diff --git a/_bibliography/citations-eu.bib b/_bibliography/citations-eu.bib index 01f7a984e..a395c92da 100644 --- a/_bibliography/citations-eu.bib +++ b/_bibliography/citations-eu.bib @@ -5,10 +5,10 @@ @article{__2023 journal = {Доклады Белорусского государственного университета информатики и радиоэлектроники}, keywords = {{\textgreater}UseGalaxy.eu}, note = {Number: 2 -Place: Республика Беларусь, Минск -Publisher: Учреждение образования «Белорусский государственный университет информатики и радиоэлектроники»}, +Place: Республика Беларусь, Минск}, number = {2}, pages = {104--113}, + publisher = {Учреждение образования «Белорусский государственный университет информатики и радиоэлектроники»}, title = {{ВЫЧИСЛИТЕЛЬНЫЙ} АНАЛИЗ СТРУКТУРНОГО {CОСТАВА} ГЕНОМОВ КОРОНАВИРУСОВ}, url = {https://cyberleninka.ru/article/n/vychislitelnyy-analiz-strukturnogo-costava-genomov-koronavirusov}, urldate = {2023-07-31}, @@ -55,6 +55,47 @@ @article{abdulhak_genomic_2025 year = {2025} } +@article{abedin_cladistic_2025, + abstract = {The endangered Peacock Softshell Turtle Nilssonia hurum (Gray, 1830) has undergone a steep population decline in recent decades because of habitat loss and anthropogenic pressures, highlighting the urgent need for scientific intervention to ensure its protection in the wild. Thus, the present study integrates mitogenomic and ecological data to guide proactive conservation strategies for this species. The study reports the first mitogenome (16,788 bp) of N. hurum from the upper Ganges region, which exhibits a typical gene composition and strong A + T bias. The mitogenome-based phylogenetic analyses reveal the monophyly of the genus Nilssonia Gray, 1872 and a close evolutionary relationship between N. hurum and N. nigricans (Anderson, 1875). The genetic distance and haplotype network analyses on the basis of the CYTB gene reveal substantial intraspecific diversity and spatial genetic structuring among populations across river basins within the easternmost range. Using species distribution modeling, the study identified 123,699 km2 (6.81\% of IUCN range) as presently suitable for N. hurum. However, future climate projections indicate drastic reductions in suitable habitat, with losses of up to 85\% due to climate change. The landscape genetic analyses revealed that the Meghna basin exhibits the highest mean functional connectivity (0.603), whereas the Brahmaputra basin shows the lowest connectivity (0.198) despite containing suitable habitat patches, consistent with its high genetic diversity. Moreover, projections under future climate scenarios, driven by anticipated losses in habitat suitability, indicate widespread declines in functional connectivity across all basins and sub-basins. The landscape geometry assessments further reveal increasing habitat fragmentation due to climate change. Therefore, populations persisting within suitable habitat patches across different river basins in the eastern range should be prioritized as distinct conservation units for future management. Overall, this study provides a critical foundation for site-specific conservation planning through landscape genetics to address habitat loss, fragmentation, and mitigating inbreeding depression for ensuring the long-term endurance of this threatened freshwater turtle in South Asia.}, + author = {Abedin, Imon and Putra, Angkasa and Kang, Hye-Eun and Singh, Arunima and Singh, Shailendra and Singha, Hilloljyoti and Kim, Hyun-Woo and Kundu, Shantanu}, + copyright = {© 2025 The Author(s). Ecology and Evolution published by British Ecological Society and John Wiley \& Sons Ltd.}, + doi = {10.1002/ece3.72751}, + issn = {2045-7758}, + journal = {Ecology and Evolution}, + keywords = {{\textgreater}UseGalaxy.eu, climate change, ecology, mitogenome, phylogeny, species distribution model, testudines}, + language = {en}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.72751}, + number = {12}, + pages = {e72751}, + shorttitle = {Cladistic {Relationships} and {Landscape} {Genetics} of the {Endangered} {Indian} {Peacock} {Softshell} {Turtle} {Nilssonia} hurum ({Gray}, 1830)}, + title = {Cladistic {Relationships} and {Landscape} {Genetics} of the {Endangered} {Indian} {Peacock} {Softshell} {Turtle} {Nilssonia} hurum ({Gray}, 1830): {Implications} for {Strategic} {Conservation} {Planning}}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.72751}, + urldate = {2025-12-26}, + volume = {15}, + year = {2025} +} + +@article{abedin_lineages_2025, + abstract = {The Tricarinate Hill Turtle (Melanochelys tricarinata), endemic to the Indian subcontinent, faces significant threats from intensifying anthropogenic pressures and severe habitat degradation. Thus, to facilitate conservation efforts for this endangered species, a comprehensive assessment of its genomics and ecology is imperative. The present study adopts two independent approaches by characterizing the complete mitogenome and evaluating current and future habitat suitability. The mitogenome (16,745 bp) comprises 37 genes, with most protein-coding genes beginning with the canonical ATG start codon. The codon usage analysis revealed that arginine, leucine, and serine are the most frequently used amino acids. The control region contains a termination-associated sequence, four conserved sequence blocks, and two distinct tandem repeat motifs. The phylogenetic assessment using both Bayesian inference and Maximum-likelihood methods consistently placed M. tricarinata in a distinct clade, separate from other geoemydids. The mitogenome-based TimeTree analysis revealed that M. tricarinata diverged from its closest relatives during the Oligocene. The comparative analyses of partial mitochondrial genes revealed substantial divergence between Melanochelys congeners (3.71–5.20\% in cox1, 7.99–9.29\% in cytb), with low haplotypic diversity in M. tricarinata and high in M. trijuga. The ensemble model identified suitable habitats under both current and future climate scenarios. Under present scenario, approximately 374,657 km2 of ideal habitat was delineated within the training extent with a mean corridor connectivity of 0.377, which was reduced to 238,039 km2 and mean connectivity of 0.518 when restricted to existing forest cover. Moreover, only 31,450 km2 of the suitable habitat for this species falls within Protected Areas, representing just 11.912\% of the total identified favorable area. The future projections suggest a potential reduction of up to 40\% in suitable habitat area due to climatic changes, accompanied by increased fragmentation, smaller patch sizes, and over 80\% decline in connectivity across future scenarios. Thus, this study provides comprehensive insights into the systematic position, evolutionary history and ecological requirements of M. tricarinata, offering a critical scientific foundation to guide effective conservation and management strategies for this imperiled species across its native range.}, + author = {Abedin, Imon and Putra, Angkasa and Kang, Hye-Eun and Singh, Arunima and Singh, Shailendra and Jung, Won-Kyo and Kim, Hyun-Woo and Kundu, Shantanu}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s41598-025-26890-5}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Ecology, Evolution, Genetics}, + language = {en}, + month = {November}, + number = {1}, + pages = {42751}, + publisher = {Nature Publishing Group}, + shorttitle = {Lineages to landscapes}, + title = {Lineages to landscapes: mitogenomic insights and climate refugia informing proactive conservation of the endangered {Tricarinate} {Hill} {Turtle} ({Melanochelys} tricarinata) in the {Indian} subcontinent}, + url = {https://www.nature.com/articles/s41598-025-26890-5}, + urldate = {2025-12-26}, + volume = {15}, + year = {2025} +} + @article{abusaleh_genetic_2024, abstract = {As a key enzyme of the renin-angiotensin system (RAS), angiotensin-converting enzyme 2 (ACE2) is a validated receptor for SARS-CoV-2, linking RAS to COVID-19. Functional ACE1/ACE2 gene polymorphisms likely cause an imbalance in the ACE1/ACE2 ratio, triggering RAS imbalance and may contribute to COVID-19 complications. This study aimed to investigate four single nucleotide polymorphisms (SNPs) of ACE1 and ACE2 genes, three for ACE1 (rs4343, rs4342, rs4341) and one for ACE2 (rs2285666), in patients with COVID-19 among the Palestinian population. A total of 130 blood samples were collected, including 50 negative controls without COVID-19 infection, 50 cases with COVID-19 infection but not hospitalized, and 30 patients with severe COVID-19 infection hospitalized in the intensive care unit. Fragments of the ACE1 and ACE2 genes, including the targeted SNPs, were amplified using multiplex PCR and subsequently genotyped by next-generation sequencing with specific virtual probes. Our results revealed that ACE2 rs2285666 GG genotype carriers were more prevalent in COVID-19 patients compared to the control group (P=0.049), while no statistical differences were observed in the distribution of ACE1 (rs4343, rs4342, rs4341) variants between COVID-19 patients and the control group. GA carriers of ACE2, rs2285666, among cases and ICU groups were at lower risk of getting COVID-19 infection (P=0.002 and P=0.013, respectively), and they were unlikely to develop fatigue (P=0.043), headache (P=0.007), loss of smell (P=0.028), and dyspnea (P=0.005). Age and comorbidities such as hypertension and coronary artery disease (CAD) were independent risk factors for COVID-19 disease. Symptoms of COVID-19 patients such as fatigue, headaches, runny noses, and loss of smell were significantly higher in non-hospitalized cases of COVID-19, while dyspnea was more frequent in the ICU patients. In conclusion, these findings indicate that the ACE2 rs2285666 GG genotype is associated with an increased risk of COVID-19 infection. This association suggests a potential genetic predisposition linked to the ACE2 gene, which may influence the susceptibility and severity of the disease.}, author = {AbuSaleh, Lama and Ereqat, Suheir and Al-Jawabreh, Amer and Nasereddin, Abedelmajeed and AbuSaleh, Lama and Ereqat, Suheir and Al-Jawabreh, Amer and Nasereddin, Abedelmajeed}, @@ -64,9 +105,9 @@ @article{abusaleh_genetic_2024 keywords = {{\textgreater}UseGalaxy.eu}, language = {en}, month = {August}, - note = {Publisher: Cureus}, number = {8}, pages = {e67670}, + publisher = {Cureus}, title = {Genetic {Polymorphisms} of {Angiotensin}-{Converting} {Enzyme} 1 ({ACE1}) and {ACE2} {Associated} {With} {Severe} {Acute} {Respiratory} {Syndrome} {COVID}-19 in the {Palestinian} {Population}}, url = {https://www.cureus.com/articles/276157-genetic-polymorphisms-of-angiotensin-converting-enzyme-1-ace1-and-ace2-associated-with-severe-acute-respiratory-syndrome-covid-19-in-the-palestinian-population}, urldate = {2024-09-02}, @@ -167,9 +208,9 @@ @article{aerts_altered_2024 keywords = {{\textgreater}UseGalaxy.eu, Amygdala, Cadherins, Interneurons, Mice, Knockout, Protocadherins, amygdala development, autism spectrum disorder, conditional knockout, non-clustered protocadherin, proteomics, ultrasonic vocalization}, language = {eng}, month = {June}, - note = {Publisher: Royal Society}, number = {6}, pages = {240113}, + publisher = {Royal Society}, title = {Altered socio-affective communication and amygdala development in mice with protocadherin10-deficient interneurons}, url = {https://royalsocietypublishing.org/doi/full/10.1098/rsob.240113}, urldate = {2024-10-20}, @@ -187,10 +228,10 @@ @article{afouda_culturing_2020 keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Siberian permafrost, culturomics, genomic evolution, resistance genes}, language = {en}, month = {October}, - note = {Number: 10 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 10}, number = {10}, pages = {1522}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Culturing {Ancient} {Bacteria} {Carrying} {Resistance} {Genes} from {Permafrost} and {Comparative} {Genomics} with {Modern} {Isolates}}, url = {https://www.mdpi.com/2076-2607/8/10/1522}, urldate = {2021-01-15}, @@ -240,8 +281,8 @@ @article{aggarwal_role_2021 keywords = {+UsePublic, +Workbench, {\textgreater}UseGalaxy.eu}, language = {English}, month = {September}, - note = {Publisher: Elsevier}, number = {0}, + publisher = {Elsevier}, title = {The role of viral genomics in understanding {COVID}-19 outbreaks in long-term care facilities}, url = {https://www.thelancet.com/journals/lanmic/article/PIIS2666-5247(21)00208-1/fulltext}, urldate = {2021-09-30}, @@ -249,6 +290,27 @@ @article{aggarwal_role_2021 year = {2021} } +@article{aguado-ramsay_erga-bge_2025, + abstract = {The reference genome of +Lewinskya acuminata +(H. Philib.) F. Lara, Garilleti \& Goffinet will enable phylogenomic, biogeographic, and evolutionary studies within the +Orthotrichaceae +and related bryophyte lineages at a depth previously inaccessible. This species of moss is among the most representative of the Mediterranean epiphytic communities and can be readily identified by its long-acuminate leaves, fusiform capsules with a vestigial exostome, a well-developed endostome of six broad segments, and a dark, puckered peristome mouth when dry. The entirety of the genome sequence was assembled into 6 contiguous chromosomal pseudomolecules, 1 mitochondrial genome, and 2 plastid genomes. This chromosome-level assembly encompasses 0.25 Gb, composed of 51 contigs and 13 scaffolds, with contig and scaffold N50 values of 11.5 Mb and 40.8 Mb, respectively.}, + author = {Aguado-Ramsay, Pablo and Lara, Francisco and Draper, Isabel and Conejero, Maria and Böhne, Astrid and Monteiro, Rita and Marcussen, Thomas and H. Struck, Torsten and A. Oomen, Rebekah and {Genomescope Sequencing Team} and Moussy, Alice and Cruaud, Corinne and Labadie, Karine and Demirdjian, Lola and Téodori, Emilie and Wincker, Patrick and H. Oliveira, Pedro and Aury, Jean-Marc and Bortoluzzi, Chiara}, + doi = {10.12688/openreseurope.21670.1}, + issn = {2732-5121}, + journal = {Open Research Europe}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {November}, + pages = {357}, + title = {{ERGA}-{BGE} reference genome of {Lewinskya} acuminata, a common epiphytic {Mediterranean} moss with disjunct populations in {California} and {Ethiopia}}, + url = {https://open-research-europe.ec.europa.eu/articles/5-357/v1}, + urldate = {2025-11-28}, + volume = {5}, + year = {2025} +} + @article{agudelo-romero_advancing_2025, author = {Agudelo-Romero, Patricia and Conradie, Talya and Caparros-Martin, Jose Antonio and Martino, David Jimmy and Kicic, Anthony and Stick, Stephen Michael and Hakkaart, Christopher and Sharma, Abhinav}, issn = {2673-7647}, @@ -299,10 +361,10 @@ @article{ahmad_biosynthetic_2023-1 keywords = {\textit{Hypogymnia physodes}, \textit{Hypogymnia tubulosa}, {\textgreater}UseGalaxy.eu, biosynthetic gene cluster, lichen, long read sequencing, polyketide synthesis, reference genome}, language = {en}, month = {May}, - note = {Number: 5 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 5}, number = {5}, pages = {546}, + publisher = {Multidisciplinary Digital Publishing Institute}, shorttitle = {Biosynthetic {Potential} of {Hypogymnia} {Holobionts}}, title = {Biosynthetic {Potential} of {Hypogymnia} {Holobionts}: {Insights} into {Secondary} {Metabolite} {Pathways}}, url = {https://www.mdpi.com/2309-608X/9/5/546}, @@ -373,10 +435,10 @@ @article{ahmed_high_2020 keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, language = {en}, month = {October}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {18637}, + publisher = {Nature Publishing Group}, title = {High prevalence of mcr-1 -encoded colistin resistance in commensal {Escherichia} coli from broiler chicken in {Bangladesh}}, url = {https://www.nature.com/articles/s41598-020-75608-2}, urldate = {2021-02-25}, @@ -411,9 +473,9 @@ @article{akol_multimodal_2023 keywords = {{\textgreater}UseGalaxy.eu, Forkhead Transcription Factors, Rett Syndrome}, language = {eng}, month = {January}, - note = {Publisher: Proceedings of the National Academy of Sciences}, number = {2}, pages = {e2122467120}, + publisher = {Proceedings of the National Academy of Sciences}, title = {Multimodal epigenetic changes and altered {NEUROD1} chromatin binding in the mouse hippocampus underlie {FOXG1} syndrome}, url = {https://www.pnas.org/doi/full/10.1073/pnas.2122467120}, urldate = {2023-03-15}, @@ -479,9 +541,9 @@ @inproceedings{alam_reusability_2023 author = {Alam, Khairul and Roy, Banani and Serebrenik, Alexander}, booktitle = {2023 30th {Asia}-{Pacific} {Software} {Engineering} {Conference} ({APSEC})}, doi = {10.1109/APSEC60848.2023.00039}, + issn = {2640-0715}, keywords = {{\textgreater}UseGalaxy.eu, Collaboration, Galaxy, Manuals, Recommender systems, Reproducibility of results, Reusability, Scientific workflow management systems, Scientific workflow repositories, Scientific workflows, Software, Task analysis, Workflow management software}, month = {December}, - note = {ISSN: 2640-0715}, pages = {289--298}, shorttitle = {Reusability {Challenges} of {Scientific} {Workflows}}, title = {Reusability {Challenges} of {Scientific} {Workflows}: {A} {Case} {Study} for {Galaxy}}, @@ -500,9 +562,9 @@ @article{alawi_private_2024 keywords = {{\textgreater}UseGalaxy.eu, Environmental sciences, Water microbiology}, language = {en}, month = {March}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {1--16}, + publisher = {Nature Publishing Group}, title = {Private and well drinking water are reservoirs for antimicrobial resistant bacteria}, url = {https://www.nature.com/articles/s44259-024-00024-9}, urldate = {2024-05-17}, @@ -517,7 +579,7 @@ @incollection{albrecht_amplicon-based_2024 booktitle = {Epigenome {Editing}: {Methods} and {Protocols}}, doi = {10.1007/978-1-0716-4051-7_21}, editor = {Jeltsch, Albert and Rots, Marianne G.}, - isbn = {978-1-07-164051-7}, + isbn = {978-1-0716-4051-7}, keywords = {{\textgreater}UseGalaxy.eu}, language = {en}, pages = {405--418}, @@ -536,9 +598,9 @@ @article{alcaraz_development_2021 journal = {Environmental Science \& Technology}, keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, month = {April}, - note = {Publisher: American Chemical Society}, number = {8}, pages = {5024--5036}, + publisher = {American Chemical Society}, title = {Development of a {Comprehensive} {Toxicity} {Pathway} {Model} for 17α-{Ethinylestradiol} in {Early} {Life} {Stage} {Fathead} {Minnows} ({Pimephales} promelas)}, url = {https://doi.org/10.1021/acs.est.0c05942}, urldate = {2021-08-20}, @@ -570,7 +632,7 @@ @incollection{ali_bioinformatics_2024 booktitle = {Trends in {Plant} {Biotechnology}}, doi = {10.1007/978-981-97-0814-7_10}, editor = {Ijaz, Siddra and Ul Haq, Imran and Mohamed Ali, Hayssam}, - isbn = {978-981-9708-14-7}, + isbn = {978-981-97-0814-7}, keywords = {{\textgreater}UseGalaxy.eu}, language = {en}, pages = {281--334}, @@ -603,7 +665,7 @@ @article{ali_characterization_2021 doi = {10.21203/rs.3.rs-380784/v1}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {April}, - note = {Publisher: Research Square Platform LLC}, + publisher = {Research Square Platform LLC}, title = {Characterization of the {Virome} {Associated} {With} {Haemagogus} {Mosquitoes} in {Trinidad}, {West} {Indies}}, url = {https://doi.org/10.21203/rs.3.rs-380784/v1}, year = {2021} @@ -702,7 +764,7 @@ @article{alminana_endometriosis-associated_2025 doi = {10.1186/s40659-025-00641-2}, issn = {0716-9760}, journal = {Biological research}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Cumulus Cells, Endometriosis-associated Infertility, Fertilized Oocyte, Mirnas., Oocyte Quality}, month = {September}, number = {1}, pages = {62}, @@ -739,7 +801,7 @@ @article{alvandi_pathovar-specific_2023 journal = {Plant Disease}, keywords = {{\textgreater}UseGalaxy.eu}, month = {January}, - note = {Publisher: Scientific Societies}, + publisher = {Scientific Societies}, title = {Pathovar-{Specific} {PCR} {Method} for {Detection} and {Identification} of {Xanthomonas} translucens pv. undulosa}, url = {https://apsjournals.apsnet.org/doi/abs/10.1094/PDIS-11-22-2677-SR}, urldate = {2023-03-15}, @@ -769,8 +831,8 @@ @article{amaral_tcti_2022 journal = {Scientific Reports}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {January}, - note = {Publisher: Springer Science and Business Media LLC}, number = {1}, + publisher = {Springer Science and Business Media LLC}, title = {{TcTI}, a {Kunitz}-type trypsin inhibitor from cocoa associated with defense against pathogens}, url = {https://doi.org/10.1038/s41598-021-04700-y}, volume = {12}, @@ -807,8 +869,6 @@ @article{ambros_distribution_2023 month = {September}, number = {4}, pages = {34}, - pmcid = {PMC10688831}, - pmid = {38045928}, title = {Distribution, inducibility, and characteristics of {Latilactobacillus} curvatus temperate phages}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10688831/}, urldate = {2023-12-28}, @@ -852,7 +912,7 @@ @article{andrade_assessing_2023 doi = {10.2139/ssrn.4350080}, journal = {SSRN Electronic Journal}, keywords = {{\textgreater}UseGalaxy.eu}, - note = {Publisher: Elsevier BV}, + publisher = {Elsevier BV}, title = {Assessing {Antimicrobial} and {Metal} {Resistance} {Genes} in {Escherichia} {Coli} from {Domestic} {Groundwater} {Supplies} in {Rural} {Ireland}}, url = {https://doi.org/10.2139/ssrn.4350080}, year = {2023} @@ -867,8 +927,8 @@ @article{andriyanov_genomic_2024 keywords = {{\textgreater}UseGalaxy.eu, Antimicrobial resistance (AMR), Delftia tsuruhatensis, Genomics, phylogenomic analysis, raw milk}, language = {English}, month = {January}, - note = {Publisher: Frontiers}, pages = {1321122}, + publisher = {Frontiers}, title = {Genomic analysis of multidrug-resistant {Delftia} tsuruhatensis isolated from raw bovine milk}, url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1321122/full}, urldate = {2024-05-17}, @@ -886,10 +946,10 @@ @article{annor_melibiosex-galmacconkey_2023 keywords = {\textit{E. coli}, \textit{Escherichia albertii}, \textit{Salmonella}, {\textgreater}UseGalaxy.eu, MacConkey Agar, culture media, food safety, poultry safety}, language = {en}, month = {March}, - note = {Number: 1 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 1}, number = {1}, pages = {119--130}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Melibiose–{X}-{Gal}–{MacConkey} {Agar} for {Presumptive} {Differentiation} of {Escherichia} albertii from {E}. coli and {Salmonella} from {Poultry} {Meat}}, url = {https://www.mdpi.com/2673-8007/3/1/10}, urldate = {2023-03-15}, @@ -935,7 +995,7 @@ @article{apletsch_type_2025 journal = {Food \& Function}, keywords = {{\textgreater}UseGalaxy.eu}, language = {en}, - note = {Publisher: Royal Society of Chemistry}, + publisher = {Royal Society of Chemistry}, title = {A type 4 resistant potato starch alters the cecal microbiome, gene expression and resistance to colitis in mice fed a {Western} diet based on {NHANES} data}, url = {https://pubs.rsc.org/en/content/articlelanding/2025/fo/d4fo04697h}, urldate = {2025-04-15}, @@ -952,10 +1012,10 @@ @article{apostolakos_functional_2022 keywords = {\textit{Weissella} spp., {\textgreater}UseGalaxy.eu, Next-Generation Sequencing, bioinformatics, fermented products, molecular microbiology, starter cultures}, language = {en}, month = {December}, - note = {Number: 4 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 4}, number = {4}, pages = {799--813}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Functional and {Safety} {Characterization} of {Weissella} paramesenteroides {Strains} {Isolated} from {Dairy} {Products} through {Whole}-{Genome} {Sequencing} and {Comparative} {Genomics}}, url = {https://www.mdpi.com/2624-862X/3/4/55}, urldate = {2024-11-17}, @@ -973,10 +1033,10 @@ @article{apostolakos_genomic_2023 keywords = {{\textgreater}UseGalaxy.eu, Mastitis, Milk, Probiotics, Staphylococcus, dairy products, lactic acid bacteria, mastitis, probiotics, sheep’s milk, staphylococci, whole-genome sequencing}, language = {en}, month = {January}, - note = {Number: 18 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 18}, number = {18}, pages = {13883}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Genomic and {Phenotypic} {Characterization} of {Mastitis}-{Causing} {Staphylococci} and {Probiotic} {Lactic} {Acid} {Bacteria} {Isolated} from {Raw} {Sheep}’s {Milk}}, url = {https://www.mdpi.com/1422-0067/24/18/13883}, urldate = {2023-10-28}, @@ -993,8 +1053,8 @@ @article{apostolakos_occurrence_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, language = {eng}, month = {September}, - note = {Publisher: Frontiers Media SA}, pages = {737720}, + publisher = {Frontiers Media SA}, title = {Occurrence of {Colibacillosis} in {Broilers} and {Its} {Relationship} {With} {Avian} {Pathogenic} {Escherichia} coli ({APEC}) {Population} {Structure} and {Molecular} {Characteristics}}, url = {https://doi.org/10.3389/fvets.2021.737720}, volume = {8}, @@ -1008,9 +1068,9 @@ @article{arai_two_2024 journal = {Royal Society Open Science}, keywords = {{\textgreater}UseGalaxy.eu, Wolbachia, evolution, genome rearrangement, male killing}, month = {January}, - note = {Publisher: Royal Society}, number = {1}, pages = {231502}, + publisher = {Royal Society}, title = {Two male-killing {Wolbachia} from {Drosophila} birauraia that are closely related but distinct in genome structure}, url = {https://royalsocietypublishing.org/doi/full/10.1098/rsos.231502}, urldate = {2024-04-28}, @@ -1026,9 +1086,9 @@ @article{arcari_ceftazidimeavibactam_2023 journal = {Microbial Genomics}, keywords = {{\textgreater}UseGalaxy.eu, Anti-Bacterial Agents, Klebsiella pneumoniae}, language = {eng}, - note = {Publisher: Microbiology Society,}, number = {2}, pages = {000931}, + publisher = {Microbiology Society,}, shorttitle = {Ceftazidime–avibactam resistance in {Klebsiella} pneumoniae sequence type 37}, title = {Ceftazidime–avibactam resistance in {Klebsiella} pneumoniae sequence type 37: a decade of persistence and concealed evolution}, url = {https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000931}, @@ -1045,10 +1105,9 @@ @article{arcari_genotypic_2023 keywords = {{\textgreater}UseGalaxy.eu, Ceftazidime, Klebsiella Infections}, language = {en}, month = {November}, - note = {Publisher: Centers for Disease Control and Prevention}, number = {11}, pages = {2266}, - pmid = {37877547}, + publisher = {Centers for Disease Control and Prevention}, title = {Genotypic {Evolution} of {Klebsiella} pneumoniae {Sequence} {Type} 512 during {Ceftazidime}/{Avibactam}, {Meropenem}/{Vaborbactam}, and {Cefiderocol} {Treatment}, {Italy}}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10617348/}, urldate = {2023-12-28}, @@ -1065,9 +1124,9 @@ @article{arcari_interplay_2022 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Anti-Bacterial Agents, COVID-19, Ceftazidime-avibactam, KPC, Klebsiella Infections, Klebsiella pneumoniae, Meropenem}, language = {eng}, month = {January}, - note = {Publisher: Springer Science and Business Media LLC}, number = {3}, pages = {495--500}, + publisher = {Springer Science and Business Media LLC}, title = {Interplay between {Klebsiella} pneumoniae producing {KPC}-31 and {KPC}-3 under treatment with high dosage meropenem: a case report}, url = {https://doi.org/10.1007/s10096-021-04388-y}, volume = {41}, @@ -1083,9 +1142,9 @@ @article{arcari_multiplicity_2023 keywords = {{\textgreater}UseGalaxy.eu, Anti-Bacterial Agents, Klebsiella Infections}, language = {eng}, month = {July}, - note = {Publisher: American Society for Microbiology}, number = {0}, pages = {e00368--23}, + publisher = {American Society for Microbiology}, title = {Multiplicity of {blaKPC} {Genes} and {pKpQIL} {Plasmid} {Plasticity} in the {Development} of {Ceftazidime}-{Avibactam} and {Meropenem} {Coresistance} in {Klebsiella} pneumoniae {Sequence} {Type} 307}, url = {https://journals.asm.org/doi/full/10.1128/aac.00368-23}, urldate = {2023-07-31}, @@ -1103,10 +1162,10 @@ @article{ardisasmita_comprehensive_2022 keywords = {{\textgreater}UseGalaxy.eu, Data integration, Hepatocytes, Induced Pluripotent Stem Cells, Pluripotent Stem Cells, RNA sequencing, Stem-cell differentiation}, language = {en}, month = {October}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {1--15}, + publisher = {Nature Publishing Group}, title = {A comprehensive transcriptomic comparison of hepatocyte model systems improves selection of models for experimental use}, url = {https://www.nature.com/articles/s42003-022-04046-9}, urldate = {2022-12-03}, @@ -1114,11 +1173,10 @@ @article{ardisasmita_comprehensive_2022 year = {2022} } -@article{ardisasmita_novel_2024, +@misc{ardisasmita_novel_2024, abstract = {Accurate liver disease modeling and drug toxicity testing still remain challenging as liver cells in vitro poorly resemble adult hepatocytes, as we previously demonstrated using whole transcriptome and cell identity analysis. To address this, we used our insights into hepatic modeling to develop hepatocyte-like liver organoids (HeLLOs), a novel human organoid model with mature hepatocyte functions superior to existing models. HeLLOs are easily established from (small) healthy or diseased liver tissues and rapidly expanded for an extended period in optimized culture conditions. Transcriptomic and functional analyses revealed that differentiated HeLLOs closely resemble fresh primary human hepatocytes (PHHs) and perform key hepatic functions such as gluconeogenesis, drug metabolism, and bile acid synthesis. We developed a HeLLO-based toxicity assay with higher sensitivity in predicting liver toxicity of known liver-toxic drugs compared to the gold-standard PHHs. By modeling disease-related mechanisms, such as bile acid transport, HeLLOs uncover transport-inhibition toxicity mechanisms of known liver toxic drugs. Single cell sequencing analysis of HeLLOs identified a heterogeneous cluster of cells with cholangiocyte-like and hepatocyte-like cells, overall resembling liver regenerative cells. As such, HeLLOs hold great promise for advancing liver disease modeling and drug testing. To our knowledge, HeLLOs are the best expandable liver model for predicting adverse drug reactions as well as modeling various liver disease mechanisms.}, author = {Ardisasmita, AI and Joore, IP and Levy, N and Myszczyszyn, A and Marsee, A and Sinnige, T and Ruiter, J and Ferdinandusse, S and Dudaryeva, O and Gruber, E and Daive, V and Levato, R and Spee, B and Verstegen, M.M.A. and van der Laan, L.J.W. and Nieuwenhuis, EES and Schene, IF and Fuchs, SA}, doi = {10.1101/2024.10.29.620824}, - journal = {bioRxiv}, keywords = {{\textgreater}UseGalaxy.eu}, title = {Novel hepatocyte-like liver organoids recapitulate crucial mature hepatic functions}, url = {http://europepmc.org/abstract/PPR/PPR932234}, @@ -1132,8 +1190,8 @@ @article{argenta_american_2024 journal = {FACETS}, keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org}, month = {January}, - note = {Publisher: Canadian Science Publishing}, pages = {1--10}, + publisher = {Canadian Science Publishing}, title = {American lobster ({Homarus} americanus) hepatopancreas transcriptome reveals the significance of chitin-related genes during impoundment shell disease}, url = {https://www.facetsjournal.com/doi/full/10.1139/facets-2024-0049}, urldate = {2024-11-02}, @@ -1183,10 +1241,10 @@ @article{aribisala_cheminformatics_2023 journal = {Molecular Simulation}, keywords = {{\textgreater}UseGalaxy.eu, Resistance, molecular docking, molecular dynamics simulation, penicillin−binding proteins, phenolics}, month = {June}, - note = {Publisher: Taylor \& Francis -\_eprint: https://doi.org/10.1080/08927022.2023.2228423}, + note = {\_eprint: https://doi.org/10.1080/08927022.2023.2228423}, number = {0}, pages = {1--17}, + publisher = {Taylor \& Francis}, title = {Cheminformatics identification of phenolics as modulators of key penicillin−binding proteins of {Escherichia} coli towards interventive antibacterial therapy}, url = {https://doi.org/10.1080/08927022.2023.2228423}, urldate = {2023-07-31}, @@ -1204,9 +1262,9 @@ @article{aribisala_silico_2024 keywords = {{\textgreater}UseGalaxy.eu, Amoxicillin, Computational biology and bioinformatics, Drug discovery, Streptococcus pneumoniae}, language = {en}, month = {April}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {8788}, + publisher = {Nature Publishing Group}, title = {In silico exploration of phenolics as modulators of penicillin binding protein ({PBP}) 2× of {Streptococcus} pneumoniae}, url = {https://www.nature.com/articles/s41598-024-59489-3}, urldate = {2024-04-28}, @@ -1241,8 +1299,8 @@ @article{arlat_generation_2024 keywords = {3D culture, {\textgreater}UseGalaxy.eu, Adipose Tissue, Bone Marrow, Cell Culture Techniques, Three Dimensional, Cell Differentiation, Macrophages, Metabolism, Phagocytosis, Resident macrophage, macrophage subpopulation}, language = {English}, month = {June}, - note = {Publisher: Frontiers}, pages = {1356397}, + publisher = {Frontiers}, title = {Generation of functionally active resident macrophages from adipose tissue by {3D} cultures}, url = {https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2024.1356397/full}, urldate = {2024-10-20}, @@ -1260,8 +1318,6 @@ @article{arnold_isolation_2023 month = {August}, number = {4}, pages = {e1372}, - pmcid = {PMC10404844}, - pmid = {null}, title = {Isolation, biochemical characterization, and genome sequencing of two high‐quality genomes of a novel chitinolytic {Jeongeupia} species}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10404844/}, urldate = {2023-08-13}, @@ -1329,9 +1385,9 @@ @article{asadi_exploring_2025 keywords = {{\textgreater}UseGalaxy.eu, Ascomycota, Fungal Proteins, Fungal genetics, Fungal pathogenesis, Gene Expression Regulation, Fungal, Hordeum, Plant Diseases, Plant molecular biology}, language = {en}, month = {May}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {17667}, + publisher = {Nature Publishing Group}, shorttitle = {Exploring effector candidates in {Rhynchosporium} commune}, title = {Exploring effector candidates in {Rhynchosporium} commune: insights into their expression dynamics during barley infection}, url = {https://www.nature.com/articles/s41598-025-02572-0}, @@ -1349,9 +1405,9 @@ @article{ashrafi_two_2022 keywords = {{\textgreater}UseGalaxy.eu, Fabaceae, Mesorhizobium, Rhizobium}, language = {eng}, month = {August}, - note = {Publisher: American Society for Microbiology}, number = {0}, pages = {e01099--22}, + publisher = {American Society for Microbiology}, title = {Two {New} {Rhizobiales} {Species} {Isolated} from {Root} {Nodules} of {Common} {Sainfoin} ({Onobrychis} viciifolia) {Show} {Different} {Plant} {Colonization} {Strategies}}, url = {https://journals.asm.org/doi/full/10.1128/spectrum.01099-22}, urldate = {2022-09-24}, @@ -1421,10 +1477,10 @@ @article{atac_identification_2024 keywords = {{\textgreater}UseGalaxy.eu, ATOH7, Basic Helix-Loop-Helix Transcription Factors, CUT\&RUN sequencing, Induced Pluripotent Stem Cells, RNA sequencing, Retina, retinal development, retinal ganglion cells, retinal organoids, retinal progenitor cells, scRNA sequencing}, language = {en}, month = {January}, - note = {Number: 13 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 13}, number = {13}, pages = {1142}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Identification and {Characterization} of {ATOH7}-{Regulated} {Target} {Genes} and {Pathways} in {Human} {Neuroretinal} {Development}}, url = {https://www.mdpi.com/2073-4409/13/13/1142}, urldate = {2024-11-17}, @@ -1442,10 +1498,10 @@ @article{atxaerandio-landa_practical_2022 keywords = {{\textgreater}UseGalaxy.eu, Galaxy, bioinformatics workflow, foodborne pathogens, whole-genome sequencing}, language = {en}, month = {December}, - note = {Number: 12 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 12}, number = {12}, pages = {2364}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {A {Practical} {Bioinformatics} {Workflow} for {Routine} {Analysis} of {Bacterial} {WGS} {Data}}, url = {https://www.mdpi.com/2076-2607/10/12/2364}, urldate = {2024-11-17}, @@ -1472,6 +1528,40 @@ @article{aurelle_erga-bge_2025 year = {2025} } +@article{avery_putative_2025, + abstract = {Sortase enzymes are cysteine transpeptidases at the cell surface of Gram-positive bacteria. Localized to distinct foci on the cell membrane, class A sortases (SrtAs) recognize a cell wall sorting signal (CWSS), and, following cleavage at this specific binding motif, target proteins are ligated to precursors of the growing peptidoglycan layer. This activity of SrtA enzymes is utilized extensively in sortase-mediated ligation (SML) strategies for a variety of protein engineering applications. Typically, engineered variants of SrtA are used for SML experiments, considering the relatively low catalytic efficiency of this enzyme. Understandably, most biochemical studies are conducted with the isolated catalytic domain of SrtA enzymes from various bacteria, and the stereochemistry of the endogenous interaction between SrtA and its substrate is not well understood. Here, we used AlphaFold2 to create a model of the full-length SrtA enzyme from Streptococcus pyogenes (spySrtA) with or without either a peptide substrate or a portion of M protein, a cellular target. We ran triplicate 500 ns molecular dynamics simulations for each model embedded in a lipid bilayer, which revealed several stereochemical features of this system. Contact map analyses revealed specific interactions between catalytic domain positions of spySrtA and the lipid bilayer, as well as between the enzyme and M protein residues outside the canonical LPXTG pentapeptide CWSS. We also characterized a putative transmembrane domain interaction between spySrtA and M protein that we predict orients and stabilizes substrate binding. If present in vivo, we predict that these interactions may increase the catalytic efficiency of the enzyme for its substrates and could provide important stereochemical insights for SML uses.}, + author = {Avery, Nathan G. and Tahti, Elise F. and Spiegel, Paul Clinton and Antos, John M. and McCarty, James and Amacher, Jeanine F.}, + doi = {10.1021/acs.jpcb.5c05800}, + issn = {1520-5207}, + journal = {The Journal of Physical Chemistry. B}, + keywords = {{\textgreater}UseGalaxy.eu, Aminoacyltransferases, Bacterial Proteins, Cysteine Endopeptidases, Molecular Dynamics Simulation, Protein Binding, Protein Domains, Streptococcus pyogenes, Substrate Specificity}, + language = {eng}, + month = {December}, + number = {51}, + pages = {13117--13127}, + title = {A {Putative} {Interaction} between the {Transmembrane} {Domains} of {Streptococcus} pyogenes {Sortase} {A} and {Its} {Endogenous} {Substrate} {M} {Protein} {Revealed} by {Molecular} {Dynamics} {Simulations}}, + volume = {129}, + year = {2025} +} + +@article{bacchetti_investigating_2025, + abstract = {Cryptosporidium parvum is a zoonotic protozoan parasite of human and veterinary public health concern that causes gastrointestinal disease. Animal contact is a major risk factor for C. parvum outbreaks which require thorough investigation through the use of molecular subtyping. Recently, a multi-locus variable-number tandem repeat analysis (MLVA) scheme was established for C. parvum, offering improved subtyping resolution compared to the commonly used single-locus 60 kDa glycoprotein gene (gp60) subtyping approach. Using the C. parvum MLVA scheme, the genetic diversity of known gp60 subtyped faecal DNA extracts collected between April 1st 2023 and March 31st 2024 was explored. A representative group of a common Scottish gp60 subtype (IIaA15G2R1, n = 28) was analysed by MLVA and found to consist of 8 distinct complete MLVA profiles, with 4-12-5-7-27-36-16 (n = 12) being the most common. Genetic diversity within samples involved in three historic animal contact outbreaks (Outbreaks A, B and C) was investigated. Outbreak A, involving a single gp60 subtype (IIaA19G1R1), consisted of only one MLVA profile (4-12-5-8-27-15-17). Outbreak B was caused by two gp60 subtypes (IIaA17G1R1 and IIaA15G2R1), which were further subdivided into four MLVA profiles, two per gp60 subtype (4-14-4-7-27-37-15 and 4-14-5-7-27-27-15, and 4-13-4-8-27-31-17 and 4-12-5-7-27-42-16, respectively). Lastly, Outbreak C, thought to have two-point sources of infection, involved one gp60 subtype (IIaA15G2R1), which was subdivided into four distinct MLVA profiles (4-12-5-7-27-36-16, 4-12-5-7-27-32-15, 4-12-5-7-27-30-15, and 4-14-5-7-36-33-15). Improved MLVA resolution allowed outbreak specimens with insufficient epidemiological data to be linked to a source through sharing a common MLVA profile.}, + author = {Bacchetti, Ross and McCormack, Paula and Connelly, Lisa and Brown, Derek J and Chaput, Dominique L and Alexander, Claire L}, + copyright = {cc by}, + doi = {10.1016/j.crpvbd.2025.100332}, + issn = {2667-114X}, + journal = {Current research in parasitology \& vector-borne diseases}, + keywords = {{\textgreater}UseGalaxy.eu, Gp60, Mlva, Outbreak Investigation, Subtyping, cryptosporidium parvum}, + language = {eng}, + month = {January}, + pages = {100332}, + title = {Investigating genetic diversity within \<i\>{Cryptosporidium} parvum\</i\> outbreaks using multi-locus variable number tandem repeat analysis}, + url = {https://europepmc.org/articles/PMC12639845}, + urldate = {2025-12-26}, + volume = {8}, + year = {2025} +} + @article{bader_phylogenetic_2021, abstract = {In Aspergillus fumigatus, the repetitive region of the \textit{csp1} gene is one of the most frequently used loci for intraspecies typing of this human pathogenic mold. Using PCR amplification and Sanger sequencing of only a single marker, \textit{csp1} typing is readily available to most laboratories and highly reproducible. Here, I evaluate the usefulness of the \textit{csp1} marker for resistance detection and epidemiologic stratification among A. fumigatus isolates. After resolving nomenclature conflicts from published studies and adding novel \textit{csp1} types, the number of known types now adds up to 38. Their distribution mostly correlates with A. fumigatus population structure, and they are also meaningful for narrowly defined cases of azole resistance phenotypes. Isolates carrying the pandemic resistance allele TR$_{\textrm{34}}$/L98H show signs of interclade crossing of strains with t02 or t04A, into the t11 clade. Furthermore, absolute differences in voriconazole MIC values between t02/t04B versus t11 TR$_{\textrm{34}}$/L98H isolates indicate that the genetic background of resistance mutations may have a pivotal role in cross-resistance phenotypes and, thus, clinical outcome and environmental selection. Despite the general genetic similarity of isolates with identical \textit{csp1} types, outcrossing into other clades is also observed. The \textit{csp1} type alone, therefore, does not sufficiently discriminate genetic clades to be used as the sole marker in epidemiologic studies. \textbf{IMPORTANCE} Aspergillus fumigatus is a ubiquitously distributed saprophytic mold and a leading cause of invasive aspergillosis in human hosts. Pandemic azole-resistant strains have emerged on a global scale, which are thought to be propagated through use of azole-based fungicides in agriculture. To perform epidemiologic studies, genetic typing of large cohorts is key. Here, I evaluate the usefulness of the frequently used \textit{csp1} marker for resistance detection and epidemiologic stratification among A. fumigatus isolates. The phylogenetic distribution of \textit{csp1} types mostly correlates with A. fumigatus population structure and is also meaningful for narrowly defined cases of azole resistance phenotypes. Nevertheless, outcrossing of \textit{csp1} into other clades is also observed. The \textit{csp1} type alone, therefore, does not sufficiently discriminate genetic clades and should not be used as the sole marker in epidemiologic studies.}, author = {Bader, Oliver}, @@ -1498,9 +1588,9 @@ @article{baei_pharmacophore_2025 keywords = {{\textgreater}ChemicalToolbox, {\textgreater}UseGalaxy.eu, Antiviral Agents, Antiviral therapy, Drug discovery, Drug research and development, Drug screening, Flavonols, Hepatitis B virus, High throughput screening, Library screening, Principal component analysis, Quantitative Structure-Activity Relationship}, language = {en}, month = {January}, - note = {Publisher: Public Library of Science}, number = {1}, pages = {e0316765}, + publisher = {Public Library of Science}, title = {Pharmacophore modeling and {QSAR} analysis of anti-{HBV} flavonols}, url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0316765}, urldate = {2025-01-19}, @@ -1568,9 +1658,9 @@ @article{bahrami_integrated_2024 journal = {Epigenomics}, keywords = {{\textgreater}UseGalaxy.eu, biomarkers, enhancer RNA, epigenomics, stomach neoplasms, systems biology}, month = {February}, - note = {Publisher: Future Medicine}, number = {3}, pages = {159--173}, + publisher = {Future Medicine}, title = {Integrated analysis of transcriptome and epigenome reveals {ENSR00000272060} as a potential biomarker in gastric cancer}, url = {https://www.futuremedicine.com/doi/full/10.2217/epi-2023-0213}, urldate = {2024-02-03}, @@ -1587,9 +1677,9 @@ @article{baig_genome-wide_2023 keywords = {{\textgreater}UseGalaxy.eu, Ascomycota, Aspergillus, Aspergillus fumigatus, Aspergillus oryzae, Fungal genetics, Fungal structure, Fusarium, Genome analysis, Protein structure, Protein structure prediction}, language = {en}, month = {June}, - note = {Publisher: Public Library of Science}, number = {6}, pages = {e0286428}, + publisher = {Public Library of Science}, title = {Genome-wide identification and comparative in-silico characterization of β-galactosidase ({GH}-35) in ascomycetes and its role in germ tube development of {Aspergillus} fumigatus via {RNA}-seq analysis}, url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0286428}, urldate = {2023-07-31}, @@ -1606,9 +1696,9 @@ @article{baker_no_2020 keywords = {+Galactic, +IsGalaxy, +Methods, +Project, +Reproducibility, +Shared, +UseMain, +UsePublic, {\textgreater}UseGalaxy.be, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org.au, COVID 19, Genome analysis, Genomics, Open source software, Preprocessing, Public Health, SARS, SARS CoV 2, Transmissible gastroenteritis coronavirus}, language = {en}, month = {August}, - note = {Publisher: Public Library of Science}, number = {8}, pages = {e1008643}, + publisher = {Public Library of Science}, shorttitle = {No more business as usual}, title = {No more business as usual: {Agile} and effective responses to emerging pathogen threats require open data and open analytics}, url = {https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1008643}, @@ -1670,6 +1760,24 @@ @phdthesis{baldwin_evaluating_2019 year = {2019} } +@article{ballesteros-gonzalez_repressor_2025, + abstract = {KRAS mutations are responsible for a quarter of all lung adenocarcinomas. However, the molecular mechanisms linking these mutations and their frequent secondary dosage amplification to tumor formation are still not fully understood. While ample evidence supports a crucial role for the MAPK pathway in tumor development, the primary effectors targeted by this pathway remain largely unexplored. Here we identify the transcriptional repressor Capicua (CIC) as a key target inactivated by KRAS/MAPK signaling in lung adenocarcinoma. We show that genetic loss of CIC recapitulates the phenotypic consequences of amplified KRAS signaling. Genetic disruption of CIC suppressed the requirement for Kras allelic imbalances and accelerated the transformation of bronchiolar Club cells. We also demonstrate that restoring CIC repressor activity impaired proliferation of CIC-deficient tumor cells and reverted resistance to MAPK pathway inhibitors. These results highlight the key role of CIC during lung tumor formation and suggest that selective pressure for effective CIC inactivation favors secondary amplification of KRAS/MAPK signaling in tumor cells.}, + author = {Ballesteros-González, Irene and Hernández-Navas, Iván and Brehey, Oksana and Lechuga, Carmen G. and Salmón, Marina and Scotece, Morena and Velasco-Vicente, Ricardo and Flores-Gómez, Alejandra A. and Cebriá, Antonio and Simón-Carrasco, Lucía and Jiménez, Gerardo and Musteanu, Monica and Guerra, Carmen and Domínguez, Orlando and Caleiras, Eduardo and Blanco-Aparicio, Carmen and Pons, Tirso and Ferrer, Irene and Paz-Ares, Luis and Torres-Ruiz, Raul and Rodríguez-Perales, Sandra and Barbacid, Mariano and Drosten, Matthias}, + doi = {10.1038/s44321-025-00326-z}, + issn = {1757-4684}, + journal = {EMBO Molecular Medicine}, + keywords = {{\textgreater}UseGalaxy.eu, Allelic Imbalance, Drug Resistance, KRAS, Lung Cancer, Repression}, + language = {en}, + month = {December}, + number = {12}, + pages = {3377--3406}, + title = {The repressor {Capicua} is a barrier to lung tumor development driven by {Kras}/{Trp53} mutations}, + url = {https://doi.org/10.1038/s44321-025-00326-z}, + urldate = {2025-12-26}, + volume = {17}, + year = {2025} +} + @article{balobaid_arabidopsis_2025, abstract = {DNA repair is crucial for genome stability, in particular for plants which are exposed to high levels of damage arising from UV irradiation, soil pollutants and reactive oxygen species. Damage that affects both strands of the DNA duplex is harder to repair due to both the lack of a template strand and the potential for physical separation of fragmented chromosomes. As such, DNA double-strand breaks (DSBs) and interstrand DNA crosslinks (ICL) are particularly cytotoxic forms of damage. Here we report the functions of FANCONI ANAEMIA I (FANCI), an Arabidopsis thaliana homologue of the mammalian ICL repair protein. We show that in plant cells, as in mammals, FANCI forms a nuclear localised complex with FANCD2. Genetic analysis of plants lacking FANCI displays significant hypersensitivity to the DNA crosslinking reagent mitomycin C. Furthermore, mutation of FANCI in combination with mutations in a second ICL repair factor, METHYL METHANESULFONATE AND UV-SENSITIVE PROTEIN 81 (MUS81), results in increased levels of programmed cell death compared to the corresponding single mutants, revealing roles in maintaining plant genome stability. Sequence analysis of mutational repair of CRISPR-Cas9-induced DSBs revealed that FANCI promotes single nucleotide insertions and reduces longer deletions. This pattern of mutations may reflect roles for FA proteins in replication-coupled repair of a subset of DSBs. Taken together, this analysis finds evidence for multiple roles for FANCI in the maintenance of plant genome stability.}, author = {Balobaid, Atheer and Waterworth, Wanda M and Vila Nova, Sophya F and Causier, Barry and Sharma, Vinay and Park, Madeline R and Pandey, Manish K and West, Christopher E}, @@ -1693,7 +1801,7 @@ @article{bamford_collaboration_2021 journal = {bioRxiv}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {July}, - note = {Publisher: Cold Spring Harbor Laboratory}, + publisher = {Cold Spring Harbor Laboratory}, title = {Collaboration {Between} {Host} and {Viral} {Factors} {Shape} {SARS}-{CoV}-2 {Evolution}}, url = {https://doi.org/10.1101/2021.07.16.452629}, year = {2021} @@ -1708,9 +1816,9 @@ @article{bamford_comparison_2022 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Evolution, Molecular}, language = {eng}, month = {February}, - note = {Publisher: MDPI AG}, number = {2}, pages = {325}, + publisher = {MDPI AG}, title = {Comparison of {SARS}-{CoV}-2 {Evolution} in {Paediatric} {Primary} {Airway} {Epithelial} {Cell} {Cultures} {Compared} with {Vero}-{Derived} {Cell} {Lines}}, url = {https://doi.org/10.3390/v14020325}, volume = {14}, @@ -1726,9 +1834,9 @@ @article{banar_novel_2025 keywords = {{\textgreater}UseGalaxy.eu, Antibiotic resistance, Antibiotics, Bacteriophages, Bovine mastitis, Mastitis, Methicillin-Resistant Staphylococcus aureus, Methicillin-resistant Staphylococcus aureus, Phage Therapy, Staphylococcal Infections, Staphylococcus, Staphylococcus Phages, Viral genomics}, language = {en}, month = {January}, - note = {Publisher: Public Library of Science}, number = {1}, pages = {e0316157}, + publisher = {Public Library of Science}, shorttitle = {A novel broad-spectrum bacteriophage cocktail against methicillin-resistant {Staphylococcus} aureus}, title = {A novel broad-spectrum bacteriophage cocktail against methicillin-resistant {Staphylococcus} aureus: {Isolation}, characterization, and therapeutic potential in a mastitis mouse model}, url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0316157}, @@ -1753,8 +1861,8 @@ @article{bandyopadhyay_polypharmacology_2021 doi = {10.1080/07391102.2021.1959401}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {August}, - note = {Publisher: Informa UK Limited}, pages = {1--17}, + publisher = {Informa UK Limited}, title = {Polypharmacology of some medicinal plant metabolites against {SARS}-{CoV}-2 and host targets: {Molecular} dynamics evaluation of {NSP9} {RNA} binding protein}, url = {https://doi.org/10.1080/07391102.2021.1959401}, year = {2021} @@ -1765,7 +1873,7 @@ @article{barbosa_new_2021 doi = {10.21203/rs.3.rs-1050608/v1}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {November}, - note = {Publisher: Research Square Platform LLC}, + publisher = {Research Square Platform LLC}, title = {New {Putative} {Long} {Non}-{Coding} {RNAs} ({lncRNA}) {Revealed} by {Pan}-{Transcriptome} of the {Emerging} {Human} {Pathogenic} {Fungus} {Talaromyces} {Marneffei}}, url = {https://doi.org/10.21203/rs.3.rs-1050608/v1}, year = {2021} @@ -1777,9 +1885,9 @@ @article{barker_mutations_2025 journal = {Antimicrobial Agents and Chemotherapy}, keywords = {{\textgreater}UseGalaxy.eu}, month = {August}, - note = {Publisher: American Society for Microbiology}, number = {0}, pages = {e00300--25}, + publisher = {American Society for Microbiology}, title = {Mutations in {TAC1B} drive increased {CDR1} and {MDR1} expression and azole resistance in {Candida} auris}, url = {https://journals.asm.org/doi/10.1128/aac.00300-25}, urldate = {2025-09-03}, @@ -1796,9 +1904,9 @@ @article{baron_multidrug-resistant_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Isoptera, Klebsiella Infections}, language = {eng}, month = {August}, - note = {Publisher: American Society for Microbiology}, number = {9}, pages = {e0255720}, + publisher = {American Society for Microbiology}, title = {Multidrug-{Resistant} {Klebsiella} pneumoniae {Clones} from {Wild} {Chimpanzees} and {Termites} in {Senegal}}, url = {https://doi.org/10.1128/aac.02557-20}, volume = {65}, @@ -1814,9 +1922,9 @@ @article{barragan-rosillo_genome_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Genome, Plant}, language = {eng}, month = {August}, - note = {Publisher: Proceedings of the National Academy of Sciences}, number = {33}, pages = {e2107558118}, + publisher = {Proceedings of the National Academy of Sciences}, title = {Genome accessibility dynamics in response to phosphate limitation is controlled by the {PHR1} family of transcription factors in {Arabidopsis}}, url = {https://doi.org/10.1073/pnas.2107558118}, volume = {118}, @@ -1928,9 +2036,9 @@ @article{bartas_changes_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Databases, Genetic, Gene Dosage, Longevity, Models, Molecular}, language = {eng}, month = {August}, - note = {Publisher: MDPI AG}, number = {16}, pages = {8512}, + publisher = {MDPI AG}, title = {The {Changes} in the p53 {Protein} across the {Animal} {Kingdom} {Point} to {Its} {Involvement} in {Longevity}}, url = {https://doi.org/10.3390/ijms22168512}, volume = {22}, @@ -1947,9 +2055,9 @@ @article{bassu_positive_2025 keywords = {{\textgreater}UseGalaxy.eu, Hydroponics, Light, Physiology, Plant sciences, Triticum}, language = {en}, month = {August}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {30768}, + publisher = {Nature Publishing Group}, title = {Positive impact of hydroponics and artificial light on yield and quality of wheat}, url = {https://www.nature.com/articles/s41598-025-16204-0}, urldate = {2025-09-03}, @@ -1997,10 +2105,10 @@ @article{batista_da_silva_discovery_2023 keywords = {{\textgreater}UseGalaxy.eu, Characidae, Long non-coding RNAs, RNA, Long Noncoding, Transcriptomics}, language = {en}, month = {July}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {12051}, + publisher = {Nature Publishing Group}, shorttitle = {Discovery of putative long non-coding {RNAs} expressed in the eyes of {Astyanax} mexicanus ({Actinopterygii}}, title = {Discovery of putative long non-coding {RNAs} expressed in the eyes of {Astyanax} mexicanus ({Actinopterygii}: {Characidae})}, url = {https://www.nature.com/articles/s41598-023-34198-5}, @@ -2037,7 +2145,6 @@ @article{batut_community-driven_2018 month = {June}, number = {6}, pages = {752--758.e1}, - pmid = {29953864}, title = {Community-{Driven} {Data} {Analysis} {Training} for {Biology}}, url = {https://www.cell.com/cell-systems/abstract/S2405-4712(18)30230-8}, urldate = {2018-07-16}, @@ -2052,7 +2159,7 @@ @incollection{batut_rna-seq_2021 booktitle = {{RNA} {Bioinformatics}}, doi = {10.1007/978-1-0716-1307-8_20}, editor = {Picardi, Ernesto}, - isbn = {978-1-07-161307-8}, + isbn = {978-1-0716-1307-8}, keywords = {+Galactic, +HowTo, +IsGalaxy, +RefPublic, {\textgreater}UseGalaxy.eu, Differential gene expression, Functional enrichment, Galaxy, Quality control, Sequence mapping, Visualizations, Workflow}, language = {en}, pages = {367--392}, @@ -2073,9 +2180,9 @@ @article{bauer_functional_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, language = {eng}, month = {July}, - note = {Publisher: MDPI AG}, number = {15}, pages = {3801}, + publisher = {MDPI AG}, title = {Functional {Analysis} of {Non}-{Genetic} {Resistance} to {Platinum} in {Epithelial} {Ovarian} {Cancer} {Reveals} a {Role} for the {MBD3}-{NuRD} {Complex} in {Resistance} {Development}}, url = {https://doi.org/10.3390/cancers13153801}, volume = {13}, @@ -2104,9 +2211,9 @@ @article{bayona-feliu_swisnf_2021 doi = {10.1038/s41588-021-00867-2}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {May}, - note = {Publisher: Springer Science and Business Media LLC}, number = {7}, pages = {1050--1063}, + publisher = {Springer Science and Business Media LLC}, title = {The {SWI}/{SNF} chromatin remodeling complex helps resolve {R}-loop-mediated transcription–replication conflicts}, url = {https://doi.org/10.1038/s41588-021-00867-2}, volume = {53}, @@ -2123,10 +2230,10 @@ @article{bazukyan_silico_2023 keywords = {\textit{L. delbrueckii} ssp. \textit{lactis}, {\textgreater}UseGalaxy.eu, endosymbionts, honeybees, probiogenomic analysis, probiotics, whole-genome sequencing}, language = {en}, month = {June}, - note = {Number: 6 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 6}, number = {6}, pages = {540}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {In {Silico} {Probiogenomic} {Characterization} of {Lactobacillus} delbrueckii subsp. lactis {A4} {Strain} {Isolated} from an {Armenian} {Honeybee} {Gut}}, url = {https://www.mdpi.com/2075-4450/14/6/540}, urldate = {2023-07-31}, @@ -2162,10 +2269,10 @@ @article{beck_trimannose-coupled_2023 keywords = {{\textgreater}UseGalaxy.eu, RNAi, Respiratory distress syndrome, Translational research, Viral infection, miRNAs}, language = {en}, month = {July}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {4564}, + publisher = {Nature Publishing Group}, title = {Trimannose-coupled {antimiR}-21 for macrophage-targeted inhalation treatment of acute inflammatory lung damage}, url = {https://www.nature.com/articles/s41467-023-40185-1}, urldate = {2023-08-01}, @@ -2183,10 +2290,10 @@ @article{becker_correlation_2024 keywords = {{\textgreater}UseGalaxy.eu, CC-chemokine ligand, acoustic neuroma, cytokines, growth differentiation factor, transforming growth factor, tumor-associated macrophages, vestibular schwannoma}, language = {en}, month = {January}, - note = {Number: 17 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 17}, number = {17}, pages = {3002}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Correlation of {Immunomodulatory} {Cytokines} with {Tumor} {Volume} and {Cerebrospinal} {Fluid} in {Vestibular} {Schwannoma} {Patients}}, url = {https://www.mdpi.com/2072-6694/16/17/3002}, urldate = {2024-09-02}, @@ -2211,7 +2318,7 @@ @article{beer_impaired_2022 year = {2022} } -@article{beer_impaired_2022-1, +@article{beer_impaired_2022, abstract = {SARS-CoV-2 is a highly contagious respiratory virus and the causative agent for COVID-19. The severity of disease varies from mildly symptomatic to lethal and shows an extraordinary correlation with increasing age, which represents the major risk factor for severe COVID-19 1 . However, the precise pathomechanisms leading to aggravated disease in the elderly are currently unknown. Delayed and insufficient antiviral immune responses early after infection as well as dysregulated and overshooting immunopathological processes late during disease were suggested as possible mechanisms. Here we show that the age-dependent increase of COVID-19 severity is caused by the disruption of a timely and well-coordinated innate and adaptive immune response due to impaired interferon (IFN) responses. To overcome the limitations of mechanistic studies in humans, we generated a mouse model for severe COVID-19 and compared the kinetics of the immune responses in adult and aged mice at different time points after infection. Aggravated disease in aged mice was characterized by a diminished IFN-γ response and excessive virus replication. Accordingly, adult IFN-γ receptor-deficient mice phenocopied the age-related disease severity and supplementation of IFN-γ reversed the increased disease susceptibility of aged mice. Mimicking impaired type I IFN immunity in adult and aged mice, a second major risk factor for severe COVID-19 2–4 , we found that therapeutic treatment with IFN-λ in adult and a combinatorial treatment with IFN-γ and IFN-λ in aged Ifnar1 -/- mice was highly efficient in protecting against severe disease. Our findings provide an explanation for the age-dependent disease severity of COVID-19 and clarify the nonredundant antiviral functions of type I, II and III IFNs during SARS-CoV-2 infection in an age-dependent manner. Based on our data, we suggest that highly vulnerable individuals combining both risk factors, advanced age and an impaired type I IFN immunity, may greatly benefit from immunotherapy combining IFN-γ and IFN-λ.}, author = {Beer, Julius and Crotta, Stefania and Breithaupt, Angele and Ohnemus, Annette and Becker, Jan and Sachs, Benedikt and Kern, Lisa and Llorian, Miriam and Ebert, Nadine and Labroussaa, Fabien and Thao, Tran Thi Nhu and Trueeb, Bettina Salome and Jores, Joerg and Thiel, Volker and Beer, Martin and Fuchs, Jonas and Kochs, Georg and Wack, Andreas and Schwemmle, Martin and Schnepf, Daniel}, doi = {10.1101/2022.04.21.489072}, @@ -2242,9 +2349,9 @@ @article{beerling_enhanced_2024 keywords = {{\textgreater}UseGalaxy.eu, Silicates, Trace Elements, Zea mays}, language = {eng}, month = {February}, - note = {Publisher: Proceedings of the National Academy of Sciences}, number = {9}, pages = {e2319436121}, + publisher = {Proceedings of the National Academy of Sciences}, title = {Enhanced weathering in the {US} {Corn} {Belt} delivers carbon removal with agronomic benefits}, url = {https://www.pnas.org/doi/full/10.1073/pnas.2319436121}, urldate = {2024-05-17}, @@ -2280,10 +2387,10 @@ @article{ben-oz_dual_2023 keywords = {{\textgreater}UseGalaxy.eu, DNA damage and repair, DNA damage response, Genes, cdc, Tumor Suppressor Protein p53}, language = {en}, month = {November}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {7628}, + publisher = {Nature Publishing Group}, title = {A dual role of {RBM42} in modulating splicing and translation of {CDKN1A}/p21 during {DNA} damage response}, url = {https://www.nature.com/articles/s41467-023-43495-6}, urldate = {2023-12-28}, @@ -2301,9 +2408,9 @@ @article{benatto_perino_suberin_2025 keywords = {{\textgreater}UseGalaxy.eu, Secondary metabolism, Wounding}, language = {en}, month = {March}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {7930}, + publisher = {Nature Publishing Group}, title = {The suberin transporter {StABCG1} is required for barrier formation in potato leaves}, url = {https://www.nature.com/articles/s41598-025-89032-x}, urldate = {2025-03-09}, @@ -2318,9 +2425,9 @@ @article{bennett-keki_sex-biased_2023 journal = {Proceedings of the Royal Society B: Biological Sciences}, keywords = {{\textgreater}UseGalaxy.eu, Cell Communication, Longevity, diet, fruitfly, lifespan, nutrient-sensing}, month = {March}, - note = {Publisher: Royal Society}, number = {1994}, pages = {20222086}, + publisher = {Royal Society}, title = {Sex-biased gene expression in nutrient-sensing pathways}, url = {https://royalsocietypublishing.org/doi/full/10.1098/rspb.2022.2086}, urldate = {2023-12-03}, @@ -2336,7 +2443,7 @@ @article{berlanga_biodiversity_2024 keywords = {{\textgreater}UseGalaxy.eu, Bacterial community diversity, Endorheic saline lagoons, bacterial community diversity, bacterial community functionality, biofilm-sediment biotope, endorheic saline lagoons, water column biotope}, language = {English}, month = {July}, - note = {Publisher: Frontiers}, + publisher = {Frontiers}, title = {Biodiversity and poten al func onality of biofilmsediment biotope in {La} {Muerte} lagoon, {Monegros} desert, {Spain}}, url = {https://www.frontiersin.org/journals/ecology-and-evolution/articles/10.3389/fevo.2024.1412124/full}, urldate = {2024-07-07}, @@ -2350,7 +2457,7 @@ @article{berlanga_changes_2025 doi = {10.3389/fnut.2025.1641612}, issn = {2296-861X}, journal = {Frontiers in nutrition}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Beta-glucans Cava Lees, Gut Functionality, Gut Microbiota Diversity, Healthy Wistar Rat, Metagenomics Analysis}, pages = {1641612}, title = {Changes in healthy {Wistar} rat gut microbiome by short-term dietary cava lees intervention}, url = {https://europepmc.org/articles/PMC12484048}, @@ -2358,11 +2465,30 @@ @article{berlanga_changes_2025 year = {2025} } -@article{berns_homozygous_2024, +@article{berlanga_disentangling_2025, + abstract = {Gut microbiota enable wood-feeding insects to digest recalcitrant diets. Two DNA-based analyses were performed. Amplicon sequencing of gut microbiota samples from Cryptocercus punctulatus showed inter-individual heterogeneity with visually distinct ordination patterns; however, no statistically significant differences were detected. Shotgun metagenomics was used to compare the taxonomic and functional profiles of C. punctulatus gut microbiota with those of other xylophagous Dictyoptera. Despite taxonomic differences, C. punctulatus microbiota revealed functional convergence with termites (Mastotermes darwiniensis and Nasutitermes sp.). Carbohydrate metabolism was performed by different bacterial phyla across all insects. All insect species possessed metabolic potential for cellulose, hemicellulose, pectin, and starch digestion, but lignin degradation capabilities were not detected. Termites showed higher abundance of chitin and xylan degradation pathways and nitrogen fixation genes, though nitrogen fixation was also present in Cryptocercus cockroaches. Genes for oxidative stress tolerance were present across all species but were most abundant in cockroaches, particularly, Cryptocercus. All insects harbored antibiotic resistance genes, with highest levels found in cockroaches. These findings indicate that metabolic requirements for wood digestion shape gut microbial community assembly across xylophagous insects, with distinct microbial taxa contributing to cellulose and hemicellulose breakdown. Moreover, the widespread presence of antibiotic resistance genes raises concerns about the potential transmission of antibiotic resistance within insect-associated microbiomes.}, + author = {Berlanga, Mercedes and Miñana-Galbis, David and Guerrero, Ricardo}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/insects16111128}, + issn = {2075-4450}, + journal = {Insects}, + keywords = {\textit{Cryptocercus}, {\textgreater}UseGalaxy.eu, functional microbiome, gut microbiota, xylophagous dyctioptera insects}, + language = {en}, + month = {November}, + number = {11}, + pages = {1128}, + publisher = {Multidisciplinary Digital Publishing Institute}, + title = {Disentangling {Gut} {Bacterial} {Community} {Patterns} in {Cryptocercus} punctulatus and {Comparing} {Their} {Metagenomes} with {Other} {Xylophagous} {Dyctioptera} {Insects}}, + url = {https://www.mdpi.com/2075-4450/16/11/1128}, + urldate = {2025-12-26}, + volume = {16}, + year = {2025} +} + +@misc{berns_homozygous_2024, abstract = {Wnt signaling plays important roles during vertebrate development, including left-right axis specification as well as heart and kidney organogenesis. We identified a homozygous human WNT11 variant in an infant with Situs inversus totalis , complex heart defects and renal hypodysplasia, and we used Xenopus embryos to functionally characterize this variant. WNT11 c.814delG encodes a loss-of-function protein with reduced stability that lost signaling activity in vivo . This is remarkable, because the variant encodes a truncated ligand with nearly identical length and predicted structure to dominant-negative Wnts. Furthermore, we demonstrate that alteration of the truncated C-terminal end can restore stability and dominant-negative signaling activity. Our study also suggests similar functions for WNT11 in human development as described in model organisms. Therefore, biallelic WNT11 dysfunction should be considered as novel genetic cause in syndromal human phenotypes presenting with congenital heart defects and renal hypoplasia, with or without laterality defects. The work presented here enhances our understanding of human development and structure-function relationships in Wnt ligands.}, author = {Berns, Henrike and Haas, Maximilian and Bakey, Zeineb and Brislinger-Engelhardt, Magdalena Maria and Schmidts, Miriam and Walentek, Peter}, doi = {10.1101/2024.11.14.623711}, - journal = {bioRxiv}, keywords = {{\textgreater}UseGalaxy.eu}, title = {A homozygous {humanWNT11loss}-of-function variant associated with laterality, heart and renal defects}, url = {http://europepmc.org/abstract/PPR/PPR939784}, @@ -2424,9 +2550,9 @@ @article{besson_pan-flavivirus_2024 journal = {Journal of Virology}, keywords = {{\textgreater}UseGalaxy.eu}, month = {October}, - note = {Publisher: American Society for Microbiology}, number = {0}, pages = {e01215--24}, + publisher = {American Society for Microbiology}, title = {Pan-flavivirus analysis reveals {sfRNA}-independent, 3′ {UTR}-biased {siRNA} production from an insect-specific flavivirus}, url = {https://journals.asm.org/doi/abs/10.1128/jvi.01215-24}, urldate = {2024-10-19}, @@ -2459,9 +2585,8 @@ @article{bhuiyan_taf2_2025 keywords = {{\textgreater}UseGalaxy.eu}, language = {English}, month = {May}, - note = {Publisher: Elsevier}, number = {5}, - pmid = {40287942}, + publisher = {Elsevier}, title = {{TAF2} condensation in nuclear speckles links basal transcription factor {TFIID} to {RNA} splicing factors}, url = {https://www.cell.com/cell-reports/abstract/S2211-1247(25)00387-0}, urldate = {2025-05-29}, @@ -2477,9 +2602,9 @@ @article{bianconi_characterization_2024 journal = {Microbial Drug Resistance}, keywords = {{\textgreater}UseGalaxy.eu}, month = {February}, - note = {Publisher: Mary Ann Liebert, Inc., publishers}, number = {2}, pages = {91--100}, + publisher = {Mary Ann Liebert, Inc., publishers}, title = {Characterization of {Verona} {Integron}-{Encoded} {Metallo}-β-{Lactamase}-{Type} {Carbapenemase}-{Producing} {Escherichia} coli {Isolates} {Collected} over a 16-{Year} {Period} in {Bolzano} ({Northern} {Italy})}, url = {https://www.liebertpub.com/doi/abs/10.1089/mdr.2023.0197}, urldate = {2024-04-28}, @@ -2524,9 +2649,9 @@ @article{bihani_metaproteomic_2023 journal = {Journal of Proteome Research}, keywords = {{\textgreater}UseGalaxy.eu}, month = {August}, - note = {Publisher: American Chemical Society}, number = {8}, pages = {2608--2619}, + publisher = {American Chemical Society}, title = {Metaproteomic {Analysis} of {Nasopharyngeal} {Swab} {Samples} to {Identify} {Microbial} {Peptides} in {COVID}-19 {Patients}}, url = {https://doi.org/10.1021/acs.jproteome.3c00040}, urldate = {2024-11-17}, @@ -2541,7 +2666,7 @@ @incollection{bihani_metaproteomics_2024 booktitle = {Metaproteomics: {Methods} and {Protocols}}, doi = {10.1007/978-1-0716-3910-8_15}, editor = {Salerno, Carlo}, - isbn = {978-1-07-163910-8}, + isbn = {978-1-0716-3910-8}, keywords = {{\textgreater}UseGalaxy.eu}, language = {en}, pages = {165--185}, @@ -2563,10 +2688,10 @@ @article{biswas_integrated_2023 keywords = {{\textgreater}UseGalaxy.eu, apoptosis, extracellular matrix organization (EMO), integrated-omics, integrin-linked kinase (ILK), meningioma, meta-analysis, proteomics, transcriptomics}, language = {en}, month = {January}, - note = {Number: 20 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 20}, number = {20}, pages = {2483}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Integrated {Meta}-{Omics} {Analysis} {Unveils} the {Pathways} {Modulating} {Tumorigenesis} and {Proliferation} in {High}-{Grade} {Meningioma}}, url = {https://www.mdpi.com/2073-4409/12/20/2483}, urldate = {2024-11-17}, @@ -2574,11 +2699,10 @@ @article{biswas_integrated_2023 year = {2023} } -@article{black_genome-wide_2024, +@misc{black_genome-wide_2024, abstract = {When exposed single-stranded DNA accumulates at stalled or collapsed replication forks, the replication stress response is triggered to prevent genome instability. Leishmania are parasitic eukaryotes where gene expression is universally polycistronic and whose plastic genomes facilitate rapid adaptations in response to stress, with evidence implicating intrinsic replication stress as a source. Little is known about the Leishmania replication stress response. In this study, we reveal the global dynamics of the replication stress response in L. major promastigotes by performing ChIP-seq on three key replication stress response proteins, γH2A, RPA1 and RAD9, in the absence and presence of replication stress. We show that common ‘hotspots’ of replication stress correlate with DNA replication initiation and transcription termination in Leishmania . When DNA replication is stalled, replication stress response factors accumulate at early S-phase origins, with a signal pattern reminiscent of bidirectional replication fork progression. Under conditions of chronic replication stress, increased accumulation of replication stress response factors emerges at wider sites of transcription initiation, suggesting Leishmania may possess compensatory strategies to limit the effects of replication stress and ensure DNA replication can complete under these conditions. In contrast, chronic replication stress enhances RSR factor accumulation at transcription termination sites, highlighting these regions as key replication stress ‘hotspots’ in Leishmania . Lastly, variations in RPA dynamics in ATR-deficient cells uncover crucial roles of this protein kinase in managing polycistronic transcription and DNA replication, particularly under replication stress, in Leishmania . {\textless}h4{\textgreater}Summary{\textless}/h4{\textgreater} Strict controls operate to precisely copy an organism’s DNA. However, cells need ways to rapidly adapt and respond to stimuli. In some cases, these beneficial adaptations come from problems during replication. Leishmania parasites cause serious neglected infections in humans and animals across the world’s tropics and sub-tropics. Remarkably, recent evidence suggests that Leishmania DNA experiences enhanced stress during replication that can drive its ability to rapidly adapt in response to stress. How L eishmania respond to DNA replication stress is still poorly understood. Here, using a genome-wide approach to map the locations of key proteins that manage DNA replication stress and maintain genome integrity, we show ‘hotspots’ of DNA replication stress coincide with start sites of DNA replication and regions of transcription termination.}, author = {Black, J.A. and Virgilio, S and Bastos, M.S. and Silva, G.L.A. and Damasceno, J.D. and Lapsley, C and McCulloch, R and Tosi, L.R.O.}, doi = {10.1101/2024.11.04.621868}, - journal = {bioRxiv}, keywords = {{\textgreater}UseGalaxy.eu}, title = {Genome-wide mapping of {RPA1} and {RAD9} reveals the management of polycistronic transcription, replication initiation, and responses to replication stress {inLeishmania}}, url = {http://europepmc.org/abstract/PPR/PPR935225}, @@ -2635,9 +2759,9 @@ @article{blomberg_connecting_2020 keywords = {+RefPublic, +Stellar, {\textgreater}UseGalaxy.eu, Pandemics}, language = {en}, month = {May}, - note = {Publisher: Nature Publishing Group}, number = {6}, pages = {1--5}, + publisher = {Nature Publishing Group}, shorttitle = {Connecting data, tools and people across {Europe}}, title = {Connecting data, tools and people across {Europe}: {ELIXIR}’s response to the {COVID}-19 pandemic}, url = {https://www.nature.com/articles/s41431-020-0637-5}, @@ -2717,7 +2841,7 @@ @incollection{boeckman_phage_2024 booktitle = {Bacteriophages: {Methods} and {Protocols}}, doi = {10.1007/978-1-0716-3549-0_8}, editor = {Tumban, Ebenezer}, - isbn = {978-1-07-163549-0}, + isbn = {978-1-0716-3549-0}, keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, Bacteriophage, DNA sequence assembly, Genomics, Phage, Whole-genome sequencing}, language = {en}, pages = {125--144}, @@ -2729,6 +2853,24 @@ @incollection{boeckman_phage_2024 year = {2024} } +@article{bogaerts_galaxy_2025, + abstract = {The influx of whole genome sequencing (WGS) data in the public health and clinical diagnostic sectors has created a need for data analysis methods and bioinformatics expertise, which can be a bottleneck for many laboratories. At Sciensano, the Belgian national public health institute, an intuitive and user-friendly bioinformatics tool portal was implemented using Galaxy, an open-source platform for data analysis and workflow creation. The Galaxy @Sciensano instance is available to both internal and external scientists and offers a wide range of tools provided by the community, complemented by over 50 custom tools and pipelines developed in-house. The tool selection is currently focused primarily on the analysis of WGS data generated using Illumina sequencing for microbial pathogen typing, characterization and outbreak detection, but it also addresses specific use cases for other data types. Our Galaxy instance includes several custom-developed 'push-button' pipelines, which are user-friendly and intuitive stand-alone tools that perform complete characterization of bacterial isolates based on WGS data and generate interactive HTML output reports with key findings. These pipelines include quality control, de novo assembly, sequence typing, antimicrobial resistance prediction and several relevant species-specific assays. They are tailored for pathogens with active genomic surveillance programs, and clinical relevance, such as Escherichia coli, Listeria monocytogenes, Salmonella spp. and Mycobacterium tuberculosis. These tools and pipelines utilize internationally recognized databases such as PubMLST, EnteroBase, and the NCBI National Database of Antibiotic Resistant Organisms, which are automatically synchronized on a regular basis to ensure up-to-date results. Many of these pipelines are part of the routine activities of Belgian national reference centers and laboratories, some of which use them under ISO accreditation. This resource is publicly available for noncommercial use at https://galaxy.sciensano.be/and can help other laboratories establish reliable, traceable and reproducible bioinformatics analyses for pathogens encountered in public health settings.}, + author = {Bogaerts, Bert and Van Braekel, Julien and Van Uffelen, Alexander and D’aes, Jolien and Godfroid, Maxime and Delcourt, Thomas and Kelchtermans, Michael and Milis, Kato and Goeders, Nathalie and De Keersmaecker, Sigrid C. J. and Roosens, Nancy H. C. and Winand, Raf and Vanneste, Kevin}, + doi = {10.1186/s12864-024-11182-5}, + issn = {1471-2164}, + journal = {BMC Genomics}, + keywords = {{\textgreater}UseGalaxy.eu, Computational Biology, Disease Outbreaks, Galaxy, Genomic surveillance, Genomics, Public health, Software, Whole genome sequencing}, + month = {January}, + number = {1}, + pages = {20}, + shorttitle = {Galaxy @{Sciensano}}, + title = {Galaxy @{Sciensano}: a comprehensive bioinformatics portal for genomics-based microbial typing, characterization, and outbreak detection}, + url = {https://doi.org/10.1186/s12864-024-11182-5}, + urldate = {2025-01-19}, + volume = {26}, + year = {2025} +} + @article{bogguri_biphasic_2024, abstract = {{\textless}p{\textgreater}Organophosphorus nerve agents (OPNA) are hazardous environmental exposures to the civilian population and have been historically weaponized as chemical warfare agents (CWA). OPNA exposure can lead to several neurological, sensory, and motor symptoms that can manifest into chronic neurological illnesses later in life. There is still a large need for technological advancement to better understand changes in brain function following OPNA exposure. The human-relevant {\textless}italic{\textgreater}in vitro{\textless}/italic{\textgreater} multi-electrode array (MEA) system, which combines the MEA technology with human stem cell technology, has the potential to monitor the acute, sub-chronic, and chronic consequences of OPNA exposure on brain activity. However, the application of this system to assess OPNA hazards and risks to human brain function remains to be investigated. In a concentration-response study, we have employed a human-relevant MEA system to monitor and detect changes in the electrical activity of engineered neural networks to increasing concentrations of the sarin surrogate 4-nitrophenyl isopropyl methylphosphonate (NIMP). We report a biphasic response in the spiking (but not bursting) activity of neurons exposed to low (i.e., 0.4 and 4 μM) versus high concentrations (i.e., 40 and 100 μM) of NIMP, which was monitored during the exposure period and up to 6 days post-exposure. Regardless of the NIMP concentration, at a network level, communication or coordination of neuronal activity decreased as early as 60 min and persisted at 24 h of NIMP exposure. Once NIMP was removed, coordinated activity was no different than control (0 μM of NIMP). Interestingly, only in the high concentration of NIMP did coordination of activity at a network level begin to decrease again at 2 days post-exposure and persisted on day 6 post-exposure. Notably, cell viability was not affected during or after NIMP exposure. Also, while the catalytic activity of AChE decreased during NIMP exposure, its activity recovered once NIMP was removed. Gene expression analysis suggests that human iPSC-derived neurons and primary human astrocytes resulted in altered genes related to the cell’s interaction with the extracellular environment, its intracellular calcium signaling pathways, and inflammation, which could have contributed to how neurons communicated at a network level.{\textless}/p{\textgreater}}, author = {Bogguri, Chandrakumar and George, Vivek Kurien and Amiri, Beheshta and Ladd, Alexander and Hum, Nicholas R. and Sebastian, Aimy and Enright, Heather A. and Valdez, Carlos A. and Mundhenk, T. Nathan and Cadena, Jose and Lam, Doris}, @@ -2738,7 +2880,7 @@ @article{bogguri_biphasic_2024 keywords = {{\textgreater}UseGalaxy.eu, Acute exposure, Human Induced Pluripotent Stem Cells, Microphysiological systems, Multi-Electrode Array, human neuronal activity, nerve agent, organophosphate}, language = {English}, month = {September}, - note = {Publisher: Frontiers}, + publisher = {Frontiers}, title = {Biphasic response of human {iPSC}-derived neural network activity following exposure to a sarin-surrogate nerve agent}, url = {https://www.frontiersin.org/journals/cellular-neuroscience/articles/10.3389/fncel.2024.1378579/full}, urldate = {2024-11-17}, @@ -2754,7 +2896,7 @@ @article{bohlender_stable_2020 journal = {Frontiers in Plant Science}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Glyco-engineering, N-glycan humanization, N-glycan sialylation, PMP, glyco-optimization, plant-made pharmaceuticals, plant-made recombinant biopharmaceuticals}, language = {English}, - note = {Publisher: Frontiers}, + publisher = {Frontiers}, title = {Stable {Protein} {Sialylation} in {Physcomitrella}}, url = {https://www.frontiersin.org/articles/10.3389/fpls.2020.610032/full}, urldate = {2021-05-12}, @@ -2848,9 +2990,9 @@ @article{boneva_3_2020 keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Gene Expression Profiling, Tissue Preservation}, language = {en}, month = {May}, - note = {Publisher: Nature Publishing Group}, number = {10}, pages = {1--11}, + publisher = {Nature Publishing Group}, title = {3′ {MACE} {RNA}-sequencing allows for transcriptome profiling in human tissue samples after long-term storage}, url = {https://www.nature.com/articles/s41374-020-0446-z}, urldate = {2020-08-12}, @@ -2868,10 +3010,10 @@ @article{boneva_mace_2020 keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Transcriptome}, language = {en}, month = {December}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {21292}, + publisher = {Nature Publishing Group}, title = {{MACE} {RNA} sequencing analysis of conjunctival squamous cell carcinoma and papilloma using formalin-fixed paraffin-embedded tumor tissue}, url = {https://www.nature.com/articles/s41598-020-78339-6}, urldate = {2021-04-08}, @@ -2905,8 +3047,8 @@ @article{boneva_transcriptional_2020 journal = {Frontiers in Immunology}, keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Gene Expression Profiling, Hyalocytes, Immune Privilege, Immunity, Innate, Myeloid Cells, Transcriptome, Viterous Body, Vitreous Macrophages, innate immunity}, language = {English}, - note = {Publisher: Frontiers}, pages = {567274}, + publisher = {Frontiers}, title = {Transcriptional {Profiling} {Uncovers} {Human} {Hyalocytes} as a {Unique} {Innate} {Immune} {Cell} {Population}}, url = {https://www.frontiersin.org/articles/10.3389/fimmu.2020.567274/full}, urldate = {2021-05-15}, @@ -2921,9 +3063,9 @@ @article{boondech_complete_2025 issn = {2516-8290}, journal = {Access Microbiology}, keywords = {{\textgreater}UseGalaxy.eu}, - note = {Publisher: Microbiology Society,}, number = {6}, pages = {000986.v4}, + publisher = {Microbiology Society,}, title = {Complete genome and comparative analysis of {Xanthomonas} oryzae pv. oryzae isolated from northern {Thailand}}, url = {https://www.microbiologyresearch.org/content/journal/acmi/10.1099/acmi.0.000986.v4}, urldate = {2025-07-12}, @@ -2940,9 +3082,9 @@ @article{borchel_sex_2022 keywords = {{\textgreater}UseGalaxy.eu, Copepoda, Eggs, Fish Diseases, Gene expression, Heterozygosity, Lice, Molting, Polymerase chain reaction, Sex ratio, Single nucleotide polymorphisms}, language = {en}, month = {March}, - note = {Publisher: Public Library of Science}, number = {3}, pages = {e0266022}, + publisher = {Public Library of Science}, shorttitle = {Sex differences in the early life stages of the salmon louse {Lepeophtheirus} salmonis ({Copepoda}}, title = {Sex differences in the early life stages of the salmon louse {Lepeophtheirus} salmonis ({Copepoda}: {Caligidae})}, url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0266022}, @@ -2990,15 +3132,15 @@ @article{bose_trna_2020 @article{bossche_critical_2021, abstract = {{\textless}p{\textgreater}Metaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear. Here, we carried out the first community-driven, multi-lab comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluated the effect of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, lab-assembled human intestinal model and a human fecal sample. We observed that variability at the peptide level was predominantly due to wet-lab workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappeared at protein group level. While differences were observed for predicted community composition, similar functional profiles were obtained across workflows. CAMPI demonstrates the robustness of present-day metaproteomics research, serves as a template for multi-lab studies in metaproteomics, and provides publicly available data sets for benchmarking future developments.{\textless}/p{\textgreater}}, author = {Bossche, Tim Van Den and Kunath, Benoit J. and Schallert, Kay and Schäpe, Stephanie S. and Abraham, Paul E. and Armengaud, Jean and Arntzen, Magnus Ø and Bassignani, Ariane and Benndorf, Dirk and Fuchs, Stephan and Giannone, Richard J. and Griffin, Timothy J. and Hagen, Live H. and Halder, Rashi and Henry, Céline and Hettich, Robert L. and Heyer, Robert and Jagtap, Pratik and Jehmlich, Nico and Jensen, Marlene and Juste, Catherine and Kleiner, Manuel and Langella, Olivier and Lehmann, Theresa and Leith, Emma and May, Patrick and Mesuere, Bart and Miotello, Guylaine and Peters, Samantha L. and Pible, Olivier and Reichl, Udo and Renard, Bernhard Y. and Schiebenhoefer, Henning and Scryba, Alexander and Tanca, Alessandro and Trappe, Kathrin and Trezzi, Jean-Pierre and Uzzau, Sergio and Verschaffelt, Pieter and Bergen, Martin von and Wilmes, Paul and Wolf, Maximilian and Martens, Lennart and Muth, Thilo}, + chapter = {New Results}, copyright = {© 2021, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/}, doi = {10.1101/2021.03.05.433915}, journal = {bioRxiv}, keywords = {+Methods, +UsePublic, {\textgreater}Galaxy-P, {\textgreater}UseGalaxy.eu}, language = {en}, month = {March}, - note = {Publisher: Cold Spring Harbor Laboratory -Section: New Results}, pages = {2021.03.05.433915}, + publisher = {Cold Spring Harbor Laboratory}, shorttitle = {Critical {Assessment} of {Metaproteome} {Investigation} ({CAMPI})}, title = {Critical {Assessment} of {Metaproteome} {Investigation} ({CAMPI}): {A} {Multi}-{Lab} {Comparison} of {Established} {Workflows}}, url = {https://www.biorxiv.org/content/10.1101/2021.03.05.433915v1}, @@ -3031,9 +3173,9 @@ @article{boulogne_meta-analysis_2025 keywords = {{\textgreater}Plant Galaxy, {\textgreater}UseGalaxy.eu, Bioinformatics, Glycobiology, Marine biology, RNA}, language = {en}, month = {January}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {3603}, + publisher = {Nature Publishing Group}, title = {Meta-analysis of {RNA}-{Seq} datasets allows a better understanding of {P}. tricornutum cellular biology, a requirement to improve the production of {Biologics}}, url = {https://www.nature.com/articles/s41598-025-87620-5}, urldate = {2025-02-01}, @@ -3088,15 +3230,23 @@ @article{bovio_isolation_2018 year = {2018} } -@article{bowran_novel_2023, - abstract = {{\textless}h4{\textgreater}ABSTRACT{\textless}/h4{\textgreater} The Type VIIb protein secretion system (T7SSb) is found in Bacillota (firmicute) bacteria and has been shown to mediate interbacterial competition. EssC is a membrane-bound ATPase that is a critical component of the T7SSb and plays a key role in substrate recognition. Prior analysis of available genome sequences of the foodborne bacterial pathogen Listeria monocytogenes has shown that although the T7SSb was encoded as part of the core genome, EssC could be found as one of seven different sequence variants. While each sequence variant was associated with a specific suite of candidate substrate proteins encoded immediately downstream of essC , many LXG-domain proteins were encoded across multiple essC sequence variants. Here we have extended this analysis using a diverse collection of 37,930 L. monocytogenes genomes. We have identified a rare eighth variant of EssC present in ten L. monocytogenes Lineage III genomes. These genomes also encode a large toxin of the rearrangement hotspot (Rhs) repeat family adjacent to essC8 , along with a probable immunity protein and three small accessory proteins. We have further identified nine novel LXG-domain proteins, and four additional chromosomal hotspots across L. monocytogenes genomes where LXG proteins can be encoded. The eight L. monocytogenes EssC variants were also found in other Listeria species, with additional novel EssC types also identified. Across the genus, species frequently encoded multiple EssC types, indicating that T7SSb diversity is a primary feature of the genus Listeria . {\textless}h4{\textgreater}DATA SUMMARY{\textless}/h4{\textgreater} All genome sequences used in this study are available via Genbank, and the assembly accession numbers are provided in Table S1. This file also lists relevant metadata (name, source category, country, year and clonal complex). {\textless}h4{\textgreater}IMPACT STATEMENT{\textless}/h4{\textgreater} Listeria monocytogenes is a soil-borne saprophytic bacterium and a food-borne pathogen of humans. Decomposing plant matter and the human GI tract are rich in diverse microbial species and to colonise these niches L. monocytogenes must be able to compete with other bacteria. The type VII secretion system (T7SS) of Bacillota has been shown to secrete protein toxins that target other bacteria. In this study we have analysed a diverse collection of L. monocytogenes genome sequences to study the diversity of the Listeria T7SS and its putative effector proteins. We show that the EssC component of the L. monocytogenes T7SS is highly diverse, clustering into one of eight sequence variants. Each EssC variant is associated with a specific toxin candidate, and the EssC8 variant T7SS likely secretes a novel rearrangement hotspot (Rhs) repeat toxin. We also identify multiple new LXG-families of T7SS toxins and describe genomic hotspots where they are encoded. We find no link between EssC variants and clinical outcome. In agreement with this, analysis of EssC variability in available genomes of other Listeria species showed that all eight L. monocytogenes EssC variants are present in non-monocytogenes Listeria species.}, - author = {Bowran, Kieran and Garrett, Stephen and Vliet, Arnoud van and Palmer, Tracy}, - doi = {10.1101/2023.02.17.528482}, - journal = {bioRxiv}, - keywords = {{\textgreater}UseGalaxy.eu}, - title = {A novel variant of {theListeria} monocytogenestype {VII} secretion system {EssC} component is associated with an {Rhs} toxin}, - url = {http://europepmc.org/abstract/PPR/PPR618080}, - year = {2023} +@article{bowden_foxi1_2026, + abstract = {Foxi1 is a master regulator of ionocytes (ISCs/INCs) across species and organs. Two subtypes of ISCs exist, and both α- and β-ISCs regulate pH- and ion-homeostasis in epithelia. Gain and loss of FOXI1 function are associated with human diseases, including Pendred syndrome, male infertility, renal acidosis, and cancers. Foxi1 was predominantly studied in the context of ISC specification, however, reports indicate additional functions in early and ectodermal development. Here, we re-investigated the functions of Foxi1 in Xenopus laevis embryonic mucociliary epidermis developpment and found a novel function for Foxi1 in the generation of Notch-ligand expressing mucociliary multipotent progenitors (MPPs). We demonstrate that MPPs are a distinct sub-population of epidermal cells in which Foxi1 has two concentration-dependent functions: At low levels, Foxi1 maintains ectodermal competence in MPPs through transcriptional and epigenetic mechanisms, while at high levels, Foxi1 induces a multi-step process of ISC specification and differentiation in cooperation with Ubp1 and Dmrt2. We further describe how foxi1 expression is affected through auto- and Notch-regulation, and how this developmental program affects mucociliary patterning. Together, we reveal novel functions for MPPs and Foxi1 in Xenopus mucociliary epidermis formation, relevant to our understanding of vertebrate development and human disease.}, + author = {Bowden, Sarah and Brislinger-Engelhardt, Magdalena Maria and Hansen, Mona and Andricek, Aisha and Temporal-Plo, Africa and Weber, Damian and Hägele, Sandra and Lorenz, Fabian and Litwin, Tim and Kreutz, Clemens and Walentek, Peter}, + doi = {10.1371/journal.pbio.3003583}, + issn = {1545-7885}, + journal = {PLOS Biology}, + keywords = {{\textgreater}UseGalaxy.eu, Cell differentiation, Embryos, Epidermis, Gene expression, Organoids, Transcription factors, Transcriptional control, Xenopus}, + language = {en}, + month = {May}, + number = {1}, + pages = {e3003583}, + publisher = {Public Library of Science}, + title = {Foxi1 regulates multipotent mucociliary progenitors and ionocyte specification through transcriptional and epigenetic mechanisms}, + url = {https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3003583}, + urldate = {2026-01-09}, + volume = {24}, + year = {2026} } @article{bowran_novel_2023, @@ -3106,9 +3256,9 @@ @article{bowran_novel_2023 issn = {2057-5858}, journal = {Microbial Genomics}, keywords = {{\textgreater}UseGalaxy.eu, Listeria monocytogenes, Type VII Secretion Systems}, - note = {Publisher: Microbiology Society,}, number = {6}, pages = {001036}, + publisher = {Microbiology Society,}, title = {A novel variant of the {Listeria} monocytogenes type {VII} secretion system {EssC} component is associated with an {Rhs} toxin}, url = {https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001036}, urldate = {2024-11-17}, @@ -3116,6 +3266,17 @@ @article{bowran_novel_2023 year = {2023} } +@article{bowran_novel_2023, + abstract = {{\textless}h4{\textgreater}ABSTRACT{\textless}/h4{\textgreater} The Type VIIb protein secretion system (T7SSb) is found in Bacillota (firmicute) bacteria and has been shown to mediate interbacterial competition. EssC is a membrane-bound ATPase that is a critical component of the T7SSb and plays a key role in substrate recognition. Prior analysis of available genome sequences of the foodborne bacterial pathogen Listeria monocytogenes has shown that although the T7SSb was encoded as part of the core genome, EssC could be found as one of seven different sequence variants. While each sequence variant was associated with a specific suite of candidate substrate proteins encoded immediately downstream of essC , many LXG-domain proteins were encoded across multiple essC sequence variants. Here we have extended this analysis using a diverse collection of 37,930 L. monocytogenes genomes. We have identified a rare eighth variant of EssC present in ten L. monocytogenes Lineage III genomes. These genomes also encode a large toxin of the rearrangement hotspot (Rhs) repeat family adjacent to essC8 , along with a probable immunity protein and three small accessory proteins. We have further identified nine novel LXG-domain proteins, and four additional chromosomal hotspots across L. monocytogenes genomes where LXG proteins can be encoded. The eight L. monocytogenes EssC variants were also found in other Listeria species, with additional novel EssC types also identified. Across the genus, species frequently encoded multiple EssC types, indicating that T7SSb diversity is a primary feature of the genus Listeria . {\textless}h4{\textgreater}DATA SUMMARY{\textless}/h4{\textgreater} All genome sequences used in this study are available via Genbank, and the assembly accession numbers are provided in Table S1. This file also lists relevant metadata (name, source category, country, year and clonal complex). {\textless}h4{\textgreater}IMPACT STATEMENT{\textless}/h4{\textgreater} Listeria monocytogenes is a soil-borne saprophytic bacterium and a food-borne pathogen of humans. Decomposing plant matter and the human GI tract are rich in diverse microbial species and to colonise these niches L. monocytogenes must be able to compete with other bacteria. The type VII secretion system (T7SS) of Bacillota has been shown to secrete protein toxins that target other bacteria. In this study we have analysed a diverse collection of L. monocytogenes genome sequences to study the diversity of the Listeria T7SS and its putative effector proteins. We show that the EssC component of the L. monocytogenes T7SS is highly diverse, clustering into one of eight sequence variants. Each EssC variant is associated with a specific toxin candidate, and the EssC8 variant T7SS likely secretes a novel rearrangement hotspot (Rhs) repeat toxin. We also identify multiple new LXG-families of T7SS toxins and describe genomic hotspots where they are encoded. We find no link between EssC variants and clinical outcome. In agreement with this, analysis of EssC variability in available genomes of other Listeria species showed that all eight L. monocytogenes EssC variants are present in non-monocytogenes Listeria species.}, + author = {Bowran, Kieran and Garrett, Stephen and Vliet, Arnoud van and Palmer, Tracy}, + doi = {10.1101/2023.02.17.528482}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {A novel variant of {theListeria} monocytogenestype {VII} secretion system {EssC} component is associated with an {Rhs} toxin}, + url = {http://europepmc.org/abstract/PPR/PPR618080}, + year = {2023} +} + @misc{boyer_pulsar_2024, abstract = {Recent evidence for the stochastic gravitational wave backgorund reported by the pulsar timing arrays (PTA) can be interpreted as a signal from the cosmological phase transition. We use up-to-date models of the gravitational wave power spectra to compare constraints on the parameters of the phase transition for the three different available PTA measurements and to work out a refined estimate of the cosmological magnetic field that should result from this transition. We find that the PTA data, combined with a constraint from the abundance of primordial black holes, are consistent with a possibility of a moderate strength first-order phase transition during quark confinement and yield a rather precise prediction for the initial parameters of the magnetic field, with the magnetic field energy density in near equipartition with photon energy density and correlation length close to one co-moving parsec.}, author = {Boyer, T. and Neronov, A.}, @@ -3172,7 +3333,7 @@ @article{bray_chemicaltoolbox_2020 doi = {10.1186/s13321-020-00442-7}, issn = {1758-2946}, journal = {Journal of Cheminformatics}, - keywords = {+Galactic, +IsGalaxy, +Tools, {\textgreater}ChemicalToolbox}, + keywords = {+Galactic, +IsGalaxy, +Tools, {\textgreater}ChemicalToolbox, {\textgreater}UseGalaxy.eu}, language = {eng}, month = {June}, number = {1}, @@ -3210,7 +3371,7 @@ @article{bray_intuitive_2020 doi = {10.1186/s13321-020-00451-6}, issn = {1758-2946}, journal = {Journal of Cheminformatics}, - keywords = {+Galactic, +HowTo, +IsGalaxy, +Shared, {\textgreater}BRIDGE, {\textgreater}ChemicalToolbox, Galaxy, Molecular Dynamics, Reproducible}, + keywords = {+Galactic, +HowTo, +IsGalaxy, +Shared, {\textgreater}BRIDGE, {\textgreater}ChemicalToolbox, {\textgreater}UseGalaxy.eu, Galaxy, Molecular Dynamics, Reproducible}, language = {eng}, month = {September}, number = {1}, @@ -3223,6 +3384,29 @@ @article{bray_intuitive_2020 year = {2020} } +@article{bray_planemo_2023, + abstract = {There are thousands of well-maintained high-quality open-source software utilities for all aspects of scientific data analysis. For more than a decade, the Galaxy Project has been providing computational infrastructure and a unified user interface for these tools to make them accessible to a wide range of researchers. To streamline the process of integrating tools and constructing workflows as much as possible, we have developed Planemo, a software development kit for tool and workflow developers and Galaxy power users. Here we outline Planemo's implementation and describe its broad range of functionality for designing, testing, and executing Galaxy tools, workflows, and training material. In addition, we discuss the philosophy underlying Galaxy tool and workflow development, and how Planemo encourages the use of development best practices, such as test-driven development, by its users, including those who are not professional software developers.}, + author = {Bray, Simon and Chilton, John and Bernt, Matthias and Soranzo, Nicola and Beek, Marius van den and Batut, Bérénice and Rasche, Helena and Čech, Martin and Cock, Peter J. A. and Grüning, Björn and Nekrutenko, Anton}, + doi = {10.1101/gr.276963.122}, + issn = {1088-9051, 1549-5469}, + journal = {Genome Research}, + keywords = {{\textgreater}UseGalaxy.eu, Computational Biology, Software}, + language = {en}, + month = {February}, + note = {Company: Cold Spring Harbor Laboratory Press +Distributor: Cold Spring Harbor Laboratory Press +Institution: Cold Spring Harbor Laboratory Press +Label: Cold Spring Harbor Laboratory Press}, + number = {2}, + pages = {261--268}, + publisher = {Cold Spring Harbor Lab}, + title = {The {Planemo} toolkit for developing, deploying, and executing scientific data analyses in {Galaxy} and beyond}, + url = {https://genome.cshlp.org/content/33/2/261}, + urldate = {2023-06-05}, + volume = {33}, + year = {2023} +} + @phdthesis{breidenbach_harmful_2023, author = {Breidenbach, Joshua David}, keywords = {{\textgreater}UseGalaxy.eu}, @@ -3279,9 +3463,9 @@ @article{breunis_patient-derived_2025 keywords = {{\textgreater}UseGalaxy.eu, Myeloid Cell Leukemia Sequence 1 Protein, Sarcoma, Sarcoma, Ewing, Targeted therapies}, language = {en}, month = {August}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {7688}, + publisher = {Nature Publishing Group}, shorttitle = {Patient-derived tumoroids from {CIC}}, title = {Patient-derived tumoroids from {CIC}::{DUX4} rearranged sarcoma identify {MCL1} as a therapeutic target}, url = {https://www.nature.com/articles/s41467-025-62629-6}, @@ -3300,8 +3484,8 @@ @article{bright_temporal_2025 keywords = {{\textgreater}UseGalaxy.eu, Cell fate and cell lineage, GABAergic Neurons, Genetics of the nervous system, Neural Stem Cells, Neurogenesis, Telencephalon}, language = {en}, month = {July}, - note = {Publisher: Nature Publishing Group}, pages = {1--13}, + publisher = {Nature Publishing Group}, title = {Temporal control of progenitor competence shapes maturation in {GABAergic} neuron development in mice}, url = {https://www.nature.com/articles/s41593-025-01999-y}, urldate = {2025-07-12}, @@ -3317,10 +3501,9 @@ @article{brimson_collective_2025 keywords = {{\textgreater}UseGalaxy.eu}, language = {English}, month = {March}, - note = {Publisher: Elsevier}, number = {6}, pages = {918--933.e4}, - pmid = {39672161}, + publisher = {Elsevier}, title = {Collective oscillatory signaling in {Dictyostelium} discoideum acts as a developmental timer initiated by weak coupling of a noisy pulsatile signal}, url = {https://www.cell.com/developmental-cell/abstract/S1534-5807(24)00698-1}, urldate = {2025-05-29}, @@ -3368,10 +3551,10 @@ @article{broche_genome-wide_2023 keywords = {{\textgreater}UseGalaxy.eu, DNA methylation, Epigenetics, Histone post-translational modifications, Transcriptional regulatory elements}, language = {en}, month = {February}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {1--12}, + publisher = {Nature Publishing Group}, title = {Genome-wide deposition of 6-methyladenine in human {DNA} reduces the viability of {HEK293} cells and directly influences gene expression}, url = {https://www.nature.com/articles/s42003-023-04466-1}, urldate = {2023-03-15}, @@ -3379,6 +3562,24 @@ @article{broche_genome-wide_2023 year = {2023} } +@article{bronnec_speckseq_2026, + abstract = {Variants of uncertain significance (VUS) are a major obstacle in genetic diagnosis, particularly when involving gain-of-function (GoF) mutations that are poorly predicted in silico. MEFV, which encodes the inflammasome sensor pyrin, is mutated in two autoinflammatory diseases, familial Mediterranean fever (FMF) and pyrin-associated autoinflammation with neutrophilic dermatosis (PAAND). Here, we developed SpeckSeq, a method that combines DNA bar-coding, ASC speck–based single-cell sorting and next-generation sequencing to systematically identify hypermorphic MEFV variants in response to different stimuli. SpeckSeq identified 49 GoF mutations separated into two distinct groups containing either PAAND variants or FMF variants. SpeckSeq was validated using patients’ cells and supported a reclassification of MEFV variant pathogenicity, leading to novel diagnoses. As a large-scale mutagenesis approach, using human genetics as a guide, SpeckSeq revealed structural and functional pyrin features, including a putative ligand-accommodating cavity in the B30.2 domain. Altogether, SpeckSeq classifies VUS to refine molecular diagnostics and improve our knowledge on the pyrin inflammasome.}, + author = {Bronnec, Pauline and Dalmon, Sarah and Briand, Chloe and Allatif, Omran and Broly, Martin and Marcotte, Melissa and Lombardi, Gianluca and Barthes, Kevin and Martel, Nora and Hughes, Sandrine and Gillet, Benjamin and Milhavet, Florian and Atilgan, Aysima and Bachelez, Hervé and Palmeri, Serena and Prigione, Ignazia and Madrange, Marine and Savey, Léa and Moutschen, Michel and Jeru, Isabelle and El Moussaoui, Majdouline and Belot, Alexandre and Sbidian, Emilie and Carbone, Alessandra and Jamilloux, Yvan and Gattorno, Marco and Smahi, Asma and Georgin-Lavialle, Sophie and Boursier, Guilaine and Magnotti, Flora and Henry, Thomas}, + doi = {10.1084/jem.20251065}, + issn = {0022-1007, 1540-9538}, + journal = {Journal of Experimental Medicine}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {February}, + number = {2}, + pages = {e20251065}, + title = {{SpeckSeq} enables high-throughput functional stratification of \textit{{MEFV}} variants in autoinflammatory diseases}, + url = {https://rupress.org/jem/article/223/2/e20251065/278546/SpeckSeq-enables-high-throughput-functional}, + urldate = {2025-12-05}, + volume = {223}, + year = {2026} +} + @article{bruck_ploidy_2023, abstract = {Vibrio natriegens is the fastest-growing bacterium, with a doubling time of approximately 12–14 min. It has a high potential for basic research and biotechnological applications, e.g., it can be used for the cell-free production of (labeled) heterologous proteins, for synthetic biological applications, and for the production of various compounds. However, the ploidy level in V. natriegens remains unknown. At nine time points throughout the growth curve, we analyzed the numbers of origins and termini of both chromosomes with qPCR and the relative abundances of all genomic sites with marker frequency analyses. During the lag phase until early exponential growth, the origin copy number and origin/terminus ratio of chromosome 1 increased severalfold, but the increase was lower for chromosome 2. This increase was paralleled by an increase in cell volume. During the exponential phase, the origin/terminus ratio and cell volume decreased again. This highly dynamic and fast regulation has not yet been described for any other species. In this study, the gene dosage increase in origin-adjacent genes during the lag phase is discussed together with the nonrandom distribution of genes on the chromosomes of V. natriegens. Taken together, the results of this study provide the first comprehensive overview of the chromosome dynamics in V. natriegens and will guide the optimization of molecular biological characterization and biotechnological applications.}, author = {Brück, Patrik and Wasser, Daniel and Soppa, Jörg}, @@ -3389,10 +3590,10 @@ @article{bruck_ploidy_2023 keywords = {\textit{Vibrio natriegens}, {\textgreater}UseGalaxy.eu, DNA Copy Number Variations, Vibrio, cell size, cell volume, chromosome copy number, dynamic regulation, growth curve, origin of replication, ploidy, polyploidy, terminus of replication}, language = {en}, month = {July}, - note = {Number: 7 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 7}, number = {7}, pages = {1437}, + publisher = {Multidisciplinary Digital Publishing Institute}, shorttitle = {Ploidy in {Vibrio} natriegens}, title = {Ploidy in {Vibrio} natriegens: {Very} {Dynamic} and {Rapidly} {Changing} {Copy} {Numbers} of {Both} {Chromosomes}}, url = {https://www.mdpi.com/2073-4425/14/7/1437}, @@ -3477,7 +3678,6 @@ @article{bruno_collisions_2023 language = {eng}, month = {December}, pages = {S1097--2765(23)01012--2}, - pmid = {38151016}, title = {Collisions of {RNA} polymerases behind the replication fork promote alternative {RNA} splicing in newly replicated chromatin}, year = {2023} } @@ -3514,6 +3714,25 @@ @article{buhl_prevotella_2020 year = {2020} } +@article{burel_trichosporon_2025, + abstract = {During 2022-2024, six cases of invasive fungal infection occurred among immunocompromised patients at Marseille University Hospital, Marseille, France. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry initially identified Trichosporon inkin fungi. However, phylogenetic analysis of intergenic spacer region 1 and whole-genome sequences revealed the genetically distinct species T. austroamericanum. Analysis of core genome and mitogenome from 6 patient isolates and 1 environmental isolate revealed substantial genetic diversity among T. austroamericanum strains, indicating a polyclonal outbreak. Furthermore, the mitochondrial genome emerged as a potential marker for intraspecies differentiation, which potentially could aid in epidemiologic investigations. Identified in 2024 but potentially underestimated, T. austroamericanum has since been reported in case clusters from hospital settings in France, highlighting the need for accurate fungal identification and suggesting previously identified T. inkin cases should be re-evaluated for T. austroamericanum. Clinical T. austroamericanum is emerging in hospital settings and should be included in the differential diagnosis of fungal infections.}, + author = {Burel, Emilie and Sartor, Catherine and Moal, Valérie and Bossi, Vincent and Sevestre, Jacques and Solignac, Justine and Charrel, Rémi and Desnos-Ollivier, Marie and Ranque, Stéphane and Menu, Estelle}, + copyright = {cc by}, + doi = {10.3201/eid3111.250503}, + issn = {1080-6059}, + journal = {Emerging infectious diseases}, + keywords = {{\textgreater}UseGalaxy.eu, Emerging Disease, France, Fungi, Opportunistic Agents, Trichosporon Austroamericanum, Trichosporonosis, Yeast, outbreak}, + language = {eng}, + month = {November}, + number = {11}, + pages = {2080--2090}, + title = {Trichosporon austroamericanum {Infections} among {Hospitalized} {Patients}, {France}, 2022-2024}, + url = {https://europepmc.org/articles/PMC12704532}, + urldate = {2025-12-26}, + volume = {31}, + year = {2025} +} + @article{busch_iclip_2019, abstract = {Precise knowledge on the binding sites of an RNA-binding protein (RBP) is key to understanding the complex post-transcriptional regulation of gene expression. This information can be obtained from individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) experiments. Here, we present a complete data analysis workflow to reliably detect RBP binding sites from iCLIP data. The workflow covers all steps from the initial quality control of the sequencing reads up to peak calling and quantification of RBP binding. For each tool, we explain the specific requirements for iCLIP data analysis and suggest optimised parameter settings.}, author = {Busch, Anke and Brüggemann, Mirko and Ebersberger, Stefanie and Zarnack, Kathi}, @@ -3540,10 +3759,10 @@ @article{buttimer_isolation_2020 keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Certrevirus, Pectobacterium atrosepticum, Vequintavirinae, homing endonuclease, phage, phytopathogen, potato blackleg, sigma70 promoter, soft rot disease}, language = {en}, month = {June}, - note = {Number: 6 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 6}, number = {6}, pages = {352}, + publisher = {Multidisciplinary Digital Publishing Institute}, shorttitle = {Isolation and {Characterization} of {Pectobacterium} {Phage} {vB}\_PatM\_CB7}, title = {Isolation and {Characterization} of {Pectobacterium} {Phage} {vB}\_PatM\_CB7: {New} {Insights} into the {Genus} {Certrevirus}}, url = {https://www.mdpi.com/2079-6382/9/6/352}, @@ -3552,6 +3771,23 @@ @article{buttimer_isolation_2020 year = {2020} } +@article{cacchiarelli_association_2026, + author = {Cacchiarelli, Paolo and Goytia Bertero, Valentina and Garcia Labari, Ignacio and Arce, Débora P. and Tapia, Elizabeth and Pratta, Guillermo R.}, + doi = {10.1007/s10722-025-02672-w}, + issn = {0925-9864, 1573-5109}, + journal = {Genetic Resources and Crop Evolution}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {February}, + number = {2}, + pages = {85}, + title = {Association between molecular and quantitative variability in a tomato broad cross identified by sequence-specific markers developed from transcriptomic polymorphism for the small {Heat} {Shock} {Protein} ({sHSP}) cluster in chromosome six}, + url = {https://link.springer.com/10.1007/s10722-025-02672-w}, + urldate = {2026-01-11}, + volume = {73}, + year = {2026} +} + @article{camacho-beltran_complete_2024, abstract = {We purified a lytic bacteriophage from soil collected in Guasave, Sinaloa: phiExGM16. This bacteriophage was isolated using the host, \textit{Exiguobacterium acetilycum}. Its 17.6 kb genome contains 33 putative genes and shows a cover of 64\% with 76.37\% of nucleotide identity to \textit{Microbacterium phage} Noelani.}, author = {Camacho-Beltrán, Erika and Morales-Aguilar, Juan José and López-Meyer, Melina and Rincón-Enríquez, Gabriel and Quiñones-Aguilar, Evangelina Esmeralda}, @@ -3569,15 +3805,15 @@ @article{camacho-beltran_complete_2024 year = {2024} } -@article{camacho-beltran_complete_2024, +@article{camacho-beltran_complete_2024-1, author = {Camacho-Beltrán, Erika and Morales-Aguilar, Juan José and López-Meyer, Melina and Rincón-Enríquez, Gabriel and Quiñones-Aguilar, Evangelina Esmeralda}, doi = {10.1128/mra.00302-24}, journal = {Microbiology Resource Announcements}, keywords = {{\textgreater}UseGalaxy.eu}, month = {May}, - note = {Publisher: American Society for Microbiology}, number = {0}, pages = {e00302--24}, + publisher = {American Society for Microbiology}, title = {Complete genome sequence of the {Microbacterium} enclense bacteriophage {phiMiGM15}}, url = {https://journals.asm.org/doi/full/10.1128/mra.00302-24}, urldate = {2024-05-06}, @@ -3595,10 +3831,10 @@ @article{camargo_genomic_2023 keywords = {{\textgreater}UseGalaxy.eu, Clinical microbiology, Policy and public health in microbiology}, language = {en}, month = {September}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {14603}, + publisher = {Nature Publishing Group}, title = {Genomic analysis and antimicrobial activity of β-lactam/β-lactamase inhibitors and other agents against {KPC}-producing {Klebsiella} pneumoniae clinical isolates from {Brazilian} hospitals}, url = {https://www.nature.com/articles/s41598-023-41903-x}, urldate = {2023-09-10}, @@ -3616,10 +3852,10 @@ @article{camargo_genomics_2023 keywords = {{\textgreater}UseGalaxy.eu, CAZ-AVI, Illumina, MEM-VAR, MLST, cefiderocol, fosfomycin, polymyxin, whole genome sequencing}, language = {en}, month = {July}, - note = {Number: 7 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 7}, number = {7}, pages = {918}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Genomics and {Antimicrobial} {Susceptibility} of {Clinical} {Pseudomonas} aeruginosa {Isolates} from {Hospitals} in {Brazil}}, url = {https://www.mdpi.com/2076-0817/12/7/918}, urldate = {2023-07-11}, @@ -3665,7 +3901,6 @@ @article{candeliere_draft_2020 month = {January}, number = {2}, pages = {e01247--19}, - pmid = {31919169}, title = {Draft {Genome} {Sequences} of 12 {Leuconostoc} carnosum {Strains} {Isolated} from {Cooked} {Ham} {Packaged} in a {Modified} {Atmosphere} and from {Fresh} {Sausages}}, url = {https://mra.asm.org/content/9/2/e01247-19}, urldate = {2020-01-25}, @@ -3682,8 +3917,8 @@ @article{candeliere_genomic_2024 keywords = {{\textgreater}UseGalaxy.eu, Clostridium celatum, Clostridium tertium, Functional Genomics, Paraclostridium bifermentans, human gut microbiota, mucin}, language = {English}, month = {March}, - note = {Publisher: Frontiers}, pages = {1359726}, + publisher = {Frontiers}, title = {Genomic and functional analysis of the mucinolytic species {Clostridium} celatum, {Clostridium} tertium, and {Paraclostridium} bifermentans}, url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2024.1359726/full}, urldate = {2024-05-17}, @@ -3756,10 +3991,10 @@ @article{capitani_genome-based_2023 keywords = {\textit{Enterobacterales}, \textit{Providencia stuartii}, \textit{bla}$_{\textrm{NDM}}$, {\textgreater}UseGalaxy.eu, IncC plasmid, antibiotic resistance, opportunistic pathogen, plasmid mediated resistance}, language = {en}, month = {May}, - note = {Number: 5 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 5}, number = {5}, pages = {943}, + publisher = {Multidisciplinary Digital Publishing Institute}, shorttitle = {Genome-{Based} {Retrospective} {Analysis} of a {Providencia} stuartii {Outbreak} in {Rome}, {Italy}}, title = {Genome-{Based} {Retrospective} {Analysis} of a {Providencia} stuartii {Outbreak} in {Rome}, {Italy}: {Broad} {Spectrum} {IncC} {Plasmids} {Spread} the {NDM} {Carbapenemase} within the {Hospital}}, url = {https://www.mdpi.com/2079-6382/12/5/943}, @@ -3774,9 +4009,9 @@ @article{capitani_vivo_2024 journal = {mSphere}, keywords = {{\textgreater}UseGalaxy.eu, Anti-Bacterial Agents, Azabicyclo Compounds, Ceftazidime, Drug Combinations, Klebsiella Infections, Klebsiella pneumoniae, Liver Abscess, Microbial Sensitivity Tests}, month = {August}, - note = {Publisher: American Society for Microbiology}, number = {9}, pages = {e00423--24}, + publisher = {American Society for Microbiology}, title = {In vivo evolution to hypermucoviscosity and ceftazidime/avibactam resistance in a liver abscess caused by {Klebsiella} pneumoniae sequence type 512}, url = {https://journals.asm.org/doi/full/10.1128/msphere.00423-24}, urldate = {2024-11-17}, @@ -3827,9 +4062,9 @@ @article{carattoli_evolutionary_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Klebsiella Infections, Klebsiella pneumoniae}, language = {eng}, month = {September}, - note = {Publisher: American Society for Microbiology}, number = {10}, pages = {e0057421}, + publisher = {American Society for Microbiology}, title = {Evolutionary {Trajectories} toward {Ceftazidime}-{Avibactam} {Resistance} in {Klebsiella} pneumoniae {Clinical} {Isolates}}, url = {https://doi.org/10.1128/aac.00574-21}, volume = {65}, @@ -3882,9 +4117,9 @@ @article{carvalho_genomics_2024 keywords = {{\textgreater}UseGalaxy.eu, Chlorella, Evolution, Molecular, Genome, Viral, Genomics, Giant Viruses, Phycodnaviridae, Phylogeny}, language = {eng}, month = {October}, - note = {Publisher: American Society for Microbiology}, number = {0}, pages = {e00361--24}, + publisher = {American Society for Microbiology}, title = {Genomics and evolutionary analysis of {Chlorella} variabilis-infecting viruses demarcate criteria for defining species of giant viruses}, url = {https://journals.asm.org/doi/full/10.1128/jvi.00361-24}, urldate = {2024-10-20}, @@ -3899,7 +4134,7 @@ @article{casal_plant_2024 keywords = {{\textgreater}UseGalaxy.eu}, language = {en}, month = {July}, - note = {Publisher: Annual Reviews}, + publisher = {Annual Reviews}, title = {Plant {Thermosensors}}, url = {https://www.annualreviews.org/content/journals/10.1146/annurev-genet-111523-102327}, urldate = {2024-11-17}, @@ -3916,10 +4151,10 @@ @article{casella_novel_2025 keywords = {\textit{Bacillus}, \textit{Listeria monocytogenes}, {\textgreater}UseGalaxy.eu, Anti-Bacterial Agents, Bacillus, Depsipeptides, MDR \textit{Staphyloccus aureus}, NRPS, Peptides, Cyclic, antimicrobials, biosurfactant, genome mining, molecular networking, nobilamides, surfactins}, language = {en}, month = {January}, - note = {Number: 1 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 1}, number = {1}, pages = {41}, + publisher = {Multidisciplinary Digital Publishing Institute}, shorttitle = {Novel {Insights} into the {Nobilamide} {Family} from a {Deep}-{Sea} {Bacillus}}, title = {Novel {Insights} into the {Nobilamide} {Family} from a {Deep}-{Sea} {Bacillus}: {Chemical} {Diversity}, {Biosynthesis} and {Antimicrobial} {Activity} {Towards} {Multidrug}-{Resistant} {Bacteria}}, url = {https://www.mdpi.com/1660-3397/23/1/41}, @@ -3938,10 +4173,10 @@ @article{castellana_pannonibacter_2024 keywords = {{\textgreater}UseGalaxy.eu, Pannonibacter, environmental bacteria, hospital acquired infections, putative novel species, whole-genome sequencing}, language = {en}, month = {April}, - note = {Number: 4 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 4}, number = {4}, pages = {799}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Pannonibacter anstelovis sp. nov. {Isolated} from {Two} {Cases} of {Bloodstream} {Infections} in {Paediatric} {Patients}}, url = {https://www.mdpi.com/2076-2607/12/4/799}, urldate = {2024-05-17}, @@ -3975,7 +4210,7 @@ @article{castillo-villamizar_unveiling_2024 keywords = {{\textgreater}UseGalaxy.eu, Agricultural practices, Biocatalysts, Biodiversity, Bioprospection, citrus cultivation, microbiome, soil-associated bacteria}, language = {English}, month = {May}, - note = {Publisher: Frontiers}, + publisher = {Frontiers}, title = {Unveiling soil bacterial ecosystems in andean citrus orchards of {Santander}, {Colombia}}, url = {https://www.frontiersin.org/journals/ecology-and-evolution/articles/10.3389/fevo.2024.1372284/full}, urldate = {2025-02-28}, @@ -3997,6 +4232,25 @@ @patent{cathomen_truly_2021 year = {2021} } +@article{cen_comparative_2025, + abstract = {Archaeognatha is phylogenetically positioned as the basal lineage relative to all extant insect orders and comprises approximately 600 described species. The internal phylogenetic relationships and divergence times within this ancient order have long been a subject of scientific debate. In this study, we assembled 14 mitochondrial genomes from species within the genera Pedetontus and Pedetontinus to clarify the phylogenetic relationship and estimate divergence times within Archaeognatha. Phylogenetic analyses revealed that both Machilidae and Machilinae are paraphyletic; Pedetontinus included in this analysis formed a well-supported monophyletic clade, whereas the sampled Pedetontus species were not recovered as a monophyletic clade. Divergence time estimates indicate that Archaeognatha originated during the Late Carboniferous (301.15 Mya, 95\% HPD: 298.88–303.67 Mya), with subsequent diversification spanning from the Mesozoic era to the present. The adaptive radiation of epiphytic bryophytes and potential coevolutionary interactions between plants and insects are proposed to have significantly contributed to the diversification of Archaeognatha. Based on multiple lines of evidence, we propose that the current morphological criteria for species delineation within Pedetontus (Pd.) require revision to better reflect its evolutionary history. In the branch-site model analysis, when Pd. silvestrii—collected from temperate regions—was designated as the foreground branch, two positively selected sites were detected at the 66th position of the Cytb and the 34th position of ATP6. When Pd. hainanensis and Pd. bawanglingensis—collected from tropical regions—were used as the foreground branches, six positively selected sites were identified at the 622nd position of Cytb, the 499th position of ATP6, and the 623rd, 873rd, 1106th, and 1141st positions of COI.}, + author = {Cen, Wei and Yang, Ting and Li, Jia-Wen and Yu, Dan-Na and Storey, Kenneth B. and Zhang, Jia-Yong}, + doi = {10.3390/insects16121194}, + issn = {2075-4450}, + journal = {Insects}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {November}, + number = {12}, + pages = {1194}, + shorttitle = {Comparative {Mitogenomics} of {Pedetontus} and {Pedetontinus} ({Insecta}}, + title = {Comparative {Mitogenomics} of {Pedetontus} and {Pedetontinus} ({Insecta}: {Archaeognatha}) {Unveils} {Phylogeny}, {Divergence} {History}, and {Adaptive} {Evolution}}, + url = {https://www.mdpi.com/2075-4450/16/12/1194}, + urldate = {2026-01-11}, + volume = {16}, + year = {2025} +} + @article{cen_morpho-molecular_2025, abstract = {Archaeognatha (bristletails) represent an evolutionarily significant but understudied insect group. Notably, the morphological identification method proposed by Mendes for Archaeognatha has certain limitations, which may lead to the underestimation or misidentification of some cryptic species. To address this issue, we employed an integrated strategy that combines morphological and molecular identification methods. Therefore, this study aimed to (1) identify cryptic diversity within Pedetontus silvestrii using mitogenomic data; (2) clarify phylogenetic relationships among Archaeognatha lineages; and (3) estimate divergence times for key taxonomic splits. We analyzed mitochondrial genomes from six P. silvestrii populations (Liaoning, Jilin, and Hebei Provinces) alongside 14 published Archaeognatha genomes. Key findings include the following: (1) Integrative analyses of genetic distances, phylogenetic reconstruction, bPTP-based molecular species delimitation, and divergence time estimation collectively revealed four evolutionarily distinct lineages within P. silvestrii. (2) Machilidae and Machilinae were non-monophyletic, whereas Petrobiellinae showed close affinity to Meinertellidae. (3) Archaeognatha originated {\textasciitilde}301.19 Mya (Late Carboniferous); the Machilinae–Petrobiinae split occurred approximately 153.99 Mya (Jurassic). This study underscores the critical importance of mitogenomic analysis in elucidating cryptic biodiversity, while emphasizing the necessity of integrating morphological identification with molecular characterization for comprehensive species delineation in future taxonomic investigations.}, author = {Cen, Wei and Li, Jia-Wen and He, Jia-Tao and Chen, Xin-Yu and Li, Luo-Ying and Storey, Kenneth B. and Yu, Dan-Na and Zhang, Jia-Yong}, @@ -4007,10 +4261,10 @@ @article{cen_morpho-molecular_2025 keywords = {{\textgreater}UseGalaxy.eu, Archaeognatha, cryptic species, divergence time, mitochondrial genome, phylogenetic relationship}, language = {en}, month = {May}, - note = {Number: 5 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 5}, number = {5}, pages = {452}, + publisher = {Multidisciplinary Digital Publishing Institute}, shorttitle = {Morpho-{Molecular} {Discordance} and {Cryptic} {Diversity} in {Jumping} {Bristletails}}, title = {Morpho-{Molecular} {Discordance} and {Cryptic} {Diversity} in {Jumping} {Bristletails}: {A} {Mitogenomic} {Analysis} of {Pedetontus} silvestrii ({Insecta}: {Archaeognatha}: {Machilidae})}, url = {https://www.mdpi.com/2075-4450/16/5/452}, @@ -4079,10 +4333,10 @@ @article{chanama_comparative_2023 keywords = {{\textgreater}UseGalaxy.eu, Actinomycetales, Bacteria, Comparative genomics, Phylogenomics}, language = {en}, month = {May}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {8794}, + publisher = {Nature Publishing Group}, title = {Comparative genome features and secondary metabolite biosynthetic potential of {Kutzneria} chonburiensis and other species of the genus {Kutzneria}}, url = {https://www.nature.com/articles/s41598-023-36039-x}, urldate = {2023-06-05}, @@ -4139,6 +4393,25 @@ @article{cheffer_dot1l_2023 year = {2023} } +@article{chen_bacillus_2025, + abstract = {BackgroundPyridine-2,6-dicarboxylic acid (DPA) is a valuable dicarboxylic acid that has the potential to serve as a precursor for bio-sustainable and bio-degradable materials and self-healing polymers. It also plays a crucial role in the heat resistance of Bacillus subtilis spores. However, extracting DPA from spores is resource-intensive and technically complex, limiting its industrial application. To overcome these challenges, this study aims to engineer B. subtilis as a microbial cell factory for the direct production of free and soluble DPA.ResultsThis study first demonstrated that blocking sporulation reduced DPA production due to the repression of dipicolinate synthase expression. To enhance extracellular DPA production, dipicolinate synthase expression was fine-tuned, increasing the extracellular DPA titer to 330 ± 10 mg/l in strain BSDYvyDVF. Transcriptomic analysis revealed that spore coat assembly genes modulate DPA production. By disrupting a spore coat assembly activator in strain BSDYvyDVF-gerE, sporulation was successfully inhibited, significantly boosting the DPA yield to 944 ± 3 mg/l. Further optimization of fermentation conditions was performed using an orthogonal design. The highest DPA titer of 1250 mg/l was achieved and validated through fed-batch fermentation in a 1.5-l bioreactor.ConclusionThis study demonstrates the potential of engineered B. subtilis BSDYvyDVF-gerE as an efficient cell factory for sustainable DPA biosynthesis. In addition, it identifies key challenges in DPA production, including synthesis efficiency (regulation of key enzyme expression) and transport (intracellular-to-extracellular export), and proposes corresponding solutions.}, + author = {Chen, Taichi and Uzunovic, Haris and Brul, Stanley and Hugenholtz, Jeroen}, + copyright = {cc by-nc-nd}, + doi = {10.1186/s12934-025-02859-x}, + issn = {1475-2859}, + journal = {Microbial cell factories}, + keywords = {{\textgreater}UseGalaxy.eu, Biopolymer, Dicarboxylic acid, Dipicolinic Acid, Fermentation optimization, Spore Coat Assembly}, + language = {eng}, + month = {November}, + number = {1}, + pages = {233}, + title = {Bacillus subtilis as cell factory for enhanced production of the biopolymer precursor pyridine-2,6-dicarboxylic acid}, + url = {https://europepmc.org/articles/PMC12613536}, + urldate = {2025-12-26}, + volume = {24}, + year = {2025} +} + @article{chen_canonical_2024, abstract = {The androgen receptor (AR) is central in prostate tissue identity and differentiation, and controls normal growth-suppressive, prostate-specific gene expression. It also drives prostate tumorigenesis when hijacked for oncogenic transcription. The execution of growth-suppressive AR transcriptional programs in prostate cancer (PCa) and the potential for reactivation remain unclear. Here, we use a genome-wide approach to modulate canonical androgen response element (ARE) motifs—the classic DNA binding elements for AR—to delineate distinct AR transcriptional programs. We find that activating these AREs promotes differentiation and growth-suppressive transcription, potentially leading to AR+ PCa cell death, while ARE repression is tolerated by PCa cells but deleterious to normal prostate cells. Gene signatures driven by ARE activity correlate with improved prognosis and luminal phenotypes in PCa patients. Canonical AREs maintain a normal, lineage-specific transcriptional program that can be reengaged in PCa cells, offering therapeutic potential and clinical relevance.}, author = {Chen, Xuanrong and Augello, Michael A. and Liu, Deli and Lin, Kevin and Hakansson, Alex and Sjöström, Martin and Khani, Francesca and Deonarine, Lesa D. and Liu, Yang and Travascio-Green, Jaida and Wu, Jiansheng and Chan, Un In and Owiredu, Jude and Loda, Massimo and Feng, Felix Y. and Robinson, Brian D. and Davicioni, Elai and Sboner, Andrea and Barbieri, Christopher E.}, @@ -4149,9 +4422,9 @@ @article{chen_canonical_2024 keywords = {{\textgreater}UseGalaxy.eu, Cancer genomics, Cell growth, Gene Expression Regulation, Neoplastic, Prostate, Prostate cancer, Prostatic Neoplasms, Receptors, Androgen, Response Elements}, language = {en}, month = {December}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {10675}, + publisher = {Nature Publishing Group}, title = {Canonical androgen response element motifs are tumor suppressive regulatory elements in the prostate}, url = {https://www.nature.com/articles/s41467-024-53734-z}, urldate = {2025-01-05}, @@ -4166,11 +4439,10 @@ @article{chen_comparative_2025 issn = {2470-1394}, journal = {Mitochondrial DNA Part A}, keywords = {{\textgreater}UseGalaxy.eu, Eulipotyphla, hibernation, lifespan, mitogenomics}, - note = {Publisher: Taylor \& Francis -\_eprint: https://doi.org/10.1080/24701394.2025.2558619}, + note = {\_eprint: https://doi.org/10.1080/24701394.2025.2558619}, number = {0}, pages = {1--13}, - pmid = {40931882}, + publisher = {Taylor \& Francis}, title = {Comparative mitogenomics of the eulipotyphlan species ({Mammalia}, {Eulipotyphla}) provides novel insights into the molecular evolution of hibernation}, url = {https://doi.org/10.1080/24701394.2025.2558619}, urldate = {2025-09-15}, @@ -4198,13 +4470,32 @@ @article{chen_first_2021 doi = {10.1017/s0007485321000808}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {September}, - note = {Publisher: Cambridge University Press (CUP)}, pages = {1--10}, + publisher = {Cambridge University Press (CUP)}, title = {First complete mitochondrial genome of {Rhodinia} species ({Lepidoptera}: {Saturniidae}): genome description and phylogenetic implication}, url = {https://doi.org/10.1017/s0007485321000808}, year = {2021} } +@article{chen_genus-wide_2024, + abstract = {Parasitism is an important lifestyle in the \textit{Trichoderma} genus but has not been studied in a genus-wide way toward \textit{Pythium} and \textit{Globisporangium} hosts. Our approach screened a genus-wide set of 30 \textit{Trichoderma} species in dual culture assays with two soil-borne \textit{Pythium} and three \textit{Globisporangium} plant-parasitic species and used exo-proteomic analyses, with the aim to correlate \textit{Trichoderma} antagonism with potential strategies for attacking \textit{Pythium} and \textit{Globisporangium}. The \textit{Trichoderma} spp. showed a wide range of antagonism from strong to weak, but the same \textit{Trichoderma} strain showed similar levels toward all the \textit{Pythium} and \textit{Globisporangium} species. The \textit{Trichoderma} enzymes from strong (\textit{Trichoderma asperellum}, \textit{Trichoderma atroviride}, and \textit{Trichoderma virens}), moderate (\textit{Trichoderma} cf. \textit{guizhouense} and \textit{Trichoderma reesei}), and weak (\textit{Trichoderma parepimyces}) antagonists were induced by the autoclaved mycelia of one of the screened \textit{Pythium} species, \textit{Pythium myriotylum}. The variable proportions of putative cellulases, proteases, and redox enzymes suggested diverse as well as shared strategies amongst the antagonists. There was a partial positive correlation between antagonism from microscopy and the cellulase activity induced by autoclaved \textit{P. myriotylum} mycelia in different \textit{Trichoderma} species. The deletion of the cellulase transcriptional activator XYR1 in \textit{T. reesei} led to lower antagonism toward \textit{Pythium} and \textit{Globisporangium}. The antagonism of \textit{Pythium} and \textit{Globisporangium} appears to be a generic property of \textit{Trichoderma} as most of the \textit{Trichoderma} species were at least moderately antagonistic. While a role for cellulases in the antagonism was uncovered, cellulases did not appear to make a major contribution to \textit{T. reesei} antagonism, and other factors are also likely contributing.IMPORTANCE\textit{Trichoderma} is an important genus widely distributed in nature with broad ecological impacts and applications in the biocontrol of plant diseases. The \textit{Pythium} and \textit{Globisporangium} genera of fungus-like water molds include many important soil-borne plant pathogens that cause various diseases. Most of the \textit{Trichoderma} species showed at least a moderate ability to compete with or antagonize the \textit{Pythium} and \textit{Globisporangium} hosts, and microscopy showed examples of parasitism (a slow type of killing) and predation (a fast type of killing). Hydrolytic enzymes such as cellulases and proteases produced by \textit{Trichoderma} likely contribute to the antagonism. A mutant deficient in cellulase activity had reduced antagonism. Interestingly, \textit{Pythium} and \textit{Globisporangium} species contain cellulose in their cell walls (unlike true fungi such as \textit{Trichoderma}), and the cellulolytic ability of \textit{Trichoderma} appears beneficial for antagonism of water molds.}, + author = {Chen, Siqiao and Daly, Paul and Anjago, Wilfred Mabeche and Wang, Rong and Zhao, Yishen and Wen, Xian and Zhou, Dongmei and Deng, Sheng and Lin, Xisha and Voglmeir, Josef and Cai, Feng and Shen, Qirong and Druzhinina, Irina S. and Wei, Lihui}, + doi = {10.1128/aem.00681-24}, + issn = {0099-2240}, + journal = {Applied and Environmental Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, Cellulases, Plant Diseases, Pythium, Trichoderma}, + language = {eng}, + month = {August}, + number = {0}, + pages = {e00681--24}, + publisher = {American Society for Microbiology}, + title = {Genus-wide analysis of {Trichoderma} antagonism toward {Pythium} and {Globisporangium} plant pathogens and the contribution of cellulases to the antagonism}, + url = {https://journals.asm.org/doi/10.1128/aem.00681-24}, + urldate = {2024-08-19}, + volume = {0}, + year = {2024} +} + @article{chen_high-light_2025, abstract = {Photosynthetic organisms have evolved mechanisms to manage excess light, crucial for maximizing photosynthetic efficiency. High-light (HL) tolerant Synechocystis sp. PCC6803 strains were developed through laboratory evolution, with tolerance attributed to specific point mutations. Key mutations affected the NDH-1L complex F1-subunit (NdhF1 F124L ) and translation elongation factor G2 (EF-G2 R461C ). Reintroducing these mutations into laboratory strains conferred HL tolerance. Comparisons with knockout and overexpressor lines showed NdhF1 F124L and EF-G2 R461C result in gain of function. Transcriptomic and proteomic analysis unveiled a network of responses contributing to HL tolerance, including maintenance of phosphate metabolism and decreased antenna size by depleting a specific linker protein in EF-G2 R461C cells. Consequently, overexpression of Pho regulon genes increased HL tolerance. NdhF1 F124L enhances cyclic electron flow (CEF) by increasing NDH-1 complex subunit accumulation. Other HL-adapted strains demonstrated that increased CEF and decreased antenna size are recurring outcomes, achievable through various mutations. This study demonstrates how limited mutations can reconfigure cells for enhanced HL tolerance, offering insights for improving photosynthetic efficiency.}, author = {Chen, Weiyang and Abdel-Salam, Eslam and Dann, Marcel and Ott, Caroline and Schwenkert, Serena and Leister, Dario}, @@ -4226,10 +4517,10 @@ @article{chen_terrestrial_2025 keywords = {\textit{Chelonoidis vicina}, {\textgreater}UseGalaxy.eu, Adaptation, Physiological, Genome, Mitochondrial, Turtles, adaptation, evolution, mitochondrial genomes, positive selection}, language = {en}, month = {February}, - note = {Number: 2 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 2}, number = {2}, pages = {173}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Terrestrial {Adaptation} in {Chelonoidis} vicina as {Revealed} {Based} on {Analysis} of the {Complete} {Mitochondrial} {Genome}}, url = {https://www.mdpi.com/2073-4425/16/2/173}, urldate = {2025-05-29}, @@ -4261,10 +4552,10 @@ @article{cheron_usp7maged1-mediated_2023 keywords = {{\textgreater}UseGalaxy.eu, Addiction, Cocaine, Cocaine-Related Disorders, Epigenetics in the nervous system, Substance-Related Disorders}, language = {en}, month = {December}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {8481}, + publisher = {Nature Publishing Group}, shorttitle = {{USP7}/{Maged1}-mediated {H2A} monoubiquitination in the paraventricular thalamus}, title = {{USP7}/{Maged1}-mediated {H2A} monoubiquitination in the paraventricular thalamus: an epigenetic mechanism involved in cocaine use disorder}, url = {https://www.nature.com/articles/s41467-023-44120-2}, @@ -4282,9 +4573,9 @@ @article{cherrad_new_2023 keywords = {{\textgreater}UseGalaxy.eu, DNA extraction, DNA isolation, Downy mildew, Fungicides, Fungicides, Industrial, Gene sequencing, Leaves, Next-generation sequencing, Oomycetes, Polymerase chain reaction, Vitis}, language = {en}, month = {January}, - note = {Publisher: Public Library of Science}, number = {1}, pages = {e0268385}, + publisher = {Public Library of Science}, title = {New insights from short and long reads sequencing to explore cytochrome b variants in {Plasmopara} viticola populations collected from vineyards and related to resistance to complex {III} inhibitors}, url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0268385}, urldate = {2023-03-15}, @@ -4302,10 +4593,10 @@ @article{chetverikov_molecular_2024 keywords = {\textit{28S}, \textit{Calacarus}, \textit{Cox1}, {\textgreater}UseGalaxy.eu, Acari, arthropod structure, endemic, erroneous sequences, female genitalia, phytoparasite diversity, phytophagous mite, reproductive system}, language = {en}, month = {February}, - note = {Number: 2 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 2}, number = {2}, pages = {329}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Molecular {Phylogenetics} and {Light} {Microscopy} {Reveal} “{True}” and “{False}” {Calacarines} and {Novel} {Genital} {Structures} in {Gall} {Mites} ({Acariformes}, {Eriophyoidea})}, url = {https://www.mdpi.com/1999-4907/15/2/329}, urldate = {2024-05-17}, @@ -4319,8 +4610,8 @@ @article{chiappa_evolutionary_2025 keywords = {{\textgreater}UseGalaxy.eu, ⛔ No DOI found}, language = {eng}, month = {January}, - note = {Accepted: 2025-02-10T15:01:17Z -Publisher: Università degli Studi di Roma "La Sapienza"}, + note = {Accepted: 2025-02-10T15:01:17Z}, + publisher = {Università degli Studi di Roma "La Sapienza"}, title = {Evolutionary biology of {Raphitoma} {Bellardi}, 1847 ({Neogastropoda}, {Conoidea})}, url = {https://iris.uniroma1.it/handle/11573/1733327}, urldate = {2025-05-29}, @@ -4337,10 +4628,10 @@ @article{chiappa_potential_2024 keywords = {{\textgreater}UseGalaxy.eu, Mollusk Venoms, Raphitomidae, Snails, conotoxin, salivary glands, transcriptome, trophic ecology, venom duct, venom evolution}, language = {en}, month = {August}, - note = {Number: 8 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 8}, number = {8}, pages = {348}, + publisher = {Multidisciplinary Digital Publishing Institute}, shorttitle = {Potential {Ancestral} {Conoidean} {Toxins} in the {Venom} {Cocktail} of the {Carnivorous} {Snail} {Raphitoma} purpurea ({Montagu}, 1803) ({Neogastropoda}}, title = {Potential {Ancestral} {Conoidean} {Toxins} in the {Venom} {Cocktail} of the {Carnivorous} {Snail} {Raphitoma} purpurea ({Montagu}, 1803) ({Neogastropoda}: {Raphitomidae})}, url = {https://www.mdpi.com/2072-6651/16/8/348}, @@ -4376,9 +4667,9 @@ @article{chisembe_nationwide_2024 keywords = {{\textgreater}UseGalaxy.eu}, language = {en}, month = {October}, - note = {Publisher: Oxford Academic}, number = {6}, pages = {dlae200}, + publisher = {Oxford Academic}, title = {A nationwide survey of antimicrobial resistance of {Escherichia} coli isolated from broiler chickens in {Malawi}}, url = {https://dx.doi.org/10.1093/jacamr/dlae200}, urldate = {2025-09-03}, @@ -4442,9 +4733,9 @@ @article{chuchaona_metagenomic_2025 keywords = {{\textgreater}UseGalaxy.eu, Diseases, Microbiology, Molecular biology, Viral infection, Virology}, language = {en}, month = {August}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {30672}, + publisher = {Nature Publishing Group}, title = {Metagenomic analysis and genomic characterization of enterovirus {A76} and {Norovirus} {GI}.6[{P11}] co-infection in a patient with acute gastroenteritis in {Thailand}}, url = {https://www.nature.com/articles/s41598-025-16816-6}, urldate = {2025-09-03}, @@ -4458,8 +4749,8 @@ @article{cigana_monitoraggio_2023 keywords = {{\textgreater}UseGalaxy.eu}, language = {it}, month = {March}, - note = {Accepted: 2023-02-19 -Publisher: Università Ca' Foscari Venezia}, + note = {Accepted: 2023-02-19}, + publisher = {Università Ca' Foscari Venezia}, title = {Monitoraggio della comunità microbiologica durante un processo di fermentazione anaerobica di scarti vitivinicoli}, url = {http://dspace.unive.it/handle/10579/23273}, urldate = {2023-07-31}, @@ -4503,9 +4794,9 @@ @article{colin_whats_2022 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, language = {eng}, month = {January}, - note = {Publisher: Springer Science and Business Media LLC}, number = {2}, pages = {167--182}, + publisher = {Springer Science and Business Media LLC}, title = {What's left in the tank? {Identification} of non-ascribed aquarium's coral collections with {DNA} barcodes as part of an integrated diagnostic approach}, url = {https://doi.org/10.1007/s12686-021-01250-3}, volume = {14}, @@ -4549,8 +4840,8 @@ @article{cordellier_next-generation_2021 journal = {Zoology}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {January}, - note = {Publisher: Elsevier BV}, pages = {125895}, + publisher = {Elsevier BV}, title = {Next-generation sequencing of {DNA} from resting eggs: signatures of eutrophication in a lake's sediment}, url = {https://doi.org/10.1016/j.zool.2021.125895}, year = {2021} @@ -4614,6 +4905,25 @@ @article{cosenza-contreras_proteometabolomics_2024 year = {2024} } +@article{costa-ribeiro_application_2025, + abstract = {Millions of foodborne infections are reported yearly worldwide due to a variety of pathogens. A promising approach to tackle this issue relies on Next Generation Sequencing (NGS). In this work a novel multi-foodborne pathogen detection was developed. The method combines a selective enrichment step in a novel broth, multiplex PCR with interlaboratory-validated primers, long-read Flongle MinION sequencing, and data analysis in three cloud-based pipelines to overcome complex, command line-based bioinformatic data analyses. The method, was evaluated in salmon samples spiked with fresh, heat and cold stressed, bacterial cultures of Salmonella spp., E. coli O157:H7 and L. monocytogenes, as well as with in-house, and commercial mock communities, doped with Y. enterocolitica and thermotolerant Campylobacter spp. No major deviations from the expected results were obtained, reaching a limit of detection  90\% regardless the bioinformatic pipeline selected and concordance values between 0.9 to 1.0. Taken together, the proposed method allows for simple and reliable implementation of NGS as testing tool to streamline foodborne pathogen detection, and overcoming the typical limitations associated with this technology.}, + author = {Costa-Ribeiro, Ana and Lamas, Alexandre and Prado, Marta and Garrido-Maestu, Alejandro}, + copyright = {cc by-nc-nd}, + doi = {10.1038/s41538-025-00452-5}, + issn = {2396-8370}, + journal = {NPJ science of food}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {October}, + number = {1}, + pages = {211}, + title = {Application of {MSB} selective enrichment followed by amplicon {MinION} sequencing for multipathogen detection in smoked salmon}, + url = {https://europepmc.org/articles/PMC12569004}, + urldate = {2025-12-26}, + volume = {9}, + year = {2025} +} + @article{costa_olfactory_2025, abstract = {Increased carbon dioxide (CO2) in the ocean is changing seawater chemistry. Behavioural alterations in CO2 exposed fish have been linked to changes in the central nervous system (CNS). However, we hypothesise that receptor cells in direct contact with the environment are more susceptible to changes in water chemistry than the CNS. Electrophysiology, histology, and transcriptomics were used to explore the effect of exposure to CO2 acidified water on the olfactory epithelium (OE) of the Senegalese sole (Solea senegalensis). The upper and lower OE of this flatfish detect different odorants and are in contact with different environments. Acute exposure to acidified water decreased olfactory sensitivity more in the upper than in the lower OE. After chronic exposure to high CO2 there was no histological changes in the upper OE, however, in the lower OE, there was a massive infiltration of melanomacrophage (MMC) and tissue disorganization. In addition, in the upper OE, differential expressed gene transcripts (DETs) were related to inflammation and innate immune processes whereas in the lower OE, DETs were related to the adaptative immune response. Differential regulation of genes related to neurogenesis and plasticity occurred in both epithelia. The effects of ocean acidification in sole OE depends on the nostril, however the occurrence of an exacerbated immune response, OE remodelling and reduced sensitivity indicate that ocean acidification is likely to have significant and unpredictable consequences for behaviour.}, author = {Costa, Rita A. and Hubbard, Peter and Manchado, Manuel and Power, Deborah M. and Velez, Zélia}, @@ -4655,9 +4965,9 @@ @article{cova_helios_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, language = {eng}, month = {August}, - note = {Publisher: Rockefeller University Press}, number = {10}, pages = {e20202317}, + publisher = {Rockefeller University Press}, title = {Helios represses megakaryocyte priming in hematopoietic stem and progenitor cells}, url = {https://doi.org/10.1084/jem.20202317}, volume = {218}, @@ -4675,8 +4985,6 @@ @article{crespo_pcid2_2024 month = {March}, number = {3}, pages = {109152}, - pmcid = {PMC10879814}, - pmid = {38384833}, title = {{PCID2} dysregulates transcription and viral {RNA} processing to promote {HIV}-1 latency}, url = {http://europepmc.org/abstract/MED/38384833}, volume = {27}, @@ -4701,8 +5009,8 @@ @article{cruz-ojeda_silico_2025 keywords = {{\textgreater}RNA Workbench, {\textgreater}UseGalaxy.eu}, language = {en}, month = {January}, - note = {Publisher: Baishideng Publishing Group Inc.}, number = {3}, + publisher = {Baishideng Publishing Group Inc.}, title = {In silico analysis of {lncRNA}-{miRNA}-{mRNA} signatures related to {Sorafenib} effectiveness in liver cancer cells}, url = {https://www.wjgnet.com/1007-9327/full/v31/i3/95207.htm}, urldate = {2025-01-05}, @@ -4720,10 +5028,10 @@ @article{cunha_characterization_2025 keywords = {\textit{Rosenblumvirus}, \textit{Staphylococcus} phage, {\textgreater}UseGalaxy.eu, biocontrol, host range}, language = {en}, month = {March}, - note = {Number: 3 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 3}, number = {3}, pages = {664}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Characterization of {Newly} {Isolated} {Rosenblumvirus} {Phage} {Infecting} {Staphylococcus} aureus from {Different} {Sources}}, url = {https://www.mdpi.com/2076-2607/13/3/664}, urldate = {2025-05-29}, @@ -4742,8 +5050,6 @@ @article{cupic_first_2023 month = {July}, number = {4}, pages = {821--833}, - pmcid = {PMC10415781}, - pmid = {37464939}, shorttitle = {The first cavefish in the {Dinaric} {Karst}?}, title = {The first cavefish in the {Dinaric} {Karst}? {Cave} colonization made possible by phenotypic plasticity in {Telestes} karsticus}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10415781/}, @@ -4769,6 +5075,24 @@ @article{dad_molecular_2020 year = {2020} } +@article{dahdouh_revisiting_2025, + abstract = {Over 60 years ago, researchers started the genetic analysis of bacterial cell division by isolating conditional, temperature-sensitive mutants of essential Escherichia coli cell division genes. These early mutants were obtained by mutagenesis with chemical agents that introduced dozens to hundreds of mutations in the bacterial genomes. In this work, we present the complete genome sequences of six of these original mutants on ftsA, ftsZ and ftsQ genes, along with two of the strains used to generate them. The genomes of mutants obtained by exposure to nitrosoguanidine had 100 to 400 mutations. Transducing target alleles into a new strain effectively reduced the number of mutations, but those near the target gene were co-transduced with it. In contrast, a mutant generated by site-directed mutagenesis maintained the genomic background intact. The genomic analysis improves our understanding of these foundational strains, offering insights into the effects of historical mutagenesis techniques. These findings underscore the importance of genomic characterization in ensuring accurate interpretations of experimental results in microbiological research.}, + author = {Dahdouh, Elias and García-Pérez, Isabel and Reyes-Zuñagua, Diana Soledad and Mingorance, Jesús and Vicente, Miguel}, + copyright = {cc by}, + doi = {10.1099/mgen.0.001558}, + issn = {2057-5858}, + journal = {Microbial genomics}, + keywords = {{\textgreater}UseGalaxy.eu, Cell division, Escherichia Coli, Genomic analysis, Mutagenesis}, + language = {eng}, + month = {November}, + number = {11}, + title = {Revisiting classical \<i\>{Escherichia} coli\</i\> cell division mutants by whole-genome sequencing}, + url = {https://europepmc.org/articles/PMC12584984}, + urldate = {2025-12-26}, + volume = {11}, + year = {2025} +} + @article{daly_dual-transcriptomic_2021, abstract = {Biological control is a promising approach to suppress diseases caused by \textit{Pythium} spp. such as Pythium soft rot of ginger caused by \textit{P. myriotylum}. Unusually for a single genus, it also includes species that can antagonize \textit{Pythium} plant pathogens, such as \textit{Pythium oligandrum}. We investigated if a new isolate of \textit{P. oligandrum} could antagonize \textit{P. myriotylum}, what changes occurred in gene expression when \textit{P. oligandrum} (antagonist) and \textit{P. myriotylum} (host) interacted, and whether \textit{P. oligandrum} could control soft-rot of ginger caused by \textit{P. myriotylum}. An isolate of \textit{P. oligandrum}, GAQ1, recovered from soil could antagonize \textit{P. myriotylum} in a plate-based confrontation assay whereby \textit{P. myriotylum} became non-viable. The loss of viability of \textit{P. myriotylum} coupled with how \textit{P. oligandrum} hyphae could coil around and penetrate the hyphae of \textit{P. myriotylum}, indicated a predatory interaction. We investigated the transcriptional responses of \textit{P. myriotylum} and \textit{P. oligandrum} using dual-RNAseq at a stage in the confrontation where similar levels of total transcripts were measured from each species. As part of the transcriptional response of \textit{P. myriotylum} to the presence of \textit{P. oligandrum}, genes including a subset of putative Kazal-type protease inhibitors were strongly upregulated along with cellulases, elicitin-like proteins and genes involved in the repair of DNA double-strand breaks. In \textit{P. oligandrum}, proteases, cellulases, and peroxidases featured prominently in the upregulated genes. The upregulation along with constitutive expression of \textit{P. oligandrum} proteases appeared to be responded to by the upregulation of putative protease inhibitors from \textit{P. myriotylum}, suggesting a \textit{P. myriotylum} defensive strategy. Notwithstanding this \textit{P. myriotylum} defensive strategy, \textit{P. oligandrum} had a strong disease control effect on soft-rot of ginger caused by \textit{P. myriotylum}. The newly isolated strain of \textit{P. oligandrum} is a promising biocontrol agent for suppressing the soft-rot of ginger. The dual-RNAseq approach highlights responses of \textit{P. myriotylum} that suggests features of a defensive strategy, and are perhaps another factor that may contribute to the variable success and durability of biological attempts to control diseases caused by \textit{Pythium} spp.}, author = {Daly, Paul and Chen, Siqiao and Xue, Taiqiang and Li, Jingjing and Sheikh, Taha Majid Mahmood and Zhang, Qimeng and Wang, Xuehai and Zhang, Jinfeng and Fitzpatrick, David A and McGowan, Jamie and Shi, Xiujuan and Deng, Sheng and Jiu, Min and Zhou, Dongmei and Druzhinina, Irina S and Wei, Lihui}, @@ -4808,7 +5132,7 @@ @article{dantanarayana_understanding_2025 journal = {ACS Electrochemistry}, keywords = {{\textgreater}UseGalaxy.eu}, month = {August}, - note = {Publisher: American Chemical Society}, + publisher = {American Chemical Society}, title = {Understanding {Palladium} {Ion} {Induced} {Bioelectrocatalysis} in {Shewanella} oneidensis {MR}-1 through {Electrochemical} and {Genetic} {Interrogations}}, url = {https://doi.org/10.1021/acselectrochem.5c00244}, urldate = {2025-09-03}, @@ -4984,9 +5308,9 @@ @article{de_azevedo_genomic_2024 keywords = {{\textgreater}UseGalaxy.eu, Genome, Viral, Viruses}, language = {eng}, month = {May}, - note = {Publisher: American Society for Microbiology}, number = {0}, pages = {e00513--24}, + publisher = {American Society for Microbiology}, title = {The genomic and phylogenetic analysis of {Marseillevirus} cajuinensis raises questions about the evolution of {Marseilleviridae} lineages and their taxonomical organization}, url = {https://journals.asm.org/doi/full/10.1128/jvi.00513-24}, urldate = {2024-06-07}, @@ -5022,10 +5346,10 @@ @article{de_jesus_bertani_whole_2023 keywords = {{\textgreater}UseGalaxy.eu, Anti-Bacterial Agents, Antimicrobials, Escherichia coli, Microbiology}, language = {en}, month = {February}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {2299}, + publisher = {Nature Publishing Group}, title = {Whole genome sequence analysis of the first reported isolate of {Salmonella} {Agona} carrying {blaCTX}-{M}-55 gene in {Brazil}}, url = {https://www.nature.com/articles/s41598-023-29599-5}, urldate = {2023-03-15}, @@ -5033,6 +5357,26 @@ @article{de_jesus_bertani_whole_2023 year = {2023} } +@article{de_koning_nanogalaxy_2020, + abstract = {AbstractBackground. Long-read sequencing can be applied to generate very long contigs and even completely assembled genomes at relatively low cost and with min}, + author = {de Koning, Willem and Miladi, Milad and Hiltemann, Saskia and Heikema, Astrid and Hays, John P. and Flemming, Stephan and van den Beek, Marius and Mustafa, Dana A. and Backofen, Rolf and Grüning, Björn and Stubbs, Andrew P.}, + doi = {10.1093/gigascience/giaa105}, + issn = {2047-217X}, + journal = {GigaScience}, + keywords = {+Galactic, +IsGalaxy, +Shared, +Tools, {\textgreater}NanoGalaxy, {\textgreater}UseGalaxy.eu, Nanopore Sequencing, Nanopores}, + language = {en}, + month = {October}, + number = {10}, + pages = {giaa105}, + publisher = {Oxford Academic}, + shorttitle = {{NanoGalaxy}}, + title = {{NanoGalaxy}: {Nanopore} long-read sequencing data analysis in {Galaxy}}, + url = {https://academic.oup.com/gigascience/article/9/10/giaa105/5928356}, + urldate = {2020-10-19}, + volume = {9}, + year = {2020} +} + @article{de_melo-ximenes_first_2025, abstract = {Genomic resources, such as draft genomes, are vital for biodiversity monitoring and conservation. For endangered species, they enable the development of tools like organellar genomes and molecular markers, which are crucial for population genetics. Advances in sequencing technologies now allow high-throughput genotyping with detailed amplicon sequences, enhancing genetic variation studies. The northern muriqui (\textit{Brachyteles hypoxanthus}), a critically endangered primate endemic to Brazil's Atlantic Forest, currently lacks both nuclear and mitochondrial genome data and species-specific microsatellite markers for population genetic studies. We assembled a 2.52 Gb draft genome for \textit{B. hypoxanthus} with 202,243 contigs (N50 = 29,134 bp), and BUSCO analyses indicated 52\% completeness and 15.5\% fragmented genes. The complete 16,635 bp mitochondrial genome retains the conserved mammalian structure with 22 tRNAs, 2 rRNAs, 13 CDS, and an origin of replication. Additionally, we designed 31 SSR primer pairs suitable for non-invasive sampling and genotyping, alongside two mtDNA and two sex-determination primers, configured into three multiplex PCR sets. These genomic resources, including the draft genome, complete mitochondrial genome, and microsatellite markers, provide essential tools for evolutionary analyses and the genetic monitoring of \textit{B. hypoxanthus} populations, supporting its conservation.}, author = {de Melo-Ximenes, Amanda Alves and Batista, Romina and Corvalán, Leonardo Carlos Jeronimo and Marques-Bonet, Tomas and Kuderna, Lukas and Farh, Kyle and Rogers, Jeffrey and Kaizer, Mariane da Cruz and Boubli, Jean Philippe and de Melo, Fabiano Rodrigues and Nunes, Rhewter and Telles, Mariana Pires de Campos}, @@ -5077,7 +5421,7 @@ @article{de_oliveira_apoplastomes_2024 keywords = {{\textgreater}UseGalaxy.eu, Apoplast, Moniliophthora perniciosa, apoplastic washing fluid, defense proteins, theobroma cacao}, language = {English}, month = {May}, - note = {Publisher: Frontiers}, + publisher = {Frontiers}, title = {Apoplastomes of contrasting cacao genotypes to witches’ broom disease reveals differential accumulation of {PR} proteins}, url = {https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1387153/full}, urldate = {2024-11-17}, @@ -5170,9 +5514,9 @@ @article{dederichs_nonpreferential_2024 journal = {Arteriosclerosis, Thrombosis, and Vascular Biology}, keywords = {{\textgreater}UseGalaxy.eu}, month = {March}, - note = {Publisher: American Heart Association}, number = {3}, pages = {690--697}, + publisher = {American Heart Association}, title = {Nonpreferential but {Detrimental} {Accumulation} of {Macrophages} {With} {Clonal} {Hematopoiesis}-{Driver} {Mutations} in {Cardiovascular} {Tissues}—{Brief} {Report}}, url = {https://www.ahajournals.org/doi/full/10.1161/ATVBAHA.123.320183}, urldate = {2024-07-09}, @@ -5231,10 +5575,10 @@ @article{delandre_long-read_2024 keywords = {\textit{Pf}3D7, \textit{Pf}W2, \textit{Plasmodium falciparum}, {\textgreater}UseGalaxy.eu, PromethION, genome assembly, long-read sequencing, nanopore}, language = {en}, month = {February}, - note = {Number: 2 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 2}, number = {2}, pages = {89}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Long-{Read} {Sequencing} and {De} {Novo} {Genome} {Assembly} {Pipeline} of {Two} {Plasmodium} falciparum {Clones} ({Pf3D7}, {PfW2}) {Using} {Only} the {PromethION} {Sequencer} from {Oxford} {Nanopore} {Technologies} without {Whole}-{Genome} {Amplification}}, url = {https://www.mdpi.com/2079-7737/13/2/89}, urldate = {2024-04-28}, @@ -5247,13 +5591,34 @@ @article{delroisse_photophore_2021 doi = {10.3389/fmars.2021.627045}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {April}, - note = {Publisher: Frontiers Media SA}, + publisher = {Frontiers Media SA}, title = {Photophore {Distribution} and {Enzymatic} {Diversity} {Within} the {Photogenic} {Integument} of the {Cookie}-{Cutter} {Shark} {Isistius} brasiliensis ({Chondrichthyes}: {Dalatiidae})}, url = {https://doi.org/10.3389/fmars.2021.627045}, volume = {8}, year = {2021} } +@article{demeter_flow_2025, + abstract = {Plasmacytoid dendritic cells (pDCs) are a unique subset of dendritic cells specialized in rapid and robust type I interferon (IFN) production, playing critical roles in the pathogenesis and pathomechanisms of many human diseases. Accurate identification of pDCs in peripheral blood mononuclear cells (PBMCs) is challenging due to dynamic and non-exclusive specific expression of surface markers such as blood dendritic cell antigen (BDCA)-2 and BDCA-4. Although BDCA-4 is generally more stably expressed than BDCA-2, prolonged stimulation or inflammatory conditions can induce its expression on multiple non-pDC cell types, reducing the accuracy of pDC identification. Here, we thoroughly investigated BDCA-4 expression dynamics on pDCs and other PBMC subsets following prolonged activation with Toll-like receptor (TLR) 7 and TLR9 agonists. Our flow cytometry analysis revealed a significant increase in BDCA-4-positive non-pDC populations after extended stimulation, primarily corresponding to CD14+ monocytes. To overcome this limitation, we performed a gating strategy combining BDCA-4 positivity with a cocktail of non-pDC markers, enabling the exclusion of non-pDCs and accurate identification of pDCs. This approach enables the reliable identification of pDCs within heterogeneous cell populations using only two fluorescent channels in healthy conditions and even during strong activation or pathological states characterized by chronic inflammation.}, + author = {Demeter, Sarolta and Fekete, Tünde and Scholtz, Beáta and Veréb, Zoltán and Kemény, Lajos and Bácsi, Attila and Pázmándi, Kitti}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/ijms262210979}, + issn = {1422-0067}, + journal = {International Journal of Molecular Sciences}, + keywords = {{\textgreater}UseGalaxy.eu, BDCA-4, flow cytometry, gating strategy, monocyte, plasmacytoid dendritic cell}, + language = {en}, + month = {January}, + number = {22}, + pages = {10979}, + publisher = {Multidisciplinary Digital Publishing Institute}, + shorttitle = {Flow {Cytometric} {Challenges} in {Plasmacytoid} {Dendritic} {Cell} ({pDC}) {Identification}}, + title = {Flow {Cytometric} {Challenges} in {Plasmacytoid} {Dendritic} {Cell} ({pDC}) {Identification}: {Limitation} of {BDCA}-4 ({CD304})-{Based} {Gating}}, + url = {https://www.mdpi.com/1422-0067/26/22/10979}, + urldate = {2025-12-26}, + volume = {26}, + year = {2025} +} + @article{deng_atlas_2024, abstract = {Endothelial cells play crucial roles in physiology and are increasingly recognized as therapeutic targets in cardiovascular disease. Here, we analyzed the regulatory landscape of cardiac endothelial cells by assessing chromatin accessibility, histone modifications, and 3D chromatin organization and confirmed the functional relevance of enhancer-promoter interactions by CRISPRi-mediated enhancer silencing. We used this dataset to explore mechanisms of transcriptional regulation in cardiovascular disease and compared six different experimental models of heart failure, hypertension, or diabetes. Enhancers that regulate gene expression in diseased endothelial cells were enriched with binding sites for a distinct set of transcription factors, including the mineralocorticoid receptor (MR), a known drug target in heart failure and hypertension. For proof of concept, we applied endothelial cell-specific MR deletion in mice to confirm MR-dependent gene expression and predicted direct MR target genes. Overall, we have compiled here a comprehensive atlas of cardiac endothelial cell enhancer elements that provides insight into the role of transcription factors in cardiovascular disease.}, author = {Deng, Lisa and Pollmeier, Luisa and Bednarz, Rebecca and Cao, Can and Laurette, Patrick and Wirth, Luisa and Mamazhakypov, Argen and Bode, Christine and Hein, Lutz and Gilsbach, Ralf and Lother, Achim}, @@ -5265,8 +5630,6 @@ @article{deng_atlas_2024 month = {March}, number = {10}, pages = {eadj5101}, - pmcid = {PMC10917356}, - pmid = {38446896}, title = {Atlas of cardiac endothelial cell enhancer elements linking the mineralocorticoid receptor to pathological gene expression}, volume = {10}, year = {2024} @@ -5297,10 +5660,10 @@ @article{deng_gene_2020 keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, language = {en}, month = {February}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {1--9}, + publisher = {Nature Publishing Group}, title = {Gene expression in immortalized versus primary isolated cardiac endothelial cells}, url = {https://www.nature.com/articles/s41598-020-59213-x}, urldate = {2020-03-02}, @@ -5314,9 +5677,9 @@ @article{deng_lamp_2022 journal = {Plant Disease}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {January}, - note = {Publisher: Scientific Societies}, number = {1}, pages = {231--246}, + publisher = {Scientific Societies}, title = {{LAMP} {Assay} for {Distinguishing} {Fusarium} oxysporum and {Fusarium} commune in {Lotus} ({Nelumbo} nucifera) {Rhizomes}}, url = {https://doi.org/10.1094/pdis-06-21-1223-re}, volume = {106}, @@ -5332,9 +5695,9 @@ @article{deng_massively_2024 keywords = {{\textgreater}UseGalaxy.eu, CRISPR-Cas Systems, Gene Editing, Homologous Recombination, Saccharomyces cerevisiae}, language = {eng}, month = {May}, - note = {Publisher: American Association for the Advancement of Science}, number = {20}, pages = {eadj9382}, + publisher = {American Association for the Advancement of Science}, title = {Massively parallel {CRISPR}-assisted homologous recombination enables saturation editing of full-length endogenous genes in yeast}, url = {https://www.science.org/doi/full/10.1126/sciadv.adj9382}, urldate = {2024-06-07}, @@ -5348,9 +5711,9 @@ @article{denis_identification_2025 journal = {Microbiology Spectrum}, keywords = {{\textgreater}UseGalaxy.eu}, month = {March}, - note = {Publisher: American Society for Microbiology}, number = {0}, pages = {e02040--24}, + publisher = {American Society for Microbiology}, title = {Identification of {Toxoplasma} gondii antigenic proteins using an in vivo approach and in silico investigation of their polymorphism}, url = {https://journals.asm.org/doi/10.1128/spectrum.02040-24}, urldate = {2025-03-29}, @@ -5443,10 +5806,10 @@ @article{dhamija_pan-cancer_2020 keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, language = {en}, month = {August}, - note = {Number: 8 -Publisher: Nature Publishing Group}, + note = {Number: 8}, number = {8}, pages = {999--1010}, + publisher = {Nature Publishing Group}, title = {A pan-cancer analysis reveals nonstop extension mutations causing {SMAD4} tumour suppressor degradation}, url = {https://www.nature.com/articles/s41556-020-0551-7}, urldate = {2020-08-12}, @@ -5492,8 +5855,8 @@ @article{dias_pathogenicity_2022 journal = {Science of The Total Environment}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {March}, - note = {Publisher: Elsevier BV}, pages = {152324}, + publisher = {Elsevier BV}, title = {Pathogenicity of {Shiga} toxin-producing {Escherichia} coli ({STEC}) from wildlife: {Should} we care?}, url = {https://doi.org/10.1016/j.scitotenv.2021.152324}, volume = {812}, @@ -5514,8 +5877,6 @@ @article{diz-kucukkaya_jak2v617f_2024 month = {August}, number = {3}, pages = {167--174}, - pmcid = {PMC11589362}, - pmid = {38801025}, title = {{JAK2V617F} {Mutation} in {Endothelial} {Cells} of {Patients} with {Atherosclerotic} {Carotid} {Disease}}, volume = {41}, year = {2024} @@ -5565,10 +5926,10 @@ @article{donatova_changes_2024 keywords = {{\textgreater}UseGalaxy.eu, Influenza A virus, Influenza, Human, NS1 protein, Neurodegenerative Diseases, adaptation, brain, immune response, inflammation, influenza virus, neurodegeneration}, language = {en}, month = {January}, - note = {Number: 5 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 5}, number = {5}, pages = {2460}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Changes in the {Expression} of {Proteins} {Associated} with {Neurodegeneration} in the {Brains} of {Mice} after {Infection} with {Influenza} {A} {Virus} with {Wild} {Type} and {Truncated} {NS1}}, url = {https://www.mdpi.com/1422-0067/25/5/2460}, urldate = {2024-05-17}, @@ -5586,10 +5947,10 @@ @article{dorn_linc00261_2020 keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, CDH1, EMT, FOXA2, LINC00261, PDAC, TGFβ, lncRNA}, language = {en}, month = {May}, - note = {Number: 5 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 5}, number = {5}, pages = {1227}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {{LINC00261} {Is} {Differentially} {Expressed} in {Pancreatic} {Cancer} {Subtypes} and {Regulates} a {Pro}-{Epithelial} {Cell} {Identity}}, url = {https://www.mdpi.com/2072-6694/12/5/1227}, urldate = {2020-05-27}, @@ -5625,9 +5986,9 @@ @article{dossmann_specific_2024 keywords = {{\textgreater}UseGalaxy.eu, DNA methylation, Enzyme mechanisms, Transferases}, language = {en}, month = {May}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {1--12}, + publisher = {Nature Publishing Group}, title = {Specific {DNMT3C} flanking sequence preferences facilitate methylation of young murine retrotransposons}, url = {https://www.nature.com/articles/s42003-024-06252-z}, urldate = {2024-05-19}, @@ -5642,9 +6003,9 @@ @article{doyle_multiple_2025 journal = {Open Biology}, keywords = {{\textgreater}UseGalaxy.eu, Episyrphus balteatus, Syrphidae, genetics of migration, insect migration, migratory hoverflies, sex bias}, month = {February}, - note = {Publisher: Royal Society}, number = {2}, pages = {240235}, + publisher = {Royal Society}, title = {Multiple factors contribute to female dominance in migratory bioflows}, url = {https://royalsocietypublishing.org/doi/10.1098/rsob.240235}, urldate = {2025-02-16}, @@ -5685,8 +6046,8 @@ @article{dugar_chromosomal_2022 author = {Dugar, Gaurav and Hofmann, Andreas and Heermann, Dieter W and Hamoen, Leendert W}, journal = {Nature Genetics}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, - note = {Publisher: Nature Publishing Group}, pages = {1--8}, + publisher = {Nature Publishing Group}, title = {A chromosomal loop anchor mediates bacterial genome organization}, year = {2022} } @@ -5697,7 +6058,7 @@ @article{dumaidi_sero-molecular_2025 doi = {10.1155/cjid/6981644}, issn = {1712-9532}, journal = {The Canadian journal of infectious diseases \& medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Haplotype Networking, Occult Hepatitis B Virus Infection (Obi), Phylogenetic analysis, Whole Genome Sequence (Wgs), hepatitis B virus (HBV)}, pages = {6981644}, title = {Sero-{Molecular} {Markers} and {Genetic} {Diversity} of {Hepatitis} {B} {Virus} {Isolated} {From} {Hemodialysis} {Patients} {From} {Jenin} {District}, {West} {Bank}, {Palestine}}, url = {https://europepmc.org/articles/PMC12473736}, @@ -5763,9 +6124,9 @@ @article{dvir_uncovering_2021 doi = {10.1016/j.celrep.2021.109198}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {June}, - note = {Publisher: Elsevier BV}, number = {9}, pages = {109198}, + publisher = {Elsevier BV}, title = {Uncovering the {RNA}-binding protein landscape in the pluripotency network of human embryonic stem cells}, url = {https://doi.org/10.1016/j.celrep.2021.109198}, volume = {35}, @@ -5781,7 +6142,7 @@ @article{dwiyanti_whole_2025 keywords = {{\textgreater}UseGalaxy.eu, Genome, Illumina, Neolamarckia, chloroplast, microsatellite, plant breeding}, language = {English}, month = {May}, - note = {Publisher: Frontiers}, + publisher = {Frontiers}, shorttitle = {Whole {Genome} {Sequencing} of {Neolamarckia} macrophylla ({Roxb}.) {Bosser} and {Neolamarckia} cadamba ({Roxb}.) {Bosser} from {Indonesia}}, title = {Whole {Genome} {Sequencing} of {Neolamarckia} macrophylla ({Roxb}.) {Bosser} and {Neolamarckia} cadamba ({Roxb}.) {Bosser} from {Indonesia}: {A} vital resource for completing chloroplast genomes and mining microsatellite markers}, url = {https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2025.1608577/full}, @@ -5811,10 +6172,10 @@ @article{dziuba_silent_2023 keywords = {{\textgreater}UseGalaxy.eu, Bacterial evolution, Bacterial genetics, Magnetosomes, Magnetospirillum, Microbial ecology}, language = {en}, month = {March}, - note = {Number: 3 -Publisher: Nature Publishing Group}, + note = {Number: 3}, number = {3}, pages = {326--339}, + publisher = {Nature Publishing Group}, title = {Silent gene clusters encode magnetic organelle biosynthesis in a non-magnetotactic phototrophic bacterium}, url = {https://www.nature.com/articles/s41396-022-01348-y}, urldate = {2023-07-31}, @@ -5832,9 +6193,9 @@ @article{edet_genomic_2024 keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, Computational biology and bioinformatics, Gene Expression Regulation, Plant, Genetics, Molecular biology, Mutation, Plant Leaves, Plant sciences, Vigna}, language = {en}, month = {May}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {10654}, + publisher = {Nature Publishing Group}, title = {Genomic analysis of a spontaneous unifoliate mutant reveals gene candidates associated with compound leaf development in {Vigna} unguiculata [{L}] {Walp}}, url = {https://www.nature.com/articles/s41598-024-61062-x}, urldate = {2024-05-17}, @@ -5863,7 +6224,7 @@ @incollection{eggenhofer_evolutionary_2024 booktitle = {{RNA} {Folding}: {Methods} and {Protocols}}, doi = {10.1007/978-1-0716-3519-3_11}, editor = {Lorenz, Ronny}, - isbn = {978-1-07-163519-3}, + isbn = {978-1-0716-3519-3}, keywords = {{\textgreater}RNA Workbench, {\textgreater}UseGalaxy.eu, Covariance models, Multiple sequence alignment, RNA families, Secondary structure, Unsupervised model construction}, language = {en}, pages = {255--284}, @@ -5884,9 +6245,9 @@ @article{ehle_downregulation_2024 keywords = {{\textgreater}UseGalaxy.eu, Hepatology, Transcription}, language = {en}, month = {May}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {1--14}, + publisher = {Nature Publishing Group}, title = {Downregulation of {HNF4A} enables transcriptomic reprogramming during the hepatic acute-phase response}, url = {https://www.nature.com/articles/s42003-024-06288-1}, urldate = {2024-05-19}, @@ -5936,9 +6297,9 @@ @article{el-sawalhi_epidemiological_2023 journal = {Microbiology Spectrum}, keywords = {{\textgreater}UseGalaxy.eu}, month = {March}, - note = {Publisher: American Society for Microbiology}, number = {2}, pages = {e01426--22}, + publisher = {American Society for Microbiology}, title = {Epidemiological {Description} and {Detection} of {Antimicrobial} {Resistance} in {Various} {Aquatic} {Sites} in {Marseille}, {France}}, url = {https://journals.asm.org/doi/full/10.1128/spectrum.01426-22}, urldate = {2024-11-17}, @@ -5946,6 +6307,23 @@ @article{el-sawalhi_epidemiological_2023 year = {2023} } +@article{elmobark_blueedge_2025, + abstract = {Owing to the increasing number of IoT gadgets and the growth of big data, we are now facing massive amounts of diverse data that require proper preprocessing before they can be analyzed. Conventional methods involve sending data directly to the cloud, where it is cleaned and sorted, resulting in a more crowded network, increased latency, and a potential threat to users’ privacy. This paper presents an enhanced version of the BlueEdge framework—a neural network solution designed for the automated classification of data types on edge devices. We achieve this by utilizing a feed-forward neural network and optimized features to identify the presence of 14 distinct data types. Because of this, input data can be preprocessed near its source, and not in the cloud. We utilized a comprehensive dataset comprising 1400 samples, encompassing various data formats from around the world. Compared with rule-based methods, experimental assessment achieves better performance, and results in reduced data transmission (reduced by 62\%) and processing latency (78 times faster than cloud-based systems), with resource efficiency comparable to low-end mobile devices. Additionally, our strategy demonstrates strong performance under various data conditions, achieving accuracy levels of over 85\% on datasets that may include variations and a noise level as high as 20\%. The approach used here is capable of processing data for IoT devices used in education, which can lead to more efficient connections with the cloud and better privacy preservation. +SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-30445-z.}, + author = {Elmobark, Nagwa and El-Ghareeb, Haitham and Elhishi, Sara}, + doi = {10.1038/s41598-025-30445-z}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Automated data type detection, Edge computing, IoT data preprocessing, Neural network classification, Resource-efficient computing}, + language = {eng}, + month = {December}, + number = {1}, + pages = {43823}, + title = {{BlueEdge} neural network approach and its application to automated data type classification in mobile edge computing}, + volume = {15}, + year = {2025} +} + @article{elnouty_assessing_2025, abstract = {Natural Killer (NK) cells are vital components of the innate immune system, playing a crucial role in defending the body against tumors and virally infected cells. While various methods exist for their isolation, the profound impact of these techniques on NK cell biology remains poorly characterized.This study presents a comprehensive analysis of the transcriptomic profiles of NK cells isolated using different positive selection methods; anti-CD56, anti-CD7 (with two distinct lineage depletion protocols), and a combination of anti-CD16 and anti-CD56 antibodies, compared to negative selection using immunomagnetic beads. Our integrated analysis of RNA-Seq datasets revealed that the isolation method is a dominant source of transcriptomic variation, accounting for 68.6 \% of the total dataset variance, with technical factors being inextricably confounded with this biological signal. We identified extensive method-specific transcriptional signatures, with minimal overlap ({\textless}0.1 \%) in differentially expressed genes (DEGs) across techniques. Functional enrichment analysis demonstrated that these signatures correspond to starkly different functional states: anti-CD16/anti-CD56 selection enriched for a highly activated, cytotoxically competent NK cell population with upregulated pathways in cytotoxicity and immune surveillance, while one anti-CD7-based method captured NK cells in a suppressed state, showing significant downregulation of lymphocyte activation and cytotoxicity pathways. Marker expression analysis further revealed extreme inter-study heterogeneity, with fold-changes in key cytotoxic genes exceeding 70,000-fold between methods. These findings highlight that the choice of isolation technique is not neutral but fundamentally determines the transcriptional and functional identity of the studied NK cell population. Our results highlight the critical importance of methodological standardization in NK cell research and provide essential guidance for selecting isolation strategies tailored to specific research or therapeutic applications.}, author = {ElNouty, Rana and Moustafa, Ahmed and Mostafa, Maha and Ouf, Amged and Abou-Aisha, Khaled and Rady, Mona}, @@ -6008,9 +6386,9 @@ @article{epihov_iron_2024 journal = {Environmental Science \& Technology}, keywords = {{\textgreater}UseGalaxy.eu, Carbon Dioxide, Soil}, month = {July}, - note = {Publisher: American Chemical Society}, number = {27}, pages = {11970--11987}, + publisher = {American Chemical Society}, shorttitle = {Iron {Chelation} in {Soil}}, title = {Iron {Chelation} in {Soil}: {Scalable} {Biotechnology} for {Accelerating} {Carbon} {Dioxide} {Removal} by {Enhanced} {Rock} {Weathering}}, url = {https://doi.org/10.1021/acs.est.3c10146}, @@ -6047,9 +6425,9 @@ @article{ereqat_association_2022 keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org}, language = {eng}, month = {July}, - note = {Publisher: Spandidos Publications}, number = {1}, pages = {1--10}, + publisher = {Spandidos Publications}, title = {Association of {DNA} methylation and genetic variations of the {\textless}em{\textgreater}{APOE}{\textless}/em{\textgreater} gene with the risk of diabetic dyslipidemia}, url = {https://www.spandidos-publications.com/10.3892/br.2022.1544}, urldate = {2022-09-24}, @@ -6065,11 +6443,10 @@ @article{erkelenz_rbm3_2024 journal = {RNA Biology}, keywords = {{\textgreater}UseGalaxy.eu, RNA-seq, Rbm3, isoform switch, splicing, transcriptional fidelity}, month = {December}, - note = {Publisher: Taylor \& Francis -\_eprint: https://doi.org/10.1080/15476286.2024.2413820}, + note = {\_eprint: https://doi.org/10.1080/15476286.2024.2413820}, number = {1}, pages = {1--13}, - pmid = {39387568}, + publisher = {Taylor \& Francis}, title = {Rbm3 deficiency leads to transcriptome-wide splicing alterations}, url = {https://doi.org/10.1080/15476286.2024.2413820}, urldate = {2024-10-14}, @@ -6077,6 +6454,21 @@ @article{erkelenz_rbm3_2024 year = {2024} } +@article{erny_downregulation_2025, + abstract = {Cardiac hypertrophy is a key mechanism that allows the heart to adapt to increased load, but in the long term is associated with a higher risk for heart failure, arrhythmia, and death. During hypertrophic growth, cardiac myocytes signal to endothelial cells via vascular endothelial growth factor (VEGF) to promote angiogenesis and maintain myocardial oxygen supply. Insufficient angiogenesis leads to a decline in capillary density and drives the progression from compensated cardiac hypertrophy to heart failure. Here, we studied the time course of endothelial cell gene expression during heart failure development and identified transcriptional regulators of cell proliferation and angiogenesis. We applied transverse aortic constriction (TAC) in mice and isolated cardiac endothelial cells for RNA sequencing after 6 h and 1, 3, 7, or 28 days to create an inventory of gene expression during the course of cardiac hypertrophy and failure. Echocardiography revealed that decompensated heart failure occurred between days 7 and 28 after TAC. At the same time, we observed a switch in endothelial cell gene expression with an upregulation of proliferation markers in the hypertrophy state but downregulation in decompensated heart failure. Of note, endothelial cell cycle arrest occurred despite strong VEGF signaling from cardiac myocytes, indicating VEGF resistance. To investigate how endothelial cell proliferation is transcriptionally regulated, we performed a weighted gene co-expression network analysis and identified a module of 180 cell cycle-related genes. We predicted transcription factor 19 (TCF19), ATPase family AAA domain containing 2 (ATAD2), and transcription factor Dp-1 (TFDP1) to be central regulators of this gene module. Knockdown of TCF19 and ATAD2 by siRNA in HUVECs led to a downregulation of the marker of proliferation MKI67 and repressed cell proliferation, tube formation, and cell migration, confirming their regulatory function. In heart tissue biopsies from patients with aortic stenosis, TCF19 and ATAD2 abundance were positively correlated with endothelial cell proliferation. TCF19 or ATAD2 control the expression of a gene network involved in endothelial cell proliferation and angiogenesis. Downregulation of TCF19 and ATAD2 is associated with endothelial cell cycle arrest and an impaired angiogenic response to VEGF signaling that may promote the transition from compensated cardiac hypertrophy to heart failure.}, + author = {Erny, Elias and Koentges, Christoph and Mukherjee, Debanjan and Wirth, Luisa and Kamaras, Christos and Zell, Franziska and Hossfeld, Madelon and Groß, Olaf and Lother, Achim}, + doi = {10.1007/s00395-025-01139-4}, + issn = {1435-1803}, + journal = {Basic Research in Cardiology}, + keywords = {{\textgreater}UseGalaxy.eu, Angiogenesis, Cell cycle, Endothelial Cells, Endothelial cells, Gene Expression, Gene expression, Heart Failure, Heart failure, Hypertrophy, hypertrophy}, + language = {en}, + month = {September}, + title = {Downregulation of {TCF19} and {ATAD2} causes endothelial cell cycle arrest at the transition from cardiac hypertrophy to heart failure}, + url = {https://doi.org/10.1007/s00395-025-01139-4}, + urldate = {2025-10-03}, + year = {2025} +} + @article{erturkmen_microbiota_2025, abstract = {Colostrum microbiota is diverse and rich in beneficial bacteria with potential probiotic properties. The current study investigates the buffalo colostrum from Turkey, assessing its cultivable microbial diversity and conducting a metagenomic analysis. The metagenomic analysis of Day 2 colostrum shows a diverse bacterial composition, dominated by Bacteroidota (49.75\%) and Firmicutes (44.934\%), followed by Proteobacteria (5.11\%) and Actinobacteriota (1.50\%). Bifidobacterium spp., Lactobacillus acidophilus, and Lactococcus spp. were counted above 7.00 log CFU/mL in culturable microbiota. Thirty-six lactic acid bacteria (LAB) strains were selected, with 14 strains showing positive bile salt hydrolase (BSH) activity with glycocholic acid (GCA) and taurocholic acid (TCA) and resistance to bile salts and acidic conditions (survival in pH 2 medium and 0.3\% (w/v) bile salt). These strains were identified with high scores ({\textgreater} 1.80 genus levels) by MALDI-TOF MS and exhibited cholesterol assimilation ranging from 49.21\% to 68.22\% and exopolysaccharide (EPS) production from 7.9 to 12.4 mg/L. L. acidophilus PB4, grouped as high cholesterol assimilation and EPS production capacity, was well-characterized for safety through whole-genome sequencing (WGS) analysis using the Illumina NovaSeq platform and assigned an average nucleotide identity (ANI) value of 99.1\%. The findings from this study could advance research on the potential of probiotic microorganisms and probiotic food products derived from them in lowering cholesterol risk.}, author = {Ertürkmen, P.}, @@ -6127,8 +6519,6 @@ @article{espadinha_casecontrol_2025 month = {April}, number = {4}, pages = {728--740}, - pmcid = {PMC11950266}, - pmid = {40133048}, title = {Case–{Control} {Study} of {Factors} {Associated} with {Hemolytic} {Uremic} {Syndrome} among {Shiga} {Toxin}–{Producing} {Escherichia} coli {Patients}, {Ireland}, 2017–2020}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11950266/}, urldate = {2025-04-13}, @@ -6179,8 +6569,8 @@ @article{estell_zc3h4_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Genetic, Transcription}, language = {eng}, month = {April}, - note = {Publisher: eLife Sciences Publications, Ltd}, pages = {e67305}, + publisher = {eLife Sciences Publications, Ltd}, title = {{ZC3H4} restricts non-coding transcription in human cells}, url = {https://doi.org/10.7554/elife.67305}, volume = {10}, @@ -6197,10 +6587,10 @@ @article{estrada_mallarino_nephronophthisis_2020 keywords = {+Methods, +UsePublic, {\textgreater}RNA Workbench}, language = {en}, month = {September}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {15954}, + publisher = {Nature Publishing Group}, title = {Nephronophthisis gene products display {RNA}-binding properties and are recruited to stress granules}, url = {https://www.nature.com/articles/s41598-020-72905-8}, urldate = {2021-04-14}, @@ -6254,15 +6644,32 @@ @article{faddetta_endophytic_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Microbiota}, language = {eng}, month = {March}, - note = {Publisher: Springer Science and Business Media LLC}, number = {1}, pages = {7078}, + publisher = {Springer Science and Business Media LLC}, title = {The endophytic microbiota of {Citrus} limon is transmitted from seed to shoot highlighting differences of bacterial and fungal community structures}, url = {https://doi.org/10.1038/s41598-021-86399-5}, volume = {11}, year = {2021} } +@article{fadilah_complete_2026, + abstract = {Red meranti is considered a primary commercial product in the timber trade, recognized as the leading roundwood commodity with a total volume of 653.49 thousand m\&\#179; in 2020 (BPS 2021). This type of wood is characterized by its straight, cylindrical trunk and is primarily sourced from natural forests. There are also efforts to cultivate red meranti through sustainable forest management practices (Wistara et al., 2016). Previous reports indicated that the survival rate of the red meranti exceeds 67\%, with a Mean Annual Diameter Increment (MADI) above 1.7 cm/year (Widiyatno et al., 2020).As a member of the Dipterocarpaceae family, red meranti comprises approximately 75 species found in the lowland tropical rainforests of the Indo-Malayan region (Steenis 1983). Rubroshorea leprosula (Miq.) P. S. Ashton and J. Heck, a synonym for Shorea leprosula Miq. (Ashton and Heckenhauer, 2022), is locally known as meranti tembaga. It is also internationally traded as part of the light red meranti timber group (Ng et al., 2021). Typically, R. leprosula grows up to 1.000 m above sea level and has an estimated extent of occurrence (EOO) of over 2 million km 2 . This species is native to Southeast Asia, with a natural distribution that includes Singapore, Peninsular Malaysia, Peninsular Thailand, the Indonesian islands of Java, Sumatra, and Borneo (Kalimantan, Brunei Darussalam, Sabah, and Sarawak) (Pooma and Newman, 2024). R. leprosula is a timber tree known for its high economic value and significant presence in both regional and international tropical timber markets (Harahap et al., 2018). It is traded and utilized as raw material for various applications, including light and heavy construction, furniture, flooring, and plywood (Purwaningsih and Kintamani, 2018;Alex et al., 2023). This species is a key product of lowland tropical rainforests and serves as symbols of these ecosystems (Yu et al., 2021). The harvested timber of R. leprosula shows promising prospects, as it is classified as commercial wood class 1 (Djarwanto et al., 2017), with a strength class of III (Wahyudi and Sitanggang, 2016) and durability class of III-IV (Kartasujana and Martawijaya, 1973). However, the high value of R. leprosula has led to overexploitation and unsustainable harvesting under the Timber Forest Product Utilization Permit (Izin Usaha Pemanfaatan Hasil Hutan Kayu -Hutan Alam, IUPHHK-HA), as well as illegal logging and trade. Logging activity continues to be reported in Gunung Leuser National Park, where loggers specifically target R. leprosula due to its accessibility and ease of processing compared to other species (Harnelly et al., 2016). Moreover, R. leprosula typically occurs in late successional stages and is considered a climax species in lowland dipterocarp forests, characterized by low regeneration rates (Nurfatma et al. 2017). It also shows low natural regeneration in degraded habitats such as Tesso Nilo National Park (Kusumo et al., 2016). Consequently, it has low dominance in protected forests like Bukit Barisan Selatan National Park (Prayoga et al., 2019). These ecological characteristics render the species highly vulnerable to habitat disturbance and overexploitation, especially in concentrated areas such as the now-abandoned PT. Patriadi concession. As a result, the population of R. leprosula has been declining due to the conversion of forest land into agricultural and industrial plantation areas (Gaveau et al., 2016;Harahap et al., 2018), which has contributed to a continuous decrease in its global population. According to the International Union for Conservation of Nature (IUCN) Red List of Threatened Species, this species is globally classified as Near Threatened (NT) and has undergone a 20-29\% reduction over the past three generations (approximately 210 years) (Pooma and Newman, 2024). Indonesia is known as a wood-producing country that exported timber products, including those from illegal logging, to partner countries such as China and Japan from 2001 to 2010, with volumes estimated at 11,000 m\&\#179; and 12,000 m\&\#179; Roundwood Equivalent (RWE), respectively (Ji et al., 2018). In 2013, about 80 million m\&\#179; of RWE was illegally produced across nine countries, with approximately 50\% of this illegal supply originating from Indonesia (Hoare 2015). However, only 3,829 m\&\#179; of illegal wood was seized in 2017 (Ministry of Environment and Forestry 2019). This situation highlights the urgent need for conservation efforts to protect and sustain the existing populations of R. leprosula. Identifying the species and origin of illegal wood is challenging without reliable identification methods. The most established method for wood identification is the study of wood anatomy, which characterizes species based on their internal structure. However, this method can sometimes be challenging in distinguishing wood species, particularly within meranti species, leading to the development of other methods, such as chemical and genetic methods. However, genetic methods are currently considered more accurate for identifying wood species and their origins (Finkeldey et al., 2009;Lowe and Cross, 2011) through genomic information.Unlocking genomic data for R. leprosula is vital for enhancing wood identification and developing genetic conservation strategies. Among various genomic resources, the chloroplast genome is particularly valuable, as it provides crucial insights into genetic variation among closely related species. In plants, the chloroplast genome or plastome is a semi-autonomous structure enclosed in double membranes, housing independent genetic material (Dobrogojski et al., 2020;Daniell et al., 2021). These organelles possess molecular machinery that regulates gene expression (Chevigny et al., 2020) and play a vital role in various physiological processes within plants (Mahapatra et al., 2021). The chloroplast genome is a valuable tool for genetic studies due to its slow evolutionary rate, maternal inheritance in most angiosperms, and its conserved structure and gene sequences (Zulfahmi et al., 2015;Song et al., 2019). In angiosperms, the chloroplast genome typically ranges from 107 kb to 218 kb and encodes 120 to 130 genes crucial for transcription, translation, and photosynthesis (Daniell et al., 2016;Li et al., 2024). Due to its conservation, the chloroplast genome serves as a reliable resource for molecular identification, genetic diversity assessment, and phylogenetic studies (Chew et al., 2023;Kim et al., 2024). The genome of Rubroshorea leprosula from Malaysia has been sequenced using the Illumina HiSeq platform to study comparative genomics and molecular dating of the evolution of the Dipterocarpaceae family, highlighting the role of drought in aseasonal tropical rainforests (Ng et al., 2021). Another Rubroshorea leprosula genome from China was sequenced by Yu et al. (2021) using the Illumina NovoSeq 6000 platform to conduct a comprehensive evolutionary analysis of chloroplast genomes from 20 species of Dipterocapoideae and to identify barcoding loci for species identification. However, data on the genomic resources for R. leprosula from Indonesia are still limited, as the Indonesian population may harbor unique genetic characteristics. This lack of information poses a significant challenge to advancing research on developing chloroplast DNA (cpDNA) markers, which are essential for genetic conservation efforts. Therefore, this study aims to assemble and characterize the complete chloroplast genome of Rubroshorea leprosula from Indonesia, generated from short-read sequencing, and to analyze its phylogenetic relationship with other species. This study enhances understanding of the genetics of R. leprosula from Indonesia and contributes to wood identification and conservation efforts. It represents a vital step toward preserving this species and enriching the knowledge of plant genetics.The plant material used in this study consisted of silica-gel dried cambium sample collected from Rubroshorea leprosula from Bukit Tigapuluh National Park, Riau Province on Sumatra Island, Indonesia (-0.814669 S, 102.528702 E), specifically from one individual mature tree with a stem diameter at the breast height of 50.8 cm and total height approximately 21 m with straight stem (Figure 1) to ensure the quality and consistency of the samples obtained. The cambium sample was scraped with a stainless-steel scalpel blade to form a sawdust-like material. The sawdust was then ground again with a Qiagen TissueLyser II. A total of 100 mg of the cambium powder sample was used for genomic DNA extraction and isolation following the modified Cetyltrimethylammonium Bromide (CTAB) protocol (Doyle and Doyle, 1990). Specifically, the modifications involve two incubations: 65 \&\#176;C for 60 min and 37 \&\#176;C for 30 min, with an additional 20 \&\#181;L of Proteinase K before the first incubation and 20 \&\#181;L of RNase A before the second. The initial quantification and assessment of genomic DNA purity were conducted using a Nanodrop 2000 spectrophotometer (Thermo Scientific), which exhibited a concentration of 300.3 ng/μL, A260/280 of 1.81, and A260/230 of 1.18, and was visualized via 1\% Tris-Borate-EDTA (TBE) agarose gel electrophoresis. To achieve accurate DNA quantification, Qubit dsDNA HS Assay Kits (Thermo Scientific) were utilized. The genomic DNA samples of R. leprosula exhibited a concentration of 13.1 ng/μL and a total amount of 458.5 μg. The high-molecular-weight genomic DNA extracted from R. leprosula was subsequently used for library preparation to facilitate subsequent short-read sequencing. Libraries were prepared according to the protocol provided by Novogen AIT, Singapore, for the Illumina NovaSeq 6000. The sequencing was done through PT. Genetika Science Indonesia, resulting in a data output of 3 GB. Short-read sequencing has been selected for this study due to its well-established application in the reconstruction of chloroplast genomes. Its high accuracy and coverage facilitate reliable assembly and annotation of the chloroplast genome, while also offering cost-effective solutions for study purposes (Wang et al., 2018). All data analysis was conducted at the Forest Genetics and Molecular Forestry Laboratory within the Department of Silviculture, Faculty of Forestry and Environment at IPB University in Bogor, West Java, Indonesia.Raw reads of the Rubroshorea leprosula from Illumina NovaSeq 6000 sequencing (Fastq) were uploaded to the Galaxy web platform, specifically the public server at usegalaxy.org v25.0.4.dev0 (https://usegalaxy.eu/) for analysis (Afgan et al. 2016). Quality control was conducted to evaluate the quality of reads. The quality of raw short-reads was assessed using FastQC v0.12.1 (Andrews, 2010), and clean reads were filtered with Fastp v0.24.0 (Chen et al., 2018) using default parameters. Clean reads were assembled using SPAdes v3.15.3 (Bankevich et al., 2012) and GetOrganelle v1.7.7.1 (Jin et al., 2020), both with default parameters. SPAdes v3.15.3 uses an adaptive multi-k-mer strategy by default. This approach was considered appropriate for the high-quality Illumina short-read data employed in this study and has been widely applied in chloroplast genome assembly. To improve accuracy, the assembled contigs were polished using Pilon v1.20.1 (Walker et al., 2014). These contigs were then mapped to the reference plastome of Shorea leprosula, a synonym of Rubroshorea leprosula (GenBank accession: MZ160997.1). The assembly results were then annotated using GeSeq (https://chlorobox.mpimp-golm.mpg.de/geseq.html) (Tillich et al., 2017). The fully annotated circular genome was visualized using OrganellarGenomeDRAW (OGDRAW) v1.3.1 accessible through the MPI-MP Chlorobox platform (Greiner et al., 2019).In order to evaluate the phylogenetic position of the reconstructed chloroplast relative to those of closely related organisms and to assess the possible effects of these differences, a phylogenetic analysis was conducted. A total of 20 chloroplast genomes of taxa closely related to Rubroshorea leprosula (from the Dipterocarpaceae family) were downloaded from GenBank (the National Center for Biotechnology Information/NCBI) and aligned with the obtained plastomes. A complete list of the accessions used is given in Supplementary Table 1. Neolamackia cadamba (NC\_041149.1) was included and used as an outgroup. The sequences were processed in Mega X v12.1.1 (Kumar et al, 2018) and aligned with MAFFT v7.526 (Katoh and Standley, 2013) using default parameters. A maximum likelihood (ML) phylogenetic tree was inferred with the IQ-TREE Web Server (Trifinopoulos et al., 2016), applying 1,000 bootstrap replicates. The phylogenetic tree was visualized using iTOL (Letunic and Bork 2024).Short-read sequencing of Rubroshorea leprosula generated a total of 20,499,674 reads, equivalent to 3 gigabase pairs (Gbp) of raw data. The mean read length was 150 bp, and the mean read quality score of the raw data was recorded at 36. After filtering, all reads passed the quality assessment with the same score. The complete chloroplast genome of R. leprosula has been successfully assembled using short-read (Illumina NovaSeq 6000) sequencing data to resolve structural regions. The Rubroshorea leprosula chloroplast genome exhibits a typical quadripartite structure (Figure 2a) with a total length of 150,691 bp. The genome consists of a Small Single-copy Region (SSC: 19,917 bp) and a Large Single-copy Region (LSC: 83,740 bp), separated by a pair of inverted repeat regions: Inverted Repeat A (IRA: 23,517 bp) and Inverted Repeat B (IRB: 23,517 bp) (Figure 2a). The GC content of the R. leprosula sequence is 34.2\%. This finding is nearly comparable in size to the Shorea leprosula syn.Rubroshorea leprosula chloroplast genome reported by Yu et al. (2021), which is 152,100 bp. Furthermore, similar chloroplast genome sizes were also found in Shorea macrophylla syn.Rubroshorea macrophylla, at 150,778 bp (Chew et al., 2023), and Rubroshorea johorensis, at 149,968 bp (Nugroho et al., 2025). These results indicate that the chloroplast genome size in the Sumatran population of Rubroshorea leprosula is relatively conserved and consistent within the Rubroshorea or Shorea group, at around 150 kb. The Rubroshorea leprosula chloroplast genome contains a total of 115 genes, including 80 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes (Supplementary Table 2). These genes are categorized into four functional groups: selfreplicating genes, photosynthetic genes, genes with other functions, and genes of unknown function (Supplementary Table 2). In the Rubroshorea leprosula chloroplast genome, of the total identified genes, 19 contain introns, suggesting that RNA processing events may play a crucial role in gene expression and regulation, as further detailed in Supplementary Table 2.Similar to other plant chloroplasts, R. leprosula likely exhibits high levels of recombination and structural rearrangements, traits characteristic of plant chloroplast genomes that contribute to genome plasticity. However, variations in gene content and intron presence may indicate species-specific adaptations that could be linked to environmental factors or evolutionary history. The results of chloroplast genome sequencing of R. leprosula indicated that, although the assembled genome remains limited, it can be used for further population genetic studies, providing essential data for designing conservation strategies for this species. This underscores the need for further research in this area.Conducting additional comparative genomic studies may provide deeper insights into the functional implications of these genomic features in R. leprosula.The phylogenetic tree of R. leprosula based on the complete chloroplast genome showed that the studied R. leprosula was in the same clade as other species within the same genus, specifically Shorea pachyphylla (NC\_040966.1) syn. Rubroshorea pachyphylla, with a bootstrap value of 100\% (Figure 2b). Additionally, R. leprosula forms a monophyletic clade with Parashorea chinensis (NC\_046579.1), Shorea zeylanica (NC\_040965.1) syn. Doona zeylanica, Hopea reticulata (NC\_052744.1), and Hopea chinensis (NC\_053766.1), emphasizing the intricate evolutionary connections among these taxa. This finding aligns with the study by Yu et al. (2021), which reported that the phylogenetic tree of the genus Rubroshorea (syn. Shorea) was not monophyletic. The present study provides an updated phylogenetic analysis of R. leprosula, contributing to a deeper understanding of the evolutionary dynamics that characterize R. leprosula and its related species.}, + author = {Fadilah, Ainun and Hikmat, Agus and Karlinasari, Lina and Dwiyanti, Fifi Gus and Pratama, Rahadian and Maulana, Faizal and Kamal, Irsyad and Syaputra, Dhika and Siregar, Iskandar Zulkarnaen}, + doi = {10.3389/fevo.2026.1751419}, + issn = {2296-701X}, + journal = {Frontiers in Ecology and Evolution}, + keywords = {{\textgreater}UseGalaxy.eu, Chloroplast genome, Dipterocarp, Illumina, Rubroshorea, phylogenetic}, + language = {English}, + month = {January}, + publisher = {Frontiers}, + title = {Complete {Chloroplast} {Genome} {Assembly} of {Rubroshorea} leprosula {Wood} from {Indonesia} for {Phylogenetic} and {Conservation} {Studies}}, + url = {https://www.frontiersin.org/journals/ecology-and-evolution/articles/10.3389/fevo.2026.1751419/full}, + urldate = {2026-01-06}, + volume = {14}, + year = {2026} +} + @article{fahrner_democratizing_2022, abstract = {{\textless}h4{\textgreater}Background{\textless}/h4{\textgreater}Data-independent acquisition (DIA) has become an important approach in global, mass spectrometric proteomic studies because it provides in-depth insights into the molecular variety of biological systems. However, DIA data analysis remains challenging owing to the high complexity and large data and sample size, which require specialized software and vast computing infrastructures. Most available open-source DIA software necessitates basic programming skills and covers only a fraction of a complete DIA data analysis. In consequence, DIA data analysis often requires usage of multiple software tools and compatibility thereof, severely limiting the usability and reproducibility.{\textless}h4{\textgreater}Findings{\textless}/h4{\textgreater}To overcome this hurdle, we have integrated a suite of open-source DIA tools in the Galaxy framework for reproducible and version-controlled data processing. The DIA suite includes OpenSwath, PyProphet, diapysef, and swath2stats. We have compiled functional Galaxy pipelines for DIA processing, which provide a web-based graphical user interface to these pre-installed and pre-configured tools for their use on freely accessible, powerful computational resources of the Galaxy framework. This approach also enables seamless sharing workflows with full configuration in addition to sharing raw data and results. We demonstrate the usability of an all-in-one DIA pipeline in Galaxy by the analysis of a spike-in case study dataset. Additionally, extensive training material is provided to further increase access for the proteomics community.{\textless}h4{\textgreater}Conclusion{\textless}/h4{\textgreater}The integration of an open-source DIA analysis suite in the web-based and user-friendly Galaxy framework in combination with extensive training material empowers a broad community of researches to perform reproducible and transparent DIA data analysis.}, author = {Fahrner, Matthias and Föll, Melanie Christine and Grüning, Björn Andreas and Bernt, Matthias and Röst, Hannes and Schilling, Oliver}, @@ -6271,8 +6678,8 @@ @article{fahrner_democratizing_2022 journal = {GigaScience}, keywords = {+IsGalaxy, +UsePublic, {\textgreater}UseGalaxy.eu, Computational Biology, Proteomics}, language = {eng}, - note = {Publisher: Oxford University Press (OUP)}, pages = {giac005}, + publisher = {Oxford University Press (OUP)}, title = {Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the {Galaxy} framework}, url = {https://doi.org/10.1093/gigascience/giac005}, volume = {11}, @@ -6289,10 +6696,10 @@ @article{fahrner_systematic_2021 keywords = {+Methods, +Shared, +Stellar, +UsePublic, {\textgreater}UseGalaxy.eu, NCI-60 reanalysis, endogenous proteolysis, fragment mass tolerance, mass spectrometry, semispecific peptide search}, language = {en}, month = {June}, - note = {Number: 2 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 2}, number = {2}, pages = {26}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {A {Systematic} {Evaluation} of {Semispecific} {Peptide} {Search} {Parameter} {Enables} {Identification} of {Previously} {Undescribed} {N}-{Terminal} {Peptides} and {Conserved} {Proteolytic} {Processing} in {Cancer} {Cell} {Lines}}, url = {https://www.mdpi.com/2227-7382/9/2/26}, urldate = {2021-05-27}, @@ -6342,7 +6749,7 @@ @article{fallmann_rna_2019 author = {Fallmann, Jörg and Videm, Pavankumar and Bagnacani, Andrea and Batut, Bérénice and Doyle, Maria A. and Klingstrom, Tomas and Eggenhofer, Florian and Stadler, Peter F. and Backofen, Rolf and Grüning, Björn}, doi = {10.1093/nar/gkz353}, journal = {Nucleic Acids Research}, - keywords = {+Education, +Galactic, +IsGalaxy, {\textgreater}RNA Workbench, Software}, + keywords = {+Education, +Galactic, +IsGalaxy, {\textgreater}RNA Workbench, {\textgreater}UseGalaxy.eu, Software}, language = {en}, month = {May}, shorttitle = {The {RNA} workbench 2.0}, @@ -6379,10 +6786,10 @@ @article{farias_basidin_2023 keywords = {\textit{Theobroma cacao}, {\textgreater}UseGalaxy.eu, basidiomycetes, effectors, hypersensitivity response, witche’s broom}, language = {en}, month = {January}, - note = {Number: 14 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 14}, number = {14}, pages = {11714}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {{BASIDIN} as a {New} {Protein} {Effector} of the {Phytopathogen} {Causing} {Witche}’s {Broom} {Disease} in {Cocoa}}, url = {https://www.mdpi.com/1422-0067/24/14/11714}, urldate = {2023-07-31}, @@ -6432,9 +6839,9 @@ @article{farmiloe_widespread_2020 journal = {Philosophical Transactions of the Royal Society B: Biological Sciences}, keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org}, month = {March}, - note = {Publisher: Royal Society}, number = {1795}, pages = {20190333}, + publisher = {Royal Society}, title = {Widespread correlation of {KRAB} zinc finger protein binding with brain-developmental gene expression patterns}, url = {https://royalsocietypublishing.org/doi/full/10.1098/rstb.2019.0333}, urldate = {2020-03-05}, @@ -6485,10 +6892,10 @@ @article{fatima_book_2023 keywords = {{\textgreater}UseGalaxy.eu}, language = {en}, month = {January}, - note = {Number: 70 -Publisher: F1000 Research Limited}, + note = {Number: 70}, number = {70}, pages = {70}, + publisher = {F1000 Research Limited}, title = {Book of {Abstracts} of the 1st {Colloquium} for {Bioinformatics} {Learning}, {Education}, and {Training}}, url = {https://f1000research.com/documents/12-70}, urldate = {2023-03-15}, @@ -6534,9 +6941,9 @@ @article{feldker_genome-wide_2020 keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, AP-1, Epithelial-Mesenchymal Transition, Genome, Human, ZEB1, breast cancer, epithelial to mesenchymal transition}, language = {eng}, month = {July}, - note = {Publisher: John Wiley \& Sons, Ltd}, number = {n/a}, pages = {e103209}, + publisher = {John Wiley \& Sons, Ltd}, title = {Genome-wide cooperation of {EMT} transcription factor {ZEB1} with {YAP} and {AP}-1 in breast cancer}, url = {https://www.embopress.org/doi/10.15252/embj.2019103209}, urldate = {2020-08-18}, @@ -6565,7 +6972,7 @@ @article{fell_fibcd1_2021 doi = {10.1101/2021.09.09.459581}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {September}, - note = {Publisher: Cold Spring Harbor Laboratory}, + publisher = {Cold Spring Harbor Laboratory}, title = {{FIBCD1} is a {Conserved} {Receptor} for {Chondroitin} {Sulphate} {Proteoglycans} of the {Brain} {Extracellular} {Matrix} and a {Candidate} {Gene} for a {Complex} {Neurodevelopmental} {Disorder}}, url = {https://doi.org/10.1101/2021.09.09.459581}, year = {2021} @@ -6581,9 +6988,9 @@ @article{feng_scarless_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, language = {eng}, month = {January}, - note = {Publisher: Oxford University Press (OUP)}, number = {3}, pages = {iyab012}, + publisher = {Oxford University Press (OUP)}, title = {Scarless engineering of the {Drosophila} genome near any site-specific integration site}, url = {https://doi.org/10.1093/genetics/iyab012}, volume = {217}, @@ -6617,10 +7024,10 @@ @article{feng_transcription_2022 keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, Drosophila Proteins, Experimental organisms, Molecular biology, Transcription Factors}, language = {en}, month = {July}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {3808}, + publisher = {Nature Publishing Group}, title = {Transcription factor paralogs orchestrate alternative gene regulatory networks by context-dependent cooperation with multiple cofactors}, url = {https://www.nature.com/articles/s41467-022-31501-2}, urldate = {2023-08-06}, @@ -6634,8 +7041,8 @@ @article{fernandes_alise_2023 keywords = {{\textgreater}UseGalaxy.eu, ⛔ No DOI found}, language = {en}, month = {August}, - note = {Accepted: 2024-04-17T00:37:44Z -Publisher: Universidade Federal de Minas Gerais}, + note = {Accepted: 2024-04-17T00:37:44Z}, + publisher = {Universidade Federal de Minas Gerais}, shorttitle = {Análise de splicing alternativo durante o processo de amadurecimento de frutos}, title = {Análise de splicing alternativo durante o processo de amadurecimento de frutos: aplicação em café e tomate}, url = {http://www.sbicafe.ufv.br/handle/123456789/14325}, @@ -6715,9 +7122,9 @@ @article{fernandez-diaz_draft_2023 keywords = {{\textgreater}UseGalaxy.eu}, language = {eng}, month = {January}, - note = {Publisher: American Society for Microbiology}, number = {2}, pages = {e01293--22}, + publisher = {American Society for Microbiology}, title = {Draft {Genome} {Sequence} of an {Isolate} of {Genotype} {VII} {Newcastle} {Disease} {Virus} {Isolated} from an {Outbreak} in {Fighting} {Cock} in {Peru}}, url = {https://journals.asm.org/doi/full/10.1128/mra.01293-22}, urldate = {2023-03-15}, @@ -6781,8 +7188,8 @@ @article{ferreira_avaliacao_2023 keywords = {{\textgreater}UseGalaxy.eu}, language = {por}, month = {February}, - note = {Accepted: 2023-05-25T16:42:56Z -Publisher: Universidade Federal do Pampa}, + note = {Accepted: 2023-05-25T16:42:56Z}, + publisher = {Universidade Federal do Pampa}, title = {Avaliação da expressão diferencial em {Physcomitrium} patens na busca das adaptações moleculares responsivas na arquitetura dos órgãos reprodutivos}, url = {https://repositorio.unipampa.edu.br/jspui/handle/riu/8369}, urldate = {2023-07-31}, @@ -6798,7 +7205,7 @@ @article{ferreira_tcserpin_2024 keywords = {{\textgreater}UseGalaxy.eu, Inglês (Estados Unidos) Inglês (Estados Unidos) Formatado: Inglês (Estados Unidos), Protease Inhibitors, Serpin, stress and defense Fonte: Itálico, theobroma cacao, thermostability}, language = {English}, month = {January}, - note = {Publisher: Frontiers}, + publisher = {Frontiers}, title = {{TcSERPIN}, an inhibitor that interacts with cocoa defense proteins and has biotechnological potential against human pathogens}, url = {https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1337750/full}, urldate = {2024-05-17}, @@ -6815,9 +7222,9 @@ @article{fiedler_taxonomic_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, language = {eng}, month = {January}, - note = {Publisher: MDPI AG}, number = {2}, pages = {246}, + publisher = {MDPI AG}, title = {Taxonomic {Evaluation} of the {Heyndrickxia} ({Basonym} {Bacillus}) sporothermodurans {Group} ({H}. sporothermodurans, {H}. vini, {H}. oleronia) {Based} on {Whole} {Genome} {Sequences}}, url = {https://doi.org/10.3390/microorganisms9020246}, volume = {9}, @@ -6852,10 +7259,10 @@ @article{fischer_expanding_2024 keywords = {{\textgreater}UseGalaxy.eu, Genetic Vectors, Recombination, Genetic, human adenoviruses, mutagenesis of viral genomes, replication-competent vectors, transgene insertion sites, viral bacmids}, language = {en}, month = {May}, - note = {Number: 5 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 5}, number = {5}, pages = {658}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Expanding the {Scope} of {Adenoviral} {Vectors} by {Utilizing} {Novel} {Tools} for {Recombination} and {Vector} {Rescue}}, url = {https://www.mdpi.com/1999-4915/16/5/658}, urldate = {2024-05-17}, @@ -6951,6 +7358,7 @@ @article{foll_moving_2021 Results Rigorous quality control in combination with careful pre-processing enabled reduction of m/z shifts and intensity batch effects. High classification accuracy was found for both, tumor vs. stroma and muscle-infiltrating vs. non-muscle invasive tumors. Some of the most discriminative m/z features for each condition could be assigned a putative identity: Stromal tissue was characterized by collagen type I peptides and tumor tissue by histone and heat shock protein beta-1 peptides.Intermediate filaments such as cytokeratins and vimentin were discriminative between the tumors with different muscle-infiltration status. To make the study fully reproducible and to advocate the criteria of FAIR (findability, accessibility, interoperability, and reusability) research data, we share the raw data, spectra annotations as well as all Galaxy histories and workflows. Data are available via ProteomeXchange with identifier PXD026459 and Galaxy results via https://github.com/foellmelanie/Bladder\_MSI\_Manuscript\_Galaxy\_links. Conclusion Here, we show that translational MSI data analysis in a fully transparent and reproducible manner is possible and we would like to encourage the community to join our efforts.}, author = {Föll, Melanie Christine and Volkmann, Veronika and Enderle-Ammour, Kathrin and Wilhelm, Konrad and Guo, Dan and Vitek, Olga and Bronsert, Peter and Schilling, Oliver}, + chapter = {New Results}, copyright = {© 2021, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/}, doi = {10.1101/2021.08.09.455649}, journal = {bioRxiv}, @@ -6959,8 +7367,7 @@ @article{foll_moving_2021 month = {August}, note = {Company: Cold Spring Harbor Laboratory Distributor: Cold Spring Harbor Laboratory -Label: Cold Spring Harbor Laboratory -Section: New Results}, +Label: Cold Spring Harbor Laboratory}, pages = {2021.08.09.455649}, shorttitle = {Moving translational mass spectrometry imaging towards transparent and reproducible data analyses}, title = {Moving translational mass spectrometry imaging towards transparent and reproducible data analyses: {A} case study of an urothelial cancer cohort analyzed in the {Galaxy} framework}, @@ -7010,8 +7417,8 @@ @article{fonseca_mineracao_2024 keywords = {{\textgreater}UseGalaxy.eu}, language = {por}, month = {September}, - note = {Accepted: 2024-11-06T15:09:43Z -Publisher: Universidade Federal do Amazonas}, + note = {Accepted: 2024-11-06T15:09:43Z}, + publisher = {Universidade Federal do Amazonas}, title = {Mineração genômica e identificação de moléculas com potencial biotecnológico da microbiota amazônica}, url = {https://tede.ufam.edu.br/handle/tede/10467}, urldate = {2024-11-17}, @@ -7058,7 +7465,7 @@ @article{foschini_methylation_2020 journal = {Frontiers in Oncology}, keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, BWA, DNA Methylation, FLNA, HDAC6, MAGE family, UXT, X-chromosome, androgen receptor, male breast cancer}, language = {English}, - note = {Publisher: Frontiers}, + publisher = {Frontiers}, title = {Methylation {Profile} of {X}-{Chromosome}–{Related} {Genes} in {Male} {Breast} {Cancer}}, url = {https://www.frontiersin.org/articles/10.3389/fonc.2020.00784/full}, urldate = {2020-08-19}, @@ -7090,8 +7497,8 @@ @article{fraccalvieri_isolamento_2025 keywords = {{\textgreater}UseGalaxy.eu, ⛔ No DOI found}, language = {ita}, month = {March}, - note = {Accepted: 2025-05-23T11:24:15Z -Publisher: Università degli studi di Bari}, + note = {Accepted: 2025-05-23T11:24:15Z}, + publisher = {Università degli studi di Bari}, shorttitle = {Isolamento di batteri appartenenti alla famiglia delle {Enterobatteriacee} resistenti agli antibiotici in alimenti di origine animale e vegetale}, title = {Isolamento di batteri appartenenti alla famiglia delle {Enterobatteriacee} resistenti agli antibiotici in alimenti di origine animale e vegetale: analisi genomica e implicazioni per la sicurezza alimentare}, url = {https://ricerca.uniba.it/handle/11586/539587}, @@ -7100,34 +7507,32 @@ @article{fraccalvieri_isolamento_2025 } @article{fraccalvieri_isolation_2025, - author = {Fraccalvieri, Rosa and Castellana, Stefano and Bianco, Angelica and Difato, Laura Maria and Capozzi, Loredana and Del Sambro, Laura and Donatiello, Adelia and Pugliese, Domenico and Tempesta, Maria and Parisi, Antonio and Caruso, Marta}, + abstract = {The emergence of colistin-resistant Enterobacteriaceae in food products is a growing concern due to the potential transfer of resistance to human pathogens. This study aimed to assess the prevalence of colistin-resistant Enterobacteriaceae in raw and ready-to-eat food samples collected from two regions of Italy (Apulia and Basilicata) and to evaluate their resistance phenotypes and genetic characteristics. A total of 1000 food samples were screened, with a prevalence of 4.4\% of colistin-resistant Enterobacteriaceae. The majority of the isolates belonged to Enterobacter spp. (60\%), followed by Moellerella wisconsensis, Atlantibacter hermannii, Klebsiella pneumoniae, and Escherichia coli, among others. Genomic sequencing and antimicrobial susceptibility testing revealed high levels of resistance to β-lactams, with most isolates exhibiting multidrug resistance (MDR). Notably, seven isolates harbored mcr genes (mcr-1, mcr-9, and mcr-10). Additionally, in four of them were predicted the IncHI2 plasmids, known to facilitate the spread of colistin resistance. Furthermore, 56 antimicrobial resistance genes were identified, suggesting the genetic mechanisms underlying resistance to several antibiotic classes. Virulence gene analysis showed that E. coli and other isolates carried genes linked to pathogenicity, increasing the potential risk to public health. This study emphasizes the role of food as a potential reservoir for colistin-resistant bacteria and the importance of monitoring the spread of AMR genes in foodborne pathogens.}, + author = {Fraccalvieri, Rosa and Bianco, Angelica and Difato, Laura Maria and Capozzi, Loredana and Del Sambro, Laura and Castellana, Stefano and Donatiello, Adelia and Serrecchia, Luigina and Pace, Lorenzo and Farina, Donatella and Galante, Domenico and Caruso, Marta and Tempesta, Maria and Parisi, Antonio}, + doi = {10.3390/microorganisms13010163}, issn = {2076-2607}, journal = {Microorganisms}, keywords = {{\textgreater}UseGalaxy.eu}, - language = {eng}, - month = {July}, - number = {8}, - title = {Isolation of {ESBL}-{Producing} {Enterobacteriaceae} in {Food} of {Animal} and {Plant} {Origin}: {Genomic} {Analysis} and {Implications} for {Food} {Safety}}, - url = {http://europepmc.org/abstract/PMC/PMC12388533}, + month = {January}, + number = {1}, + pages = {163}, + title = {Isolation and {Characterization} of {Colistin}-{Resistant} {Enterobacteriaceae} from {Foods} in {Two} {Italian} {Regions} in the {South} of {Italy}}, + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11767609/}, + urldate = {2025-02-16}, volume = {13}, year = {2025} } @article{fraccalvieri_isolation_2025, - abstract = {The emergence of colistin-resistant Enterobacteriaceae in food products is a growing concern due to the potential transfer of resistance to human pathogens. This study aimed to assess the prevalence of colistin-resistant Enterobacteriaceae in raw and ready-to-eat food samples collected from two regions of Italy (Apulia and Basilicata) and to evaluate their resistance phenotypes and genetic characteristics. A total of 1000 food samples were screened, with a prevalence of 4.4\% of colistin-resistant Enterobacteriaceae. The majority of the isolates belonged to Enterobacter spp. (60\%), followed by Moellerella wisconsensis, Atlantibacter hermannii, Klebsiella pneumoniae, and Escherichia coli, among others. Genomic sequencing and antimicrobial susceptibility testing revealed high levels of resistance to β-lactams, with most isolates exhibiting multidrug resistance (MDR). Notably, seven isolates harbored mcr genes (mcr-1, mcr-9, and mcr-10). Additionally, in four of them were predicted the IncHI2 plasmids, known to facilitate the spread of colistin resistance. Furthermore, 56 antimicrobial resistance genes were identified, suggesting the genetic mechanisms underlying resistance to several antibiotic classes. Virulence gene analysis showed that E. coli and other isolates carried genes linked to pathogenicity, increasing the potential risk to public health. This study emphasizes the role of food as a potential reservoir for colistin-resistant bacteria and the importance of monitoring the spread of AMR genes in foodborne pathogens.}, - author = {Fraccalvieri, Rosa and Bianco, Angelica and Difato, Laura Maria and Capozzi, Loredana and Del Sambro, Laura and Castellana, Stefano and Donatiello, Adelia and Serrecchia, Luigina and Pace, Lorenzo and Farina, Donatella and Galante, Domenico and Caruso, Marta and Tempesta, Maria and Parisi, Antonio}, - doi = {10.3390/microorganisms13010163}, + author = {Fraccalvieri, Rosa and Castellana, Stefano and Bianco, Angelica and Difato, Laura Maria and Capozzi, Loredana and Del Sambro, Laura and Donatiello, Adelia and Pugliese, Domenico and Tempesta, Maria and Parisi, Antonio and Caruso, Marta}, issn = {2076-2607}, journal = {Microorganisms}, keywords = {{\textgreater}UseGalaxy.eu}, - month = {January}, - number = {1}, - pages = {163}, - pmcid = {PMC11767609}, - pmid = {39858930}, - title = {Isolation and {Characterization} of {Colistin}-{Resistant} {Enterobacteriaceae} from {Foods} in {Two} {Italian} {Regions} in the {South} of {Italy}}, - url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11767609/}, - urldate = {2025-02-16}, + language = {eng}, + month = {July}, + number = {8}, + title = {Isolation of {ESBL}-{Producing} {Enterobacteriaceae} in {Food} of {Animal} and {Plant} {Origin}: {Genomic} {Analysis} and {Implications} for {Food} {Safety}}, + url = {http://europepmc.org/abstract/PMC/PMC12388533}, volume = {13}, year = {2025} } @@ -7153,9 +7558,9 @@ @article{freedman_plasmid_2025 journal = {Microbiology Resource Announcements}, keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org}, month = {June}, - note = {Publisher: American Society for Microbiology}, number = {0}, pages = {e00341--25}, + publisher = {American Society for Microbiology}, title = {Plasmid and chromosomal sequences of {Pantoea} agglomerans isolated from air in {Fort} {Collins}, {Colorado}}, url = {https://journals.asm.org/doi/full/10.1128/mra.00341-25}, urldate = {2025-06-12}, @@ -7172,9 +7577,9 @@ @article{friedrich_identification_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, language = {eng}, month = {July}, - note = {Publisher: Springer Science and Business Media LLC}, number = {1}, pages = {15139}, + publisher = {Springer Science and Business Media LLC}, title = {Identification of pathological transcription in autosomal dominant polycystic kidney disease epithelia}, url = {https://doi.org/10.1038/s41598-021-94442-8}, volume = {11}, @@ -7191,8 +7596,8 @@ @article{friedrich_tryptophan_2021 keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, language = {en}, month = {May}, - note = {Publisher: Nature Publishing Group}, pages = {1--18}, + publisher = {Nature Publishing Group}, title = {Tryptophan metabolism drives dynamic immunosuppressive myeloid states in {IDH}-mutant gliomas}, url = {https://www.nature.com/articles/s43018-021-00201-z}, urldate = {2021-05-30}, @@ -7209,10 +7614,10 @@ @article{frohlich_benchmarking_2022 keywords = {{\textgreater}UseGalaxy.eu, Data processing, Mass spectrometry, Proteomics}, language = {en}, month = {May}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {2622}, + publisher = {Nature Publishing Group}, title = {Benchmarking of analysis strategies for data-independent acquisition proteomics using a large-scale dataset comprising inter-patient heterogeneity}, url = {https://www.nature.com/articles/s41467-022-30094-0}, urldate = {2022-11-06}, @@ -7247,7 +7652,6 @@ @article{fuchs_varvamp_2025 month = {May}, number = {1}, pages = {5067}, - pmid = {40449995}, shorttitle = {{varVAMP}}, title = {{varVAMP}: degenerate primer design for tiled full genome sequencing and {qPCR}}, volume = {16}, @@ -7298,8 +7702,8 @@ @article{gaafar_novel_2020 keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, language = {en}, month = {October}, - note = {Publisher: PeerJ Inc.}, pages = {e10096}, + publisher = {PeerJ Inc.}, shorttitle = {Novel targets for engineering {Physostegia} chlorotic mottle and tomato brown rugose fruit virus-resistant tomatoes}, title = {Novel targets for engineering {Physostegia} chlorotic mottle and tomato brown rugose fruit virus-resistant tomatoes: in silico prediction of tomato {microRNA} targets}, url = {https://peerj.com/articles/10096}, @@ -7351,17 +7755,6 @@ @article{gains_identification_2023 year = {2023} } -@article{galaxy_and_hyphy_developments_teams_no_2020, - abstract = {The current state of much of the Wuhan pneumonia virus (COVID-19) research shows a regrettable lack of data sharing and considerable analytical obfuscation. This impedes global research cooperation, which is essential for tackling public health emergencies, and requires unimpeded access to data, analysis tools, and computational infrastructure. Here we show that community efforts in developing open analytical software tools over the past ten years, combined with national investments into scientific computational infrastructure, can overcome these deficiencies and provide an accessible platform for tackling global health emergencies in an open and transparent manner. Specifically, we use all COVID-19 genomic data available in the public domain so far to (1) underscore the importance of access to raw data and to (2) demonstrate that existing community efforts in curation and deployment of biomedical software can reliably support rapid, reproducible research during global health crises. All our analyses are fully documented at https://github.com/galaxyproject/SARS-CoV-2 .}, - author = {{=Galaxy and HyPhy developments teams} and Nekrutenko, Anton and Kosakovsky Pond, Sergei}, - doi = {10.1101/2020.02.21.959973}, - journal = {bioRxiv}, - keywords = {{\textgreater}UseGalaxy.eu}, - title = {No more business as usual: agile and effective responses to emerging pathogen threats require open data and open analytics}, - url = {http://europepmc.org/abstract/PPR/PPR114129}, - year = {2020} -} - @article{galaxy_community_galaxy_2024, abstract = {Galaxy (https://galaxyproject.org) is deployed globally, predominantly through free-to-use services, supporting user-driven research that broadens in scope each year. Users are attracted to public Galaxy services by platform stability, tool and reference dataset diversity, training, support and integration, which enables complex, reproducible, shareable data analysis. Applying the principles of user experience design (UXD), has driven improvements in accessibility, tool discoverability through Galaxy Labs/subdomains, and a redesigned Galaxy ToolShed. Galaxy tool capabilities are progressing in two strategic directions: integrating general purpose graphical processing units (GPGPU) access for cutting-edge methods, and licensed tool support. Engagement with global research consortia is being increased by developing more workflows in Galaxy and by resourcing the public Galaxy services to run them. The Galaxy Training Network (GTN) portfolio has grown in both size, and accessibility, through learning paths and direct integration with Galaxy tools that feature in training courses. Code development continues in line with the Galaxy Project roadmap, with improvements to job scheduling and the user interface. Environmental impact assessment is also helping engage users and developers, reminding them of their role in sustainability, by displaying estimated CO2 emissions generated by each Galaxy job.}, author = {{=Galaxy Community}}, @@ -7389,10 +7782,10 @@ @article{galgano_pilot_2023 keywords = {\textit{Escherichia coli}, \textit{Mammaliicoccus lentus}, \textit{Salmonella} Derby, {\textgreater}UseGalaxy.eu, antimicrobial activity, essential oils, poultry farms}, language = {en}, month = {March}, - note = {Number: 3 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 3}, number = {3}, pages = {436}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Pilot {Study} on the {Action} of {Thymus} vulgaris {Essential} {Oil} in {Treating} the {Most} {Common} {Bacterial} {Contaminants} and {Salmonella} enterica subsp. enterica {Serovar} {Derby} in {Poultry} {Litter}}, url = {https://www.mdpi.com/2079-6382/12/3/436}, urldate = {2023-03-15}, @@ -7442,9 +7835,9 @@ @article{gallus_fructobacillus_2022 journal = {International Journal of Systematic and Evolutionary Microbiology}, keywords = {{\textgreater}UseGalaxy.eu}, month = {October}, - note = {Publisher: Microbiology Society,}, number = {10}, pages = {005553}, + publisher = {Microbiology Society,}, title = {Fructobacillus cardui sp. nov., isolated from a thistle ({Carduus} nutans) flower}, url = {https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.005553}, urldate = {2022-11-06}, @@ -7465,7 +7858,6 @@ @article{galvis_dimet_2024 language = {eng}, month = {April}, pages = {btae282}, - pmid = {38656970}, shorttitle = {{DIMet}}, title = {{DIMet}: {An} open-source tool for {Differential} analysis of targeted {Isotope}-labeled {Metabolomics} data}, year = {2024} @@ -7483,8 +7875,6 @@ @article{galvis_using_2025 month = {January}, number = {2}, pages = {e5168}, - pmcid = {PMC11769753}, - pmid = {39872723}, shorttitle = {Using {DIMet} for {Differential} {Analysis} of {Labeled} {Metabolomics} {Data}}, title = {Using {DIMet} for {Differential} {Analysis} of {Labeled} {Metabolomics} {Data}: {A} {Step}-by-step {Guide} {Showcasing} the {Glioblastoma} {Metabolism}}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11769753/}, @@ -7513,15 +7903,15 @@ @article{gao_comprehensive_2020 @article{gao_comprehensive_2020, abstract = {{\textless}p{\textgreater}Mammalian DNA methylation patterns are established by two \textit{de novo} DNA methyltransferases DNMT3A and DNMT3B, which exhibit both redundant and distinctive methylation activities. However, the related molecular basis remains undetermined. Through comprehensive structural, enzymology and cellular characterization of DNMT3A and DNMT3B, we here report a multi-layered substrate-recognition mechanism underpinning their divergent genomic methylation activities. A hydrogen bond in the catalytic loop of DNMT3B causes a lower CpG specificity than DNMT3A, while the interplay of target recognition domain and homodimeric interface fine-tunes the distinct target selection between the two enzymes, with Lysine 777 of DNMT3B acting as a unique sensor of the +1 flanking base. The divergent substrate preference between DNMT3A and DNMT3B provides an explanation for site-specific epigenomic alterations seen in ICF syndrome with DNMT3B mutations. Together, this study reveals crucial and distinctive substrate-readout mechanisms of the two DNMT3 enzymes, implicative of their differential roles during development and pathogenesis.{\textless}/p{\textgreater}}, author = {Gao, Linfeng and Emperle, Max and Guo, Yiran and Grimm, Sara A. and Ren, Wendan and Adam, Sabrina and Uryu, Hidetaka and Zhang, Zhi-Min and Chen, Dongliang and Yin, Jiekai and Dukatz, Michael and Anteneh, Hiwot and Jurkowska, Renata Z. and Lu, Jiuwei and Wang, Yinsheng and Bashtrykov, Pavel and Wade, Paul A. and Wang, Gang Greg and Jeltsch, Albert and Song, Jikui}, + chapter = {New Results}, copyright = {© 2020, Posted by Cold Spring Harbor Laboratory. The copyright holder for this pre-print is the author. All rights reserved. The material may not be redistributed, re-used or adapted without the author's permission.}, doi = {10.1101/2020.04.27.064386}, journal = {bioRxiv}, keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, language = {en}, month = {April}, - note = {Publisher: Cold Spring Harbor Laboratory -Section: New Results}, pages = {2020.04.27.064386}, + publisher = {Cold Spring Harbor Laboratory}, title = {Comprehensive structure-function characterization of {DNMT3B} and {DNMT3A} reveals distinctive de novo {DNA} methylation mechanisms}, url = {https://www.biorxiv.org/content/10.1101/2020.04.27.064386v1}, urldate = {2020-05-22}, @@ -7547,15 +7937,15 @@ @article{gao_land_2024 @article{gao_pluripotency_2020, abstract = {{\textless}p{\textgreater}Awakening of zygotic transcription in animal embryos relies on maternal pioneer transcription factors. The interplay of global and specific functions of these proteins remains poorly understood. Here, we analyzed nucleosome positioning, H3K27 acetylation, transcription, and gastrulation rates in zebrafish embryos lacking pluripotency factors Pou5f3 and Sox19b. We show that the bulk transcriptional onset does not require Sox19b and Pou5f3, but is sensitive to their balance. Pou5f3 docks H3K27ac on the enhancers of genes involved in gastrulation and ventral fate specification. Sox19b facilitates Pou5f3 access to one-third of these enhancers. The genes regulating mesendodermal and dorsal fates are primed for activation independently on Pou5f3 and Sox19b. Strikingly, the loss of either factor results in activation of silent enhancers; simultaneous loss of both leads to premature expression of differentiation genes. Our results uncover how independent activities of maternal Pou5f3 and Sox19b add up or antagonize to determine the early gene expression repertoire.{\textless}/p{\textgreater}}, author = {Gao, Meijiang and Veil, Marina and Rosenblatt, Marcus and Gebhard, Anna and Hass, Helge and Buryanova, Lenka and Yampolsky, Lev Y. and Grüning, Björn and Timmer, Jens and Onichtchouk, Daria}, + chapter = {New Results}, copyright = {© 2020, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/}, doi = {10.1101/2020.02.16.949362}, journal = {bioRxiv}, keywords = {+Methods, +Stellar, +Tools, +UsePublic, {\textgreater}UseGalaxy.eu}, language = {en}, month = {May}, - note = {Publisher: Cold Spring Harbor Laboratory -Section: New Results}, pages = {2020.02.16.949362}, + publisher = {Cold Spring Harbor Laboratory}, title = {Pluripotency factors select gene expression repertoire at {Zygotic} {Genome} {Activation}}, url = {https://www.biorxiv.org/content/10.1101/2020.02.16.949362v2}, urldate = {2020-05-28}, @@ -7571,9 +7961,9 @@ @article{gao_pluripotency_2022 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Gene Expression Regulation, Developmental, Genome}, language = {eng}, month = {February}, - note = {Publisher: Springer Science and Business Media LLC}, number = {1}, pages = {788}, + publisher = {Springer Science and Business Media LLC}, title = {Pluripotency factors determine gene expression repertoire at zygotic genome activation}, url = {https://doi.org/10.1038/s41467-022-28434-1}, volume = {13}, @@ -7589,8 +7979,8 @@ @article{garcia-fernandez_antibiotic_2024 keywords = {{\textgreater}UseGalaxy.eu, Campylobacter, Virulence, antibiotic resistance (AMR), cgMLST, gyrA, pTet, pVir, tet(O)}, language = {English}, month = {January}, - note = {Publisher: Frontiers}, pages = {1293666}, + publisher = {Frontiers}, title = {Antibiotic resistance, plasmids, and virulence-associated markers in human strains of {Campylobacter} jejuni and {Campylobacter} coli isolated in {Italy}}, url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1293666/full}, urldate = {2024-05-17}, @@ -7607,7 +7997,7 @@ @article{garcia-jimenez_exploring_2025 keywords = {{\textgreater}UseGalaxy.eu, LTR type, evolutionary dynamics, gene products, seaweed, stress response, transposons}, language = {English}, month = {June}, - note = {Publisher: Frontiers}, + publisher = {Frontiers}, shorttitle = {Exploring transposons in macroalgae}, title = {Exploring transposons in macroalgae: {LTR} elements and neighboring genes in red seaweeds}, url = {https://www.frontiersin.org/journals/marine-science/articles/10.3389/fmars.2025.1592442/full}, @@ -7616,6 +8006,23 @@ @article{garcia-jimenez_exploring_2025 year = {2025} } +@article{garcia_empowering_2025, + abstract = {Background: Rising obesity rates among young adults increase long-term health risks, especially cardiometabolic conditions such as type 2 diabetes mellitus. Digital interventions can offer scalable solutions to promote and support healthy behaviors by integrating personalized diet, physical activity promotion, and behavioral support. Objective: To assess the feasibility, user friendliness, adherence, and satisfaction of the Healthy Lifestyle Recommender System (HLRS). Secondary outcomes will include measures of metabolic health and obesity. Methods: A 3-month, single-arm pilot study conducted across European countries, including Bulgaria, Germany, Italy, Netherlands, Portugal, and Spain, enrolling 351 young adults (18-25 years old, BMI 18.5-29.9 kg/m2). The intervention includes a mobile app for meal planning (Nutrida v.1), gamified physical activity encouragement (GameBus), and real-time monitoring via a wearable smartwatch device. Primary outcomes are adherence and engagement, measured through app usage and participant feedback; secondary outcomes include anthropometry, physical activity, dietary patterns, psychological well-being, and selected biomarkers of metabolic health. Expected Outcomes: Improved engagement is expected to enhance lifestyle behaviors, supporting weight management and overall well-being. Findings will guide future large-scale interventions. Conclusions: This study will contribute to minimizing the impact of obesity in Europe.}, + author = {García, Silvia and Ródenas-Munar, Marina and Bohn, Torsten and Kemperman, Astrid and Rodrigues, Daniela and Evers, Suzan and Lamy, Elsa and Pérez-Jiménez, María and Forberger, Sarah and Onorati, Maria Giovanna and Devecchi, Andrea and De Magistris, Tiziana and Halimi, Jihan and Ivanova, Yoanna and Doychinov, Boyko and Bouzas, Cristina and Tur, Josep A.}, + doi = {10.3390/jpm15120625}, + issn = {2075-4426}, + journal = {Journal of Personalized Medicine}, + keywords = {{\textgreater}UseGalaxy.eu, digital health, gamification, mHealth, obesity prevention, sedentary behavior, young adults}, + language = {eng}, + month = {December}, + number = {12}, + pages = {625}, + shorttitle = {Empowering {Healthy} {Lifestyle} {Behavior} {Through} {Personalized} {Intervention} {Portfolios} {Using} a {Healthy} {Lifestyle} {Recommender} {System} to {Prevent} and {Control} {Obesity} in {Young} {Adults}}, + title = {Empowering {Healthy} {Lifestyle} {Behavior} {Through} {Personalized} {Intervention} {Portfolios} {Using} a {Healthy} {Lifestyle} {Recommender} {System} to {Prevent} and {Control} {Obesity} in {Young} {Adults}: {Pilot} {Study} {Protocol} from the {HealthyW8} {Project}}, + volume = {15}, + year = {2025} +} + @incollection{garcia_exploring_2025, abstract = {Overexpressing a gene in a mammalian cell line can be an extremely powerful technique to investigate and explore a gene’s biological functions and associated pathways. Here we describe how combining wet-lab methodology and in-silico transcriptomic approaches can aid in the discovery of unknown gene functions, perturbation of molecular processes or the elucidation of mechanism of action.}, address = {New York, NY}, @@ -7634,6 +8041,24 @@ @incollection{garcia_exploring_2025 year = {2025} } +@article{garrard_fostering_2025, + abstract = {Communities of experts collaborating on scientific or technical projects are drivers of innovation across the life sciences. The ELIXIR research infrastructure organises scientific- and technological-themed communities as one of its key mechanisms to ensure that services are user-focused, while at the same time facilitating collaboration and creating scientific impact through the life science data generated across Europe. ELIXIR has rapidly expanded its communities portfolio in response to unmet needs and has developed a comprehensive process framework to facilitate the work of these communities. The ELIXIR Communities framework is made up of a suite of tools and processes that ensure effective community evolution and management, covering how communities are established, led, supported, and can collaborate across ELIXIR and beyond. Being aware of similar approaches in other contexts and in the interests of furthering community development in other research infrastructures and similar organisations, we share insights into the ELIXIR Communities framework and outline the skill set of a community manager and what this looks like in the ELIXIR context. Finally, to show the benefits of the communities, we share concrete examples of how the ELIXIR Communities have had an impact on the scientific landscape. By showcasing these outcomes we hope to demonstrate not only to other research infrastructures, but also to funders, that supporting scientific communities provides a valuable return on investment. We hope that these examples will encourage life scientists who may be interested in joining the ELIXIR Communities, and research infrastructure professionals whose roles require structured engagement with domain experts and users.}, + author = {Garrard, Clare and Heil, Katharina F and Aspromonte, Maria Cristina and Batut, Bérénice and Chegkazi, Magda and Hancock, John M and Harrison, Elaine and Ishaque, Naveed and Kerry, Giselle and Korpelainen, Eija and Lanfear, Jerry and Martin, Corinne and Schaaf, Sebastian and Scollen, Serena and Tseng, Yun-Yun and Velankar, Sameer and Vizcaíno, Juan Antonio and Waterhouse, Robert M and Willighagen, Egon and Blomberg, Niklas and Maccallum, Peter}, + doi = {10.12688/f1000research.168288.1}, + issn = {2046-1402}, + journal = {F1000Research}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {September}, + pages = {884}, + shorttitle = {Fostering and sustaining collaborative innovation}, + title = {Fostering and sustaining collaborative innovation: {Insights} from {ELIXIR} {Europe}'s life science {Communities}}, + url = {https://f1000research.com/articles/14-884/v1}, + urldate = {2026-01-11}, + volume = {14}, + year = {2025} +} + @article{garrido-gala_comprehensive_2022, abstract = {WRKY transcription factors play critical roles in plant growth and development or stress responses. Using up-to-date genomic data, a total of 64 and 257 WRKY genes have been identified in the diploid woodland strawberry, \textit{Fragaria vesca}, and the more complex allo-octoploid commercial strawberry, \textit{Fragaria} × \textit{ananassa} cv. Camarosa, respectively. The completeness of the new genomes and annotations has enabled us to perform a more detailed evolutionary and functional study of the strawberry WRKY family members, particularly in the case of the cultivated hybrid, in which homoeologous and paralogous \textit{FaWRKY} genes have been characterized. Analysis of the available expression profiles has revealed that many strawberry \textit{WRKY} genes show preferential or tissue-specific expression. Furthermore, significant differential expression of several \textit{FaWRKY} genes has been clearly detected in fruit receptacles and achenes during the ripening process and pathogen challenged, supporting a precise functional role of these strawberry genes in such processes. Further, an extensive analysis of predicted development, stress and hormone-responsive cis-acting elements in the strawberry WRKY family is shown. Our results provide a deeper and more comprehensive knowledge of the \textit{WRKY} gene family in strawberry.}, author = {Garrido-Gala, José and Higuera, José-Javier and Rodríguez-Franco, Antonio and Muñoz-Blanco, Juan and Amil-Ruiz, Francisco and Caballero, José L}, @@ -7661,10 +8086,10 @@ @article{garrido_identification_2020 keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Gene Expression Regulation, Plant, Genes, Essential, Meiosis, Transcriptome}, language = {en}, month = {February}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {1--12}, + publisher = {Nature Publishing Group}, title = {Identification and validation of reference genes for {RT}-{qPCR} normalization in wheat meiosis}, url = {https://www.nature.com/articles/s41598-020-59580-5}, urldate = {2020-03-24}, @@ -7726,7 +8151,7 @@ @article{geiszelhardt_glia_2025 doi = {10.3390/ijms26199684}, issn = {1422-0067}, journal = {International journal of molecular sciences}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Cell-type Dependent Sensitivity, Crystal structure, In Vitro Cell Viability, Nanoparticles, Neural cells, Titanium dioxide}, month = {October}, number = {19}, pages = {9684}, @@ -7755,15 +8180,15 @@ @article{gener_full-coverage_2019 @article{genolet_identification_2020, abstract = {{\textless}p{\textgreater}X-chromosomal genes contribute to sex differences, in particular during early development, when both X chromosomes are active in females. Here, double X-dosage shifts female pluripotent cells towards the naive stem cell state by increasing pluripotency factor expression, inhibiting the differentiation-promoting MAP kinase (MAPK) signalling pathway and delaying differentiation. To identify the genetic basis of these sex differences, we have performed a series of CRISPR knockout screens in murine embryonic stem cells to comprehensively identify X-linked genes that cause the female pluripotency phenotype. We found multiple genes that act in concert, among which Klhl13 plays a central role. We show that this E3 ubiquitin ligase substrate adaptor protein promotes pluripotency factor expression, delays differentiation and represses MAPK target genes, and we identify putative substrates. We thus elucidate the mechanisms that drive sex-induced differences in pluripotent cells with implications for gender medicine in the context of induced pluripotent stem cell based therapies.{\textless}/p{\textgreater}}, author = {Genolet, Oriana and Monaco, Anna A. and Dunkel, Ilona and Boettcher, Michael and Schulz, Edda G.}, + chapter = {New Results}, copyright = {© 2020, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/}, doi = {10.1101/2020.03.09.983544}, journal = {bioRxiv}, keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, language = {en}, month = {March}, - note = {Publisher: Cold Spring Harbor Laboratory -Section: New Results}, pages = {2020.03.09.983544}, + publisher = {Cold Spring Harbor Laboratory}, title = {Identification of {X}-chromosomal genes that drive global {X}-dosage effects in mammals}, url = {https://www.biorxiv.org/content/10.1101/2020.03.09.983544v1}, urldate = {2020-03-24}, @@ -7779,9 +8204,9 @@ @article{genolet_identification_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Clustered Regularly Interspaced Short Palindromic Repeats, Genes, X-Linked, Sex Characteristics}, language = {eng}, month = {April}, - note = {Publisher: Springer Science and Business Media LLC}, number = {1}, pages = {110}, + publisher = {Springer Science and Business Media LLC}, title = {Identification of {X}-chromosomal genes that drive sex differences in embryonic stem cells through a hierarchical {CRISPR} screening approach}, url = {https://doi.org/10.1186/s13059-021-02321-2}, volume = {22}, @@ -7835,9 +8260,9 @@ @article{gessara_highly_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Genome}, language = {eng}, month = {April}, - note = {Publisher: Elsevier BV}, number = {4}, pages = {784--796}, + publisher = {Elsevier BV}, title = {Highly {Efficient} {Genome} {Modification} of {Cultured} {Primordial} {Germ} {Cells} with {Lentiviral} {Vectors} to {Generate} {Transgenic} {Songbirds}}, url = {https://doi.org/10.1016/j.stemcr.2021.02.015}, volume = {16}, @@ -7890,9 +8315,9 @@ @article{ghosh_suppressive_2024 keywords = {{\textgreater}UseGalaxy.eu, Cancer genetics, Cancer genomics, Evolutionary genetics, Functional genomics, Mutation}, language = {en}, month = {October}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {9209}, + publisher = {Nature Publishing Group}, title = {Suppressive cancer nonstop extension mutations increase {C}-terminal hydrophobicity and disrupt evolutionarily conserved amino acid patterns}, url = {https://www.nature.com/articles/s41467-024-52779-4}, urldate = {2024-10-27}, @@ -7909,9 +8334,9 @@ @article{gilbertson_conservation_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Gene Expression Regulation, Immune System}, language = {eng}, month = {December}, - note = {Publisher: Elsevier BV}, number = {12}, pages = {1077--1087}, + publisher = {Elsevier BV}, title = {Conservation and divergence in gene regulation between mouse and human immune cells deserves equal emphasis}, url = {https://doi.org/10.1016/j.it.2021.10.007}, volume = {42}, @@ -7961,10 +8386,10 @@ @article{giufre_detection_2024 keywords = {{\textgreater}UseGalaxy.eu, ESKAPE, KPC-216, cefiderocol, ceftazidime-avibactam, cross-resistance}, language = {en}, month = {June}, - note = {Number: 6 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 6}, number = {6}, pages = {507}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Detection of {KPC}-216, a {Novel} {KPC}-3 {Variant}, in a {Clinical} {Isolate} of {Klebsiella} pneumoniae {ST101} {Co}-{Resistant} to {Ceftazidime}-{Avibactam} and {Cefiderocol}}, url = {https://www.mdpi.com/2079-6382/13/6/507}, urldate = {2024-06-07}, @@ -7994,7 +8419,7 @@ @article{gjaltema_distal_2021 doi = {10.1101/2021.03.29.437476}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {March}, - note = {Publisher: Cold Spring Harbor Laboratory}, + publisher = {Cold Spring Harbor Laboratory}, title = {Distal and proximal cis-regulatory elements sense {X}-chromosomal dosage and developmental state at {theXistlocus}}, url = {https://doi.org/10.1101/2021.03.29.437476}, year = {2021} @@ -8045,9 +8470,9 @@ @article{glaros_limited_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, language = {eng}, month = {September}, - note = {Publisher: Elsevier BV}, number = {9}, pages = {2005--2023.e10}, + publisher = {Elsevier BV}, title = {Limited access to antigen drives generation of early {B} cell memory while restraining the plasmablast response}, url = {https://doi.org/10.1016/j.immuni.2021.08.017}, volume = {54}, @@ -8113,9 +8538,9 @@ @article{godbole_multiomic_2024 keywords = {{\textgreater}UseGalaxy.eu, CNS cancer, Data integration, Glycomics, Proteomics, Tumour heterogeneity}, language = {en}, month = {July}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {6237}, + publisher = {Nature Publishing Group}, title = {Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and {N}-glycan level}, url = {https://www.nature.com/articles/s41467-024-50554-z}, urldate = {2024-07-27}, @@ -8138,6 +8563,21 @@ @article{goglio_performance_2024 year = {2024} } +@article{goldspink_multi-locus_2025, + abstract = {The interactions between powdery mildews (Ascomycota, Erysiphaceae), obligate biotrophic pathogens of many plants, and pycnidial fungi belonging to the genus Ampelomyces, are classic examples of specific mycoparasitic relationships. These interactions are common and finely tuned tritrophic relationships amongst host plants, powdery mildews, and Ampelomyces mycoparasites wherever these organisms co-occur in the field. Selected Ampelomyces strains have already been developed as biocontrol agents of powdery mildew infections of some crops. In Australia, their study has received little attention so far. Only a single Ampelomyces strain, included in a whole-genome sequencing (WGS) project, was known from this continent. Here, we report the isolation of 20 more Ampelomyces strains from eight powdery mildew species in Australia. Multi-locus phylogenetic network analyses of all the 21 Australian Ampelomyces strains carried out in combination with 32 reference strains from overseas revealed that the Australian strains belonged to four molecular taxonomic units (MOTUs). All those MOTUs were delimited earlier based on Ampelomyces strains isolated in Europe, North America, and elsewhere. Based on the phylogenetic analyses, two Australian strains belonging to different MOTUs were selected for WGS. Long-read (MinION) and short-read (Illumina) technologies were used to provide genome assemblies with high completeness. Both assemblies have a bipartite structure, i.e., consisted of AT-rich, gene-sparse regions interspersed with GC-balanced, gene-rich regions. These new high-quality assemblies and evidence-based annotations are important resources for future analyses of mycoparasitic interactions to disentangle molecular mechanisms underlying mycoparasitism, possible new biocontrol applications, and naturally occurring tritrophic relationships.}, + author = {Goldspink, Lauren and Sotiropoulos, Alexandros G. and Idnurm, Alexander and Ash, Gavin J. and Dearnaley, John D. W. and Boddington, Morwenna and Ahmad, Aftab and Németh, Márk Z. and Pintye, Alexandra and Gorfer, Markus and Shin, Hyeon-Dong and Kovács, Gábor M. and Vaghefi, Niloofar and Kiss, Levente}, + doi = {10.1371/journal.pone.0322842}, + issn = {1932-6203}, + journal = {PloS One}, + keywords = {{\textgreater}UseGalaxy.eu, Ascomycota, Australia, Genome, Fungal, Phylogeny, Plant Diseases, Whole Genome Sequencing}, + language = {eng}, + number = {12}, + pages = {e0322842}, + title = {Multi-locus phylogenetic network analysis of {Ampelomyces} mycoparasites isolated from diverse powdery mildews in {Australia} and the generation of two de novo genome assemblies}, + volume = {20}, + year = {2025} +} + @article{gomes_shigella_2023, abstract = {Trained immunity is a long-term memory of innate immune cells, generating an improved response upon reinfection. \textit{Shigella} is an important human pathogen and inflammatory paradigm for which there is no effective vaccine. Using zebrafish larvae, we demonstrate that after \textit{Shigella} training, neutrophils are more efficient at bacterial clearance. We observe that \textit{Shigella}-induced protection is nonspecific and has differences with training by BCG and β-glucan. Analysis of histone ChIP-seq on trained neutrophils revealed that \textit{Shigella} training deposits the active H3K4me3 mark on promoter regions of 1612 genes, dramatically changing the epigenetic landscape of neutrophils toward enhanced microbial recognition and mitochondrial ROS production. Last, we demonstrate that mitochondrial ROS plays a key role in enhanced antimicrobial activity of trained neutrophils. It is envisioned that signals and mechanisms we discover here can be used in other vertebrates, including humans, to suggest new therapeutic strategies involving neutrophils to control bacterial infection.}, author = {Gomes, Margarida C and Brokatzky, Dominik and Bielecka, Magdalena K and Wardle, Fiona C and Mostowy, Serge}, @@ -8185,6 +8625,23 @@ @article{gomes_unlocking_2025 year = {2025} } +@article{gonzalez-vinceiro_plamseq_2025, + abstract = {Chromatin immunoprecipitation and coimmunoprecipitation assays are common approaches to characterize the genomic localization and protein interactors, respectively, for a protein of interest. However, these approaches require the use of specific antibodies, which often face sensitivity and specificity issues. On the basis of TurboID, we developed proximity-labeled affinity-purified mass spectrometry and sequencing (PLAMseq), which enables, in the same workflow, identification of the genomic loci and the interacting proteome of a protein of interest. Moreover, PLAMseq can also be applied to specifically map protein interactions and ubiquitin(-like)–modified proteins. We validated PLAMseq with two well-characterized proteins, RNA polymerase II, and CTCF, with excellent robustness and reproducibility. Next, we applied PLAMseq to characterize histone H1 SUMOylation, in which study has remained elusive due to the lack of specific reagents, and found that SETDB1 binds to SUMOylated histones H1.2 and H1.4 that also colocalize with H3K9me3 at repetitive regions of the genome.}, + author = {González-Vinceiro, Lourdes and Espejo-Serrano, Carmen and Soler-Oliva, María Eugenia and Soto-Hidalgo, Emily and Mateos-Martín, María Luisa and Rico, Daniel and González-Aguilera, Cristina and González-Prieto, Román}, + doi = {10.1126/sciadv.ady4151}, + journal = {Science Advances}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {November}, + number = {45}, + pages = {eady4151}, + publisher = {American Association for the Advancement of Science}, + title = {{PLAMseq} enables the proteo-genomic characterization of chromatin-associated proteins and protein interactions in a single workflow}, + url = {https://www.science.org/doi/10.1126/sciadv.ady4151}, + urldate = {2025-12-26}, + volume = {11}, + year = {2025} +} + @misc{gonzalez-vinceiro_plamseq_2025, abstract = {Chromatin Immunoprecipitation (ChIP) and Co-Immunoprecipitation (CoIP) assays are the most common approaches to characterize the genomic localization and protein interactors, respectively, for a protein of interest. However, these approaches require the use of specific antibodies, which are costly reagents that often face sensitivity and specificity issues. Based on TurboID, we developed PLAMseq (Proximity Labelled Affinity-purified Mass spectrometry plus sequencing), which enables, in the same workflow, to identify the genomic loci and the interacting proteome of a protein of interest. Moreover, PLAMseq can also be applied to specifically map protein interactions across the genome or to specifically detect proteins which are ubiquitin(-like) modified. After a short biotin pulse, DNA-protein crosslinks are induced by formaldehyde and the interactors of a protein of interest, together with their associated DNA sequences, are purified simultaneously and identified by mass spectrometry-based proteomics and Next Generation Sequencing, respectively. To validate PLAMseq, we performed the proteo-genomic characterization of two proteins which genomic loci are very well characterized, namely, RNA polymerase II and CTCF, with excellent robustness and reproducibility. Next, we applied PLAMseq to characterize Histone H1 SUMOylation, a histone post-translational modification which study has remained elusive due to the lack of specific reagents. We found that SETDB1 binds to SUMOylated histone H1.2 and H1.4 and, accordingly, SUMOylated histone H1 colocalizes with H3K9me3 at repetitive regions of the genome.}, author = {González-Vinceiro, Lourdes and Espejo-Serrano, Carmen and Soler-Oliva, María Eugenia and Mateos-Martín, María Luisa and Rico, Daniel and González-Aguilera, Cristina and Prieto, Román González}, @@ -8212,10 +8669,10 @@ @article{goossens_obligate_2023 keywords = {{\textgreater}UseGalaxy.eu, Effectors in plant pathology, Microbe, Microbiome, Pathogens, Symbiosis}, language = {en}, month = {December}, - note = {Number: 12 -Publisher: Nature Publishing Group}, + note = {Number: 12}, number = {12}, pages = {2349--2364}, + publisher = {Nature Publishing Group}, title = {Obligate biotroph downy mildew consistently induces near-identical protective microbiomes in {Arabidopsis} thaliana}, url = {https://www.nature.com/articles/s41564-023-01502-y}, urldate = {2023-12-28}, @@ -8248,8 +8705,8 @@ @article{goshi_direct_2025 keywords = {{\textgreater}UseGalaxy.eu, Astrocytes, Cell culture, Chemokines, Chronic fatigue syndrome, Chronic infection, Cognitive ability, Cytokines, Encephalomyelitis, Firing pattern, Gene expression, IL-6, Immune response, Infections, Interleukin 6, Neurons, Severe acute respiratory syndrome coronavirus 2, TNF-α, Tumor necrosis factor-TNF, Tumor necrosis factor-α, Viral infections, cytokine, human iPSC derived neurons, inflammation, long-COVID, multi-electrode array, neuron networks}, language = {English}, month = {February}, - note = {Place: Lausanne, Switzerland -Publisher: Frontiers Research Foundation}, + note = {Place: Lausanne, Switzerland}, + publisher = {Frontiers Research Foundation}, title = {Direct effects of prolonged {TNF}-α and {IL}-6 exposure on neural activity in human {iPSC}-derived neuron-astrocyte co-cultures}, url = {https://www.proquest.com/docview/3165948049/abstract/9D6077E8D5E84209PQ/1}, urldate = {2025-02-24}, @@ -8300,10 +8757,10 @@ @article{greenfield_modification_2020 keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, JAK inhibition, epigenetics, histone modification, myeloproliferative neoplasms}, language = {en}, month = {September}, - note = {Number: 9 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 9}, number = {9}, pages = {2669}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Modification of the {Histone} {Landscape} with {JAK} {Inhibition} in {Myeloproliferative} {Neoplasms}}, url = {https://www.mdpi.com/2072-6694/12/9/2669}, urldate = {2021-04-09}, @@ -8329,6 +8786,31 @@ @article{greenfield_p989_2022 year = {2022} } +@article{gregoric_erga-bge_2025, + abstract = {The +Leviellus thorelli +reference genome provides the first high-quality genomic resource for +Zygiellidae +, a family of orb-weaving spiders with a dynamic systematic history and distinct for constructing webs with a characteristic spiral-free sector. As part of the European Reference Genome Atlas (ERGA), we generated a chromosome-level assembly for +L. thorelli +that is organized into 13 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 2.20 Gb and is composed of 939 contigs and 130 scaffolds, with contig and scaffold N50 values of 5.4 Mb and 167.1 Mb, respectively. This genome represents a valuable addition to the growing collection of spider genomes. With +Zygiellidae +now included among the available genomes of true orb-weavers, this is a key resource for comparative studies into the genomic basis of orb web and silk evolution.}, + author = {Gregorič, Matjaz and Bužan, Elena and Böhne, Astrid and Monteiro, Rita and Fernández, Rosa and Escudero, Nuria and Gut, Marta and Aguilera, Laura and Câmara Ferreira, Francisco and Cruz, Fernando and Gómez-Garrido, Jèssica and S. Alioto, Tyler and Bortoluzzi, Chiara}, + doi = {10.12688/openreseurope.21671.1}, + issn = {2732-5121}, + journal = {Open Research Europe}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {November}, + pages = {365}, + title = {{ERGA}-{BGE} reference genome of {Leviellus} thorelli, a common orb-weaving spider representing the {Zygiellidae} family}, + url = {https://open-research-europe.ec.europa.eu/articles/5-365/v1}, + urldate = {2025-11-30}, + volume = {5}, + year = {2025} +} + @article{gress_prostaglandin_2024, abstract = {Increased production of Prostaglandin D2 (PGD2) is linked to development and progression of asthma and allergy. PGD2 is rapidly degraded to its metabolites, which initiate type 2 innate lymphoid cells (ILC2) migration and IL-5/IL-13 cytokine secretion in a PGD2 receptor 2 (DP2)-dependent manner. Blockade of DP2 has shown therapeutic benefit in subsets of asthma patients. Cellular mechanisms of ILC2 activity in response to PGD2 and its metabolites are still unclear. We hypothesized that ILC2 respond non-uniformly to PGD2 metabolites. ILC2s were isolated from peripheral blood of patients with atopic asthma. ILC2s were stimulated with PGD2 and four PGD2 metabolites (Δ12-PGJ2, Δ12-PGD2, 15-deoxyΔ12,14-PGD2, 9α,11β-PGF2) with or without the selective DP2 antagonist fevipiprant. Total RNA was sequenced, and differentially expressed genes (DEG) were identified by DeSeq2. Differential gene expression analysis revealed an upregulation of pro-inflammatory DEGs in ILC2s stimulated with PGD2 (14 DEGs), Δ12-PGD2 (27 DEGs), 15-deoxyΔ12,14-PGD2 (56 DEGs) and Δ12-PGJ2 (136 DEGs), but not with 9α,11β-PGF2. Common upregulated DEGs were i.e. ARG2, SLC43A2, LAYN, IGFLR1, or EPHX2. Inhibition of DP2 via fevipiprant mainly resulted in downregulation of pro-inflammatory genes such as DUSP4, SPRED2, DUSP6, ETV1, ASB2, CD38, ADGRG1, DDIT4, TRPM2, or CD69. DEGs were related to migration and various immune response-relevant pathways such as “chemokine (C-C motif) ligand 4 production”, “cell migration”, “interleukin-13 production”, “regulation of receptor signaling pathway via JAK-STAT”, or “lymphocyte apoptotic process”, underlining the pro-inflammatory effects of PGD2 metabolite-induced immune responses in ILC2s as well as the anti-inflammatory effects of DP2 inhibition via fevipiprant. Furthermore, PGD2 and metabolites showed distinct profiles in ILC2 activation. Overall, these results expand our understanding of DP2 initiated ILC2 activity.}, author = {Gress, Christina and Fuchs, Maximilian and Carstensen-Aurèche, Saskia and Müller, Meike and Hohlfeld, Jens M.}, @@ -8338,9 +8820,9 @@ @article{gress_prostaglandin_2024 keywords = {{\textgreater}UseGalaxy.eu, Asthma, Cell metabolism, Cytokines, Gene expression, Immune response, Immunity, Innate, Lymphocytes, Metabolic pathways, Metabolites, Prostaglandin D2, RNA sequencing, Receptors, Immunologic, Receptors, Prostaglandin, Signal Transduction}, language = {en}, month = {July}, - note = {Publisher: Public Library of Science}, number = {7}, pages = {e0307750}, + publisher = {Public Library of Science}, title = {Prostaglandin {D2} receptor 2 downstream signaling and modulation of type 2 innate lymphoid cells from patients with asthma}, url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0307750}, urldate = {2024-07-29}, @@ -8358,10 +8840,10 @@ @article{gress_transcriptomic_2024 keywords = {{\textgreater}UseGalaxy.eu, Asthma, Biomarkers, Experimental models of disease, Gene regulation in immune cells, Inflammation, Pneumonia, Pulmonary Disease, Chronic Obstructive, RNA sequencing}, language = {en}, month = {January}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {1721}, + publisher = {Nature Publishing Group}, title = {Transcriptomic characterization of the human segmental endotoxin challenge model}, url = {https://www.nature.com/articles/s41598-024-51547-0}, urldate = {2024-01-23}, @@ -8375,6 +8857,7 @@ @article{greve_decitabine_2021 Hypomethylating agents (HMA) have become the backbone of nonintensive acute myeloid leukemia/myelodysplastic syndrome (AML/MDS) treatment, also by virtue of their activity in patients with adverse genetics, for example, monosomal karyotypes, often with losses on chromosome 7, 5, or 17. No comparable activity is observed with cytarabine, a cytidine analogue without DNA-hypomethylating properties. As evidence exists for compounding hypermethylation and gene silencing of hemizygous tumor suppressor genes (TSG), we thus hypothesized that this effect may preferentially be reversed by the HMAs decitabine and azacitidine. An unbiased RNA-sequencing approach was developed to interrogate decitabine-induced transcriptome changes in AML cell lines with or without a deletion of chromosomes 7q, 5q or 17p. HMA treatment preferentially upregulated several hemizygous TSG in this genomic region, significantly derepressing endogenous retrovirus (ERV)3–1, with promoter demethylation, enhanced chromatin accessibility, and increased H3K4me3 levels. Decitabine globally reactivated multiple transposable elements, with activation of the dsRNA sensor RIG-I and interferon regulatory factor (IRF)7. Induction of ERV3–1 and RIG-I mRNA was also observed during decitabine treatment in vivo in serially sorted peripheral blood AML blasts. In patient-derived monosomal karyotype AML murine xenografts, decitabine treatment resulted in superior survival rates compared with cytarabine. Collectively, these data demonstrate preferential gene derepression and ERV reactivation in AML with chromosomal deletions, providing a mechanistic explanation that supports the clinical observation of superiority of HMA over cytarabine in this difficult-to-treat patient group. Significance: These findings unravel the molecular mechanism underlying the intriguing clinical activity of HMAs in AML/MDS patients with chromosome 7 deletions and other monosomal karyotypes.See related commentary by O'Hagan et al., p. 813}, author = {Greve, Gabriele and Schüler, Julia and Grüning, Björn A. and Berberich, Bettina and Stomper, Julia and Zimmer, Dennis and Gutenkunst, Lea and Bönisch, Ulrike and Meier, Ruth and Blagitko-Dorfs, Nadja and Grishina, Olga and Pfeifer, Dietmar and Weichenhan, Dieter and Plass, Christoph and Lübbert, Michael}, + chapter = {Genome and Epigenome}, copyright = {©2020 American Association for Cancer Research.}, doi = {10.1158/0008-5472.CAN-20-1430}, issn = {0008-5472, 1538-7445}, @@ -8382,11 +8865,9 @@ @article{greve_decitabine_2021 keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, language = {en}, month = {February}, - note = {Publisher: American Association for Cancer Research -Section: Genome and Epigenome}, number = {4}, pages = {834--846}, - pmid = {33203699}, + publisher = {American Association for Cancer Research}, shorttitle = {Decitabine {Induces} {Gene} {Derepression} on {Monosomic} {Chromosomes}}, title = {Decitabine {Induces} {Gene} {Derepression} on {Monosomic} {Chromosomes}: {In} {Vitro} and {In} {Vivo} {Effects} in {Adverse}-{Risk} {Cytogenetics} {AML}}, url = {https://cancerres.aacrjournals.org/content/81/4/834}, @@ -8404,7 +8885,7 @@ @article{greve_three_2024 keywords = {{\textgreater}NanoGalaxy, {\textgreater}UseGalaxy.eu, Armadillidium vulgare, Effectors, Feminization, Genomics, Wolbachia, f Element, isopod crustacean}, language = {English}, month = {August}, - note = {Publisher: Frontiers}, + publisher = {Frontiers}, shorttitle = {Three feminizing {Wolbachia} strains in a single host species}, title = {Three feminizing {Wolbachia} strains in a single host species: comparative genomics paves the way for identifying sex reversal factors}, url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2024.1416057/full}, @@ -8433,9 +8914,9 @@ @article{gruber_complete_2025 journal = {Microbiology Resource Announcements}, keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org}, month = {April}, - note = {Publisher: American Society for Microbiology}, number = {0}, pages = {e00193--25}, + publisher = {American Society for Microbiology}, title = {Complete genome sequence of {Planococcus} koreensis isolated from soil in {Fort} {Collins}, {Colorado}}, url = {https://journals.asm.org/doi/full/10.1128/mra.00193-25}, urldate = {2025-04-21}, @@ -8467,9 +8948,9 @@ @article{gu_galaxy-ml_2021 keywords = {+Galactic, +IsGalaxy, +Project, +Shared, +Tools, {\textgreater}ML Workbench, {\textgreater}UseGalaxy.eu, Cancers and neoplasms, Decision trees, Deep learning, Galaxies, Machine Learning, Machine learning, Medicine and health sciences, Scientists, Supervised machine learning}, language = {en}, month = {June}, - note = {Publisher: Public Library of Science}, number = {6}, pages = {e1009014}, + publisher = {Public Library of Science}, shorttitle = {Galaxy-{ML}}, title = {Galaxy-{ML}: {An} accessible, reproducible, and scalable machine learning toolkit for biomedicine}, url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009014}, @@ -8483,9 +8964,9 @@ @inproceedings{gu_proswats_2024 author = {Gu, Yang and Cao, Jian and Qian, Shiyou and Zhu, Nengjun and Guan, Wei}, booktitle = {2024 {IEEE} {International} {Conference} on {Web} {Services} ({ICWS})}, doi = {10.1109/ICWS62655.2024.00111}, + issn = {2836-3868}, keywords = {{\textgreater}UseGalaxy.eu, Adaptation models, Bridges, Confidence-aware Learning, Learning systems, Natural languages, Predictive models, Proxy Mechanism, Quality of service, Reliability, Scientific Workflow Retrieval, Semantic Gap, Semantics, Services Composition, Training, Web services}, month = {July}, - note = {ISSN: 2836-3868}, pages = {932--943}, shorttitle = {{ProSwats}}, title = {{ProSwats}: {A} {Proxy}-based {Scientific} {Workflow} {Retrieval} {Approach} by {Bridging} the {Gap} between {Textual} and {Structural} {Semantics}}, @@ -8573,9 +9054,9 @@ @article{guesdon_combining_2023 journal = {ACS Synthetic Biology}, keywords = {{\textgreater}UseGalaxy.eu, CRISPR-Cas Systems, Saccharomyces cerevisiae}, month = {November}, - note = {Publisher: American Chemical Society}, number = {11}, pages = {3252--3266}, + publisher = {American Chemical Society}, title = {Combining {Fusion} of {Cells} with {CRISPR}-{Cas9} {Editing} for the {Cloning} of {Large} {DNA} {Fragments} or {Complete} {Bacterial} {Genomes} in {Yeast}}, url = {https://doi.org/10.1021/acssynbio.3c00248}, urldate = {2024-11-17}, @@ -8661,10 +9142,10 @@ @article{guo_mitogenome-based_2024 keywords = {{\textgreater}UseGalaxy.eu, Heptageniidae, cryptic species, divergence time, mitogenomes, phylogenetic relationship}, language = {en}, month = {October}, - note = {Number: 10 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 10}, number = {10}, pages = {745}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Mitogenome-{Based} {Phylogeny} with {Divergence} {Time} {Estimates} {Revealed} the {Presence} of {Cryptic} {Species} within {Heptageniidae} ({Insecta}, {Ephemeroptera})}, url = {https://www.mdpi.com/2075-4450/15/10/745}, urldate = {2024-11-17}, @@ -8682,8 +9163,8 @@ @article{gupta_targeted_2025 keywords = {{\textgreater}UseGalaxy.eu, Genetic engineering, Synthetic biology}, language = {en}, month = {September}, - note = {Publisher: Nature Publishing Group}, pages = {1--12}, + publisher = {Nature Publishing Group}, title = {Targeted {DNA} {ADP}-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes}, url = {https://www.nature.com/articles/s41587-025-02802-w}, urldate = {2025-09-10}, @@ -8697,7 +9178,7 @@ @article{gussak_precision_2023 journal = {ACS Synthetic Biology}, keywords = {{\textgreater}UseGalaxy.eu, Streptococcus suis}, month = {August}, - note = {Publisher: American Chemical Society}, + publisher = {American Chemical Society}, title = {Precision {Genome} {Engineering} in {Streptococcus} suis {Based} on a {Broad}-{Host}-{Range} {Vector} and {CRISPR}-{Cas9} {Technology}}, url = {https://doi.org/10.1021/acssynbio.3c00110}, urldate = {2023-08-24}, @@ -8746,8 +9227,8 @@ @article{hahn_dna_2020 journal = {Frontiers in Cell and Developmental Biology}, keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Aging, Cerebral Cortex, DNA Methylation, GABA, inhibitory interneurons, proteostasis, synapse, transcriptional control}, language = {English}, - note = {Publisher: Frontiers}, pages = {639}, + publisher = {Frontiers}, title = {{DNA} {Methyltransferase} 1 ({DNMT1}) {Function} {Is} {Implicated} in the {Age}-{Related} {Loss} of {Cortical} {Interneurons}}, url = {https://www.frontiersin.org/articles/10.3389/fcell.2020.00639/full}, urldate = {2021-02-08}, @@ -8765,9 +9246,9 @@ @article{haidar_neural_2025 keywords = {{\textgreater}UseGalaxy.eu, Autonomic nervous system, Cancer microenvironment}, language = {en}, month = {August}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {7094}, + publisher = {Nature Publishing Group}, title = {Neural function of {Netrin}-1 in precancerous lesions of the pancreas}, url = {https://www.nature.com/articles/s41467-025-62299-4}, urldate = {2025-09-03}, @@ -8865,10 +9346,9 @@ @article{han_dna-directed_2023 keywords = {{\textgreater}UseGalaxy.eu, CPSF73, DSIF, RNA Polymerase II, RNA polymerase II, Rat1, Saccharomyces cerevisiae Proteins, Spt5, TFIIS, XRN2, intrinsic termination site, termination, torpedo}, language = {English}, month = {September}, - note = {Publisher: Elsevier}, number = {18}, pages = {3253--3267.e7}, - pmid = {37683646}, + publisher = {Elsevier}, title = {{DNA}-directed termination of {RNA} polymerase {II} transcription}, url = {https://www.cell.com/molecular-cell/abstract/S1097-2765(23)00644-5}, urldate = {2023-11-18}, @@ -8961,7 +9441,7 @@ @article{hashimoto_oncoprotein_2025 keywords = {{\textgreater}UseGalaxy.eu}, language = {en}, month = {May}, - note = {Publisher: John Wiley \& Sons, Ltd}, + publisher = {John Wiley \& Sons, Ltd}, title = {The oncoprotein {DEK} controls growth-regulated gene expression by enhancing the {DNA}-binding activity of basic leucine zipper transcription factors}, url = {https://febs.onlinelibrary.wiley.com/doi/10.1111/febs.70124}, urldate = {2025-05-29}, @@ -8975,9 +9455,9 @@ @article{hassan_genome-wide_2023 journal = {Phytopathogenomics and Disease Control}, keywords = {{\textgreater}UseGalaxy.eu}, month = {December}, - note = {Publisher: Journal of Global Innovations in Agricultural and Social Sciences (JGIASS)}, number = {2}, pages = {1--12}, + publisher = {Journal of Global Innovations in Agricultural and Social Sciences (JGIASS)}, title = {Genome-wide identification and characterization of the plant defensins ({Pdfs}) gene family in selected {Leguminous} crops and their expression profiles in response to biotic and abiotic stresses}, url = {http://dx.doi.org/10.22194/Pdc/3.1017}, volume = {2}, @@ -9022,6 +9502,26 @@ @article{hausdorf_erga-bge_2025 year = {2025} } +@article{haydar_chamber-specific_2026, + abstract = {Cis-regulatory elements (CREs) are noncoding DNA regions regulating cell-type-specific gene expression programs by interacting with distal gene promoters. Here, we aim to decode the function and spatial organization of CRE-promoter interactions in human cardiomyocytes. We analyzed the epigenome and chromatin interactions of human male atrial, ventricular, and failing cardiomyocytes. Atrial and ventricular cardiomyocytes harbored chamber-specific CRE-promoter interactions modulating gene expression as confirmed by functional epigenetic silencing. These CRE-promoter interactions explain the distinct contribution of non-coding genetic variants to atrial and ventricular diseases, such as dilated cardiomyopathy and arrhythmias. We dissected the prototypic KCNJ2 locus, encoding a potassium channel associated with ventricular arrhythmia susceptibility. Functional epigenetic silencing confirmed that CREs, harboring QT-duration-associated genetic risk factors, modulate KCNJ2 gene expression levels, alter KCNJ2-dependent channel currents, and affect cardiomyocyte repolarization. The presented human CM-specific chromatin interaction analysis provides key insights into regulatory mechanisms and aids in interpreting genetic risk factors.}, + author = {Haydar, S. and Bednarz, R. and Laurette, P. and Sobitov, I. and Díaz i Pedrosa, N. and Videm, P. and Lueneburg, T. and Kuß, S. and Lahm, H. and Dreßen, M. and Krane, M. and Schmidt, C. and Grüning, B. A. and Voigt, N. and Streckfuss-Bömeke, K. and Gilsbach, R.}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s41467-025-67220-7}, + issn = {2041-1723}, + journal = {Nature Communications}, + keywords = {{\textgreater}UseGalaxy.eu, Cardiovascular biology, Epigenetics}, + language = {en}, + month = {January}, + number = {1}, + pages = {117}, + publisher = {Nature Publishing Group}, + title = {Chamber-specific chromatin architecture guides functional interpretation of disease-associated {Cis}-regulatory elements in human cardiomyocytes}, + url = {https://www.nature.com/articles/s41467-025-67220-7}, + urldate = {2026-01-12}, + volume = {17}, + year = {2026} +} + @article{he_complete_2024, abstract = {In this study, we sequenced and analyzed the mitochondrial genome of the Satanas beetle, Dynastes satanas Moser, 1909, which was intercepted by Chinese Customs during an attempted smuggling operati...}, author = {He, Xunuo and Wei, Shuang and Li, Panpan and Li, Xianfeng}, @@ -9032,9 +9532,9 @@ @article{he_complete_2024 keywords = {{\textgreater}UseGalaxy.eu}, language = {EN}, month = {December}, - note = {Publisher: Taylor \& Francis}, number = {12}, pages = {1627--1631}, + publisher = {Taylor \& Francis}, shorttitle = {Complete mitochondrial genome of the {Satanas} beetle, {Dynastes} satanas {Moser}, 1909 ({Coleoptera}}, title = {Complete mitochondrial genome of the {Satanas} beetle, {Dynastes} satanas {Moser}, 1909 ({Coleoptera}: {Scarabaeidae})}, url = {https://www.tandfonline.com/doi/abs/10.1080/23802359.2024.2432373}, @@ -9117,10 +9617,10 @@ @article{hedhly_s-locus_2023 keywords = {\textit{Prunus salicina}, \textit{S}-allele, \textit{S}-genotyping-by-sequencing, {\textgreater}UseGalaxy.eu, Japanese plum, Prunus, Prunus domestica, self-incompatibility}, language = {en}, month = {January}, - note = {Number: 4 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 4}, number = {4}, pages = {3932}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {S-{Locus} {Genotyping} in {Japanese} {Plum} by {High} {Throughput} {Sequencing} {Using} a {Synthetic} {S}-{Loci} {Reference} {Sequence}}, url = {https://www.mdpi.com/1422-0067/24/4/3932}, urldate = {2023-03-15}, @@ -9137,7 +9637,7 @@ @article{heine_activation_2024 keywords = {10-Cl-BBQ, {\textgreater}UseGalaxy.eu, AhR knockout mice, Allergic Airway Inflammation, Aryl hydrocarbon receptor, Immunomodulation, adjuvant, allergen-specific immunotherapy}, language = {English}, month = {June}, - note = {Publisher: Frontiers}, + publisher = {Frontiers}, shorttitle = {Activation of the aryl hydrocarbon receptor improves allergen-specific immunotherapy of murine allergic airway inflammation}, title = {Activation of the aryl hydrocarbon receptor improves allergen-specific immunotherapy of murine allergic airway inflammation: a novel adjuvant option?}, url = {https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2024.1397072/full}, @@ -9192,9 +9692,9 @@ @article{henriques_revealing_2025 keywords = {{\textgreater}UseGalaxy.eu, Microbiology, Viral evolution, Virology}, language = {en}, month = {February}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {1--11}, + publisher = {Nature Publishing Group}, title = {Revealing the hidden diversity of {Chlorella} heliozoae-infecting giant viruses}, url = {https://www.nature.com/articles/s44298-025-00088-y}, urldate = {2025-02-28}, @@ -9207,8 +9707,8 @@ @article{hering_eikenella_2021 doi = {10.1099/ijsem.0.004977}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {September}, - note = {Publisher: Microbiology Society}, number = {9}, + publisher = {Microbiology Society}, title = {Eikenella glucosivorans sp. nov., isolated from a human throat swab, and emendation of the genus {Eikenella} to include saccharolytic species}, url = {https://doi.org/10.1099/ijsem.0.004977}, volume = {71}, @@ -9225,9 +9725,9 @@ @article{hermawaty_novo_2025 keywords = {{\textgreater}UseGalaxy.eu, Metabolomics, Plant biotechnology, Plant genetics, Plant physiology, Plant stress responses, Plant symbiosis, Seedlings, Sequencing, Thymelaeaceae, Transcriptome, Wood}, language = {en}, month = {January}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {2977}, + publisher = {Nature Publishing Group}, title = {De novo transcriptome assembly and analysis during agarwood induction in {Gyrinops} versteegii {Gilg}. seedling}, url = {https://www.nature.com/articles/s41598-025-87486-7}, urldate = {2025-01-27}, @@ -9243,8 +9743,8 @@ @article{hernandez_design_2020 journal = {Frontiers in Microbiology}, keywords = {+HowTo, +RefPublic, +Stellar, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org.au, Bacterial strain-specific, NGS, biocontrol, marker, qPCR, risk assesment}, language = {English}, - note = {Publisher: Frontiers}, pages = {208}, + publisher = {Frontiers}, title = {Design of {Bacterial} {Strain}-{Specific} {qPCR} {Assays} {Using} {NGS} {Data} and {Publicly} {Available} {Resources} and {Its} {Application} to {Track} {Biocontrol} {Strains}}, url = {https://www.frontiersin.org/articles/10.3389/fmicb.2020.00208/full}, urldate = {2020-03-23}, @@ -9262,10 +9762,10 @@ @article{herwibawa_association_2024 keywords = {{\textgreater}UseGalaxy.eu, Arabidopsis, CRE, Oryza, SNP, TFBS, cullin, indel, phylogenetic}, language = {en}, month = {January}, - note = {Number: 2 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 2}, number = {2}, pages = {1040}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Association of a {Specific} {OsCULLIN3c} {Haplotype} with {Salt} {Stress} {Responses} in {Local} {Thai} {Rice}}, url = {https://www.mdpi.com/1422-0067/25/2/1040}, urldate = {2024-05-17}, @@ -9336,8 +9836,8 @@ @article{hetz_burkholderiaceae_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, language = {eng}, month = {February}, - note = {Publisher: Frontiers Media SA}, pages = {628269}, + publisher = {Frontiers Media SA}, title = {Burkholderiaceae {Are} {Key} {Acetate} {Assimilators} {During} {Complete} {Denitrification} in {Acidic} {Cryoturbated} {Peat} {Circles} of the {Arctic} {Tundra}}, url = {https://doi.org/10.3389/fmicb.2021.628269}, volume = {12}, @@ -9408,6 +9908,26 @@ @article{hiltemann_galaxy_2023 year = {2023} } +@article{hoang_comprehensive_2025, + abstract = {Colibacillosis, caused by avian pathogenic Escherichia coli (APEC), represents a major threat to poultry production, leading to significant mortality and economic losses. This study aimed to characterize an APEC strain, HPVN24, isolated from diarrheic chickens at a farm in Hai Phong, Vietnam. The strain was investigated through phenotypic assays, antibiotic susceptibility profiling, and whole-genome sequencing using the Illumina platform. HPVN24 exhibited β-hemolytic activity and resistance to trimethoprim, ampicillin, and ciprofloxacin. Whole-genome analysis identified the strain as serotype O78:H9 and sequence type ST23, with a genome size of 5.05 Mb and a GC content of 50.57\%. Genome annotation revealed a wide repertoire of genes involved in metabolism, secretion systems, virulence, and biofilm formation. Virulence-associated genes included those related to adhesion, iron acquisition, hemolysin production, and stress response. Analysis predicted multidrug resistance to 18 antibiotic classes, with particularly strong resistance to fluoroquinolones. Phylogenetic comparison demonstrated that HPVN24 clustered closely with O78:H9 strains isolated from poultry in other regions, suggesting potential transmission across populations. These findings indicate that HPVN24 is a multidrug-resistant and highly virulent APEC strain linked to colibacillosis outbreaks in Vietnam and highlight the need for ongoing surveillance, judicious antibiotic usage, and alternative strategies to ensure poultry health and food safety.}, + author = {Hoang, Minh Duc and Lanh, Pham Thi and Hien, Vu Thi and Kao, Cheng-Yen and Quyen, Dong Van}, + copyright = {cc by}, + doi = {10.3390/microorganisms13102265}, + issn = {2076-2607}, + journal = {Microorganisms}, + keywords = {{\textgreater}UseGalaxy.eu, Antibiotic Resistance, Avian Pathogenic Escherichia Coli, Colibacillosis, Vietnam Poultry, Whole Genome Sequencing, virulence factors}, + language = {eng}, + month = {September}, + number = {10}, + pages = {2265}, + shorttitle = {Comprehensive {Genomic} and {Phenotypic} {Characterization} of \<i\>{Escherichia} coli\</i\> {O78}}, + title = {Comprehensive {Genomic} and {Phenotypic} {Characterization} of \<i\>{Escherichia} coli\</i\> {O78}:{H9} {Strain} {HPVN24} {Isolated} from {Diarrheic} {Poultry} in {Vietnam}}, + url = {https://europepmc.org/articles/PMC12565876}, + urldate = {2025-12-26}, + volume = {13}, + year = {2025} +} + @article{hodzhev_analysis_2023, abstract = {Pulmonary sarcoidosis is a complex inflammatory disease characterized by granulomas in the lung tissue, leading to breathing difficulties and chest pain. Its etiology remains not fully understood, with factors such as allergies, autoimmune responses and genetics playing a role. This study explores the potential of blood microbiome dysbiosis, defined as an imbalance in the microbial ecosystem, as a missing piece of the puzzle in understanding the etiology of the disease. Our objective was to apply a decision-tree supervised machine learning hierarchical model to distinguish potential patterns of microbiome dysbiosis in blood samples from patients with pulmonary sarcoidosis as compared to healthy age-matched controls. Blood microbiome analysis, being individually-specific and stable, offers a unique perspective. Utilizing 16S rRNA gene amplicon sequencing, we analyzed the blood microbiome composition characterized by non-normally distributed and sparse data. Because of the rarity of the disease in Bulgaria, we studied a relatively small patient group, n = 7. The findings were compared to 21 healthy age-matched controls. Bioinformatics and statistical analysis play a pivotal role in microbiome analysis, especially when discerning associations between taxonomic composition and disorders such as pulmonary sarcoidosis. By analyzing the microbial diversity, we identified alterations in the blood microbiome composition between healthy individuals and those with sarcoidosis, which potentially may trigger the disease. Advanced machine learning techniques provided additional power to the analysis, that might be overlooked by the usual group statistics, confirming the differentiation of the diversity within the studied microbiome.}, author = {Hodzhev, Yordan}, @@ -9416,10 +9936,10 @@ @article{hodzhev_analysis_2023 journal = {Biotechnology \& Biotechnological Equipment}, keywords = {{\textgreater}UseGalaxy.eu, Pulmonary sarcoidosis, blood microbiome dysbiosis, classification, decision tree model}, month = {December}, - note = {Publisher: Taylor \& Francis -\_eprint: https://doi.org/10.1080/13102818.2023.2283133}, + note = {\_eprint: https://doi.org/10.1080/13102818.2023.2283133}, number = {1}, pages = {2283133}, + publisher = {Taylor \& Francis}, title = {Analysis of blood microbiome dysbiosis in pulmonary sarcoidosis by decision tree model}, url = {https://doi.org/10.1080/13102818.2023.2283133}, urldate = {2023-12-03}, @@ -9475,7 +9995,7 @@ @article{hoffmann_role_2024 keywords = {{\textgreater}UseGalaxy.eu}, language = {EN}, month = {December}, - note = {Publisher: Taylor \& Francis}, + publisher = {Taylor \& Francis}, title = {The role of the 5’ sensing function of ribonuclease {E} in cyanobacteria}, url = {https://www.tandfonline.com/doi/abs/10.1080/15476286.2024.2328438}, urldate = {2024-05-17}, @@ -9508,9 +10028,9 @@ @article{holper_genome-wide_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Genome, Viral, Host Microbial Interactions, Mutation}, language = {eng}, month = {August}, - note = {Publisher: MDPI AG}, number = {8}, pages = {1574}, + publisher = {MDPI AG}, title = {A {Genome}-{Wide} {CRISPR}/{Cas9} {Screen} {Reveals} the {Requirement} of {Host} {Sphingomyelin} {Synthase} 1 for {Infection} with {Pseudorabies} {Virus} {Mutant} {gD}–{Pass}}, url = {https://doi.org/10.3390/v13081574}, volume = {13}, @@ -9580,9 +10100,9 @@ @article{honecker_entamoeba_2025 keywords = {{\textgreater}UseGalaxy.eu, Cloning, Cytokines, Entamoeba histolytica, MicroRNAs, Monocytes, Neutrophils, Proteomes, Trophozoites}, language = {en}, month = {October}, - note = {Publisher: Public Library of Science}, number = {4}, pages = {e0012997}, + publisher = {Public Library of Science}, title = {Entamoeba histolytica extracellular vesicles drive pro-inflammatory monocyte signaling}, url = {https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0012997}, urldate = {2025-05-29}, @@ -9637,9 +10157,8 @@ @article{hosseini_astrocytes_2024 keywords = {{\textgreater}RNA Workbench, {\textgreater}UseGalaxy.eu, CSPGs remodeling, LAR and PTP-σ receptors, astrocytes, neural precursor cells, neurogenesis, spinal cord injury}, language = {English}, month = {September}, - note = {Publisher: Elsevier}, number = {0}, - pmid = {39303705}, + publisher = {Elsevier}, title = {Astrocytes originated from neural stem cells drive the regenerative remodeling of pathologic {CSPGs} in spinal cord injury}, url = {https://www.cell.com/stem-cell-reports/abstract/S2213-6711(24)00244-3}, urldate = {2024-09-23}, @@ -9671,9 +10190,9 @@ @article{hosseinzadeh_whole_2024 keywords = {{\textgreater}UseGalaxy.eu, Animal breeding, Genetics, MicroRNAs, RNA, Long Noncoding}, language = {en}, month = {March}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {6544}, + publisher = {Nature Publishing Group}, title = {Whole genome discovery of regulatory genes responsible for the response of chicken to heat stress}, url = {https://www.nature.com/articles/s41598-024-56757-0}, urldate = {2024-04-28}, @@ -9687,9 +10206,9 @@ @article{howard_complete_2023 journal = {Microbiology Resource Announcements}, keywords = {{\textgreater}UseGalaxy.eu}, month = {August}, - note = {Publisher: American Society for Microbiology}, number = {0}, pages = {e00293--23}, + publisher = {American Society for Microbiology}, title = {Complete genome sequence of a human bacteremia isolate of {Kalamiella} piersonii}, url = {https://journals.asm.org/doi/10.1128/mra.00293-23}, urldate = {2023-09-05}, @@ -9767,10 +10286,10 @@ @article{huang_translational_2023 keywords = {{\textgreater}UseGalaxy.eu, Oryza, Plant hormones, Plant molecular biology, Translation}, language = {en}, month = {August}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {4674}, + publisher = {Nature Publishing Group}, title = {A translational regulator {MHZ9} modulates ethylene signaling in rice}, url = {https://www.nature.com/articles/s41467-023-40429-0}, urldate = {2023-11-18}, @@ -9795,6 +10314,23 @@ @unj-jena.de. year = {2021} } +@article{hui_complete_2025, + abstract = {Hasora schoenherr is a Hesperiidae species belonging to the subfamily Coeliadinae. Here, we report the complete mitogenome dataset of Hasora schoenherr sampled from Endau-Rompin Johor National Park, Malaysia, sequenced using the Illumina NovaSeq 6000 technology. The mitogenome is 15,353 bp long, comprising a set of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region. All PCGs were initiated by the typical ATN codon, except for COX1 which started with a CGA start codon. Out of the 13 PCGs, three PCGs (COX1, COX2 and NADH4) were terminated with an incomplete stop codon T. Phylogenetic analysis supported the placement of Hasora schonherr within Coeliadinae with a high support value and it is clustered with the Hasora vitta (NC027170) sample from China.}, + author = {Hui, Lam Boon and Miga, Marylin and Siang, Chan Vei and Rahman, Aqilah Awg Abdul and Parimannan, Sivachandran and Rajandas, Heera and Sitam, Frankie Thomas and Tokiman, Lili and Kemalok, Jai and Shamsir, Mohd Shahir and Salleh, Faezah Mohd}, + doi = {10.1016/j.dib.2025.112218}, + issn = {2352-3409}, + journal = {Data in Brief}, + keywords = {{\textgreater}UseGalaxy.eu, Assembly, Endau-rompin, Johor national park, Phylogeny}, + month = {December}, + pages = {112218}, + shorttitle = {The complete mitogenome dataset of \textit{{Hasora} {Schoenherr}} ({Latreille}, 1824) ({Lepidoptera}}, + title = {The complete mitogenome dataset of \textit{{Hasora} {Schoenherr}} ({Latreille}, 1824) ({Lepidoptera}: {Hesperiidae}: {Coeliadinae}) from {Malaysia}}, + url = {https://www.sciencedirect.com/science/article/pii/S2352340925009394}, + urldate = {2025-12-22}, + volume = {63}, + year = {2025} +} + @article{humphrey_characterisation_2024, abstract = {Genome sequencing of Clostridium clostridioforme strain LM41 revealed the presence of an atypically high proportion of mobile genetic elements for this species, with a particularly high abundance of prophages. Bioinformatic analysis of prophage sequences sought to characterise these elements and identify prophage-linked genes contributing to enhanced fitness of the host bacteria in the dysbiotic gut. This work has identified 15 prophages, of which 4 are predicted to be intact, 2 are predicted to be defective, and 9 are unclassified. qPCR analysis revealed spontaneous release of four of the LM41 prophages into the culture supernatant, the majority of which had morphology akin to podoviruses when visualised using Transmission Electron Microscopy. We observed diversity in the lysogeny mechanisms utilised by the prophages, with examples of the classical λ-like CI/Cro system, the ICE Bs 1 ImmR/ImmA-like system, and the Mu-like C/Ner system. Classical morons, such as toxins or immune evasion factors, were not observed. We did, however, identify a variety of genes with roles in mediating restriction modification and genetic diversity, as well as some candidate genes with potential roles in host adaptation. Despite being the most abundant entities in the intestine, there is a dearth of information about phages associated with members of the microbiome. This work begins to shed light on the contribution of these elements to the lifestyle of C. clostridioforme LM41.}, author = {Humphrey, Suzanne and Marouli, Angeliki and Thümmler, Katja and Mullin, Margaret and Wall, Daniel}, @@ -9813,9 +10349,9 @@ @article{humphrey_genomic_2024 issn = {1465-2080}, journal = {Microbiology}, keywords = {{\textgreater}UseGalaxy.eu, Clostridium, Gastrointestinal Microbiome, Prophages}, - note = {Publisher: Microbiology Society,}, number = {8}, pages = {001486}, + publisher = {Microbiology Society,}, shorttitle = {Genomic characterization of prophage elements in {Clostridium} clostridioforme}, title = {Genomic characterization of prophage elements in {Clostridium} clostridioforme: an understudied component of the intestinal microbiome}, url = {https://www.microbiologyresearch.org/content/journal/micro/10.1099/mic.0.001486}, @@ -9834,9 +10370,9 @@ @article{hunold_dynatag_2025 keywords = {{\textgreater}UseGalaxy.eu, Chromatin, Epigenetics analysis, Gene regulation, Stem-cell differentiation, Transcription factors}, language = {en}, month = {July}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {6585}, + publisher = {Nature Publishing Group}, title = {{DynaTag} for efficient mapping of transcription factors in low-input samples and at single-cell resolution}, url = {https://www.nature.com/articles/s41467-025-61797-9}, urldate = {2025-08-04}, @@ -9852,7 +10388,7 @@ @article{hurtado_one_2025 keywords = {{\textgreater}UseGalaxy.eu, Campylobacter coli, Campylobacter jejuni, Nanopore long-fragment sequencing, antimicrobial resistance, one health, pangenome, resistome, whole-genome sequencing}, language = {English}, month = {January}, - note = {Publisher: Frontiers}, + publisher = {Frontiers}, title = {A {One} {Health} approach for the genomic characterization of antibiotic-resistant {Campylobacter} isolates using {Nanopore} whole-genome sequencing}, url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2025.1540210/full}, urldate = {2025-02-16}, @@ -9869,9 +10405,9 @@ @article{husaini_investigating_2023 keywords = {{\textgreater}UseGalaxy.eu}, language = {en}, month = {December}, - note = {Publisher: IOP Publishing}, number = {1}, pages = {012006}, + publisher = {IOP Publishing}, title = {Investigating the patterns of simple sequence repeats ({SSRs}) inferred from the whole genome of a critically endangered species {Cassine} koordersii kosterm}, url = {https://dx.doi.org/10.1088/1755-1315/1271/1/012006}, urldate = {2024-11-17}, @@ -9926,8 +10462,8 @@ @article{hwang_reduction_2024 keywords = {{\textgreater}UseGalaxy.eu, Apolipoproteins E, Biomarkers, Brain, Diseases, Fetal Alcohol Spectrum Disorders, Genome-Wide Association Study, Neuroscience, Prenatal Exposure Delayed Effects}, language = {en}, month = {May}, - note = {Publisher: Nature Publishing Group}, pages = {1--17}, + publisher = {Nature Publishing Group}, title = {Reduction of {APOE} accounts for neurobehavioral deficits in fetal alcohol spectrum disorders}, url = {https://www.nature.com/articles/s41380-024-02586-6}, urldate = {2024-05-17}, @@ -9943,7 +10479,7 @@ @article{iaffaldano_crispr_2023 keywords = {{\textgreater}UseGalaxy.eu, CRISPR library screening, Gene Activation, Lentiviral vectors, gene knockout, vector titers}, language = {English}, month = {July}, - note = {Publisher: Frontiers}, + publisher = {Frontiers}, title = {{CRISPR} library screening to develop {HEK293}-derived cell lines with improved lentiviral vector titers}, url = {https://www.frontiersin.org/journals/genome-editing/articles/10.3389/fgeed.2023.1218328/full}, urldate = {2024-11-17}, @@ -9961,9 +10497,9 @@ @article{iliev_first_2025 keywords = {16S sequencing, {\textgreater}UseGalaxy.eu, Black Sea microbiology, culturable microbiota, shotgun metagenome sequencing, submerged petrified forest}, language = {en}, month = {August}, - note = {Publisher: Multidisciplinary Digital Publishing Institute}, number = {8}, pages = {583}, + publisher = {Multidisciplinary Digital Publishing Institute}, shorttitle = {First {Microbial} {Survey} of a {Submerged} {Petrified} {Forest} in the {Black} {Sea}}, title = {First {Microbial} {Survey} of a {Submerged} {Petrified} {Forest} in the {Black} {Sea}: {Culture}-{Based} and {Metagenomic} {Insights}}, url = {https://www.mdpi.com/1424-2818/17/8/583}, @@ -9981,10 +10517,10 @@ @article{ilikkan_laktik_2023 keywords = {{\textgreater}UseGalaxy.eu}, language = {tr}, month = {June}, - note = {Number: 2 -Publisher: Igdir University}, + note = {Number: 2}, number = {2}, pages = {932--940}, + publisher = {Igdir University}, title = {Laktik {Asit} {Bakterilerinde} {Tetrasiklin} {Direncinin} {Fenotipik} ve {Tüm} {Genom} {Dizilerinde} in silico {Genotipik} {Olarak} {Araştırılması}}, url = {https://dergipark.org.tr/en/pub/jist/issue/77307/1233617}, urldate = {2023-07-31}, @@ -10002,9 +10538,9 @@ @article{imre_epigenetic_2024 keywords = {{\textgreater}UseGalaxy.eu, Epigenesis, Genetic, Epigenetics, Gene regulation, Heterochromatin, Histones, Nuclear organization, Nucleosomes}, language = {en}, month = {October}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {9171}, + publisher = {Nature Publishing Group}, title = {Epigenetic modulation via the {C}-terminal tail of {H2A}.{Z}}, url = {https://www.nature.com/articles/s41467-024-53514-9}, urldate = {2024-11-17}, @@ -10056,8 +10592,6 @@ @article{ioos_harnessing_2023 keywords = {{\textgreater}UseGalaxy.eu}, month = {October}, pages = {e16354}, - pmcid = {PMC10601906}, - pmid = {null}, title = {Harnessing the power of comparative genomics to support the distinction of sister species within {Phyllosticta} and development of highly specific detection of {Phyllosticta} citricarpa causing citrus black spot by real-time {PCR}}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10601906/}, urldate = {2023-10-28}, @@ -10090,9 +10624,9 @@ @article{ipoutcha_synthetic_2024 keywords = {{\textgreater}UseGalaxy.eu, Bacterial Infections, Bacteriophages, Pseudomonas Infections, Pseudomonas Phages}, language = {eng}, month = {January}, - note = {Publisher: American Society for Microbiology}, number = {3}, pages = {e02897--23}, + publisher = {American Society for Microbiology}, title = {A synthetic biology approach to assemble and reboot clinically relevant {Pseudomonas} aeruginosa tailed phages}, url = {https://journals.asm.org/doi/full/10.1128/spectrum.02897-23}, urldate = {2024-05-17}, @@ -10110,10 +10644,10 @@ @article{ishola_comparative_2024 keywords = {{\textgreater}UseGalaxy.eu, auxiliary metabolic genes (AMGs), bacteriophages, metagenomics, murine models, prophages, virome}, language = {en}, month = {February}, - note = {Number: 2 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 2}, number = {2}, pages = {255}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Comparative {Metagenomic} {Analysis} of {Bacteriophages} and {Prophages} in {Gnotobiotic} {Mouse} {Models}}, url = {https://www.mdpi.com/2076-2607/12/2/255}, urldate = {2024-01-30}, @@ -10232,10 +10766,10 @@ @article{jaki_total_2023 keywords = {{\textgreater}UseGalaxy.eu, COVID-19, Immune evasion, Outcomes research, SARS-CoV-2, Viral evolution, Viral infection}, language = {en}, month = {April}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {1999}, + publisher = {Nature Publishing Group}, title = {Total escape of {SARS}-{CoV}-2 from dual monoclonal antibody therapy in an immunocompromised patient}, url = {https://www.nature.com/articles/s41467-023-37591-w}, urldate = {2023-06-05}, @@ -10252,9 +10786,9 @@ @article{jalili_galaxy_2020 keywords = {+Education, +Galactic, +IsGalaxy, +Project, +RefPublic, +Tools, {\textgreater}Live EU, {\textgreater}Metabolomics EU, {\textgreater}Metagenomics EU, {\textgreater}Proteomics EU, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au, Software}, language = {en}, month = {July}, - note = {Publisher: Oxford Academic}, number = {W1}, pages = {W395--W402}, + publisher = {Oxford Academic}, shorttitle = {The {Galaxy} platform for accessible, reproducible and collaborative biomedical analyses}, title = {The {Galaxy} platform for accessible, reproducible and collaborative biomedical analyses: 2020 update}, url = {https://academic.oup.com/nar/article/48/W1/W395/5849904}, @@ -10272,9 +10806,9 @@ @article{janet-maitre_strain-specific_2025 keywords = {{\textgreater}UseGalaxy.eu, Complement System Proteins, Pseudomonas Infections, Pseudomonas aeruginosa}, language = {eng}, month = {August}, - note = {Publisher: American Society for Microbiology}, number = {0}, pages = {e00055--25}, + publisher = {American Society for Microbiology}, title = {Strain-specific variation in the complement resistome of {Pseudomonas} aeruginosa}, url = {https://journals.asm.org/doi/full/10.1128/iai.00055-25}, urldate = {2025-09-03}, @@ -10292,10 +10826,10 @@ @article{jarvis_semi-automated_2022 keywords = {{\textgreater}UseGalaxy.eu, Centromeres, Genetic variation, Genome assembly algorithms, Genomics}, language = {en}, month = {November}, - note = {Number: 7936 -Publisher: Nature Publishing Group}, + note = {Number: 7936}, number = {7936}, pages = {519--531}, + publisher = {Nature Publishing Group}, title = {Semi-automated assembly of high-quality diploid human reference genomes}, url = {https://www.nature.com/articles/s41586-022-05325-5}, urldate = {2022-12-03}, @@ -10348,10 +10882,10 @@ @article{jeon_tailored_2023 keywords = {\textit{N} gene, \textit{RdRp} gene, {\textgreater}UseGalaxy.eu, SARS-CoV-2, internal positive control, multiplex real-time RT-PCR}, language = {en}, month = {January}, - note = {Number: 4 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 4}, number = {4}, pages = {602}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Tailored {Multiplex} {Real}-{Time} {RT}-{PCR} with {Species}-{Specific} {Internal} {Positive} {Controls} for {Detecting} {SARS}-{CoV}-2 in {Canine} and {Feline} {Clinical} {Samples}}, url = {https://www.mdpi.com/2076-2615/13/4/602}, urldate = {2023-03-15}, @@ -10383,10 +10917,10 @@ @article{jesudoss_chelladurai_comparative_2023 keywords = {\textit{Dipylidium caninum}, {\textgreater}UseGalaxy.eu, cat and dog, cestode, flea tapeworm, genome comparison, species delimitation}, language = {en}, month = {May}, - note = {Number: 5 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 5}, number = {5}, pages = {675}, + publisher = {Multidisciplinary Digital Publishing Institute}, shorttitle = {Comparative {Genomic} {Analysis} and {Species} {Delimitation}}, title = {Comparative {Genomic} {Analysis} and {Species} {Delimitation}: {A} {Case} for {Two} {Species} in the {Zoonotic} {Cestode} {Dipylidium} caninum}, url = {https://www.mdpi.com/2076-0817/12/5/675}, @@ -10402,11 +10936,10 @@ @article{jhinjharia_high-throughput_2023 issn = {0739-1102}, journal = {Journal of Biomolecular Structure and Dynamics}, keywords = {{\textgreater}ChemicalToolbox, FFAR4, HTVS, diabetes, machine-learning, molecular dynamic simulations}, - note = {Publisher: Taylor \& Francis -\_eprint: https://doi.org/10.1080/07391102.2023.2280707}, + note = {\_eprint: https://doi.org/10.1080/07391102.2023.2280707}, number = {0}, pages = {1--21}, - pmid = {37978906}, + publisher = {Taylor \& Francis}, title = {A high-throughput structural dynamics approach for identification of potential agonists of {FFAR4} for type 2 diabetes mellitus therapy}, url = {https://doi.org/10.1080/07391102.2023.2280707}, urldate = {2023-11-22}, @@ -10424,10 +10957,10 @@ @article{ji_unusual_2025 keywords = {{\textgreater}UseGalaxy.eu, Chilopoda, cryptic species, divergence time, mitogenomes, phylogeny}, language = {en}, month = {May}, - note = {Number: 5 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 5}, number = {5}, pages = {486}, + publisher = {Multidisciplinary Digital Publishing Institute}, shorttitle = {Unusual {Genetic} {Diversity} {Within} {Thereuopoda} clunifera ({Wood}, 1862) ({Chilopoda}}, title = {Unusual {Genetic} {Diversity} {Within} {Thereuopoda} clunifera ({Wood}, 1862) ({Chilopoda}: {Scutigeromorpha}) {Revealed} by {Phylogeny} and {Divergence} {Times} {Using} {Mitochondrial} {Genomes}}, url = {https://www.mdpi.com/2075-4450/16/5/486}, @@ -10468,13 +11001,30 @@ @article{jiang_-depth_2022 year = {2022} } +@article{johnson_improve_2018, + author = {Johnson, James E. and Kumar, Praveen and Easterly, Caleb and Esler, Mark and Mehta, Subina and Eschenlauer, Arthur C. and Hegeman, Adrian D. and Jagtap, Pratik D. and Griffin, Timothy J.}, + doi = {10.12688/f1000research.16450.2}, + issn = {2046-1402}, + journal = {F1000Research}, + keywords = {+IsGalaxy, +Stellar, +Tools, {\textgreater}UseGalaxy.eu}, + language = {en}, + month = {October}, + pages = {1604}, + shorttitle = {Improve your {Galaxy} text life}, + title = {Improve your {Galaxy} text life: {The} {Query} {Tabular} {Tool}}, + url = {https://f1000research.com/articles/7-1604/v1}, + urldate = {2018-10-05}, + volume = {7}, + year = {2018} +} + @article{jonsson_enhanced_2025, author = {Jönsson, Alexander and Iatrou, Antonia and Wildfang, Louise and J. Neumann, Dana and Gürbüz, Hakan and A. Schoenmaker, Carina A. and Danner Dalgaard, Marlene and Rose Jensen, Pernille and Dufva, Martin}, doi = {10.1039/D4MA01191K}, journal = {Materials Advances}, keywords = {{\textgreater}UseGalaxy.eu}, language = {en}, - note = {Publisher: Royal Society of Chemistry}, + publisher = {Royal Society of Chemistry}, shorttitle = {Enhanced biocompatibility of {3D} printed resin parts via wet autoclave postprocessing}, title = {Enhanced biocompatibility of {3D} printed resin parts via wet autoclave postprocessing: implications for stem cell organ-on-a-chip culture}, url = {https://pubs.rsc.org/en/content/articlelanding/2025/ma/d4ma01191k}, @@ -10492,9 +11042,9 @@ @article{joshi_insights_2025 keywords = {{\textgreater}UseGalaxy.eu, Bacteria, Biofilms, Candida, Microbial communities, Urinary Catheters}, language = {en}, month = {May}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {15375}, + publisher = {Nature Publishing Group}, title = {Insights into urinary catheter colonisation and polymicrobial biofilms of {Candida}- bacteria under flow condition}, url = {https://www.nature.com/articles/s41598-025-00457-w}, urldate = {2025-05-28}, @@ -10545,7 +11095,7 @@ @article{joshi_tracing_2024 keywords = {{\textgreater}UseGalaxy.eu, Flaxseed, Hypertension, addictions, cardiovascular, side effects}, language = {English}, month = {January}, - note = {Publisher: Frontiers}, + publisher = {Frontiers}, title = {Tracing the pathways and mechanisms involved in medicinal uses of flaxseed with computational methods and bioinformatics tools}, url = {https://www.frontiersin.org/articles/10.3389/fchem.2023.1276052}, urldate = {2024-05-17}, @@ -10563,9 +11113,9 @@ @article{jovovic_novo_2024 keywords = {{\textgreater}UseGalaxy.eu, Molecular ecology, Molecular evolution, Transcriptomics}, language = {en}, month = {June}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {595}, + publisher = {Nature Publishing Group}, shorttitle = {De novo transcriptomes of cave and surface isopod crustaceans}, title = {De novo transcriptomes of cave and surface isopod crustaceans: insights from 11 species across three suborders}, url = {https://www.nature.com/articles/s41597-024-03393-y}, @@ -10639,9 +11189,9 @@ @article{justen_genetics_2025 keywords = {{\textgreater}UseGalaxy.eu, Evolutionary genetics, Molecular evolution, Speciation}, language = {en}, month = {August}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {7897}, + publisher = {Nature Publishing Group}, title = {The genetics of extrinsic postzygotic selection in a migratory divide between subspecies of the {Swainson}’s thrush}, url = {https://www.nature.com/articles/s41467-025-63188-6}, urldate = {2025-09-03}, @@ -10683,11 +11233,10 @@ @article{kabir_genome_2025 year = {2025} } -@article{kaczmarczyk_genome-wide_2025, +@misc{kaczmarczyk_genome-wide_2025, abstract = {{\textless}h4{\textgreater}ABSTRACT{\textless}/h4{\textgreater} Pseudomonas aeruginosa is a metabolically versatile opportunistic human pathogen. It causes acute and chronic infections and is notorious for its multidrug resistance and tolerance. To systematically uncover genetic vulnerabilities that could be exploited as therapeutic targets, we present a portable high-density CRISPR interference (CRISPRi) library comprising {\textgreater}80’000 single-guide RNAs (sgRNAs) targeting virtually all annotated coding sequences and intergenic regions of P. aeruginosa PAO1. This library was used to assess the genome-wide fitness landscapes under different growth conditions, uncovering gain- and loss- of-function phenotypes for more than a thousand genes upon depletion. Many of the phenotypes are likely caused by hypomorphic (partial loss-of-function) alleles that would not be easily accessible by traditional transposon sequencing (Tn-Seq). Focusing on central carbon metabolism, we reveal two glyceraldehyde-3-phosphate dehydrogenases as central, non-redundant nodes in glycolytic and gluconeogenic growth conditions that might be promising targets to redirect carbon flux away from metabolically persistent states associated with chronic infections. More generally, our comprehensive sgRNA libraries are a valuable resource to access genome-wide quantitative phenotypes through CRISPRi beyond the binary phenotypes offered by Tn-Seq.}, author = {Kaczmarczyk, Andreas and Klotz, Alexander and Manfredi, Pablo and Jenal, Urs}, doi = {10.1101/2025.08.12.669819}, - journal = {bioRxiv}, keywords = {{\textgreater}UseGalaxy.eu}, title = {Genome-wide high-density {CRISPR} interference screens reveal condition-specific metabolic vulnerabilities in {Pseudomonas} aeruginosa {PAO1}}, url = {http://europepmc.org/abstract/PPR/PPR1064713}, @@ -10734,7 +11283,7 @@ @article{kaiser_mutational_2021 doi = {10.1101/2021.06.10.447556}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {June}, - note = {Publisher: Cold Spring Harbor Laboratory}, + publisher = {Cold Spring Harbor Laboratory}, title = {Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome}, url = {https://doi.org/10.1101/2021.06.10.447556}, year = {2021} @@ -10778,7 +11327,6 @@ @article{kalmbach_genome-wide_2019 language = {english}, number = {1}, pages = {1--11}, - pmid = {31658463}, title = {Genome-{Wide} {Analysis} of the {Nucleosome} {Landscape} in {Individuals} with {Coffin}-{Siris} {Syndrome}}, url = {https://www.karger.com/Article/FullText/503266}, urldate = {2019-11-26}, @@ -10830,10 +11378,10 @@ @article{kandinov_azithromycin_2023 keywords = {\textit{Neisseria gonorrhoeae}, \textit{mtrR} and \textit{mtrD} alleles, {\textgreater}UseGalaxy.eu, azithromycin resistance, efflux pump, resistance determinants}, language = {en}, month = {January}, - note = {Number: 1 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 1}, number = {1}, pages = {170}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Azithromycin {Susceptibility} {Testing} and {Molecular} {Investigation} of {Neisseria} gonorrhoeae {Isolates} {Collected} in {Russia}, 2020–2021}, url = {https://www.mdpi.com/2079-6382/12/1/170}, urldate = {2023-03-15}, @@ -10851,10 +11399,10 @@ @article{kandinov_emergence_2023 keywords = {\textit{Neisseria gonorrhoeae}, {\textgreater}UseGalaxy.eu, G12302 genogroup, NG-MAST, azithromycin resistance, genetic determinants of antimicrobial resistance, phylogenetic analysis}, language = {en}, month = {May}, - note = {Number: 5 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 5}, number = {5}, pages = {1226}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Emergence of {Azithromycin}-{Resistant} {Neisseria} gonorrhoeae {Isolates} {Belonging} to the {NG}-{MAST} {Genogroup} 12302 in {Russia}}, url = {https://www.mdpi.com/2076-2607/11/5/1226}, urldate = {2023-07-31}, @@ -10872,10 +11420,10 @@ @article{kandinov_mini-multilocus_2024 keywords = {\textit{Neisseria gonorrhoeae}, {\textgreater}UseGalaxy.eu, Gonorrhea, Multilocus Sequence Typing, Neisseria gonorrhoeae, Phylogeny, antimicrobial resistance, genogroups, informative polymorphisms, multilocus sequence typing, oligonucleotide microarray, phylogenetic analysis}, language = {en}, month = {January}, - note = {Number: 11 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 11}, number = {11}, pages = {5781}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Mini-{Multilocus} {Sequence} {Typing} {Scheme} for the {Global} {Population} of {Neisseria} gonorrhoeae}, url = {https://www.mdpi.com/1422-0067/25/11/5781}, urldate = {2024-06-07}, @@ -10891,7 +11439,7 @@ @article{kandinov_molecular_2025 keywords = {{\textgreater}UseGalaxy.eu, Gonorrhea, Neisseria gonorrhoeae, antibiotic resistance, genetic determinants of drug resistance, genotyping, molecular epidemiology}, language = {English}, month = {February}, - note = {Publisher: Frontiers}, + publisher = {Frontiers}, shorttitle = {Molecular epidemiology of {Neisseria} gonorrhoeae isolates in {Russia}, 2015–2023}, title = {Molecular epidemiology of {Neisseria} gonorrhoeae isolates in {Russia}, 2015–2023: current trends and forecasting}, url = {https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2025.1526859/full}, @@ -10900,6 +11448,25 @@ @article{kandinov_molecular_2025 year = {2025} } +@article{kansou_human_2025, + abstract = {A link between idiopathic male infertility and viral infections exhibiting seminal carriage has emerged recently. In this respect, human papillomavirus (HPV) appears to be the most prevalent sexually transmitted agent worldwide. The viruses present in the genital environment comprise the genital virome. HPV infection reportedly disrupts homeostasis of the virome in women but this topic has not previously been studied in men.}, + author = {Kansou, Elissa and Aubry, Aurélien and Brochot, Etienne and Priam, Armin and Cabry-Goubet, Rosalie and Bosquet, Dorian and Demey, Baptiste}, + doi = {10.1186/s12958-025-01488-8}, + issn = {1477-7827}, + journal = {Reproductive Biology and Endocrinology}, + keywords = {{\textgreater}UseGalaxy.eu, High-throughput sequencing, Human papillomavirus, Male infertility, Metagenomic, Sperm, Virome}, + language = {en}, + month = {November}, + number = {1}, + pages = {154}, + shorttitle = {Human papillomavirus seminal carriage alters virome diversity and male fertility}, + title = {Human papillomavirus seminal carriage alters virome diversity and male fertility: a case-control study}, + url = {https://doi.org/10.1186/s12958-025-01488-8}, + urldate = {2025-12-26}, + volume = {23}, + year = {2025} +} + @article{kao_influence_2025, abstract = {Staphylococcus aureus is the leading cause of infectious-related deaths. Vaccine development has been hampered by the recall of nonprotective immune responses from prior exposure, suggesting an effective vaccine may need to be given early in life. The goal of this pilot study was to correlate the maternal serologic response against S. aureus to an infant’s risk for skin and soft tissue infection (SSTI) and colonization in the first year of life.Pregnant women were enrolled and maternal-infant dyads followed for 12 months. Maternal 3rd trimester and cord blood were obtained to determine the anti-S. aureus IgG and anti-α-toxin (Hla) neutralizing antibody (NAb) titers. Serial surveys and skin swabs were obtained from mothers at enrollment and from infants longitudinally to ascertain S. aureus colonization status and the incidence of SSTI.63 pregnant women were enrolled, 54\% with history of SSTI or asymptomatic S. aureus colonization at enrollment. Within 48-hours of delivery, 23\% of infants had S. aureus colonization and 43\% at 1-month. Maternal S. aureus colonization resulted in 7.4 increased odds of infant colonization at delivery. Higher cord blood anti-Hla Nab titer was associated with significantly lower risk for infant SSTI in the first year of life.S. aureus colonization occurs early in life, with over 40\% of infants colonized by 1-month. These results are the first to demonstrate an association between higher transplacental anti-Hla NAb and protection against infant SSTI in the first year of life. Overall, these findings support Hla as a promising vaccine target.}, author = {Kao, Carol M and Wylie, Kristine M and Boyle, Mary G and Schneider, Alaina and Uhlir, Rachel and Crick, Scott L and Bubeck Wardenburg, Juliane and Fritz, Stephanie A}, @@ -10985,9 +11552,9 @@ @article{katsanos_gene_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, language = {eng}, month = {September}, - note = {Publisher: The Company of Biologists}, number = {17}, pages = {dev199452}, + publisher = {The Company of Biologists}, title = {Gene expression profiling of epidermal cell types in {C}. elegans using {Targeted} {DamID}}, url = {https://doi.org/10.1242/dev.199452}, volume = {148}, @@ -11003,9 +11570,9 @@ @article{katsanos_targeted_2022 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Caenorhabditis elegans, Caenorhabditis elegans Proteins}, language = {eng}, month = {February}, - note = {Publisher: American Association for the Advancement of Science (AAAS)}, number = {5}, pages = {eabk3141}, + publisher = {American Association for the Advancement of Science (AAAS)}, title = {Targeted {DamID} in {C}. elegans reveals a direct role for {LIN}-22 and {NHR}-25 in antagonizing the epidermal stem cell fate}, url = {https://doi.org/10.1126/sciadv.abk3141}, volume = {8}, @@ -11021,9 +11588,9 @@ @article{kavas_genome-wide_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, language = {eng}, month = {September}, - note = {Publisher: Springer Science and Business Media LLC}, number = {9}, pages = {1885--1902}, + publisher = {Springer Science and Business Media LLC}, title = {Genome-wide identification of the {BURP} domain-containing genes in {Phaseolus} vulgaris}, url = {https://doi.org/10.1007/s12298-021-01052-9}, volume = {27}, @@ -11050,9 +11617,9 @@ @phdthesis{kefi_improving_2023 address = {Ann Arbor, United States}, author = {Kefi, Amira}, copyright = {Database copyright ProQuest LLC; ProQuest does not claim copyright in the individual underlying works.}, + isbn = {979-8-3797-4596-7}, keywords = {{\textgreater}UseGalaxy.eu, Deep learning, Genome annotation, ISOseq, Machine learning, RNAseq, Ribo-seq}, language = {Englisch}, - note = {ISBN: 9798379745967}, title = {Improving the {Human} {Genome} {Annotation} {Using} {Integrative} {Analysis} and {Deep} {Learning} {Methods}}, type = {Ph.{D}.}, url = {https://www.proquest.com/docview/2830283170/abstract/B6B2BD2F6A44FF9PQ/1}, @@ -11070,10 +11637,10 @@ @article{khan_comparative_2023 keywords = {{\textgreater}UseGalaxy.eu, Brassica, Molecular biology, Plant sciences, Seeds}, language = {en}, month = {March}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {3577}, + publisher = {Nature Publishing Group}, title = {Comparative phylogenomic insights of {KCS} and {ELO} gene families in {Brassica} species indicate their role in seed development and stress responsiveness}, url = {https://www.nature.com/articles/s41598-023-28665-2}, urldate = {2023-03-15}, @@ -11108,10 +11675,10 @@ @article{khine_comparative_2023 keywords = {{\textgreater}UseGalaxy.eu, Environmental sciences, Escherichia coli, Escherichia coli Proteins, Evolution, Genetics, Microbiology}, language = {en}, month = {March}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {5124}, + publisher = {Nature Publishing Group}, title = {Comparative genomic analysis of {Colistin} resistant {Escherichia} coli isolated from pigs, a human and wastewater on colistin withdrawn pig farm}, url = {https://www.nature.com/articles/s41598-023-32406-w}, urldate = {2023-07-31}, @@ -11128,8 +11695,8 @@ @article{khine_genetic_2024 keywords = {{\textgreater}UseGalaxy.eu, Escherichia coli, Klebsiella pneumoniae, carbapenemase-producing Enterobacteriaceae, clonal relatedness, genetic characterization}, language = {English}, month = {November}, - note = {Publisher: Frontiers}, pages = {1464934}, + publisher = {Frontiers}, title = {Genetic characterization and clonal analysis of carbapenemase-producing {Escherichia} coli and {Klebsiella} pneumoniae from canine and human origins}, url = {https://www.frontiersin.org/journals/veterinary-science/articles/10.3389/fvets.2024.1464934/full}, urldate = {2025-09-03}, @@ -11147,9 +11714,9 @@ @article{kifle_shotgun_2024 keywords = {{\textgreater}UseGalaxy.eu, Biotechnology, Computational biology and bioinformatics}, language = {en}, month = {July}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {15096}, + publisher = {Nature Publishing Group}, title = {Shotgun metagenomic insights into secondary metabolite biosynthetic gene clusters reveal taxonomic and functional profiles of microbiomes in natural farmland soil}, url = {https://www.nature.com/articles/s41598-024-63254-x}, urldate = {2024-11-17}, @@ -11164,9 +11731,9 @@ @article{kim_complete_2022 journal = {Microbiology Resource Announcements}, keywords = {{\textgreater}UseGalaxy.eu}, month = {October}, - note = {Publisher: American Society for Microbiology}, number = {0}, pages = {e00794--22}, + publisher = {American Society for Microbiology}, title = {Complete {Genome} {Sequence} of {Metabacillus} litoralis {Strain} {NCTR108}, {Isolated} from {Commercial} {Tattoo} {Ink}}, url = {https://journals.asm.org/doi/full/10.1128/mra.00794-22}, urldate = {2022-11-06}, @@ -11181,9 +11748,9 @@ @article{kim_complete_2022-1 journal = {Microbiology Resource Announcements}, keywords = {{\textgreater}UseGalaxy.eu}, month = {October}, - note = {Publisher: American Society for Microbiology}, number = {0}, pages = {e00859--22}, + publisher = {American Society for Microbiology}, title = {Complete {Genome} {Sequence} of {Terrisporobacter} glycolicus {Strain} {WW3900}, {Isolated} from {Influent} {Wastewater} at a {Research} {Center} with {Multiple}-{Species} {Research} {Animal} {Facilities}}, url = {https://journals.asm.org/doi/full/10.1128/mra.00859-22}, urldate = {2022-11-06}, @@ -11235,10 +11802,10 @@ @article{kimura_overexpression_2021 keywords = {{\textgreater}UseGalaxy.eu, Cardiomyopathies, Experimental models of disease, Gene therapy}, language = {en}, month = {June}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {3575}, + publisher = {Nature Publishing Group}, title = {Overexpression of human {BAG3P209L} in mice causes restrictive cardiomyopathy}, url = {https://www.nature.com/articles/s41467-021-23858-7}, urldate = {2023-06-05}, @@ -11255,8 +11822,8 @@ @article{king_resistome_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Klebsiella}, language = {eng}, month = {March}, - note = {Publisher: Elsevier BV}, pages = {321--324}, + publisher = {Elsevier BV}, title = {Resistome of a carbapenemase-producing novel {ST232} {Klebsiella} michiganensis isolate from urban hospital effluent in {South} {Africa}}, url = {https://doi.org/10.1016/j.jgar.2021.01.004}, volume = {24}, @@ -11322,8 +11889,8 @@ @article{klein_pruriception_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, language = {eng}, month = {April}, - note = {Publisher: eLife Sciences Publications, Ltd}, pages = {e64506}, + publisher = {eLife Sciences Publications, Ltd}, title = {Pruriception and neuronal coding in nociceptor subtypes in human and nonhuman primates}, url = {https://doi.org/10.7554/elife.64506}, volume = {10}, @@ -11339,7 +11906,7 @@ @article{klemm_proteinortho6_2023 keywords = {{\textgreater}UseGalaxy.eu, Algebraic connectivity, Orthology, Sequence similarity, homology, spectral clustering}, language = {English}, month = {December}, - note = {Publisher: Frontiers}, + publisher = {Frontiers}, shorttitle = {Proteinortho6}, title = {Proteinortho6: pseudo-reciprocal best alignment heuristic for graph-based detection of (co-)orthologs}, url = {https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2023.1322477/full}, @@ -11465,9 +12032,9 @@ @article{koeppel_sars-cov-2_2022 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, SARS-CoV-2, reverse zoonosis, wildlife}, language = {eng}, month = {January}, - note = {Publisher: MDPI AG}, number = {1}, pages = {120}, + publisher = {MDPI AG}, title = {{SARS}-{CoV}-2 {Reverse} {Zoonoses} to {Pumas} and {Lions}, {South} {Africa}}, url = {https://doi.org/10.3390/v14010120}, volume = {14}, @@ -11482,9 +12049,9 @@ @article{kohler_msstatsshiny_2023 journal = {Journal of Proteome Research}, keywords = {{\textgreater}UseGalaxy.eu}, month = {February}, - note = {Publisher: American Chemical Society}, number = {2}, pages = {551--556}, + publisher = {American Chemical Society}, shorttitle = {{MSstatsShiny}}, title = {{MSstatsShiny}: {A} {GUI} for {Versatile}, {Scalable}, and {Reproducible} {Statistical} {Analyses} of {Quantitative} {Proteomic} {Experiments}}, url = {https://doi.org/10.1021/acs.jproteome.2c00603}, @@ -11496,10 +12063,10 @@ @article{kohler_msstatsshiny_2023 @phdthesis{kohler_novel_2024, author = {Köhler, Anja R.}, copyright = {info:eu-repo/semantics/openAccess}, + isbn = {978-1-914065-28-6}, keywords = {{\textgreater}UseGalaxy.eu}, language = {en}, - note = {Accepted: 2025-01-09T12:48:00Z -ISBN: 9781914065286}, + note = {Accepted: 2025-01-09T12:48:00Z}, title = {Novel approaches to investigate the cellular effects of epigenome modifications}, type = {{doctoralThesis}}, url = {http://elib.uni-stuttgart.de/handle/11682/15507}, @@ -11539,7 +12106,6 @@ @article{kolosov_malpighian_2019 language = {en}, month = {November}, number = {22}, - pmid = {31636157}, shorttitle = {Malpighian tubules of caterpillars}, title = {Malpighian tubules of caterpillars: blending {RNAseq} and physiology to reveal regional functional diversity and novel epithelial ion transport control mechanisms}, url = {https://jeb.biologists.org/content/222/22/jeb211623}, @@ -11575,9 +12141,9 @@ @article{kongsomboonchoke_rapid_2025 keywords = {{\textgreater}UseGalaxy.eu, Bacteriophages, Escherichia coli Infections, Phage Therapy, Phage biology, Urinary Tract Infections, Uropathogenic Escherichia coli}, language = {en}, month = {April}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {12832}, + publisher = {Nature Publishing Group}, title = {Rapid formulation of a genetically diverse phage cocktail targeting uropathogenic {Escherichia} coli infections using the {UTI89} model}, url = {https://www.nature.com/articles/s41598-025-96561-y}, urldate = {2025-05-29}, @@ -11645,9 +12211,9 @@ @inproceedings{kostrykin_robust_2024 author = {Kostrykin, Leonid and Rohr, Karl}, booktitle = {2024 {IEEE} {International} {Symposium} on {Biomedical} {Imaging} ({ISBI})}, doi = {10.1109/ISBI56570.2024.10635542}, + issn = {1945-8452}, keywords = {{\textgreater}UseGalaxy.eu, Approximation algorithms, Cell segmentation, Clustering algorithms, Computational modeling, Deformable models, Image segmentation, Microscopy, Shape, cell cluster splitting, deformable models, fluorescence microscopy, model fitting}, month = {May}, - note = {ISSN: 1945-8452}, pages = {1--4}, title = {Robust {Graph} {Pruning} for {Efficient} {Segmentation} and {Cluster} {Splitting} of {Cell} {Nuclei} {Using} {Deformable} {Shape} {Models}}, url = {https://ieeexplore.ieee.org/abstract/document/10635542?casa_token=No9ffOZBJ8cAAAAA:XunOjedwbPvqGotuE4zqmazz2og3Q3Z7CA5kVubhQkjLl2-zm-b7Dc8--PxUKrYtyv-0TkBa}, @@ -11664,7 +12230,7 @@ @article{koutras_integrated_2023 keywords = {{\textgreater}UseGalaxy.eu, B-cell receptor, ER-phagy, Signal Transduction, Transcriptomics, src-Family Kinases}, language = {English}, month = {August}, - note = {Publisher: Frontiers}, + publisher = {Frontiers}, title = {Integrated signaling and transcriptome analysis reveals {Src} family kinase individualities and novel pathways controlled by their constitutive activity}, url = {https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2023.1224520/full}, urldate = {2024-11-17}, @@ -11697,9 +12263,9 @@ @article{kowalski_eplerenone_2021 journal = {Hypertension}, keywords = {{\textgreater}UseGalaxy.eu, aldosterone, cardiovascular disease, endothelial cells, mineralocorticoid receptor, pulmonary hypertension}, month = {August}, - note = {Publisher: American Heart Association}, number = {2}, pages = {456--465}, + publisher = {American Heart Association}, title = {Eplerenone {Improves} {Pulmonary} {Vascular} {Remodeling} and {Hypertension} by {Inhibition} of the {Mineralocorticoid} {Receptor} in {Endothelial} {Cells}}, url = {https://www.ahajournals.org/doi/10.1161/HYPERTENSIONAHA.120.16196}, urldate = {2023-06-05}, @@ -11717,9 +12283,9 @@ @article{kramer_cyclic_2024 keywords = {{\textgreater}UseGalaxy.eu, Light responses, Non-photochemical quenching}, language = {en}, month = {November}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {29274}, + publisher = {Nature Publishing Group}, title = {Cyclic electron flow compensates loss of {PGDH3} and concomitant stromal {NADH} reduction}, url = {https://www.nature.com/articles/s41598-024-80836-x}, urldate = {2024-11-29}, @@ -11750,9 +12316,9 @@ @article{kruk_integrated_2024 keywords = {{\textgreater}UseGalaxy.eu, Bronchoalveolar Lavage Fluid, Cystic Fibrosis, Proteomics, Tandem Mass Spectrometry, Workflow}, language = {eng}, month = {June}, - note = {Publisher: American Society for Microbiology}, number = {0}, pages = {e00929--23}, + publisher = {American Society for Microbiology}, title = {An integrated metaproteomics workflow for studying host-microbe dynamics in bronchoalveolar lavage samples applied to cystic fibrosis disease}, url = {https://journals.asm.org/doi/10.1128/msystems.00929-23}, urldate = {2024-07-01}, @@ -11770,10 +12336,10 @@ @article{kruse_synaptopodin_2024 keywords = {{\textgreater}UseGalaxy.eu, Mossy Fibers, Hippocampal, Neuronal Plasticity, Synapses, denervation, lesion-induced plasticity, local protein synthesis, synaptopodin}, language = {en}, month = {January}, - note = {Number: 2 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 2}, number = {2}, pages = {114}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Synaptopodin {Regulates} {Denervation}-{Induced} {Plasticity} at {Hippocampal} {Mossy} {Fiber} {Synapses}}, url = {https://www.mdpi.com/2073-4409/13/2/114}, urldate = {2024-01-14}, @@ -11813,8 +12379,6 @@ @article{kumar_accessible_2022 language = {eng}, month = {December}, pages = {giad028}, - pmcid = {PMC10132306}, - pmid = {37099385}, title = {An accessible infrastructure for artificial intelligence using a {Docker}-based {JupyterLab} in {Galaxy}}, volume = {12}, year = {2022} @@ -11828,7 +12392,7 @@ @article{kumar_community_2020 keywords = {+IsGalaxy, +Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, language = {en}, month = {May}, - note = {Publisher: Preprints}, + publisher = {Preprints}, shorttitle = {Community {Research} {Amid} {COVID}-19 {Pandemic}}, title = {Community {Research} {Amid} {COVID}-19 {Pandemic}: {Genomics} {Analysis} of {SARS}-{CoV}-2 over {Public} {GALAXY} server}, url = {https://www.preprints.org/manuscript/202005.0343/v1}, @@ -11903,17 +12467,6 @@ @article{kumar_quantp:_2018 year = {2018} } -@article{kumar_tool_2019, - abstract = {Galaxy is a web-based and open-source scientific data-processing platform. Researchers compose pipelines in Galaxy to analyse scientific data. These pipelines, also known as workflows, can be complex and difficult to create from thousands of tools, especially for researchers new to Galaxy. To make creating workflows easier, faster and less error-prone, a predictive system is developed to recommend tools facilitating further analysis. A model is created to recommend tools by analysing workflows, composed by researchers on the European Galaxy server, using a deep learning approach. The higher-order dependencies in workflows, represented as directed acyclic graphs, are learned by training a gated recurrent units (GRU) neural network, a variant of a recurrent neural network (RNN). The weights of tools used in the neural network training are derived from their usage frequencies over a period of time. The hyper-parameters of the neural network are optimised using Bayesian optimisation. An accuracy of 97\% in predicting tools is achieved by the model for precision@1, precision@2 and precision@3 metrics. It is accessed by a Galaxy API to recommend tools in real-time. Multiple user interface (UI) integrations on the server communicate with this API to apprise researchers of these recommended tools interactively. {\textless}h4{\textgreater}Contact{\textless}/h4{\textgreater} kumara@informatik.uni-freiburg.de gruening@informatik.uni-freiburg.de backofen@informatik.uni-freiburg.de}, - author = {Kumar, Anup and Grüning, Björn and Backofen, Rolf}, - doi = {10.1101/838599}, - journal = {bioRxiv}, - keywords = {{\textgreater}UseGalaxy.eu}, - title = {Tool recommender system in {Galaxy} using deep learning}, - url = {http://europepmc.org/abstract/PPR/PPR101761}, - year = {2019} -} - @article{kumar_tool_2021, abstract = {Galaxy is a web-based and open-source scientific data-processing platform. Researchers compose pipelines in Galaxy to analyse scientific data. These pipelines, also known as workflows, can be complex and difficult to create from thousands of tools, especially for researchers new to Galaxy. To help researchers with creating workflows, a system is developed to recommend tools that can facilitate further data analysis.A model is developed to recommend tools using a deep learning approach by analysing workflows composed by researchers on the European Galaxy server. The higher-order dependencies in workflows, represented as directed acyclic graphs, are learned by training a gated recurrent units neural network, a variant of a recurrent neural network. In the neural network training, the weights of tools used are derived from their usage frequencies over time and the sequences of tools are uniformly sampled from training data. Hyperparameters of the neural network are optimized using Bayesian optimization. Mean accuracy of 98\% in recommending tools is achieved for the top-1 metric.The model is accessed by a Galaxy API to provide researchers with recommended tools in an interactive manner using multiple user interface integrations on the European Galaxy server. High-quality and highly used tools are shown at the top of the recommendations. The scripts and data to create the recommendation system are available under MIT license at https://github.com/anuprulez/galaxy\_tool\_recommendation.}, author = {Kumar, Anup and Rasche, Helena and Grüning, Björn and Backofen, Rolf}, @@ -11956,9 +12509,9 @@ @article{kumaran_vitro_2022 journal = {Genomics}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {March}, - note = {Publisher: Elsevier BV}, number = {2}, pages = {110266}, + publisher = {Elsevier BV}, title = {In vitro and in silico analysis of {Brilliant} {Black} degradation by {Actinobacteria} and a {Paraburkholderia} sp.}, url = {https://doi.org/10.1016/j.ygeno.2022.01.003}, volume = {114}, @@ -11973,9 +12526,9 @@ @article{kumarhalder_oxa-376_2022 journal = {RSC Advances}, keywords = {{\textgreater}UseGalaxy.eu}, language = {en}, - note = {Publisher: Royal Society of Chemistry}, number = {37}, pages = {24319--24338}, + publisher = {Royal Society of Chemistry}, shorttitle = {Oxa-376 and {Oxa}-530 variants of β-lactamase}, title = {Oxa-376 and {Oxa}-530 variants of β-lactamase: computational study uncovers potential therapeutic targets of {Acinetobacter} baumannii}, url = {https://pubs.rsc.org/en/content/articlelanding/2022/ra/d2ra02939a}, @@ -12030,9 +12583,9 @@ @article{kunz_avirulence_2025 keywords = {{\textgreater}UseGalaxy.eu, Ascomycota, Disease Resistance, Gene sequencing, Genetic loci, Genetic mapping, Genomics, Plant Diseases, Plant pathogens, Powdery mildew, Single nucleotide polymorphisms, Triticum, Wheat}, language = {en}, month = {July}, - note = {Publisher: Public Library of Science}, number = {1}, pages = {e1012799}, + publisher = {Public Library of Science}, shorttitle = {Avirulence depletion assay}, title = {Avirulence depletion assay: {Combining} {R} gene-mediated selection with bulk sequencing for rapid avirulence gene identification in wheat powdery mildew}, url = {https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1012799}, @@ -12136,10 +12689,9 @@ @article{lahm_congenital_2020 keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Genetic Loci, Polymorphism, Single Nucleotide}, language = {en}, month = {November}, - note = {Publisher: American Society for Clinical Investigation}, number = {2}, pages = {141837}, - pmid = {0}, + publisher = {American Society for Clinical Investigation}, title = {Congenital heart disease risk loci identified by genome-wide association study in {European} patients}, url = {https://www.jci.org/articles/view/141837}, urldate = {2021-01-12}, @@ -12150,15 +12702,15 @@ @article{lahm_congenital_2020 @article{lahm_genome-wide_2020, abstract = {{\textless}h3{\textgreater}Abstract{\textless}/h3{\textgreater} {\textless}h3{\textgreater}Rationale{\textless}/h3{\textgreater} {\textless}p{\textgreater}Genetic factors undoubtedly contribute to the development of congenital heart disease (CHD), but still remain mostly ill-defined.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Objective{\textless}/h3{\textgreater} {\textless}p{\textgreater}Identification of genetic risk factors associated with CHD and functional analysis of SNP-carrying genes.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Methods and Results{\textless}/h3{\textgreater} {\textless}p{\textgreater}Genetic association study of 1,440 Caucasian CHD patients from the German Heart Center Munich collected from March 2009 to June 2016, 2,594 patients of previous studies provided by the Newcastle University and 8,486 controls underwent meta-analysis to detect single nucleotide polymorphisms (SNPs) associated with CHD.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Results{\textless}/h3{\textgreater} {\textless}p{\textgreater}4,034 Caucasian CHD patients strictly classified according to the Society of Thoracic Surgeons nomenclature and 8,486 controls were included. One SNP on chromosome 5 reached genome-wide significance across all CHD phenotypes (rs185531658,OR:2.16, \textit{p}=5.28×10$^{\textrm{−9}}$) and was also indicative for septal defects (OR:2.16, \textit{p}=6.15×10$^{\textrm{−8}}$). One region on chromosome 20 pointing to the \textit{MACROD2} locus, identified four SNPs (rs150246290,OR:3.78, \textit{p}=1.27×10$^{\textrm{−10}}$; rs149890280,OR:3.74, \textit{p}=1.8×10$^{\textrm{−10}}$; rs149467721,OR:3.53; \textit{p}=1.39×10$^{\textrm{−9}}$, rs77094733,OR:3.53, \textit{p}=1.73×10$^{\textrm{−9}}$) in patients with transposition of the great arteries (TGA). A second region was detected on chromosome 8 located at \textit{ZBTB10} (rs148563140,OR:3.42, \textit{p}=3.28×10$^{\textrm{−8}}$; rs143638934,OR:3.42, \textit{p}=3.51×10$^{\textrm{−8}}$) in the same subgroup. Three highly significant risk variants on chromosome 17 (rs76774446,OR:1.60, \textit{p}=9.95×10$^{\textrm{−8}}$; rs11874,OR:1.60, \textit{p}=6.64×10$^{\textrm{−8}}$; rs17677363,OR:1.60, \textit{p}=9.81×10$^{\textrm{−8}}$) within the \textit{GOSR2} locus were identified in patients with anomalies of thoracic arteries and veins (ATAV). Genetic variants associated with ATAV are suggested to influence expression of \textit{WNT3}, and variant rs870142 related to septal defects is proposed to influence expression of \textit{MSX1}. Cardiac differentiation of human and murine induced pluripotent stem cells and single cell RNAseq analyses of developing murine and human hearts show essential functional roles for \textit{MACROD2, GOSR2, WNT3} and \textit{MSX1} at all developmental stages.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Conclusions{\textless}/h3{\textgreater} {\textless}p{\textgreater}For the first time genetic risk factors in CHD patients with TGA and ATAV were identified. Several candidate genes play an essential functional role in heart development at the embryonic, newborn and adult stage.{\textless}/p{\textgreater}}, author = {Lahm, Harald and Jia, Meiwen and Dreßen, Martina and Wirth, Felix and Puluca, Nazan and Gilsbach, Ralf and Keavney, Bernard D. and Cleuziou, Julie and Beck, Nicole and Bondareva, Olga and Dzilic, Elda and Burri, Melchior and König, Karl C. and Ziegelmüller, Johannes A. and Abou-Ajram, Claudia and Neb, Irina and Zhang, Zhong and Doppler, Stefanie A. and Mastantuono, Elisa and Lichtner, Peter and Eckstein, Gertrud and Hörer, Jürgen and Ewert, Peter and Priest, James R. and Hein, Lutz and Lange, Rüdiger and Meitinger, Thomas and Cordell, Heather J. and Müller-Myhsok, Bertram and Krane, Markus}, + chapter = {New Results}, copyright = {© 2020, Posted by Cold Spring Harbor Laboratory. The copyright holder for this pre-print is the author. All rights reserved. The material may not be redistributed, re-used or adapted without the author's permission.}, doi = {10.1101/2020.06.19.161067}, journal = {bioRxiv}, keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, language = {en}, month = {June}, - note = {Publisher: Cold Spring Harbor Laboratory -Section: New Results}, pages = {2020.06.19.161067}, + publisher = {Cold Spring Harbor Laboratory}, title = {Genome-wide association study in {European} patients with congenital heart disease identifies risk loci for transposition of the great arteries and anomalies of the thoracic arteries and veins and expression of discovered candidate genes in the developing heart}, url = {https://www.biorxiv.org/content/10.1101/2020.06.19.161067v1}, urldate = {2020-08-18}, @@ -12191,8 +12743,8 @@ @article{lalli_reappraisal_2023 keywords = {{\textgreater}UseGalaxy.eu, Adrenal Cortex Neoplasms, Adrenocortical Carcinoma, Genomics, Nuclear Receptors, Transcriptional regulation, beta-Catenin}, language = {English}, month = {December}, - note = {Publisher: Frontiers}, pages = {1303332}, + publisher = {Frontiers}, title = {A reappraisal of transcriptional regulation by {NR5A1} and beta-catenin in adrenocortical carcinoma}, url = {https://www.frontiersin.org/journals/endocrinology/articles/10.3389/fendo.2023.1303332/full}, urldate = {2024-10-27}, @@ -12239,8 +12791,7 @@ @article{lamas_whole_2023 journal = {Frontiers in Microbiology}, keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, Flongle, MinION, Salmonella spp., Serotyping, antimicrobial resistance, virulence Con formato: Fuente: Cursiva Con formato: Fuente: Cursiva, whole genome sequencing}, language = {en}, - note = {Publisher: Frontiers Media SA}, - pmid = {38107857}, + publisher = {Frontiers Media SA}, shorttitle = {Whole genome sequencing in the palm of your hand}, title = {Whole genome sequencing in the palm of your hand: how to implement a {MinION} {Galaxy}-based workflow in a food safety laboratory for rapid {Salmonella} spp. serotyping, virulence, and antimicrobial resistance gene identification}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10722185/}, @@ -12278,9 +12829,9 @@ @article{lanave_discovery_2025 keywords = {{\textgreater}NanoGalaxy, {\textgreater}UseGalaxy.eu, Pathogens, Virology}, language = {en}, month = {March}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {9650}, + publisher = {Nature Publishing Group}, title = {Discovery of a human parvovirus {B19} analog ({Erythroparvovirus}) in cats}, url = {https://www.nature.com/articles/s41598-025-94123-w}, urldate = {2025-03-29}, @@ -12368,8 +12919,8 @@ @article{lapp_transcriptional_2024 keywords = {{\textgreater}UseGalaxy.eu, Bacterial keratitis, Corneal Ulcer, Eye Infections, Bacterial, Eye Infections, Fungal, FFPE (formalin fixed paraffin embedded), Infectious keratitis, Keratitis, Keratoplasty, RNA sequencing, Viral keratitis, host response, human}, language = {English}, month = {January}, - note = {Publisher: Frontiers}, pages = {1285676}, + publisher = {Frontiers}, title = {Transcriptional profiling specifies the pathogen-specific human host response to infectious keratitis}, url = {https://www.frontiersin.org/articles/10.3389/fcimb.2023.1285676}, urldate = {2024-05-17}, @@ -12397,8 +12948,8 @@ @article{lariviere_scalable_2024 keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au, Computational Biology, Computational platforms and environments, Genome assembly algorithms, Software}, language = {en}, month = {January}, - note = {Publisher: Nature Publishing Group}, pages = {1--4}, + publisher = {Nature Publishing Group}, title = {Scalable, accessible and reproducible reference genome assembly and evaluation in {Galaxy}}, url = {https://www.nature.com/articles/s41587-023-02100-3}, urldate = {2024-01-26}, @@ -12449,9 +13000,9 @@ @article{lasolle_dual_2024 keywords = {{\textgreater}UseGalaxy.eu, Cancer models, Phenotypic screening, Proto-Oncogene Proteins B-raf, Thyroid Neoplasms}, language = {en}, month = {January}, - note = {Publisher: Nature Publishing Group}, number = {3}, pages = {155--170}, + publisher = {Nature Publishing Group}, title = {Dual targeting of {MAPK} and {PI3K} pathways unlocks redifferentiation of {Braf}-mutated thyroid cancer organoids}, url = {https://www.nature.com/articles/s41388-023-02889-y}, urldate = {2024-05-17}, @@ -12467,7 +13018,7 @@ @article{lastic_entropic_2020 keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, language = {en}, month = {September}, - note = {Publisher: Preprints}, + publisher = {Preprints}, shorttitle = {Entropic {Ranks}}, title = {Entropic {Ranks}: {A} {Methodology} for {Enhanced}, {Threshold}-{Free}, {Information}-{Rich} {Data} {Partition} and {Interpretation}}, url = {https://www.preprints.org/manuscript/202009.0424/v1}, @@ -12475,12 +13026,33 @@ @article{lastic_entropic_2020 year = {2020} } +@article{lata_surveillance_2025, + abstract = {Antimicrobial resistance (AMR) is a growing concern in human and veterinary medicine. Misuse and overuse of antimicrobials in human medicine, veterinary medicine, agriculture, and aquaculture are major drivers of AMR development, with resistant bacteria also being selected in livestock and transmitted through meat. Research on AMR in livestock and animal-derived foods is lacking in Fiji; thus, the associated risks remain unclear. Chicken is widely consumed in Fiji and is predominantly served frozen. This study is aimed at determining the prevalence and resistance profiles of Escherichia coli in frozen chicken meat from Fijian supermarkets. A total of 100 frozen chicken meat samples were purchased from supermarkets and retail outlets in Fiji for this study. E. coli was isolated from 72\% of the samples. The E. coli isolates showed relatively high levels of resistance to ampicillin (36\%), tetracycline (24\%), and streptomycin (17\%). Only one cefotaxime-resistant isolate was obtained, which was identified as an extended-spectrum β-lactamase (ESBL)–producing bacterium. This isolate harbored the ESBL-producing gene blaCTX-M-1 and was classified as ST2522. One colistin-resistant isolate was obtained, and its resistance was attributed to a chromosomal mutation in the pmrB gene. The high level of intestinal bacterial contamination in frozen chicken meat suggests that improved hygiene management is necessary throughout the production and distribution chains. Furthermore, because resistance to antimicrobials is important in both human and veterinary medicine (cefotaxime- and colistin-resistant E. coli), careful monitoring of AMR trends in Fiji is essential. These results suggest that AMR surveillance in meat and livestock is necessary to prevent its spread in Fiji.}, + author = {Lata, Deepika Darshani and Sabala, Rana Fahmi and Fukuda, Akira and Nakajima, Chie and Suzuki, Yasuhiko and Usui, Masaru}, + copyright = {Copyright © 2025 Deepika Darshani Lata et al. International Journal of Food Science published by John Wiley \& Sons Ltd.}, + doi = {10.1155/ijfo/5487064}, + issn = {2314-5765}, + journal = {International Journal of Food Science}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1155/ijfo/5487064}, + number = {1}, + pages = {5487064}, + shorttitle = {Surveillance of {Escherichia} coli {From} {Frozen} {Chicken} {Meat} in {Fiji}}, + title = {Surveillance of {Escherichia} coli {From} {Frozen} {Chicken} {Meat} in {Fiji}: {Resistance} {Characteristics} and {Public} {Health} {Concerns}}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1155/ijfo/5487064}, + urldate = {2025-12-26}, + volume = {2025}, + year = {2025} +} + @article{latif_nfatc1_2022, abstract = {Objectives Non-alcoholic fatty liver disease (NAFLD) can persist in the stage of simple hepatic steatosis or progress to steatohepatitis (NASH) with an increased risk for cirrhosis and cancer. We examined the mechanisms controlling the progression to severe NASH in order to develop future treatment strategies for this disease. Design NFATc1 activation and regulation was examined in livers from patients with NAFLD, cultured and primary hepatocytes and in transgenic mice with differential hepatocyte-specific expression of the transcription factor (Alb-cre, NFATc1c.a. and NFATc1Δ/Δ). Animals were fed with high-fat western diet (WD) alone or in combination with tauroursodeoxycholic acid (TUDCA), a candidate drug for NAFLD treatment. NFATc1-dependent ER stress-responses, NLRP3 inflammasome activation and disease progression were assessed both in vitro and in vivo. Results NFATc1 expression was weak in healthy livers but strongly induced in advanced NAFLD stages, where it correlates with liver enzyme values as well as hepatic inflammation and fibrosis. Moreover, high-fat WD increased NFATc1 expression, nuclear localisation and activation to promote NAFLD progression, whereas hepatocyte-specific depletion of the transcription factor can prevent mice from disease acceleration. Mechanistically, NFATc1 drives liver cell damage and inflammation through ER stress sensing and activation of the PERK-CHOP unfolded protein response (UPR). Finally, NFATc1-induced disease progression towards NASH can be blocked by TUDCA administration. Conclusion NFATc1 stimulates NAFLD progression through chronic ER stress sensing and subsequent activation of terminal UPR signalling in hepatocytes. Interfering with ER stress-responses, for example, by TUDCA, protects fatty livers from progression towards manifest NASH.}, author = {Latif, Muhammad Umair and Schmidt, Geske Elisabeth and Mercan, Sercan and Rahman, Raza and Gibhardt, Christine Silvia and Stejerean-Todoran, Ioana and Reutlinger, Kristina and Hessmann, Elisabeth and Singh, Shiv K. and Moeed, Abdul and Rehman, Abdul and Butt, Umer Javed and Bohnenberger, Hanibal and Stroebel, Philipp and Bremer, Sebastian Christopher and Neesse, Albrecht and Bogeski, Ivan and Ellenrieder, Volker}, + chapter = {Hepatology}, copyright = {© Author(s) (or their employer(s)) 2022. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.. http://creativecommons.org/licenses/by-nc/4.0/This is an open access article distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited, appropriate credit is given, any changes made indicated, and the use is non-commercial. See: http://creativecommons.org/licenses/by-nc/4.0/.}, doi = {10.1136/gutjnl-2021-325013}, issn = {0017-5749, 1468-3288}, @@ -12488,11 +13060,9 @@ @article{latif_nfatc1_2022 keywords = {{\textgreater}UseGalaxy.eu, Non-alcoholic Fatty Liver Disease, fatty liver, hepatic fibrosis, inflammation, nonalcoholic steatohepatitis}, language = {en}, month = {March}, - note = {Publisher: BMJ Publishing Group -Section: Hepatology}, number = {12}, pages = {2561--2573}, - pmid = {35365570}, + publisher = {BMJ Publishing Group}, title = {{NFATc1} signaling drives chronic {ER} stress responses to promote {NAFLD} progression}, url = {https://gut.bmj.com/content/early/2022/03/31/gutjnl-2021-325013}, urldate = {2022-09-24}, @@ -12500,15 +13070,32 @@ @article{latif_nfatc1_2022 year = {2022} } +@article{laugero_lncrna_2025, + abstract = {Lymphedema is a lymphatic dysfunction leading to an accumulation of fluid and fat in the arm or leg. Here, we performed noncoding RNA profiling of human breast cancer–induced secondary lymphedema. We identified the long intergenic non–protein coding RNA, P53-induced transcript (LINC-PINT), as essential for the lymphedema development. LINC-PINT is the most expressed lncRNA in human lymphatic endothelial cells (LECs) under stress condition. Knocking down LINC-PINT in LECs promotes the expression of inflammation-related genes. Mechanistically, ATAC-seq revealed that LINC-PINT induces the transcription of genes involved in lymphangiogenesis and immune cell adhesion by increasing chromatin accessibility. Notably, LINC-PINT deficiency impairs LEC proliferation, migration, and sprouting. Conditional deletion of Lnc-Pint in mouse lymphatic endothelium (Lnc-Pintlecko) leads to a reduction in dermal lymphatic network density. Lnc-Pintlecko mice exhibit decreased lymphedema, reduced dermal backflow, fibrosis, and inflammation. Our findings unveil a crucial molecular role of LINC-PINT in lymphatic function and hold substantial clinical implications for lncRNA as biomarker of lymphedema.}, + author = {Laugero, Nathalie and Peghaire, Claire and Verdu, Léna and Balzan, Elisa and Draia-Nicolau, Tangra and Sylvestre, Roxane and Malloizel-Delaunay, Julie and Bura-Rivière, Alessandra and Morfoisse, Florent and Prats, Anne-Catherine and Lacazette, Eric and Garmy-Susini, Barbara}, + doi = {10.1126/sciadv.aea2960}, + journal = {Science Advances}, + keywords = {{\textgreater}UseGalaxy.eu, Animals, Cell Movement, Cell Proliferation, Disease Models, Animal, Endothelial Cells, Female, Humans, Inflammation, Lymphangiogenesis, Lymphatic Vessels, Lymphedema, Mice, RNA, Long Noncoding}, + month = {December}, + number = {51}, + pages = {eaea2960}, + publisher = {American Association for the Advancement of Science}, + title = {{lncRNA} {LINC}-{PINT} controls lymphatic function and inflammatory profile in lymphedema}, + url = {https://www.science.org/doi/10.1126/sciadv.aea2960}, + urldate = {2025-12-26}, + volume = {11}, + year = {2025} +} + @article{laurette_vivo_2024, author = {Laurette, P. and Cao, C. and Ramanujam, D. and Schwaderer, M. and Lueneburg, T. and Kuss, S. and Weiss, L. and Dilshat, R. and Furlong, E.E.M. and Rezende, F. and Engelhardt, S. and Gilsbach, R.}, doi = {10.1161/CIRCRESAHA.123.323854}, journal = {Circulation Research}, keywords = {{\textgreater}UseGalaxy.eu}, month = {January}, - note = {Publisher: American Heart Association}, number = {2}, pages = {223--225}, + publisher = {American Heart Association}, title = {In {Vivo} {Silencing} of {Regulatory} {Elements} {Using} a {Single} {AAV}-{CRISPRi} {Vector}}, url = {https://www.ahajournals.org/doi/full/10.1161/CIRCRESAHA.123.323854}, urldate = {2024-07-09}, @@ -12526,10 +13113,10 @@ @article{le_corre_mechanism-based_2023 keywords = {{\textgreater}UseGalaxy.eu, Biochemistry, Chem-informatics, Enzyme mechanisms, Enzymes, Mechanism of action, Small molecules, chemicaltoolbox}, language = {en}, month = {May}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {7287}, + publisher = {Nature Publishing Group}, shorttitle = {Mechanism-based and computational modeling of hydrogen sulfide biogenesis inhibition}, title = {Mechanism-based and computational modeling of hydrogen sulfide biogenesis inhibition: interfacial inhibition}, url = {https://www.nature.com/articles/s41598-023-34405-3}, @@ -12569,10 +13156,10 @@ @article{lee_genomic_2022 keywords = {{\textgreater}UseGalaxy.eu, COVID-19, Infectious diseases, SARS-CoV-2, Viral epidemiology, Virology}, language = {en}, month = {December}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {22414}, + publisher = {Nature Publishing Group}, title = {Genomic epidemiology of {SARS}- {CoV}-2 {Omicron} variants in the {Republic} of {Korea}}, url = {https://www.nature.com/articles/s41598-022-26803-w}, urldate = {2023-08-06}, @@ -12703,6 +13290,7 @@ @article{lenz_amyloid_2023 abstract = {The perforant path provides the primary cortical excitatory input to the hippocampus. Because of its important role in information processing and coding, entorhinal projections to the dentate gyrus have been studied in considerable detail. Nevertheless, synaptic transmission between individual connected pairs of entorhinal stellate cells and dentate granule cells remains to be characterized. Here, we have used mouse organotypic entorhino-hippocampal tissue cultures of either sex, in which the entorhinal cortex (EC) to dentate granule cell (GC; EC–GC) projection is present, and EC–GC pairs can be studied using whole-cell patch-clamp recordings. By using cultures of wild-type mice, the properties of EC–GC synapses formed by afferents from the lateral and medial entorhinal cortex were compared, and differences in short-term plasticity were identified. As the perforant path is severely affected in Alzheimer's disease, we used tissue cultures of amyloid precursor protein (APP)–deficient mice to examine the role of APP at this synapse. APP deficiency altered excitatory neurotransmission at medial perforant path synapses, which was accompanied by transcriptomic and ultrastructural changes. Moreover, presynaptic but not postsynaptic APP deletion through the local injection of Cre-expressing adeno-associated viruses in conditional APPflox/flox tissue cultures increased the neurotransmission efficacy at perforant path synapses. In summary, these data suggest a physiological role for presynaptic APP at medial perforant path synapses that may be adversely affected under altered APP processing conditions. SIGNIFICANCE STATEMENT The hippocampus receives input from the entorhinal cortex via the perforant path. These projections to hippocampal dentate granule cells are of utmost importance for learning and memory formation. Although there is detailed knowledge about perforant path projections, the functional synaptic properties at the level of individual connected pairs of neurons are not well understood. In this study, we investigated the role of APP in mediating functional properties and transmission rules in individually connected neurons using paired whole-cell patch-clamp recordings and genetic tools in organotypic tissue cultures. Our results show that presynaptic APP expression limits excitatory neurotransmission via the perforant path, which could be compromised in pathologic conditions such as Alzheimer's disease.}, author = {Lenz, Maximilian and Eichler, Amelie and Kruse, Pia and Galanis, Christos and Kleidonas, Dimitrios and Andrieux, Geoffroy and Boerries, Melanie and Jedlicka, Peter and Müller, Ulrike and Deller, Thomas and Vlachos, Andreas}, + chapter = {Research Articles}, copyright = {Copyright © 2023 the authors. SfN exclusive license.}, doi = {10.1523/JNEUROSCI.1824-22.2023}, issn = {0270-6474, 1529-2401}, @@ -12710,11 +13298,9 @@ @article{lenz_amyloid_2023 keywords = {{\textgreater}UseGalaxy.eu, Alzheimer Disease, Perforant Pathway, amyloid precursor protein, dentate gyrus, entorhinal cortex, hilar mossy cell, perforant path, stellate cells}, language = {en}, month = {July}, - note = {Publisher: Society for Neuroscience -Section: Research Articles}, number = {29}, pages = {5290--5304}, - pmid = {37369586}, + publisher = {Society for Neuroscience}, title = {The {Amyloid} {Precursor} {Protein} {Regulates} {Synaptic} {Transmission} at {Medial} {Perforant} {Path} {Synapses}}, url = {https://www.jneurosci.org/content/43/29/5290}, urldate = {2023-07-31}, @@ -12729,8 +13315,7 @@ @article{lenz_denervated_2023 journal = {Frontiers in Molecular Neuroscience}, keywords = {{\textgreater}UseGalaxy.eu, Microglia, RNA oxidation, Schaffer collateral lesion, entorhinal cortex lesion, transcriptome analysis}, language = {en}, - note = {Publisher: Frontiers Media SA}, - pmid = {37122623}, + publisher = {Frontiers Media SA}, title = {Denervated mouse {CA1} pyramidal neurons express homeostatic synaptic plasticity following entorhinal cortex lesion}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10130538/}, urldate = {2023-06-05}, @@ -12738,6 +13323,25 @@ @article{lenz_denervated_2023 year = {2023} } +@article{lenz_hangover_2025, + abstract = {The RNA-binding protein Hangover (Hang) is essential for several stress responses in Drosophila melanogaster. Here, we discover a novel function of Hang in the regulation of gene expression. Hang binds to {\textgreater}2000 genes in the Drosophila genome and modulates transcription. We identify a diverse set of chromatin regulators as Hang interactors, including NSL, dMec, Sin3A, dREAM, and Ino80. Among these, the non-specific lethal complex (NSL) is the most prominent one. We show that Hang attenuates NSL-mediated H4K16 acetylation at transcriptional start sites to downregulate gene expression. Our work uncovers novel roles for Hang in epigenetic gene regulation and suggests that it coordinates the function of multiple chromatin regulators.}, + author = {Lenz, Jonathan and Schmelzer, Laura and Forné, Ignasi and Nist, Andrea and Imhof, Axel and Stiewe, Thorsten and Brehm, Alexander}, + copyright = {cc by-nc}, + doi = {10.1093/nar/gkaf1349}, + issn = {1362-4962}, + journal = {Nucleic acids research}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {November}, + number = {22}, + pages = {gkaf1349}, + title = {Hangover regulates gene expression by limiting {NSL}-mediated {H4K16} acetylation}, + url = {https://europepmc.org/articles/PMC12709178}, + urldate = {2025-12-26}, + volume = {53}, + year = {2025} +} + @misc{lenz_hangover_2025, abstract = {The RNA-binding protein hangover is essential for several stress responses in Drosophila melanogaster. Here, we discover a novel function of hangover in the regulation of gene expression. Hangover binds to more than 2.000 genes in the Drosophila genome and modulates transcription. We identify a diverse set of chromatin regulators as hangover interactors, including NSL, dMec, Sin3A, dREAM and Ino80. Among these, the non-specific lethal complex (NSL) is the most prominent one. We show that hangover attenuates NSL-mediated H4K16 acetylation at transcriptional start sites to downregulate gene expression. Our work uncovers novel roles for hangover in epigenetic gene regulation and suggests that it coordinates the function of multiple chromatin regulators. @@ -12799,7 +13403,7 @@ @article{lestin_modulation_2025 doi = {10.7717/peerj.20129}, issn = {2167-8359}, journal = {PeerJ}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Biofilm, Carbon-to-nitrogen Ratio, Denitrification, Marine, Methanol, Methylophaga, Methylotrophs, Nitrate}, pages = {e20129}, title = {Modulation of carbon-to-nitrogen ratio shapes the microbial ecology in a methanol-fed recirculating marine denitrifying reactor}, url = {https://europepmc.org/articles/PMC12530212}, @@ -12813,9 +13417,9 @@ @article{levi_genome-wide_2025 journal = {mBio}, keywords = {{\textgreater}UseGalaxy.eu}, month = {August}, - note = {Publisher: American Society for Microbiology}, number = {0}, pages = {e01909--25}, + publisher = {American Society for Microbiology}, title = {Genome-wide {CRISPRi} screen and proteomic profiling identify key genes related to ferulic acid’s antifungal activity}, url = {https://journals.asm.org/doi/full/10.1128/mbio.01909-25}, urldate = {2025-09-12}, @@ -12826,6 +13430,7 @@ @article{levi_genome-wide_2025 @article{lezameta_draft_2020, abstract = {Providencia stuartii is an opportunistic pathogen of the Enterobacteriales order. Here, we report the 4,594,658-bp draft genome sequence of a New Delhi metallo-β-lactamase (NDM-1)-producing Providencia stuartii strain that was isolated from an emergency patient in a private clinic in Lima, Peru.}, author = {Lezameta, Lizet and Cuicapuza, Diego and Dávila-Barclay, Alejandra and Torres, Susan and Salvatierra, Guillermo and Tsukayama, Pablo and Tamariz, Jesús}, + chapter = {Genome Sequences}, copyright = {Copyright © 2020 Lezameta et al.. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.}, doi = {10.1128/MRA.00788-20}, issn = {2576-098X}, @@ -12833,11 +13438,9 @@ @article{lezameta_draft_2020 keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, language = {en}, month = {September}, - note = {Publisher: American Society for Microbiology -Section: Genome Sequences}, number = {39}, pages = {e00788--20}, - pmid = {32972938}, + publisher = {American Society for Microbiology}, title = {Draft {Genome} {Sequence} of a {New} {Delhi} {Metallo}-β-{Lactamase} ({NDM}-1)-{Producing} {Providencia} stuartii {Strain} {Isolated} in {Lima}, {Peru}}, url = {https://mra.asm.org/content/9/39/e00788-20}, urldate = {2021-02-08}, @@ -12845,6 +13448,23 @@ @article{lezameta_draft_2020 year = {2020} } +@article{lheraud_identification_2025, + abstract = {Sex-determining genes remain largely uncharacterized outside classical models in vertebrates and insects, leaving a gap in our understanding of their evolutionary emergence. The terrestrial isopod Armadillidium vulgare provides an excellent model for investigating this question, as it presents multiple genetic sex determinants. Some lineages possess a masculinizing dominant allele at a locus called the ‘M gene’, which is analogous to an XY system. This allele is hypothesized to have been selected due to the deficit of males caused by a non-Mendelian feminizing factor previously described. The existence of the M gene was inferred from crosses carried out in the 1990s, but its molecular nature remains unresolved. Here, we conducted a genome-wide single-nucleotide polymorphisms analysis combining pooled sequencing of male and female progenies with sequencing of individual parents across two families. Bayesian estimation of haplotype frequencies in progenies pinpointed a candidate genomic region of approximately two megabases. Notably, this region contains the gene encoding the androgenic gland hormone, a protein involved in male sexual differentiation. Our findings lay the groundwork for functional investigations of the M gene, offering novel insights into the dynamics of sex determination in terrestrial isopods and into the turnover of sex chromosomes in response to sex-ratio distortion.}, + author = {Lhéraud, Baptiste and Dussert, Yann and Chebbi, Mohamed Amine and Giraud, Isabelle and Cordaux, Richard and Peccoud, Jean}, + doi = {10.1098/rsbl.2025.0287}, + issn = {1744-9561}, + journal = {Biology Letters}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {October}, + number = {10}, + pages = {20250287}, + title = {Identification of a sex-determining region potentially involved in resolving genetic conflicts over sex ratio}, + url = {https://doi.org/10.1098/rsbl.2025.0287}, + urldate = {2025-12-22}, + volume = {21}, + year = {2025} +} + @article{li_functional_2025, abstract = {Camptothecin (CAM), a well-known plant-derived antitumor compound, is a structurally complex pentacyclic pyrroloquinoline monoterpene indole alkaloid (MIA) found in various plant species. As a specific MIA, CAM had been thought to share a common upstream biosynthetic pathway with other MIAs such as the antitumor vinblastine and vincristine from Catharanthus roseus. Nevertheless the key enzymes responsible for the consecutive three-step oxidation of the –CH3 of nepetalactol to form the –COOH of 7-deoxyloganetic acid and the subsequent glycosylation of 7-deoxyloganetic acid to yield 7-deoxyloganic acid have yet to be functionally characterized. Here we established an in vivo tandem catalysis assay for the enzymatic catalytic activity characterization of 7-deoxyloganetic acid synthase (7DLS) and 7-deoxyloganetic acid glucosyltransferase (7DLGT), two crucial catalytic enzymes in MIAs biosynthesis, thereby avoiding the difficulty in the detection of the unstable biosynthetic intermediates. The enzyme activity assay platform was conducted through the co-expression of functionally characterized Cr7DLS and Cr7DLGT in Saccharomyces cerevisiae WAT11, substrate feeding, and enzymatic product verification. Two cytochrome P450 enzymes (CYPs) from Camptotheca acuminata, the prestigious resource for CAM, CaCYP76A75 and CaCYP76A76, were identified and functionally characterized to be responsible for the consecutive three-step oxidation of nepetalactol to yield 7-deoxyloganetic acid through reciprocal replacement of Cr7DLS in the in vivo tandem enzyme activity assay platform. Two uridine 5′-diphosphate glycosyltransferases (UGTs), CaUGT709C10 and CaUGT709C11, were functionally characterized to be capable of glycosylating 7-deoxyloganetic acid to yield 7-deoxyloganic acid. This study provides two CYPs as 7DLSs and two UGTs as 7DLGTs, offering potential applications in MIAs biosynthesis.}, author = {Li, Yi and Wang, Xuefei and Jiang, Honglan and Xu, Shuangyu and Xu, Ying and Liu, Zhan and Luo, Yinggang}, @@ -12866,15 +13486,35 @@ @article{li_mitochondrial_2021 doi = {10.3920/jiff2020.0054}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {March}, - note = {Publisher: Wageningen Academic Publishers}, number = {2}, pages = {233--243}, + publisher = {Wageningen Academic Publishers}, title = {The mitochondrial genome of {Qinghuang}\_1, the first modern improved strain of {Chinese} oak silkworm, {Antheraea} pernyi ({Lepidoptera}: {Saturniidae})}, url = {https://doi.org/10.3920/jiff2020.0054}, volume = {7}, year = {2021} } +@article{li_new_2025, + abstract = {Macellicephaloides Uschakov, 1955 (Annelida: Polynoidae) is a genus of deep-sea polychaetes characterized by a specialized pharynx bearing two pairs of jaws (with the dorsal pair fused) and three pairs of lateral papillae, the middle pair of which is greatly elongated, and remarkable adaptability to diverse deep-sea habitats. Most species in this genus inhabit abyssal depths ({\textgreater}7200 m), with high diversity in western Pacific trenches, while a few occur in relatively shallow habitats such as deep-sea seamounts and hydrothermal vents. This paper presents a new species, Macellicephaloides lingshuiensis sp. nov., found in deep-sea cold seeps in the South China Sea, representing the shallowest distribution record for the genus to date and the first record from cold seep environments. The classification and phylogeny of Macellicephaloides and related genera have long been the subject of debate. A previous study suggested that Macellicephaloides is nested within the Macellicephala clade, but our analyses-based on 13 mitochondrial protein-coding genes, 12S, 16S, 18S, 28S rRNA, and ITS1-ITS2 sequences-tentatively indicate that these two genera form independent evolutionary clades. Additionally, our phylogeny indicates a close evolutionary relationship between deep-sea Macellicephaloides and cave-dwelling polynoids (e.g., Gesiella), highlighting ecological connections between deep-sea and cave habitats. These conclusions are supported by morphological comparisons and genetic distance analyses. Although the subfamily Macellicephalinae is recovered as a monophyletic group, intergeneric phylogenetic relationships within it remain unresolved, highlighting the need for additional data from more species and genera. We amend the generic diagnosis of Macellicephaloides and provide an identification key to all valid species in the genus. This study clarifies the taxonomy and phylogeny of Macellicephaloides and related taxa, emphasizing the importance of continued sampling in understudied deep-sea habitats to enhance our understanding of their biodiversity.}, + author = {Li, Jie and Zhang, Linlin and Wang, Mingxiao and Wu, Xuwen}, + copyright = {cc by}, + doi = {10.3390/cimb47110897}, + issn = {1467-3045}, + journal = {Current issues in molecular biology}, + keywords = {{\textgreater}UseGalaxy.eu, Chemosynthetic Environment, Deep-sea, Morphology, Polychaetes, Systematics}, + language = {eng}, + month = {October}, + number = {11}, + pages = {897}, + shorttitle = {A {New} {Species} of \<i\>{Macellicephaloides}\</i\> {Uschakov}, 1955 ({Annelida}, {Polynoidae}) from {Cold} {Seeps} in the {South} {China} {Sea}}, + title = {A {New} {Species} of \<i\>{Macellicephaloides}\</i\> {Uschakov}, 1955 ({Annelida}, {Polynoidae}) from {Cold} {Seeps} in the {South} {China} {Sea}: {Insights} into the {Taxonomy} and {Phylogeny} of \<i\>{Macellicephaloides}\</i\> and {Related} {Genera}}, + url = {https://europepmc.org/articles/PMC12651276}, + urldate = {2025-12-26}, + volume = {47}, + year = {2025} +} + @article{li_proteogenomic_2023, author = {Li, Yize and Dou, Yongchao and Leprevost, Felipe Da Veiga and Geffen, Yifat and Calinawan, Anna P. and Aguet, François and Akiyama, Yo and Anand, Shankara and Birger, Chet and Cao, Song and Chaudhary, Rekha and Chilappagari, Padmini and Cieslik, Marcin and Colaprico, Antonio and Zhou, Daniel Cui and Day, Corbin and Domagalski, Marcin J. and Selvan, Myvizhi Esai and Fenyö, David and Foltz, Steven M. and Francis, Alicia and Gonzalez-Robles, Tania and Gümüş, Zeynep H. and Heiman, David and Holck, Michael and Hong, Runyu and Hu, Yingwei and Jaehnig, Eric J. and Ji, Jiayi and Jiang, Wen and Katsnelson, Lizabeth and Ketchum, Karen A. and Klein, Robert J. and Lei, Jonathan T. and Liang, Wen-Wei and Liao, Yuxing and Lindgren, Caleb M. and Ma, Weiping and Ma, Lei and MacCoss, Michael J. and Rodrigues, Fernanda Martins and McKerrow, Wilson and Nguyen, Ngoc and Oldroyd, Robert and Pilozzi, Alexander and Pugliese, Pietro and Reva, Boris and Rudnick, Paul and Ruggles, Kelly V. and Rykunov, Dmitry and Savage, Sara R. and Schnaubelt, Michael and Schraink, Tobias and Shi, Zhiao and Singhal, Deepak and Song, Xiaoyu and Storrs, Erik and Terekhanova, Nadezhda V. and Thangudu, Ratna R. and Thiagarajan, Mathangi and Wang, Liang-Bo and Wang, Joshua M. and Wang, Ying and Wen, Bo and Wu, Yige and Wyczalkowski, Matthew A. and Xin, Yi and Yao, Lijun and Yi, Xinpei and Zhang, Hui and Zhang, Qing and Zuhl, Maya and Getz, Gad and Ding, Li and Nesvizhskii, Alexey I. and Wang, Pei and Robles, Ana I. and Zhang, Bing and Payne, Samuel H. and Lazar, Alexander J. and Paulovich, Amanda G. and Colaprico, Antonio and Iavarone, Antonio and Chinnaiyan, Arul M. and Druker, Brian J. and Kumar-Sinha, Chandan and Newton, Chelsea J. and Huang, Chen and Mani, D. R. and Smith, Richard D. and Huntsman, Emily and Schadt, Eric E. and An, Eunkyung and Petralia, Francesca and Hostetter, Galen and Omenn, Gilbert S. and Cho, Hanbyul and Rodriguez, Henry and Zhang, Hui and Kolodziejczak, Iga and Johnson, Jared L. and Bavarva, Jasmin and Tan, Jimin and Rodland, Karin D. and Clauser, Karl R. and Krug, Karsten and Cantley, Lewis C. and Wiznerowicz, Maciej and Ellis, Matthew J. and Anurag, Meenakshi and Mesri, Mehdi and Gillette, Michael A. and Birrer, Michael J. and Ceccarelli, Michele and Dhanasekaran, Saravana M. and Edwards, Nathan and Tignor, Nicole and Babur, Özgün and Pugliese, Pietro and Gosline, Sara J. C. and Jewell, Scott D. and Satpathy, Shankha and Chowdhury, Shrabanti and Schürer, Stephan and Carr, Steven A. and Liu, Tao and Hiltke, Tara and Yaron, Tomer M. and Stathias, Vasileios and Liu, Wenke and Zhang, Xu and Song, Yizhe and Zhang, Zhen and Chan, Daniel W.}, doi = {10.1016/j.ccell.2023.06.009}, @@ -12883,10 +13523,9 @@ @article{li_proteogenomic_2023 keywords = {{\textgreater}UseGalaxy.eu, CPTAC, data harmonization, multi-omics, open data, pan-cancer, proteogenomics}, language = {English}, month = {August}, - note = {Publisher: Elsevier}, number = {8}, pages = {1397--1406}, - pmid = {37582339}, + publisher = {Elsevier}, title = {Proteogenomic data and resources for pan-cancer analysis}, url = {https://www.cell.com/cancer-cell/abstract/S1535-6108(23)00219-2}, urldate = {2023-12-03}, @@ -12904,9 +13543,9 @@ @article{li_stram_2025 keywords = {{\textgreater}UseGalaxy.eu, Cancer genomics, Personalized medicine}, language = {en}, month = {August}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {1232}, + publisher = {Nature Publishing Group}, shorttitle = {{STRaM}}, title = {{STRaM}: {A} genetic framework for improved cell product provenance for research and clinical translations}, url = {https://www.nature.com/articles/s42003-025-08547-1}, @@ -12956,10 +13595,9 @@ @article{liang_pickle-mediated_2024 keywords = {{\textgreater}UseGalaxy.eu, Arabidopsis, H3K27me3 spreading, LEC2, PICKLE, Polycomb silencing memory, chromatin remodeling, differentiation, nucleosome condensing, seed germination}, language = {English}, month = {September}, - note = {Publisher: Elsevier}, number = {18}, pages = {3438--3454.e8}, - pmid = {39232583}, + publisher = {Elsevier}, title = {{PICKLE}-mediated nucleosome condensing drives {H3K27me3} spreading for the inheritance of {Polycomb} memory during differentiation}, url = {https://www.cell.com/molecular-cell/abstract/S1097-2765(24)00692-0}, urldate = {2024-10-20}, @@ -13044,9 +13682,9 @@ @article{lin_integrative_2025 keywords = {{\textgreater}UseGalaxy.eu}, language = {en}, month = {February}, - note = {Publisher: CSIRO PUBLISHING}, number = {2}, pages = {NULL--NULL}, + publisher = {CSIRO PUBLISHING}, title = {Integrative morphological, mitogenomic and phylogenetic analyses reveal new vent-dwelling scallop species}, url = {https://www.publish.csiro.au/is/IS24091}, urldate = {2025-02-16}, @@ -13143,11 +13781,10 @@ @article{liu_complete_2025 journal = {Mitochondrial DNA Part B}, keywords = {{\textgreater}UseGalaxy.eu, Crocidura rapax, mitogenome, phylogenetic trees}, month = {April}, - note = {Publisher: Taylor \& Francis -\_eprint: https://doi.org/10.1080/23802359.2025.2475839}, + note = {\_eprint: https://doi.org/10.1080/23802359.2025.2475839}, number = {4}, pages = {288--291}, - pmid = {40084134}, + publisher = {Taylor \& Francis}, title = {The complete mitochondrial genome of {Crocidura} rapax {Allen}, 1923 and its phylogenetic analyses}, url = {https://doi.org/10.1080/23802359.2025.2475839}, urldate = {2025-03-29}, @@ -13209,9 +13846,9 @@ @article{livingstone_novo_2023 journal = {Microbiology Resource Announcements}, keywords = {{\textgreater}UseGalaxy.eu}, month = {April}, - note = {Publisher: American Society for Microbiology}, number = {5}, pages = {e00098--23}, + publisher = {American Society for Microbiology}, shorttitle = {De {Novo} {Whole}-{Genome} {Sequencing} of {Two} {Pathogenic} {Pasteurella} multocida {Type} {D}}, title = {De {Novo} {Whole}-{Genome} {Sequencing} of {Two} {Pathogenic} {Pasteurella} multocida {Type} {D}:6 {Strains} {Isolated} from {Pigs}}, url = {https://journals.asm.org/doi/full/10.1128/mra.00098-23}, @@ -13228,9 +13865,8 @@ @article{loach_galaxy_2025 keywords = {{\textgreater}UseGalaxy.eu, Galaxy platform, RDM, data life cycle, global collaboration, multiomics, open-source software, reproducibility, research data management, single-cell, spatial, training resources}, language = {English}, month = {September}, - note = {Publisher: Elsevier}, number = {0}, - pmid = {40997812}, + publisher = {Elsevier}, shorttitle = {Galaxy single-cell \& spatial omics community update}, title = {Galaxy single-cell \& spatial omics community update: {Navigating} new frontiers in 2025}, url = {https://www.cell.com/cell-genomics/abstract/S2666-979X(25)00261-7}, @@ -13397,9 +14033,8 @@ @article{lother_diabetes_2020 keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, language = {English}, month = {November}, - note = {Publisher: Elsevier}, number = {0}, - pmid = {33197445}, + publisher = {Elsevier}, title = {Diabetes changes gene expression but not {DNA} methylation in cardiac cells}, url = {https://www.jmmc-online.com/article/S0022-2828(20)30327-8/abstract}, urldate = {2020-11-23}, @@ -13458,7 +14093,7 @@ @aglucaci/rascl doi = {10.1101/2022.01.15.476448}, journal = {bioRxiv}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, - note = {Publisher: Cold Spring Harbor Laboratory}, + publisher = {Cold Spring Harbor Laboratory}, title = {{RASCL}: {Rapid} {Assessment} {Of} {SARS}-{CoV}-2 {Clades} {Through} {Molecular} {Sequence} {Analysis}}, url = {http://europepmc.org/abstract/PPR/PPR443709}, year = {2022} @@ -13473,8 +14108,8 @@ @article{luenstedt_partial_2024 keywords = {{\textgreater}UseGalaxy.eu, Colorectal Neoplasms, Hepatectomy, Liver Neoplasms, Partial hepatectomy, Tight Junctions, colorectal cancer, liver metastasis, premetastatic niche}, language = {English}, month = {June}, - note = {Publisher: Frontiers}, pages = {1388272}, + publisher = {Frontiers}, title = {Partial hepatectomy accelerates colorectal metastasis by priming an inflammatory premetastatic niche in the liver}, url = {https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2024.1388272/full}, urldate = {2024-06-17}, @@ -13510,10 +14145,10 @@ @article{luo_comparative_2025 keywords = {{\textgreater}UseGalaxy.eu, Genome, Mitochondrial, Phylogeny, mitogenome, phylogenetic analysis, stick insects}, language = {en}, month = {May}, - note = {Number: 5 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 5}, number = {5}, pages = {565}, + publisher = {Multidisciplinary Digital Publishing Institute}, shorttitle = {Comparative {Mitochondrial} {Genomic} and {Phylogenetic} {Study} of {Eight} {Species} of the {Family} {Lonchodidae} ({Phasmatodea}}, title = {Comparative {Mitochondrial} {Genomic} and {Phylogenetic} {Study} of {Eight} {Species} of the {Family} {Lonchodidae} ({Phasmatodea}: {Euphasmatodea})}, url = {https://www.mdpi.com/2073-4425/16/5/565}, @@ -13522,6 +14157,45 @@ @article{luo_comparative_2025 year = {2025} } +@article{lv_first_2025, + abstract = {Baetidae is a globally diverse mayfly family. While COI DNA barcode studies are abundant, its mitogenomic data remain scarce. In this study, we present the first mitochondrial genome of Cloeon viridulum Navás, 1931. The mitogenome of C. viridulum spans 14,431 bp and includes 13 protein-coding genes, 22 transfer RNA genes, and one 16S ribosomal RNA (rRNA) gene. However, it features an incomplete 12S rRNA gene and lacks a control region. This mitogenome has a GC content of 32.4\%. Phylogenetic analysis strongly supports a sister relationship between C. viridulum and C. dipterum. Our findings offer genomic insights into Baetidae evolution.}, + author = {Lv, Mengyu and Zhu, Tianzhe}, + doi = {10.1080/23802359.2025.2602240}, + issn = {null}, + journal = {Mitochondrial DNA Part B}, + keywords = {{\textgreater}UseGalaxy.eu, Baetidae, mitochondrial genome, phylogeny}, + month = {December}, + note = {\_eprint: https://doi.org/10.1080/23802359.2025.2602240}, + number = {1}, + pages = {74--78}, + publisher = {Taylor \& Francis}, + shorttitle = {First report of mitochondrial genome of {Cloeon} viridulum ({Ephemeroptera}}, + title = {First report of mitochondrial genome of {Cloeon} viridulum ({Ephemeroptera}: {Baetidae}) from {Hebei}, {China}}, + url = {https://doi.org/10.1080/23802359.2025.2602240}, + urldate = {2025-12-26}, + volume = {11}, + year = {2025} +} + +@article{lydon_comparative_2025, + abstract = {Vibrionaceae are a diverse family of bacteria that contain pathogenic species, including those within the Vulnificus clade: Vibrio vulnificus, Vibrio navarrensis, and Vibrio cidicii. While V. vulnificus is a generally well-characterized environmental pathogen, V. cidicii and V. navarrensis are relatively rare, recently identified species that our current understanding of virulence and environmental adaptation is limited. Here, we investigate genetic relatedness across these three species to identify shared and species-specific genes, including markers of virulence. Using publicly available genome assemblies (n = 76), we evaluated phylogenetic and genomic diversity across this clade. We sampled all available V. navarrensis and V. cidicii genomes and a biodiverse curated set of four V. vulnificus ecotypes to ensure representative coverage. Our results indicate that all three species share 2,313 core genes, many of which are core bacterial functions in addition to pathways important to environmental response, host immune evasion, and iron acquisition. Moreover, V. cidicii and V. navarrensis have extensive genetic similarity between them, including average nucleotide identities {\textgreater}95\% and 370 shared genes. Despite this similarity, they both remain more phylogenetically distant from V. vulnificus and lack key virulence genes, such as rtxA, indicating alternative pathogenic potential. Overall, these findings reveal distinct evolutionary strategies within the Vulnificus clade, with V. vulnificus specializing in enhanced pathogenesis, while V. navarrensis and V. cidicii have evolved enhanced environmental persistence capabilities.ImportanceVibrio species are important environmental aquatic bacteria that pose a threat to human and animal health across the globe. This study applied comparative genomics to investigate the genetic relatedness of Vibrio vulnificus, Vibrio navarrensis, and Vibrio cidicii, with special focus on genes associated with environmental adaptation and virulence between and within each species. Results indicate V. navarrensis and V. cidicii share many genes, are phylogenetically close, and exhibit genomic signatures of enhanced environmental persistence and stress tolerance in addition to survival in anthropogenically impacted marine systems. Furthermore, V. vulnificus possesses an overall different virulence potential with the presence of RTX systems. This adds to our understanding of genetic diversity and pathogenic mechanisms within an important group of marine pathogens.}, + author = {Lydon, Keri Ann and Lott, Megan E J}, + copyright = {cc by}, + doi = {10.1128/aem.01827-25}, + issn = {1098-5336}, + journal = {Applied and environmental microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, Comparative genomics, One Health, Vibrio Cidicii, Vibrio Navarrensis, Vibrio vulnificus, Virulence Potential}, + language = {eng}, + month = {December}, + number = {12}, + pages = {e0182725}, + title = {Comparative genomics reveals specialization and divergent virulence potential in \<i\>{Vibrio} vulnificus\</i\>, \<i\>{Vibrio} navarrensis\</i\>, and \<i\>{Vibrio} cidicii\</i\>}, + url = {https://europepmc.org/articles/PMC12724252}, + urldate = {2025-12-26}, + volume = {91}, + year = {2025} +} + @article{ma_somatostatin_2020, abstract = {Somatostatin is a neuropeptide and a key regulator of the growth axis. Six Sst encoding genes (sst1 to sst6) have been identified in teleost fish genomes but little is known about their function. The present study aimed at replicating the context of the inflammatory bowel disease (IBD) and clarifying the involvement of sst3 in the intestine innate defence barrier in zebrafish larvae. We first established a CRISP/Cas9 sst3 deficient line (MT) and analysed the morphological and transcriptomic response to 0.4\% dextran sulfate sodium (DSS). Alcian blue staining of larval sections 6 days post fertilization showed an increased in acidic mucins in the intestinal bulb and mid-intestine, with a much stronger response in the MT compared to wild type (WT). The transcriptomic analysis revealed that WT and MT shared enriched gene ontology (GO) terms and pathways linked to catabolism, chondrocyte development, innate immune system, xenobiotic metabolism and oxidative stress. In contrast, the WT specific response to DSS was enriched in GO terms and pathways linked to transcription and translation, various developmental processes, regulation of biosynthetic processes, apelin signalling and apoptosis while the MT specific response included terms and pathways linked to protein metabolism and catabolic processes, extracellular matrix – receptor interaction and proteasome and chondrocyte development. Overall, this study demonstrated that Sst3 deficiency impairs insulin growth factor and adipocytokine signalling exacerbating the inflammatory response to DSS.}, author = {Ma, Jing and Chen, Jie and Louro, Bruno and Martins, Rute S. T. and Canario, Adelino V. M.}, @@ -13592,9 +14266,9 @@ @article{mack_regulation_2022 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Longevity}, language = {eng}, month = {January}, - note = {Publisher: Springer Science and Business Media LLC}, number = {1}, pages = {25}, + publisher = {Springer Science and Business Media LLC}, title = {Regulation of fatty acid desaturase- and immunity gene-expression by mbk-1/{DYRK1A} in {Caenorhabditis} elegans}, url = {https://doi.org/10.1186/s12864-021-08176-y}, volume = {23}, @@ -13611,9 +14285,9 @@ @article{macnee_simtext_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Data Mining, Software}, language = {eng}, month = {May}, - note = {Publisher: Oxford University Press (OUP)}, number = {22}, pages = {4285--4287}, + publisher = {Oxford University Press (OUP)}, title = {{SimText}: a text mining framework for interactive analysis and visualization of similarities among biomedical entities}, url = {https://doi.org/10.1093/bioinformatics/btab365}, volume = {37}, @@ -13626,9 +14300,9 @@ @article{maffei_complete_2024 journal = {Microbiology Resource Announcements}, keywords = {{\textgreater}UseGalaxy.eu}, month = {February}, - note = {Publisher: American Society for Microbiology}, number = {4}, pages = {e01174--23}, + publisher = {American Society for Microbiology}, title = {Complete genome sequence of {Pseudomonas} aeruginosa phage {Knedl}}, url = {https://journals.asm.org/doi/full/10.1128/mra.01174-23}, urldate = {2024-04-28}, @@ -13670,26 +14344,15 @@ @article{mahilkar_experimental_2021 year = {2021} } -@article{mahilkar_rapid_2023, - abstract = {Adaptive divergence leading to speciation is the major evolutionary process generating diversity in life forms. The most commonly observed form of speciation is allopatric speciation which requires that gene flow be prevented between populations by physical or temporal barriers, as they adapt to their respective environments. Eventually, these adaptive responses drive the populations far apart in the genotypic space such that individuals from the two populations become reproductively isolated. A widely accepted theory is that speciation simply occurs as a by-product of adaptive response of the populations 1,2 . Several ecological and laboratory examples of allopatric speciation exist 3–6 . However, we know little about the nature (pre- or post-zygotic) of barriers that arise first in this process. Understanding the first barriers that arise between populations is key, as populations diverge towards becoming distinct species. In recent years, fungi been used as model organisms to answer questions related to evolution of reproductive isolation 3,7–9 . Here we show rapid evolution of pre-zygotic barriers between allopatric yeast populations. We further demonstrate that these pre-zygotic barriers arise due to altered mating kinetics of the evolved population. Moreover, our non-adaptive evolution experiments with yeast under limited selection pressure also show rapid emergence of reproductive isolation. Overall, our results show that evolution of pre-zygotic reproductive barriers can occur as result of natural selection or drift. These barriers result because of altered mating kinetics or mate preference. {\textless}h4{\textgreater}One sentence summary{\textless}/h4{\textgreater} Pre-zygotic barriers to gene flow can arise due to adaptation or drift.}, - author = {Mahilkar, Anjali and Nagendra, Prachitha and Venkataraman, Pavithra and Deshmukh, Saniya and Saini, Supreet}, - doi = {10.1101/2023.03.18.533249}, - journal = {bioRxiv}, - keywords = {{\textgreater}UseGalaxy.eu}, - title = {Rapid evolution of pre-zygotic reproductive barriers in allopatric populations}, - url = {http://europepmc.org/abstract/PPR/PPR632875}, - year = {2023} -} - @article{mahilkar_rapid_2023, author = {Mahilkar, Anjali and Nagendra, Prachitha and Venkataraman, Pavithra and Deshmukh, Saniya and Saini, Supreet}, doi = {10.1128/spectrum.01950-23}, journal = {Microbiology Spectrum}, keywords = {{\textgreater}UseGalaxy.eu, Reproduction, Saccharomyces cerevisiae}, month = {October}, - note = {Publisher: American Society for Microbiology}, number = {6}, pages = {e01950--23}, + publisher = {American Society for Microbiology}, title = {Rapid evolution of pre-zygotic reproductive barriers in allopatric populations}, url = {https://journals.asm.org/doi/full/10.1128/spectrum.01950-23}, urldate = {2024-11-17}, @@ -13697,18 +14360,48 @@ @article{mahilkar_rapid_2023 year = {2023} } +@article{mahilkar_rapid_2023, + abstract = {Adaptive divergence leading to speciation is the major evolutionary process generating diversity in life forms. The most commonly observed form of speciation is allopatric speciation which requires that gene flow be prevented between populations by physical or temporal barriers, as they adapt to their respective environments. Eventually, these adaptive responses drive the populations far apart in the genotypic space such that individuals from the two populations become reproductively isolated. A widely accepted theory is that speciation simply occurs as a by-product of adaptive response of the populations 1,2 . Several ecological and laboratory examples of allopatric speciation exist 3–6 . However, we know little about the nature (pre- or post-zygotic) of barriers that arise first in this process. Understanding the first barriers that arise between populations is key, as populations diverge towards becoming distinct species. In recent years, fungi been used as model organisms to answer questions related to evolution of reproductive isolation 3,7–9 . Here we show rapid evolution of pre-zygotic barriers between allopatric yeast populations. We further demonstrate that these pre-zygotic barriers arise due to altered mating kinetics of the evolved population. Moreover, our non-adaptive evolution experiments with yeast under limited selection pressure also show rapid emergence of reproductive isolation. Overall, our results show that evolution of pre-zygotic reproductive barriers can occur as result of natural selection or drift. These barriers result because of altered mating kinetics or mate preference. {\textless}h4{\textgreater}One sentence summary{\textless}/h4{\textgreater} Pre-zygotic barriers to gene flow can arise due to adaptation or drift.}, + author = {Mahilkar, Anjali and Nagendra, Prachitha and Venkataraman, Pavithra and Deshmukh, Saniya and Saini, Supreet}, + doi = {10.1101/2023.03.18.533249}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Rapid evolution of pre-zygotic reproductive barriers in allopatric populations}, + url = {http://europepmc.org/abstract/PPR/PPR632875}, + year = {2023} +} + +@article{mahtab_complete_2025, + abstract = {Here, we report the complete genome sequence of bacteriophage PaFZ4, a lytic bacteriophage infecting Pseudomonas aeruginosa strains. The PaFZ4 was isolated from hospital wastewater in Dhaka, Bangladesh, and predicted to be under the genus Phikmvvirus (family Autographiviridae). The genome of PaFZ4 has a 43,335-bp linear genome with 65 coding sequences.}, + author = {Mahtab, Zuhayr and Tamanna, Fahmida Haque and Jabeen, Ishrat and Islam, Sohidul and Rahman, Sezanur and Rahman, Mustafizur and Shuvo, Sabbir R}, + copyright = {cc by}, + doi = {10.1128/mra.00993-25}, + issn = {2576-098X}, + journal = {Microbiology resource announcements}, + keywords = {{\textgreater}UseGalaxy.eu, Bacteriophages, Bangladesh, Phage Genomics, Phikmvvirus, Pseudomonas aeruginosa, Whole-genome Sequencing}, + language = {eng}, + month = {December}, + number = {12}, + pages = {e0099325}, + title = {Complete genome sequence of \<i\>{Pseudomonas} aeruginosa\</i\> bacteriophage {PaFZ4} isolated from {Dhaka}, {Bangladesh}}, + url = {https://europepmc.org/articles/PMC12697138}, + urldate = {2025-12-26}, + volume = {14}, + year = {2025} +} + @article{maier_freely_2021, abstract = {{\textless}p{\textgreater}The COVID-19 pandemic is the first global health crisis to occur in the age of big genomic data. Although data generation capacity is well established and sufficiently standardized, analytical capacity is not. To establish analytical capacity it is necessary to pull together global computational resources and deliver the best open source tools and analysis workflows within a ready to use, universally accessible resource. Such a resource should not be controlled by a single research group, institution, or country. Instead it should be maintained by a community of users and developers who ensure that the system remains operational and populated with current tools. A community is also essential for facilitating the types of discourse needed to establish best analytical practices. Bringing together public computational research infrastructure from the USA, Europe, and Australia, we developed a distributed data analysis platform that accomplishes these goals. It is immediately accessible to anyone in the world and is designed for the analysis of rapidly growing collections of deep sequencing datasets. We demonstrate its utility by detecting allelic variants in high-quality existing SARS-CoV-2 sequencing datasets and by continuous reanalysis of COG-UK data. All workflows, data, and documentation is available at https://covid19.galaxyproject.org.{\textless}/p{\textgreater}}, author = {Maier, Wolfgang and Bray, Simon and Beek, Marius van den and Bouvier, Dave and Coraor, Nathaniel and Miladi, Milad and Singh, Babita and Argila, Jordi Rambla De and Baker, Dannon and Roach, Nathan and Gladman, Simon and Coppens, Frederik and Martin, Darren and Lonie, Andrew and Gruning, Bjorn and Pond, Sergei Kosakovsky and Nekrutenko, Anton}, + chapter = {New Results}, copyright = {© 2021, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/}, doi = {10.1101/2021.03.25.437046}, journal = {bioRxiv}, keywords = {+Education, +Galactic, +Methods, +Project, +UsePublic, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au}, language = {en}, month = {March}, - note = {Publisher: Cold Spring Harbor Laboratory -Section: New Results}, pages = {2021.03.25.437046}, + publisher = {Cold Spring Harbor Laboratory}, title = {Freely accessible ready to use global infrastructure for {SARS}-{CoV}-2 monitoring}, url = {https://www.biorxiv.org/content/10.1101/2021.03.25.437046v1}, urldate = {2021-03-26}, @@ -13727,11 +14420,11 @@ @article{maier_ready--use_2021 note = {Bandiera\_abtest: a Cg\_type: Nature Research Journals Primary\_atype: Correspondence -Publisher: Nature Publishing Group Subject\_term: Genomic analysis;SARS-CoV-2 Subject\_term\_id: genomic-analysis;sars-cov-2}, number = {10}, pages = {1--2}, + publisher = {Nature Publishing Group}, title = {Ready-to-use public infrastructure for global {SARS}-{CoV}-2 monitoring}, url = {https://www.nature.com/articles/s41587-021-01069-1}, urldate = {2021-10-01}, @@ -13739,6 +14432,23 @@ @article{maier_ready--use_2021 year = {2021} } +@article{maki_inhibition_2025, + abstract = {Escherichia coli O157:H7 is a major food safety concern through contamination of beef and produce. Non-antibiotic interventions to minimize O157:H7 in food animals and products are highly desired and one strategy to improve food safety is to reduce O157:H7 in cattle, a main asymptomatic reservoir, through probiotic administration. Non-pathogenic E. coli populating the intestine represent a compelling probiotic source, as these strains are already host-adapted. The challenge is to identify non-pathogenic strains capable of competing with O157:H7 for nutrients or those producing compounds to inhibit O157:H7 growth. Here, E. coli isolated from cattle fecal and recto-anal junction swab samples were sequenced and screened for the ability to compete with O157:H7. Fourteen genetically distinct, non-Shiga toxin-encoding, non-O157:H7 E. coli strains were recovered, and individual isolates representative of each strain were assessed. Nearly all strains possessed complete genetic pathways for the utilization of carbon and nitrogen sources required for O157:H7 colonization of the cattle intestine. Growth curve assays were conducted, and growth metrics were compared between bovine non-O157:H7 E. coli isolates and two O157:H7 isolates. While no strain outperformed both O157:H7 strains for all nutrients tested, at least one strain outperformed O157:H7 for each of the carbon sources tested. No strain grew significantly better than O157:H7 in media supplemented with ethanolamine. A "highly competitive" consortium of 4 non-O157:H7 isolates that grew significantly better than O157:H7 reduced O157:H7 counts CFU/mL by 1.53 log10 and {\textgreater}0.72 log10 under anaerobic and aerobic conditions, respectively, in competition assays. A consortium of "low-competitive" strains reduced O157:H7 counts by {\textgreater}0.47 log10 and {\textgreater}0.51 log10 under anaerobic and aerobic conditions. These results suggest that cattle harbor non-O157:H7 E. coli strains capable of limiting O157:H7 growth in vitro. Surveys of commensal non-O157:H7 isolates from cattle using growth-based phenotypic assays may be useful in identifying E. coli strains capable of outcompeting O157:H7 in the bovine intestine for further in vivo testing as probiotics.}, + author = {Maki, Joel J. and Mou, Kathy T. and Trachsel, Julian and Loving, Crystal L.}, + doi = {10.3390/microorganisms13122811}, + issn = {2076-2607}, + journal = {Microorganisms}, + keywords = {{\textgreater}UseGalaxy.eu, Escherichia coli, Escherichia coli O157:H7, bacteriocin, cattle, commensal, nutrient competition, nutrient exclusion, probiotics}, + language = {eng}, + month = {December}, + number = {12}, + pages = {2811}, + shorttitle = {Inhibition of {Escherichia} coli {O157}}, + title = {Inhibition of {Escherichia} coli {O157}:{H7} {Growth} {Through} {Nutrient} {Competition} by {Non}-{O157} {E}. coli {Isolated} from {Cattle}}, + volume = {13}, + year = {2025} +} + @article{maki_species_2023, abstract = {Campylobacter ureolyticus is an emerging pathogen increasingly appreciated as a common cause of gastroenteritis and extra-intestinal infections in humans. Outside the setting of gastroenteritis, little work has been done to describe the genomic content and relatedness of the species, especially regarding clinical isolates. We reviewed the epidemiology of clinical C. ureolyticus cultured by our institution over the past 10 years. Fifty-one unique C. ureolyticus isolates were identified between January 2010 and August 2022, mostly originating from abscesses and blood cultures. To clarify the taxonomic relationships between isolates and to attribute specific genes with different clinical manifestations, we sequenced 19 available isolates from a variety of clinical specimen types and conducted a pangenomic analysis with publicly available C. ureolyticus genomes. Digital DNA:DNA hybridization suggested that these C. ureolyticus comprised a species complex of 10 species clusters (SCs) and several subspecies clusters. Although some orthologous genes or gene functions were enriched in isolates found in different SCs and clinical specimens, no association was significant. Nearly a third of the isolates possessed antimicrobial resistance genes, including the ermA resistance gene, potentially conferring resistance to macrolides, the treatment of choice for severe human campylobacteriosis. This work effectively doubles the number of publicly available C. ureolyticus genomes, provides further clarification of taxonomic relationships within this bacterial complex, and identifies target SCs for future analysis.}, author = {Maki, Joel J. and Howard, Mondraya and Connelly, Sara and Pettengill, Matthew A. and Hardy, Dwight J. and Cameron, Andrew}, @@ -13746,9 +14456,9 @@ @article{maki_species_2023 journal = {Journal of Clinical Microbiology}, keywords = {{\textgreater}UseGalaxy.eu, Campylobacter, Campylobacter Infections, Campylobacter jejuni, Gastroenteritis}, month = {April}, - note = {Publisher: American Society for Microbiology}, number = {5}, pages = {e00046--23}, + publisher = {American Society for Microbiology}, title = {Species {Delineation} and {Comparative} {Genomics} within the {Campylobacter} ureolyticus {Complex}}, url = {https://journals.asm.org/doi/full/10.1128/jcm.00046-23}, urldate = {2023-06-05}, @@ -13765,8 +14475,8 @@ @article{maldonado-pava_exploring_2024 keywords = {{\textgreater}UseGalaxy.eu, Biocatalyst, Metagenomics, Microbial Diversity, Phosphorus metabolism, Phytate hydrolysis, agricultural sustainability, phytase}, language = {English}, month = {June}, - note = {Publisher: Frontiers}, pages = {1426208}, + publisher = {Frontiers}, title = {Exploring the biotechnological potential of novel soil-derived {Klebsiella} sp. and {Chryseobacterium} sp. strains using phytate as sole carbon source}, url = {https://www.frontiersin.org/journals/bioengineering-and-biotechnology/articles/10.3389/fbioe.2024.1426208/full}, urldate = {2024-07-01}, @@ -13783,8 +14493,8 @@ @article{mamut_comparative_2025 keywords = {{\textgreater}UseGalaxy.eu, Peltigera, genomics, mitochondrial genome, phylogeny, repeat sequences}, language = {English}, month = {July}, - note = {Publisher: Frontiers}, pages = {1599036}, + publisher = {Frontiers}, title = {Comparative mitogenomics analysis of {Peltigera} species and new insights into the lichen phylogenetics}, url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2025.1599036/full}, urldate = {2025-09-03}, @@ -13924,10 +14634,10 @@ @article{marimon_pertussis_2024 keywords = {\textit{Bordetella pertussis}, {\textgreater}UseGalaxy.eu, outbreak, vaccination}, language = {en}, month = {October}, - note = {Number: 10 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 10}, number = {10}, pages = {1192}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Pertussis {Outbreak} {During} 2023 in {Gipuzkoa}, {North} {Spain}}, url = {https://www.mdpi.com/2076-393X/12/10/1192}, urldate = {2024-10-20}, @@ -13995,10 +14705,10 @@ @article{martin_elixirs_2023 keywords = {{\textgreater}UseGalaxy.eu}, language = {en}, month = {November}, - note = {Number: 1512 -Publisher: F1000 Research Limited}, + note = {Number: 1512}, number = {1512}, pages = {1512}, + publisher = {F1000 Research Limited}, title = {{ELIXIR}’s {List} of indicators, and other evidence, for monitoring performance and impact in a distributed data research infrastructure for the life sciences}, url = {https://f1000research.com/documents/12-1512}, urldate = {2024-11-17}, @@ -14029,7 +14739,7 @@ @article{martin_selection_2022 doi = {10.1101/2022.01.14.476382}, journal = {bioRxiv}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, - note = {Publisher: Cold Spring Harbor Laboratory}, + publisher = {Cold Spring Harbor Laboratory}, title = {Selection analysis identifies unusual clustered mutational changes in {Omicron} lineage {BA}. 1 that likely impact {Spike} function}, url = {http://europepmc.org/abstract/PPR/PPR444222}, year = {2022} @@ -14140,6 +14850,7 @@ @article{martins_laminin-2_2024 Graphical Abstract {\textless}img class="highwire-fragment fragment-image" alt="Figure" src="https://www.life-science-alliance.org/content/lsa/7/12/e202402829/F1.medium.gif" width="440" height="427"/{\textgreater}Download figureOpen in new tabDownload PowerPoint}, author = {Martins, Susana G. and Ribeiro, Vanessa and Melo, Catarina and Paulino-Cavaco, Cláudia and Antonini, Dario and Naidu, Sharadha Dayalan and Murtinheira, Fernanda and Fonseca, Inês and Saget, Bérénice and Pita, Mafalda and Fernandes, Diogo R. and Santos, Pedro Gameiro dos and Rodrigues, Gabriela and Zilhão, Rita and Herrera, Federico and Dinkova-Kostova, Albena T. and Carlos, Ana Rita and Thorsteinsdóttir, Sólveig}, + chapter = {Research Articles}, copyright = {© 2024 Martins et al.. https://creativecommons.org/licenses/by/4.0/This article is available under a Creative Commons License (Attribution 4.0 International, as described at https://creativecommons.org/licenses/by/4.0/).}, doi = {10.26508/lsa.202402829}, issn = {2575-1077}, @@ -14147,11 +14858,9 @@ @article{martins_laminin-2_2024 keywords = {{\textgreater}UseGalaxy.eu, Cell Differentiation, Laminin, Muscle, Skeletal, Myoblasts, Oxidative Stress}, language = {en}, month = {December}, - note = {Publisher: Life Science Alliance -Section: Research Articles}, number = {12}, pages = {e202402829}, - pmid = {39379105}, + publisher = {Life Science Alliance}, title = {Laminin-α2 chain deficiency in skeletal muscle causes dysregulation of multiple cellular mechanisms}, url = {https://www.life-science-alliance.org/content/7/12/e202402829}, urldate = {2024-10-11}, @@ -14165,7 +14874,7 @@ @article{martins_rodrigues_dataplant_2021 doi = {10.17192/BFDM.2021.2.8335}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, language = {de}, - note = {Publisher: Philipps-Universität Marburg}, + publisher = {Philipps-Universität Marburg}, title = {{DataPLANT} – {Ein} {NFDI}-{Konsortium} der {Pflanzen}-{Grundlagenforschung}}, url = {https://bausteine-fdm.de/article/view/8335}, year = {2021} @@ -14228,10 +14937,10 @@ @article{mathlouthi_colorectal_2023 keywords = {\textit{Halobacteria}, \textit{Natrialba magadii}, {\textgreater}UseGalaxy.eu, archaeome, colorectal cancer, formalin-fixed paraffin embedded tissues, gut microbiome, metagenomic, prognosis}, language = {en}, month = {September}, - note = {Number: 9 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 9}, number = {9}, pages = {7572--7581}, + publisher = {Multidisciplinary Digital Publishing Institute}, shorttitle = {Colorectal {Cancer} {Archaeome}}, title = {Colorectal {Cancer} {Archaeome}: {A} {Metagenomic} {Exploration}, {Tunisia}}, url = {https://www.mdpi.com/1467-3045/45/9/477}, @@ -14249,9 +14958,9 @@ @article{mathura_characterization_2023 keywords = {{\textgreater}UseGalaxy.eu, Abscisic Acid, Gene expression, Ipomoea batatas, Potato, Protein interaction networks, Sequence motif analysis, Signaling networks, Stress signaling cascade, Sweet potato, Tubers}, language = {en}, month = {March}, - note = {Publisher: Public Library of Science}, number = {11}, pages = {e0288481}, + publisher = {Public Library of Science}, title = {Characterization and expression analysis of {SnRK2}, {PYL}, and {ABF}/ {AREB}/ {ABI5} gene families in sweet potato}, url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0288481}, urldate = {2023-11-11}, @@ -14301,10 +15010,10 @@ @article{matsuura-suzuki_mirna-mediated_2024 keywords = {{\textgreater}UseGalaxy.eu, Development, Drosophila Proteins, Drosophila melanogaster, GW182, Gene Silencing, Larva, MicroRNA, MicroRNAs}, language = {eng}, month = {September}, - note = {Num Pages: 19 -Publisher: John Wiley \& Sons, Ltd}, + note = {Num Pages: 19}, number = {23}, pages = {1--19}, + publisher = {John Wiley \& Sons, Ltd}, title = {{miRNA}-mediated gene silencing in {Drosophila} larval development involves {GW182}-dependent and independent mechanisms}, url = {https://www.embopress.org/doi/full/10.1038/s44318-024-00249-4}, urldate = {2024-10-20}, @@ -14352,9 +15061,9 @@ @article{mauer_genomics_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Acanthocephala, Rotifera}, language = {eng}, month = {August}, - note = {Publisher: Springer Science and Business Media LLC}, number = {1}, pages = {604}, + publisher = {Springer Science and Business Media LLC}, title = {Genomics and transcriptomics of epizoic {Seisonidea} ({Rotifera}, syn. {Syndermata}) reveal strain formation and gradual gene loss with growing ties to the host}, url = {https://doi.org/10.1186/s12864-021-07857-y}, volume = {22}, @@ -14375,6 +15084,25 @@ @article{mavroidi_genomic_2025 year = {2025} } +@article{mayer_gene_2025, + abstract = {BackgroundProtein kinase CK2 is known to exist as a tetramer of two catalytic α- or α'- subunits and two non-catalytic β-subunits, or as multimers of this tetramer. Moreover, CK2α (CSNK2A1) and CK2α' (CSNK2A2) are also active in the absence of CK2β (CSNK2B). Very little is known about specific functions of the individual subunits of protein kinase CK2.ResultsIn order to study the effects of CK2α and CK2α' on gene expression, we used the Mus musculus pancreatic α-cell line αTC1 and two derivatives with either CK2α (KO1 cells) or CK2α' (KO2 cells) expression knocked-out by CRISPR/Cas technology. We found numerous genes deregulated in both KO1 and KO2 cells compared to the parental cells. Applying stringent thresholds, 266 genes were found down-regulated and 153 genes up-regulated in KO1 cells, 233 genes were found down-regulated and 84 genes up-regulated in KO2 cells. Dozens of genes were found deregulated in a similar fashion in both KO1 and KO2 cells. We found altered expression of genes involved in the differentiation of pancreatic cells, including Hox genes, and in the regulation of glucagon synthesis or secretion. Moreover, many of the deregulated genes play an important role in developmental processes and in neuronal cell biology.ConclusionOur findings reveal individual and shared functions of the CK2α and CK2α' catalytic subunits, in particular regarding their involvement in regulating gene expression.}, + author = {Mayer, Jens and Pack, Mandy and Montenarh, Mathias and Götz, Claudia}, + copyright = {cc by}, + doi = {10.1186/s40659-025-00654-x}, + issn = {0717-6287}, + journal = {Biological research}, + keywords = {{\textgreater}UseGalaxy.eu, Ck2 Knock-out, Ck2α Isoforms, Gene expression profile, Pancreatic Α-cells, protein kinase CK2}, + language = {eng}, + month = {November}, + number = {1}, + pages = {69}, + title = {Gene expression changes in pancreatic α-cell lines following knock-out {Of} either {CK2α} or {CK2α}'}, + url = {https://europepmc.org/articles/PMC12616906}, + urldate = {2025-12-26}, + volume = {58}, + year = {2025} +} + @article{mc_cartney_european_2023, abstract = {A global genome database of all of Earth's species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all {\textasciitilde}1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 34 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.}, author = {Mc Cartney, Ann and Formenti, Giulio and Mouton, Alice and De Panis, Diego and De Panis, Diego and Marins, Luisa and Leitao, Henrique and Diedericks, Genevieve and Kirangwa, Joseph and Morselli, Marco and Salces, Judit and Escudero, Nuria and Iannucci, Alessio and Natali, Chiara and Svardal, Hannes and Fernandez, Rosa and De Pooter, Tim and Joris, Geert and Strazisar, Mojca and Wood, Jo and Herron, Katie and Seehausen, Ole and Watts, Phillip and Shaw, Felix and Davey, Robert and Minotto, Alice and Fernandez Gonzalez, Jose Maria and Bohne, Astrid and Alegria, Carla and Alioto, Tyler and Alves, Paulo and Amorim, Isabel and Aury, Jean-Marc and Backstrom, Niclas and Baldrian, Petr and Ballarin, Loriano and Baltrunaite, Laima and Barta, Endre and BedHom, Bertrand and Belser, Caroline and Bergsten, Johannes and Bertrand, Laurie and Bilandija, Helena and Binzer-Panchal, Mahesh and Bista, Iliana and Blaxter, Mark and Borges, Paulo AV and Borges Dias, Guilherme and Bosse, Mirte and Brown, Tom and Bruggmann, Remy and Buena-Atienza, Elena and Burgin, Josephine and Buzan, Elena and Cariani, Alessia and Casadei, Nicolas and Chiara, Matteo and Chozas, Sergio and Ciampor, Fedor and Crottini, Angelica and Cruaud, Corinne and Cruz, Fernando and Dalen, Love and De Biase, Alessio and del Campo, Javier and Delic, Teo and Dennis, Alice and Derks, Martijn FL and Diroma, Maria Angela and Djan, Mihajla and Duprat, Simone and Eleftheriadi, Klara and Feulner, Philine GD and Flot, Jean-Francois and Forni, Giobbe and Fosso, Bruno and Fournier, Pascal and Fournier-Chambrillon, Christine and Gabaldon, Toni and Garg, Shilpa and Gissi, Carmela and Giupponi, Luca and Gomez-Garrido, Jessica and Gonzalez, Josefa and Grilo, Miguel and Gruening, Bjoern and Guerin, Thomas and Guiglielmoni, Nadege and Gut, Marta and Haesler, Marcel and Hahn, Christoph and Halpern, Balint and Harrison, Peter and Heintz, Julia and Hindrikson, Maris and Hoglund, Jacob and Howe, Kerstin and Hughes, Graham and Istace, Benjamin and Cock, Mark and Jancekovic, Franc and Jonsson, Zophonias and Joye-Dind, Sagane and Koskimaki, Janne and Krystufek, Boris and Kubacka, Justyna and Kuhl, Heiner and Kusza, Szilvia and Labadie, Karine and Lahteenaro, Meri and Lantz, Henrik and Lavrinienko, Anton and Leclere, Lucas and Lopes, Ricardo Jorge and Madsen, Ole and Magdelenat, Ghislaine and Magoga, Giulia and Manousaki, Tereza and Mappes, Tapio and Marques, Joao Pedro and Martinez Redondo, Gemma and Maumus, Florian and McCarthy, Shane and Megens, Hendrik-Jan and Melo-Ferreira, Jose and Mendes, Sofia and Montagna, Matteo and Moreno, Joao and Mosbech, Mai-Britt and Moura, Monica and Musilova, Zuzana and Myers, Eugene and Nash, Will and Nater, Alexander and Nicholson, Pamela and Niell, Manuel and Nijland, Reindert and Noel, Benjamin and Noren, Karin and Oliveira, Pedro and Olsen, Remi-Andre and Ometto, Lino and Oomen, Rebekah and Ossowski, Stephan and Palinauskas, Vaidas and Palsson, Snaebjorn and Panibe, Jerome and Pauperio, Joana and Pavlek, Martina and Payen, Emilie and Pawlowska, Julia and Pellicer, Jaume and Pesole, Graziano and Pimenta, Joao and Pippel, Martin and Pirttila, Anna Maria and Poulakakis, Nikos and Rajan, Jeena and Rego, Ruben MC and Resendes, Roberto and Resl, Philipp and Riesgo, Ana and Rodin-Morch, Patrik and Soares, Andre ER and Rodriguez Fernandes, Carlos and Romeiras, Maria and Roxo, Guilherme and Ruber, Lukas and Ruiz-Lopez, Maria Jose and Saarma, Urmas and Silva, Luis and Sim-Sim, Manuela and Soler, Lucile and Sousa, Vitor and Sousa Santos, Carla and Spada, Alberto and Stefanovic, Milomir and Steger, Viktor and Stiller, Josefin and Stock, Matthias and Struck, Torsten Hugo and Sudasinghe, Hiranya and Tapanainen, Riikka and Tellgren-Roth, Christian and Trindade, Helena and Tukalenko, Yevhen and Urso, Ilenia and Vacherie, Benoit and Van Belleghem, Steven and van Oers, Kees and Vargas-Chavez, Carlos and Velickovic, Nevena and Vella, Noel and Vella, Adriana and Vernesi, Cristiano and Vicente, Sara and Villa, Sara and Vinnere Pettersson, Olga and Volckaert, Filip AM and Voros, Judit and Wincker, Patrick and Winkler, Sylke and Ciofi, Claudio and Waterhouse, Robert and Mazzoni, Camila}, @@ -14406,7 +15134,7 @@ @article{mcdonald_ultraviolet_2022 journal = {Journal of Experimental Biology}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {January}, - note = {Publisher: The Company of Biologists}, + publisher = {The Company of Biologists}, title = {Ultraviolet vision in larval {Neogonodactylus} oerstedii}, url = {https://doi.org/10.1242/jeb.243256}, year = {2022} @@ -14415,15 +15143,15 @@ @article{mcdonald_ultraviolet_2022 @article{mcerlean_epigenetic_2020, abstract = {{\textless}h3{\textgreater}Abstract{\textless}/h3{\textgreater} {\textless}p{\textgreater}Airway macrophages (AMs) are key regulators of the lung environment and are implicated in the pathogenesis of idiopathic pulmonary fibrosis (IPF), a fatal respiratory disease with no cure. However, the epigenetics of AMs development and function in IPF are limited. Here, we characterised the DNA-methylation (DNAm) profile of AMs from IPF (n=30) and healthy (n=14) donors. Our analysis revealed epigenetic heterogeneity was a key characteristic of IPF AMs. DNAm ‘clock’ analysis indicated epigenetic alterations in IPF-AMs was not associated with accelerated ageing. In differential DNAm analysis, we identified numerous differentially methylated positions (DMPs, n=11) and regions (DMRs, n=49) between healthy and IPF AMs respectively. DMPs and DMRs encompassed genes involved in lipid (\textit{LPCAT1}) and glucose (\textit{PFKB3}) metabolism and importantly, DNAm status was associated with disease severity in IPF. Collectively, our data identify that profound changes in the epigenome underpin the development and function of AMs in the IPF lung.{\textless}/p{\textgreater}}, author = {McErlean, Peter and Bell, Christopher G. and Hewitt, Richard J. and Busharat, Zabreen and Ogger, Patricia P. and Ghai, Poonam and Albers, Gesa and Kingston, Shaun and Molyneaux, Philip L. and Beck, Stephan and Lloyd, Clare M. and Maher, Toby M. and Byrne, Adam J.}, + chapter = {New Results}, copyright = {© 2020, Posted by Cold Spring Harbor Laboratory. The copyright holder for this pre-print is the author. All rights reserved. The material may not be redistributed, re-used or adapted without the author's permission.}, doi = {10.1101/2020.12.04.410191}, journal = {bioRxiv}, keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, language = {en}, month = {December}, - note = {Publisher: Cold Spring Harbor Laboratory -Section: New Results}, pages = {2020.12.04.410191}, + publisher = {Cold Spring Harbor Laboratory}, title = {Epigenetic alterations underlie airway macrophage differentiation and phenotype during lung fibrosis}, url = {https://www.biorxiv.org/content/10.1101/2020.12.04.410191v1}, urldate = {2021-02-11}, @@ -14455,9 +15183,9 @@ @article{mcgowan_multi-omics_2020 keywords = {+Galactic, +IsGalaxy, +RefPublic, +Shared, +Tools, +Visualization, {\textgreater}Galaxy-P, {\textgreater}UseGalaxy.eu, Data Visualization, Proteomics}, language = {en}, month = {April}, - note = {Publisher: Oxford Academic}, number = {4}, pages = {giaa025}, + publisher = {Oxford Academic}, shorttitle = {Multi-omics {Visualization} {Platform}}, title = {Multi-omics {Visualization} {Platform}: {An} extensible {Galaxy} plug-in for multi-omics data visualization and exploration}, url = {https://academic.oup.com/gigascience/article/9/4/giaa025/5813097}, @@ -14466,15 +15194,21 @@ @article{mcgowan_multi-omics_2020 year = {2020} } -@article{mcquarrie_rapid_2024, - abstract = {Seminal fluid proteins (Sfps) are essential for reproductive success and evolve fast, possibly driven by post-copulatory sexual selection (PCSS) originating from sperm competition and cryptic female choice. Counterintuitively, however, the coding region only in few Sfps evolves adaptively. Hence, additional genomic and functional factors must play a role in Sfp evolution independent of the protein coding region. To shed light on drivers of Sfp evolution we focus on those Sfps predominantly expressed in male accessory glands, because this allows examination of their evolution in the tissue which produces the majority of Sfps. Moreover, accessory glands develop normally in hybrids in contrast to testis allowing to control for changes in cellular environment arising during speciation. Here, we discover that Acp promoters contain hot spots for rapid evolution from accumulation of sequence changes and insertions/deletions (indels). We further show that changes in promoter sequences are accompanied by gene expression divergence among closely related Drosophila species. We then validate these observations in Drosophila hybrids to show that species-specific expression divergence of Acps with rapidly evolving promoters are maintained in hybrids for some Acps, while others show dominance of one allele, a phenomenon termed transvection. These results indicate that cis -regulatory evolution, rather than genome background variation, drives Acp expression changes and promotes their rapid evolution.}, - author = {McQuarrie, David and Stephens, Frannie and Ferguson, Alexander and Arnold, Roland and Civetta, Alberto and Soller, Matthias}, - doi = {10.1101/2024.10.14.618274}, - journal = {bioRxiv}, - keywords = {{\textgreater}UseGalaxy.eu}, - title = {Rapid promoter evolution of male accessory gland genes is accompanied by divergent expression in closely {relatedDrosophilaspecies}}, - url = {http://europepmc.org/abstract/PPR/PPR926281}, - year = {2024} +@article{mcquarrie_rapid_2025, + abstract = {Seminal fluid proteins (Sfps) are essential for reproductive success and evolve fast on average, possibly driven by post-copulatory sexual selection (PCSS) originating from sperm competition and cryptic female choice. Counterintuitively, however, the coding region only in few Sfps evolves adaptively. Hence, additional genomic and functional factors must play a role in Sfp evolution independent of the protein coding region. To shed light on drivers of Sfp evolution we focus on those Sfps predominantly expressed in male accessory glands of Drosophila to examine their evolution in the tissue which produces the majority of Sfps. Unlike the testis, the accessory glands are known to develop normally in hybrids, allowing us to control for cellular environment differences arising during speciation. Here, we identify hotspots of rapid evolution in accessory gland protein genes (Acp) promoters, driven by base changes and insertions/deletions (indels). We further show that changes in promoter sequences are accompanied by gene expression divergence among closely related species. Using hybrids, we demonstrate that species-specific expression divergence is maintained for some Acps, while others exhibit dominance of one allele. These results indicate that regulatory evolution, rather than genome background variation, drives Acp expression changes and promotes their rapid evolution.}, + author = {McQuarrie, David W J and Stephens, Frannie H S and Ferguson, Alexander D and Arnold, Roland and Civetta, Alberto and Soller, Matthias}, + doi = {10.1093/genetics/iyaf226}, + issn = {1943-2631}, + journal = {Genetics}, + keywords = {{\textgreater}UseGalaxy.eu, Animals, Drosophila, Drosophila Proteins, Evolution, Molecular, Female, Intercellular Signaling Peptides and Proteins, Male, Promoter Regions, Genetic, Seminal Plasma Proteins, accessory gland proteins, evolution hot-spot, hybrid dysgenesis, post-mating response, promoter evolution, seminal fluid proteins}, + month = {December}, + number = {4}, + pages = {iyaf226}, + title = {Rapid promoter evolution of male accessory gland genes is accompanied by divergent expression in closely related {Drosophila} species}, + url = {https://doi.org/10.1093/genetics/iyaf226}, + urldate = {2025-12-26}, + volume = {231}, + year = {2025} } @article{mcvey_genetic_2024, @@ -14487,9 +15221,9 @@ @article{mcvey_genetic_2024 keywords = {{\textgreater}UseGalaxy.eu, Apoptosis, Cell death}, language = {en}, month = {June}, - note = {Publisher: Nature Publishing Group}, number = {6}, pages = {1--12}, + publisher = {Nature Publishing Group}, title = {Genetic influence on vascular smooth muscle cell apoptosis}, url = {https://www.nature.com/articles/s41419-024-06799-z}, urldate = {2024-07-09}, @@ -14585,8 +15319,6 @@ @article{mehta_catching_2022 month = {October}, number = {10}, pages = {2205}, - pmcid = {PMC9609567}, - pmid = {36298760}, shorttitle = {Catching the {Wave}}, title = {Catching the {Wave}: {Detecting} {Strain}-{Specific} {SARS}-{CoV}-2 {Peptides} in {Clinical} {Samples} {Collected} during {Infection} {Waves} from {Diverse} {Geographical} {Locations}}, url = {http://europepmc.org/abstract/MED/36298760}, @@ -14600,11 +15332,10 @@ @article{mehta_galaxy_2023 issn = {1478-9450}, journal = {Expert Review of Proteomics}, keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au, Bioinformatics, Galaxy platform, computational workflows, mass spectrometry, multi-omics, proteomics, reproducibility}, - note = {Publisher: Taylor \& Francis -\_eprint: https://doi.org/10.1080/14789450.2023.2265062}, + note = {\_eprint: https://doi.org/10.1080/14789450.2023.2265062}, number = {0}, pages = {1--16}, - pmid = {37787106}, + publisher = {Taylor \& Francis}, title = {A {Galaxy} of informatics resources for {MS}-based proteomics}, url = {https://doi.org/10.1080/14789450.2023.2265062}, urldate = {2023-10-12}, @@ -14622,10 +15353,10 @@ @article{mehta_precursor_2020 keywords = {+Galactic, +Tools, {\textgreater}Galaxy-P, {\textgreater}UseGalaxy.be, {\textgreater}UseGalaxy.eu, galaxy framework, label-free quantification, proteomics, workflows}, language = {en}, month = {September}, - note = {Number: 3 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 3}, number = {3}, pages = {15}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Precursor {Intensity}-{Based} {Label}-{Free} {Quantification} {Software} {Tools} for {Proteomic} and {Multi}-{Omic} {Analysis} within the {Galaxy} {Platform}}, url = {https://www.mdpi.com/2227-7382/8/3/15}, urldate = {2021-05-04}, @@ -14641,7 +15372,7 @@ @article{mehta_updates_2021 journal = {Journal of Proteome Research}, keywords = {+Education, +IsGalaxy, +Methods, +RefPublic, +Stellar, +Tools, +UsePublic, {\textgreater}ASaiM, {\textgreater}UseGalaxy.eu}, month = {March}, - note = {Publisher: American Chemical Society}, + publisher = {American Chemical Society}, title = {Updates on {metaQuantome} {Software} for {Quantitative} {Metaproteomics}}, url = {https://doi.org/10.1021/acs.jproteome.0c00960}, urldate = {2021-03-09}, @@ -14729,8 +15460,8 @@ @article{metris_aircraft_2023 keywords = {{\textgreater}UseGalaxy.eu, Atmosphere, DNA, Environmental, Environmental Monitoring}, language = {en}, month = {April}, - note = {Publisher: PeerJ Inc.}, pages = {e15171}, + publisher = {PeerJ Inc.}, shorttitle = {Aircraft surveys for air {eDNA}}, title = {Aircraft surveys for air {eDNA}: probing biodiversity in the sky}, url = {https://peerj.com/articles/15171}, @@ -14812,15 +15543,35 @@ @article{migur_temperature-regulated_2021 journal = {Journal of Experimental Botany}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {September}, - note = {Publisher: Oxford University Press (OUP)}, + publisher = {Oxford University Press (OUP)}, title = {The temperature-regulated {DEAD}-box {RNA} helicase {CrhR} interactome: autoregulation and photosynthesis-related transcripts}, url = {https://doi.org/10.1093/jxb/erab416}, year = {2021} } -@article{miladi_landscape_2020, - abstract = {In 2019 the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the first documented cases of severe lung disease COVID-19. Since then, SARS-CoV-2 has been spreading around the globe resulting in a severe pandemic with over 500.000 fatalities and large economical and social disruptions in human societies. Gaining knowledge on how SARS-Cov-2 interacts with its host cells and causes COVID-19 is crucial for the intervention of novel therapeutic strategies. SARS-CoV-2, like other coronaviruses, is a positive-strand RNA virus. The viral RNA is modified by RNA-modifying enzymes provided by the host cell. Direct RNA sequencing (DRS) using nanopores enables unbiased sensing of canonical and modified RNA bases of the viral transcripts. In this work, we used DRS to precisely annotate the open reading frames and the landscape of SARS-CoV-2 RNA modifications. We provide the first DRS data of SARS-CoV-2 in infected human lung epithelial cells. From sequencing three isolates, we derive a robust identification of SARS-CoV-2 modification sites within a physiologically relevant host cell type. A comparison of our data with the DRS data from a previous SARS-CoV-2 isolate, both raised in monkey renal cells, reveals consistent RNA modifications across the viral genome. Conservation of the RNA modification pattern during progression of the current pandemic suggests that this pattern is likely essential for the life cycle of SARS-CoV-2 and represents a possible target for drug interventions.}, - author = {Miladi, Milad and Fuchs, Jonas and Maier, Wolfgang and Weigang, Sebastian and Pedrosa, Núria Díaz and Weiss, Lisa and Lother, Achim and Nekrutenko, Anton and Ruzsics, Zsolt and Panning, Marcus and Kochs, Georg and Gilsbach, Ralf and Grüning, Björn}, +@article{miladi_graphclust2_2019, + abstract = {AbstractBackground. RNA plays essential roles in all known forms of life. Clustering RNA sequences with common sequence and structure is an essential step towa}, + author = {Miladi, Milad and Sokhoyan, Eteri and Houwaart, Torsten and Heyne, Steffen and Costa, Fabrizio and Grüning, Björn and Backofen, Rolf}, + doi = {10.1093/gigascience/giz150}, + issn = {2047-217X}, + journal = {GigaScience}, + keywords = {+Galactic, +IsGalaxy, +Tools, {\textgreater}GraphClust, {\textgreater}UseGalaxy.eu}, + language = {en}, + month = {December}, + number = {12}, + pages = {giz150}, + publisher = {Oxford Academic}, + shorttitle = {{GraphClust2}}, + title = {{GraphClust2}: {Annotation} and discovery of structured {RNAs} with scalable and accessible integrative clustering}, + url = {https://academic.oup.com/gigascience/article/8/12/giz150/5663672}, + urldate = {2020-04-10}, + volume = {8}, + year = {2019} +} + +@article{miladi_landscape_2020, + abstract = {In 2019 the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the first documented cases of severe lung disease COVID-19. Since then, SARS-CoV-2 has been spreading around the globe resulting in a severe pandemic with over 500.000 fatalities and large economical and social disruptions in human societies. Gaining knowledge on how SARS-Cov-2 interacts with its host cells and causes COVID-19 is crucial for the intervention of novel therapeutic strategies. SARS-CoV-2, like other coronaviruses, is a positive-strand RNA virus. The viral RNA is modified by RNA-modifying enzymes provided by the host cell. Direct RNA sequencing (DRS) using nanopores enables unbiased sensing of canonical and modified RNA bases of the viral transcripts. In this work, we used DRS to precisely annotate the open reading frames and the landscape of SARS-CoV-2 RNA modifications. We provide the first DRS data of SARS-CoV-2 in infected human lung epithelial cells. From sequencing three isolates, we derive a robust identification of SARS-CoV-2 modification sites within a physiologically relevant host cell type. A comparison of our data with the DRS data from a previous SARS-CoV-2 isolate, both raised in monkey renal cells, reveals consistent RNA modifications across the viral genome. Conservation of the RNA modification pattern during progression of the current pandemic suggests that this pattern is likely essential for the life cycle of SARS-CoV-2 and represents a possible target for drug interventions.}, + author = {Miladi, Milad and Fuchs, Jonas and Maier, Wolfgang and Weigang, Sebastian and Pedrosa, Núria Díaz and Weiss, Lisa and Lother, Achim and Nekrutenko, Anton and Ruzsics, Zsolt and Panning, Marcus and Kochs, Georg and Gilsbach, Ralf and Grüning, Björn}, doi = {10.1101/2020.07.18.204362}, journal = {bioRxiv}, keywords = {{\textgreater}UseGalaxy.eu}, @@ -14837,11 +15588,10 @@ @article{minisy_transcription_2024 journal = {Molecular and Cellular Biology}, keywords = {{\textgreater}UseGalaxy.eu, Myometrium, Parturition, TCF23, bHLH, dystocia, extracellular matrix, myometrium remodeling, parturition, progesterone, resorption, smooth muscle cells}, month = {August}, - note = {Publisher: Taylor \& Francis -\_eprint: https://doi.org/10.1080/10985549.2024.2376146}, + note = {\_eprint: https://doi.org/10.1080/10985549.2024.2376146}, number = {8}, pages = {316--333}, - pmid = {39014976}, + publisher = {Taylor \& Francis}, title = {Transcription {Factor} 23 is an {Essential} {Determinant} of {Murine} {Term} {Parturition}}, url = {https://doi.org/10.1080/10985549.2024.2376146}, urldate = {2024-11-17}, @@ -14857,7 +15607,7 @@ @article{miranda_assessment_2024 journal = {Journal of Agricultural and Food Chemistry}, keywords = {{\textgreater}UseGalaxy.eu}, month = {May}, - note = {Publisher: American Chemical Society}, + publisher = {American Chemical Society}, title = {Assessment and {Partial} {Characterization} of {Candidate} {Genes} in {Dihydrochalcone} and {Arbutin} {Biosynthesis} in an {Apple}–{Pear} {Hybrid} by {De} {Novo} {Transcriptome} {Assembly}}, url = {https://doi.org/10.1021/acs.jafc.4c01006}, urldate = {2024-05-17}, @@ -14905,7 +15655,7 @@ @article{mitra_diversity_2025 keywords = {232, 5, 7, {\textgreater}UseGalaxy.eu, blaKPC-2-harboring Escherichia coli, blaNDM-1, blaOXA-181, core genome phylogeny, insertion sequence element, plasmids, transposons}, language = {English}, month = {May}, - note = {Publisher: Frontiers}, + publisher = {Frontiers}, title = {Diversity of mobile genetic elements in carbapenem-resistant {Enterobacterales} isolated from the intensive care units of a tertiary care hospital in {Northeast} {India}}, url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2025.1543427/full}, urldate = {2025-07-12}, @@ -14932,6 +15682,26 @@ @informatik.uni-freiburg.de).Supplementary year = {2022} } +@article{mitsuwan_recombinant_2025, + abstract = {Background/Objectives: Streptococcus suis is a zoonotic pathogen that causes infections in pigs and humans, leading to significant economic losses. S. suis can evade the immune system of hosts and induce persistent infections. Early detection and vaccination are crucial for controlling the disease in swine industries. This study aimed to investigate candidate recombinant protein for antibodies against S. suis detection and subunit vaccine development. Methods: The whole genome of S. suis BM407 was analyzed using bioinformatic tools to predict suitable proteins and genes for recombinant protein expression. Partial extracellular factor protein (epf) genes of S. suis serotype 2 DMST18783 were amplified. A 3301 bp amplicon was digested, and a specific 615 bp fragment was inserted into a pQE81L-KAN vector. Then, the constructed plasmid was cloned and expressed in Escherichia coli DH10β. Purified protein was analyzed using SDS-PAGE. In addition, translated amino acid sequences were analyzed for immune response properties, molecular docking, molecular dynamic simulation, and epitope prediction. Results: The amino acid sequence of recombinant extracellular factor protein (rEF) was revealed as a promising antigen containing putative protective regions as linear epitopes. Furthermore, the rEF was expressed as a histidine-tagged recombinant protein, and its properties were nearly similar to the predicted rEF using bioinformatic tools. Binding of the recombinant EF (rEF) protein was found to reduce fluctuations in the swine toll-like receptor 2. Furthermore, the rEF contained several regions that were predicted to be epitopes for both B-cells and T-cells. Conclusions: This study indicates that the recombinant EF fragment is a promising candidate for detecting antibodies against S. suis and as a component of a subunit vaccine.}, + author = {Mitsuwan, Watcharapong and Saengsawang, Phirabhat and Boripun, Ratchadaporn and Rodríguez-Ortega, Manuel J and Nwabor, Ozioma F}, + copyright = {cc by}, + doi = {10.3390/vaccines13111128}, + issn = {2076-393X}, + journal = {Vaccines}, + keywords = {{\textgreater}UseGalaxy.eu, Candidate Protein, EPF, Extracellular Factor Protein, Recombinant protein, Streptococcus suis}, + language = {eng}, + month = {November}, + number = {11}, + pages = {1128}, + shorttitle = {Recombinant {Extracellular} {Factor} {Protein} of \<i\>{Streptococcus} suis\</i\> as {Potential} {Candidate} {Protein} for {Antibodies} {Against} \<i\>{S}. suis\</i\> {Detection} and {Subunit} {Vaccine} {Development}}, + title = {Recombinant {Extracellular} {Factor} {Protein} of \<i\>{Streptococcus} suis\</i\> as {Potential} {Candidate} {Protein} for {Antibodies} {Against} \<i\>{S}. suis\</i\> {Detection} and {Subunit} {Vaccine} {Development}: \<i\>{In} {Silico}\</i\> and \<i\>{In} {Vitro}\</i\> {Approaches}}, + url = {https://europepmc.org/articles/PMC12656778}, + urldate = {2025-12-26}, + volume = {13}, + year = {2025} +} + @incollection{mohamad_azmi_molecular_2025, abstract = {The increasing prevalence of pathogenic Escherichia coli (E. coli) in water and food sources poses a significant threat to public health, necessitating the development of rapid and accurate biosensor detection methods such as aptamer-based biosensors due to their high specificity and sensitivity. Aptamers are nucleic acids that can bind with high affinity and specificity to a range of target molecules. This research aims to investigate biophysical mechanisms by utilizing biophysics simulations such as molecular free energy calculation and molecular docking to elucidate the interaction between specific aptamer with E. coli protein such as Shiga Toxin (Stx). The methodology involves characterizing aptamer-E. coli interactions, identifying key aptamer structural features and docking analysis of binding process between aptamer and E. coli. In conclusion, this research bridges theory for future applications, providing a framework for developing advanced biosensing technologies, by using the in-silico strategies that allowed the detection of aptamer-target interaction during molecular docking processes.}, author = {Mohamad Azmi, Muhammad Fakhrullah and Wan Ayub, Wan Mardhiyana and Ibrahim, Izzah Afifah and Redzuan, Muhammad Fadzlisyam and Ismadi, Irfan Danial and Mohd Ghazali, Mohd Ifwat and Mohamad Jamali, Muhamad Arif and Azmi, Liyana and Zainal, Nur Zaireena and Abdul Hamid, Nazefah and Abdullah, Shahino Mah}, @@ -14958,10 +15728,10 @@ @article{mohamed_candidate_2023 keywords = {\textit{Oryza sativa}, {\textgreater}UseGalaxy.eu, bioinformatics, miRNA, rice tungro disease}, language = {en}, month = {March}, - note = {Number: 3 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 3}, number = {3}, pages = {651}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Candidate {miRNAs} from {Oryza} sativa for {Silencing} the {Rice} {Tungro} {Viruses}}, url = {https://www.mdpi.com/2077-0472/13/3/651}, urldate = {2023-03-15}, @@ -14997,10 +15767,10 @@ @article{mohebifar_construction_2023 keywords = {{\textgreater}UseGalaxy.eu, Breast cancer, Long non-coding RNAs}, language = {en}, month = {December}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {21874}, + publisher = {Nature Publishing Group}, title = {Construction and analysis of pseudogene-related {ceRNA} network in breast cancer}, url = {https://www.nature.com/articles/s41598-023-49110-4}, urldate = {2023-12-14}, @@ -15014,7 +15784,7 @@ @article{molina_valencia_anotacion_2024 keywords = {{\textgreater}UseGalaxy.eu}, language = {spa}, month = {August}, - note = {Publisher: Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Biotecnología}, + publisher = {Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Biotecnología}, title = {Anotación genómica de genes expresados en la biosíntesis de compuestos fenólicos en pitahaya ({Hylocereus} spp.) expuesta a condiciones de estrés}, url = {https://repositorio.uta.edu.ec/handle/123456789/42325}, urldate = {2024-11-17}, @@ -15030,9 +15800,9 @@ @article{molla_harnessing_2024 keywords = {{\textgreater}UseGalaxy.eu}, language = {en}, month = {September}, - note = {Publisher: IOP Publishing}, number = {9}, pages = {095501}, + publisher = {IOP Publishing}, shorttitle = {Harnessing {Lignocellulolytic} and {Electrogenic} {Potential}}, title = {Harnessing {Lignocellulolytic} and {Electrogenic} {Potential}: {Insights} from {Shewanella} oneidensis {MR}-1 and {Cellulomonas} {Strains} on {Lignocellulosic} {Biomass}}, url = {https://dx.doi.org/10.1149/1945-7111/ad7909}, @@ -15100,10 +15870,10 @@ @article{morandi_evolutionary_2020 keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, DNA methylation, bisulfite sequencing, evolutionary epigenetics, squamous cell carcinoma, ultra-conserved non-coding elements}, language = {en}, month = {September}, - note = {Number: 9 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 9}, number = {9}, pages = {2092}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {An {Evolutionary} {Cancer} {Epigenetic} {Approach} {Revealed} {DNA} {Hypermethylation} of {Ultra}-{Conserved} {Non}-{Coding} {Elements} in {Squamous} {Cell} {Carcinoma} of {Different} {Mammalian} {Species}}, url = {https://www.mdpi.com/2073-4409/9/9/2092}, urldate = {2020-12-29}, @@ -15117,9 +15887,9 @@ @article{moreno_expression_2021 journal = {Nucleic Acids Research}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {November}, - note = {Publisher: Oxford University Press (OUP)}, number = {D1}, pages = {D129--D140}, + publisher = {Oxford University Press (OUP)}, title = {Expression {Atlas} update: gene and protein expression in multiple species}, url = {https://doi.org/10.1093/nar/gkab1030}, volume = {50}, @@ -15135,8 +15905,8 @@ @article{moreno_user-friendly_2021 keywords = {+Galactic, +IsGalaxy, +Shared, +Tools, +UsePublic, {\textgreater}Human Cell Atlas, {\textgreater}UseGalaxy.eu}, language = {en}, month = {March}, - note = {Publisher: Nature Publishing Group}, pages = {1--2}, + publisher = {Nature Publishing Group}, title = {User-friendly, scalable tools and workflows for single-cell {RNA}-seq analysis}, url = {https://www.nature.com/articles/s41592-021-01102-w}, urldate = {2021-04-01}, @@ -15153,10 +15923,10 @@ @article{moris_intrasexual_2023 keywords = {{\textgreater}UseGalaxy.eu, Gene expression, Phylogenetics, RNAi, Wasps}, language = {en}, month = {February}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {1--15}, + publisher = {Nature Publishing Group}, title = {Intrasexual cuticular hydrocarbon dimorphism in a wasp sheds light on hydrocarbon biosynthesis genes in {Hymenoptera}}, url = {https://www.nature.com/articles/s42003-022-04370-0}, urldate = {2023-03-15}, @@ -15208,10 +15978,10 @@ @article{morsli_direct_2021 keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Echovirus 12, cerebrospinal fluid, enterovirus meningitis, metagenomic next-generation sequencing, whole genome sequencing}, language = {en}, month = {May}, - note = {Number: 5 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 5}, number = {5}, pages = {610}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Direct {Diagnosis} of {Echovirus} 12 {Meningitis} {Using} {Metagenomic} {Next} {Generation} {Sequencing}}, url = {https://www.mdpi.com/2076-0817/10/5/610}, urldate = {2021-08-23}, @@ -15295,7 +16065,7 @@ @article{mukhopadhyay_mitogenomes_2023 keywords = {{\textgreater}UseGalaxy.eu, Leptographium, Mobile introns, Ophiostomatales, complex introns, phylogeny}, language = {English}, month = {August}, - note = {Publisher: Frontiers}, + publisher = {Frontiers}, shorttitle = {The mitogenomes of {Leptographium} aureum, {Leptographium} sp., and {Grosmannia} fruticeta}, title = {The mitogenomes of {Leptographium} aureum, {Leptographium} sp., and {Grosmannia} fruticeta: expansion by introns}, url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1240407/full}, @@ -15370,9 +16140,9 @@ @article{musmeci_draft_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, language = {eng}, month = {August}, - note = {Publisher: American Society for Microbiology}, number = {32}, pages = {e0064221}, + publisher = {American Society for Microbiology}, title = {Draft {Genome} {Sequence} of the {Mucin} {Degrader} {Clostridium} tertium {WC0709}}, url = {https://doi.org/10.1128/mra.00642-21}, volume = {10}, @@ -15441,10 +16211,10 @@ @article{naorem_immunoinformatics_2024 keywords = {\textit{Streptococcus mutans}, {\textgreater}UseGalaxy.eu, Epitopes, B-Lymphocyte, Epitopes, T-Lymphocyte, Streptococcus mutans, dental caries, immunoinformatics, molecular docking simulation, molecular dynamic simulation, multiepitope vaccine}, language = {en}, month = {October}, - note = {Number: 10 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 10}, number = {10}, pages = {916}, + publisher = {Multidisciplinary Digital Publishing Institute}, shorttitle = {Immunoinformatics {Design} of a {Multiepitope} {Vaccine} ({MEV}) {Targeting} {Streptococcus} mutans}, title = {Immunoinformatics {Design} of a {Multiepitope} {Vaccine} ({MEV}) {Targeting} {Streptococcus} mutans: {A} {Novel} {Computational} {Approach}}, url = {https://www.mdpi.com/2076-0817/13/10/916}, @@ -15463,10 +16233,10 @@ @article{napoli_absence_2022 keywords = {{\textgreater}UseGalaxy.eu, Astrobiology, Genome informatics}, language = {en}, month = {May}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {8437}, + publisher = {Nature Publishing Group}, title = {Absence of increased genomic variants in the cyanobacterium {Chroococcidiopsis} exposed to {Mars}-like conditions outside the space station}, url = {https://www.nature.com/articles/s41598-022-12631-5}, urldate = {2022-12-03}, @@ -15501,9 +16271,9 @@ @article{nasereddin_identification_2022 keywords = {{\textgreater}UseGalaxy.eu, COVID-19, SARS-CoV-2}, language = {eng}, month = {June}, - note = {Publisher: American Society for Microbiology}, number = {4}, pages = {e00736--22}, + publisher = {American Society for Microbiology}, title = {Identification of {SARS}-{CoV}-2 {Variants} of {Concern} {Using} {Amplicon} {Next}-{Generation} {Sequencing}}, url = {https://journals.asm.org/doi/full/10.1128/spectrum.00736-22}, urldate = {2022-09-24}, @@ -15527,6 +16297,36 @@ @article{nasereddin_tracking_2022 year = {2022} } +@article{nasr_pathogfair_2025, + abstract = {Abstract + +Background +Food contamination by pathogens poses a global health threat, affecting an estimated 600 million people annually. During a foodborne outbreak investigation, microbiological analysis of food vehicles detects responsible pathogens and traces contamination sources. Metagenomic approaches offer a comprehensive view of the genomic composition of microbial communities, facilitating the detection of potential pathogens in samples. Combined with sequencing techniques like Oxford Nanopore sequencing, such metagenomic approaches become faster and easier to apply. A key limitation of these approaches is the lack of accessible, easy-to-use, and openly available pipelines for pathogen identification and tracking from (meta)genomic data. + + +Findings +PathoGFAIR is a collection of Galaxy-based Findable, Accessible, Interoperable, and Reusable (FAIR) workflows employing state-of-the-art tools to detect and track pathogens from metagenomic Nanopore sequencing. Although initially developed to detect pathogens in food datasets, the workflows can be applied to other metagenomic Nanopore pathogenic data. PathoGFAIR incorporates visualizations and reports for comprehensive results. We tested PathoGFAIR on 130 samples containing different pathogens from multiple hosts under various experimental conditions. For all but 1 sample, workflows have successfully detected expected pathogens at least at the species rank. Further taxonomic ranks are detected for samples with sufficiently high colony-forming unit and low cycle threshold values. + + +Conclusions +PathoGFAIR detects the pathogens at species and subspecies taxonomic ranks in all but 1 tested sample, regardless of whether the pathogen is isolated or the sample is incubated before sequencing. Importantly, PathoGFAIR is easy to use and can be straightforwardly adapted and extended for other types of analysis and sequencing techniques, making it usable in various pathogen detection scenarios.}, + author = {Nasr, Engy and Henger, Anna and Grüning, Björn and Zierep, Paul and Batut, Bérénice}, + copyright = {https://creativecommons.org/licenses/by/4.0/}, + doi = {10.1093/gigascience/giaf017}, + issn = {2047-217X}, + journal = {GigaScience}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {January}, + pages = {giaf017}, + shorttitle = {{PathoGFAIR}}, + title = {{PathoGFAIR}: a collection of {FAIR} and adaptable (meta)genomics workflows for (foodborne) pathogens detection and tracking}, + url = {https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giaf017/8266457}, + urldate = {2026-01-11}, + volume = {14}, + year = {2025} +} + @article{nayak_bms345541_2024, abstract = {Glioblastoma (GBM) is one of the most aggressive and fatal cancers, for which Temozolomide (TMZ) chemo drug is commonly used for its treatment. However, patients gradually develop resistance to this drug, leading to tumor relapse. In our previous study, we have identified lncRNAs that regulate chemoresistance through the competing endogenous RNA (ceRNA) mechanism. In this study, we tried to find FDA-approved drugs against the target proteins of these ceRNA networks through drug repurposing using differential gene expression profiles, which could be used to nullify the effect of lncRNAs and promote the sensitivity of TMZ in GBM. We performed molecular docking and simulation studies of predicted repurposed drugs and their targets. Among the predicted repurposed drugs, we found BMS345541 has a higher binding affinity towards its target protein - FOXG1, making it a more stable complex with FOXG1-DNA. The ADMET analysis of this drug BMS345541 shows a higher half-life and lower cytotoxicity level than other predicted repurposed drugs. Hence, we conjecture that this could be a better drug for increasing the sensitivity of TMZ for treating GBM patients.}, author = {Nayak, Rojalin and Mallick, Bibekanand}, @@ -15599,6 +16399,21 @@ @article{nekrutenko_biology_2018 year = {2018} } +@article{nekrutenko_standardizing_2025, + abstract = {Candidozyma auris has emerged as a critical global health threat due to multidrug resistance and healthcare-associated transmission. While RNA-seq has become the primary tool for studying C. auris pathogenesis, inconsistent use of reference genomes and bioinformatics tools complicate cross-study comparisons. Here we demonstrate how BRC-Analytics, a platform for pathogen genomics, combined with an agentic AI assistant, enables reproducible RNA-seq analysis. By re-analyzing data from two publications we achieved near-perfect correlation with published results despite annotation version differences. We addressed provenance challenges associated with using AI agents with Galaxy by forcing them to invoke Galaxy's native tools rather than manipulating data directly. For custom analyses outside Galaxy's toolset, we provide standalone JupyterLite notebooks that reproduce our analysis without AI involvement. This framework-combining AI-assisted automation with rigorous provenance tracking-establishes a template for standardized, reproducible fungal pathogen genomics. To the best of our knowledge, this is the first example of integration between public data repositories, reproducible analysis workflows, and agentic AI tools. Our subsequent efforts will focus on improving the seamlessness of this integration.}, + author = {Nekrutenko, Anton and Callan, Danielle and Van Den Beek, Marius and Baker, Dannon and Rogers, David and Guerler, Aysam and Chilton, John and Clawson, Hiram and Cain, Scott and O'Meara, Teresa and Beavers, Kelsey and Schatz, Michael and Haeussler, Maximilian and Gruning, Bjorn and Goecks, Jeremy and Pond, Sergei Kosakovsky}, + doi = {10.64898/2025.12.30.697050}, + issn = {2692-8205}, + journal = {bioRxiv: The Preprint Server for Biology}, + keywords = {+IsGalaxy, {\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {December}, + pages = {2025.12.30.697050}, + shorttitle = {Standardizing {RNA}-seq {Analysis} of {Fungal} {Pathogens} {Using} {BRC}-{Analytics} and {Agentic} {AI}}, + title = {Standardizing {RNA}-seq {Analysis} of {Fungal} {Pathogens} {Using} {BRC}-{Analytics} and {Agentic} {AI}: {A} {Candidozyma} auris {Case} {Study}}, + year = {2025} +} + @article{nemours_use_2024, abstract = {Paclitaxel is a widely used chemotherapeutic agent for the treatment of breast cancer (BC), including as a front-line treatment for triple-negative breast cancer (TNBC) patients. However, resistance to paclitaxel remains one of the major causes of death associated with treatment failure. Multiple studies have demonstrated that miRNAs play a role in paclitaxel resistance and are associated with both disease progression and metastasis. In the present study, we used a miRNA-encoding lentiviral library as a gain-of-function screen for paclitaxel resistance in the MDA-MB-231 TNBC cell line. We identified that \textit{miR-181b}, \textit{miR-29a}, \textit{miR-30c}, \textit{miR-196} and \textit{miR-1295} conferred a resistant phenotype to cells. The expression of \textit{miR-29a} also induced resistance to eribulin and vinorelbine, while \textit{miR-181b} and \textit{miR-30c} induced resistance to vinorelbine. We measured the levels of these miRNAs in breast cancer patients and observed higher levels of \textit{miR-29a} in treatment-refractory patients. Taken together, we suggest that \textit{miR-29a} and \textit{miR-181b} may be good candidates for miRNA inhibition to overcome resistance to chemotherapy.}, author = {Nemours, Stéphane and Solé, Carla and Goicoechea, Ibai and Armesto, María and Arestin, María and Urruticoechea, Ander and Rezola, Marta and López, Isabel Álvarez and Schaapveld, Roel and Schultz, Iman and Zhang, Lei and Lawrie, Charles H}, @@ -15633,9 +16448,9 @@ @article{ngo_histone_2022 journal = {Journal of the American Heart Association}, keywords = {{\textgreater}UseGalaxy.eu, bromodomain‐containing protein, cardiac myocyte, epigenetics, heart, heart failure, histone deacetylase}, month = {June}, - note = {Publisher: American Heart Association}, number = {12}, pages = {e025857}, + publisher = {American Heart Association}, title = {Histone {Deacetylase} 6 {Inhibitor} {JS28} {Prevents} {Pathological} {Gene} {Expression} in {Cardiac} {Myocytes}}, url = {https://www.ahajournals.org/doi/full/10.1161/JAHA.122.025857}, urldate = {2022-11-06}, @@ -15699,7 +16514,7 @@ @article{nicholson_contribution_2024 keywords = {{\textgreater}UseGalaxy.eu, Bordetella bronchiseptica, RNA-Seq, and biofilm, cyclic-di-GMP, motility}, language = {English}, month = {March}, - note = {Publisher: Frontiers}, + publisher = {Frontiers}, title = {The contribution of {BvgR}, {RisA}, and {RisS} to global gene regulation, intracellular cyclic-di-{GMP} levels, motility, and biofilm formation in {Bordetella} bronchiseptica}, url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2024.1305097/full}, urldate = {2024-05-17}, @@ -15715,9 +16530,8 @@ @article{nielsen_delayed_2023 keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org}, language = {en}, month = {January}, - note = {Publisher: American Society for Clinical Investigation}, number = {2}, - pmid = {0}, + publisher = {American Society for Clinical Investigation}, title = {Delayed boosting improves human antigen-specific {Ig} and {B} cell responses to the {RH5}.1/{AS01}$_{\textrm{{B}}}$ malaria vaccine}, url = {https://insight.jci.org/articles/view/163859}, urldate = {2023-01-28}, @@ -15740,11 +16554,11 @@ @article{niemoller_bisulfite-free_2021 Cg\_type: Nature Research Journals Number: 1 Primary\_atype: Research -Publisher: Nature Publishing Group Subject\_term: Acute myeloid leukaemia;Cancer epigenetics;Methylation analysis;Tumour heterogeneity;Whole genome amplification Subject\_term\_id: acute-myeloid-leukaemia;cancer-epigenetics;methylation-analysis;tumour-heterogeneity;whole-genome-amplification}, number = {1}, pages = {1--10}, + publisher = {Nature Publishing Group}, title = {Bisulfite-free epigenomics and genomics of single cells through methylation-sensitive restriction}, url = {https://www.nature.com/articles/s42003-021-01661-w}, urldate = {2021-07-21}, @@ -15773,6 +16587,25 @@ @article{nieva_de_la_hidalga_facilitating_2025 year = {2025} } +@article{nilchi_dissecting_2025, + abstract = {Emerging evidence supports the role of type 2 diabetes (T2D) mellitus as a risk factor for cancer progression. In this study, we investigated and identified biomarkers related to diabetes and pancreatic ductal adenocarcinoma (PDAC) using systems biology to understand better the molecular landscape of PDAC and its connections with T2D.RNA-seq data related to blood samples of diabetes and pancreatic cancer were analyzed using bioinformatics tools in the Galaxy platform. After differential expression analysis using the DESeq2, the co-expression network associated with T2D and PDAC data was reconstructed using the WGCNA. Then, by visualizing the protein-protein interaction network in modules specifically related to T2D and PDAC, the key genes involved in these two diseases were identified, and their interaction network with long non-coding RNAs was reconstructed. Finally, the results of bioinformatics analysis were verified by qPCR in four groups, including T2D, PDAC, PDAC-T2D, and control groups.In this study, 1905 and 18,558 genes with significant differential expression were identified in the data of T2D and PDAC, respectively ({\textbar}logFC{\textbar} {\textgreater} 0.58, adj. p value {\textless} 0.05). The WGCNA showed 32 and 20 co-expression modules in diabetes and pancreatic cancer data, respectively. Among these, 303 genes were co-expressed, related to diabetes and pancreatic cancer. Based on the protein-protein interaction pattern, five hub genes were identified (using the CytoHubba Cytoscape plugin and the Maximal Clique Centrality (MCC) parameter). Finally, the co-expression network was reconstructed between these five genes and other lncRNAs. The qPCR showed that the expression of the CEBPZ gene was significantly increased in the blood samples of the diabetic (log2FC = 1.163, adj. p value = 0.0006), pancreatic cancer (log2FC = 3.22, adj. p value {\textless} 0.0001), and pancreatic cancer-diabetic (log2FC = 2.73, adj. p value {\textless} 0.0001) groups compared to the control group.For the first time, this study suggested that CEBPZ expression may serve as a diagnostic biomarker for assessing PDAC in individuals with T2D, given its differential expression in this specific cohort.}, + author = {Nilchi, Amirhossein Naghsh and Dehghanian, Fariba and Vallian, Sadeq and Bahreini, Amin}, + copyright = {cc by-nc-nd}, + doi = {10.1038/s41598-025-21200-5}, + issn = {2045-2322}, + journal = {Scientific reports}, + keywords = {{\textgreater}UseGalaxy.eu, Cebpz Gene, Co-expression, Differential expression, Pancreatic cancer, Type 2 diabetes, Wgcna}, + language = {eng}, + month = {October}, + number = {1}, + pages = {37288}, + title = {Dissecting {lncRNA}-{mRNA} regulatory network in type 2 diabetes as the risk factor of pancreatic cancer}, + url = {https://europepmc.org/articles/PMC12552502}, + urldate = {2025-12-26}, + volume = {15}, + year = {2025} +} + @book{nilsson_benchmarking_2024, abstract = {DiVA portal is a finding tool for research publications and student theses written at the following 50 universities and research institutions.}, author = {Nilsson, Alma}, @@ -15785,6 +16618,21 @@ @book{nilsson_benchmarking_2024 year = {2024} } +@article{noauthor_58_2025, + issn = {1660-3818}, + journal = {Transfusion medicine and hemotherapy}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {September}, + number = {Suppl 1}, + pages = {1--88}, + title = {58. {Jahrestagung} der {Deutschen} {Gesellschaft} für {Transfusionsmedizin} und {Immunhämatologie} e.{V}. ({DGTI}}, + url = {https://europepmc.org/articles/PMC12580739}, + urldate = {2025-12-26}, + volume = {52}, + year = {2025} +} + @article{noauthor_abstract_2022, issn = {2572-9241}, journal = {Hemasphere}, @@ -15798,6 +16646,20 @@ @article{noauthor_abstract_2022 year = {2022} } +@article{noauthor_abstracts_2025, + doi = {10.1186/s12936-025-05498-0}, + issn = {1475-2875}, + journal = {Malaria Journal}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {December}, + number = {Suppl 1}, + pages = {423}, + title = {Abstracts of the 9th {International} {Conference} on {Plasmodium} vivax {Research} ({ICPvR}) 2025}, + volume = {24}, + year = {2025} +} + @misc{noauthor_amazonian_2024, keywords = {{\textgreater}UseGalaxy.eu}, month = {October}, @@ -15870,8 +16732,8 @@ @article{noauthor_clostridium_2025 keywords = {{\textgreater}UseGalaxy.eu}, language = {en-US}, month = {January}, - note = {Publisher: Elsevier}, pages = {100339}, + publisher = {Elsevier}, shorttitle = {Clostridium tetani bacteraemia in the plague area in {France}}, title = {Clostridium tetani bacteraemia in the plague area in {France}: {Two} cases}, url = {https://www.sciencedirect.com/science/article/pii/S266651742500001X}, @@ -15919,6 +16781,15 @@ @misc{noauthor_effect_2024 year = {2024} } +@misc{noauthor_erga-bge_2025, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {December}, + title = {{ERGA}-{BGE} reference genome of {Hirudo} verbana, ... {\textbar} {Open} {Research} {Europe}}, + url = {https://open-research-europe.ec.europa.eu/articles/5-395}, + urldate = {2025-12-25}, + year = {2025} +} + @misc{noauthor_exome_2025, abstract = {Inherited Retinal Dystrophies (IRD) are rare and heterogeneous blindness-causing diseases caused by pathogenic variants in genes involved in retina function.}, journal = {Scilit}, @@ -16067,8 +16938,8 @@ @article{nogell_structure_2024 keywords = {{\textgreater}UseGalaxy.eu}, language = {en\_US}, month = {September}, - note = {Accepted: 2024-10-04T07:42:23Z -Publisher: Univerzita Karlova, Přírodovědecká fakulta}, + note = {Accepted: 2024-10-04T07:42:23Z}, + publisher = {Univerzita Karlova, Přírodovědecká fakulta}, title = {Structure and function of the ribosomal intergenic {DNA}}, url = {https://dspace.cuni.cz/handle/20.500.11956/194217}, urldate = {2024-11-17}, @@ -16137,9 +17008,9 @@ @article{nuhrenberg_impact_2022 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, language = {eng}, month = {January}, - note = {Publisher: Public Library of Science (PLoS)}, number = {1}, pages = {e0260222}, + publisher = {Public Library of Science (PLoS)}, title = {Impact of high platelet turnover on the platelet transcriptome: {Results} from platelet {RNA}-sequencing in patients with sepsis}, url = {https://doi.org/10.1371/journal.pone.0260222}, volume = {17}, @@ -16156,10 +17027,10 @@ @article{nunez-sanchez_characterizing_2020 keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Enterococcus faecalis, Herelleviridae, IBD, bacteriophage, intestinal model, phage therapy}, language = {en}, month = {September}, - note = {Number: 9 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 9}, number = {9}, pages = {1374}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Characterizing {Phage}-{Host} {Interactions} in a {Simplified} {Human} {Intestinal} {Barrier} {Model}}, url = {https://www.mdpi.com/2076-2607/8/9/1374}, urldate = {2021-01-07}, @@ -16229,9 +17100,9 @@ @article{ocejo_whole-genome_2024 journal = {Microbiology Spectrum}, keywords = {{\textgreater}UseGalaxy.eu, Anti-Infective Agents, Daptomycin, Enterococcus faecium, Gram-Positive Bacterial Infections}, month = {January}, - note = {Publisher: American Society for Microbiology}, number = {2}, pages = {e03672--23}, + publisher = {American Society for Microbiology}, title = {Whole-genome long-read sequencing to unveil {Enterococcus} antimicrobial resistance in dairy cattle farms exposed a widespread occurrence of {Enterococcus} lactis}, url = {https://journals.asm.org/doi/full/10.1128/spectrum.03672-23}, urldate = {2025-02-28}, @@ -16247,9 +17118,9 @@ @article{oeyen_sawfly_2020 keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, language = {en}, month = {July}, - note = {Publisher: Oxford Academic}, number = {7}, pages = {1099--1188}, + publisher = {Oxford Academic}, title = {Sawfly {Genomes} {Reveal} {Evolutionary} {Acquisitions} {That} {Fostered} the {Mega}-{Radiation} of {Parasitoid} and {Eusocial} {Hymenoptera}}, url = {https://academic.oup.com/gbe/article/12/7/1099/5842140}, urldate = {2020-08-20}, @@ -16282,7 +17153,7 @@ @article{ogunnupebi_silico_2024 keywords = {{\textgreater}UseGalaxy.eu, ADMET properties, benzothiazole, insecticidal activity, malaria, vector control}, language = {English}, month = {August}, - note = {Publisher: Frontiers}, + publisher = {Frontiers}, title = {In silico studies of benzothiazole derivatives as potential inhibitors of {Anopheles} funestus and {Anopheles} gambiae trehalase}, url = {https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2024.1428539/full}, urldate = {2025-02-28}, @@ -16297,7 +17168,7 @@ @incollection{ohta_hybrid_2023 booktitle = {Nanopore {Sequencing}: {Methods} and {Protocols}}, doi = {10.1007/978-1-0716-2996-3_2}, editor = {Arakawa, Kazuharu}, - isbn = {978-1-07-162996-3}, + isbn = {978-1-0716-2996-3}, keywords = {{\textgreater}UseGalaxy.eu, Galaxy, Hybrid genome assembly, Long-read sequencing, Nanopore sequencing, Visualizations, Workflow}, language = {en}, pages = {15--30}, @@ -16318,8 +17189,6 @@ @article{okafor_targeting_2025 keywords = {{\textgreater}UseGalaxy.eu}, month = {August}, pages = {1038}, - pmcid = {PMC12366235}, - pmid = {40830840}, shorttitle = {Targeting invasion-associated proteins {PfSUB2} and {PfTRAMP} in {Plasmodium} falciparum}, title = {Targeting invasion-associated proteins {PfSUB2} and {PfTRAMP} in {Plasmodium} falciparum: identification of potential inhibitors via molecular docking}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12366235/}, @@ -16364,6 +17233,7 @@ @misc{oliveira_cocoa_2023 @article{oliveira_integrated_2024, abstract = {During the COVID-19 pandemic, RNA-seq datasets were produced to investigate the virus–host relationship. However, much of these data remains underexplored. To improve the search for molecular targets and biomarkers, we performed an integrated analysis of multiple RNA-seq datasets, expanding the cohort and including patients from different countries, encompassing severe and mild COVID-19 patients. Our analysis revealed that severe COVID-19 patients exhibit overexpression of genes coding for proteins of extracellular exosomes, endomembrane system, and neutrophil granules (e.g., S100A9, LY96, and RAB1B), which may play an essential role in the cellular response to infection. Concurrently, these patients exhibit down-regulation of genes encoding components of the T cell receptor complex and nucleolus, including TP53, IL2RB, and NCL. Finally, SPI1 may emerge as a central transcriptional factor associated with the up-regulated genes, whereas TP53, MYC, and MAX were associated with the down-regulated genes during COVID-19. This study identified targets and transcriptional factors, lighting on the molecular pathophysiology of syndrome coronavirus 2 infection.}, author = {Oliveira, Thais Teixeira and Freitas, Júlia Firme and Medeiros, Viviane Priscila Barros de and Xavier, Thiago Jesus da Silva and Agnez-Lima, Lucymara Fassarella}, + chapter = {Research Articles}, copyright = {© 2024 Oliveira et al.. https://creativecommons.org/licenses/by/4.0/This article is available under a Creative Commons License (Attribution 4.0 International, as described at https://creativecommons.org/licenses/by/4.0/).}, doi = {10.26508/lsa.202302358}, issn = {2575-1077}, @@ -16371,11 +17241,9 @@ @article{oliveira_integrated_2024 keywords = {{\textgreater}UseGalaxy.eu, COVID-19}, language = {en}, month = {April}, - note = {Publisher: Life Science Alliance -Section: Research Articles}, number = {4}, pages = {e202302358}, - pmid = {38262689}, + publisher = {Life Science Alliance}, title = {Integrated analysis of {RNA}-seq datasets reveals novel targets and regulators of {COVID}-19 severity}, url = {https://www.life-science-alliance.org/content/7/4/e202302358}, urldate = {2024-05-17}, @@ -16393,10 +17261,10 @@ @article{olszak-przybys_diversity_2024 keywords = {\textit{Glycine max} (L.) Merrill, {\textgreater}UseGalaxy.eu, Fungi, Glycine max, Seeds, fungal barcoding, seed-borne fungi, soybean, storage fungi}, language = {en}, month = {September}, - note = {Number: 9 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 9}, number = {9}, pages = {769}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {The {Diversity} of {Seed}-{Borne} {Fungi} {Associated} with {Soybean} {Grown} in {Southern} {Poland}}, url = {https://www.mdpi.com/2076-0817/13/9/769}, urldate = {2024-10-20}, @@ -16414,10 +17282,10 @@ @article{olszak-przybys_identification_2023 keywords = {\textit{Fusarium} species, \textit{Glycine max} (L.) Merrill, {\textgreater}UseGalaxy.eu, RNA polymerase second largest subunit, pathogenicity, root rot, soil-borne fungi, soybean, translation elongation factor 1-alpha}, language = {en}, month = {September}, - note = {Number: 9 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 9}, number = {9}, pages = {1162}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Identification and {Pathogenicity} of {Fusarium} {Isolated} from {Soybean} in {Poland}}, url = {https://www.mdpi.com/2076-0817/12/9/1162}, urldate = {2024-11-17}, @@ -16435,9 +17303,9 @@ @article{omenge_seor2_2025 keywords = {{\textgreater}UseGalaxy.eu, Arabidopsis, Arabidopsis Proteins, Calcium, Phytoplasma, Plant Diseases, Plant sciences, Plant stress responses}, language = {en}, month = {May}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {17829}, + publisher = {Nature Publishing Group}, title = {{SEOR2} in {Arabidopsis} mediates {Ca2}+ dependent defense against phytoplasmas and reduction of plant growth}, url = {https://www.nature.com/articles/s41598-025-01374-8}, urldate = {2025-05-28}, @@ -16489,6 +17357,25 @@ @article{ortega_ramirez_molecular_2024 year = {2024} } +@article{orwa_chaetomium_2025, + abstract = {Late blight is a disease whose causative agent is the oomycete Phytophthora infestans. It is one of the most destructive pathogenic oomycetes and a major challenge to global tomato production. The pathogen is difficult to manage because of its ability to evolve thereby evading host resistance. The aim of this study was to screen for potential antagonists of P. infestans using a combination of culture and microbiome-based approaches. Samples were collected from healthy and P. infestans-infected tomato plants grown in soil collected from two organic tomato growers in the Rhine-Main area in Germany. A total of 246 fungal isolates were screened for their antagonistic activity against P. infestans. Most of the isolates that exhibited in vitro antagonistic activity were from the genera Penicillium, Trichoderma, Chlonostachys, Mortierella, and Pseudogymnoascus. Following a stepwise in vitro screening strategy that accounted for growth features, ecological aspects, taxonomic data, potential health risks, commercial properties, and antagonistic efficacy, five fungal isolates were eventually selected for plant trials. Chaetomium subaffine showed the highest inhibitory effect against P. infestans across three trials whereby the percentage of diseased leaf area reduced by 90\% compared to the control. Chlonostachys and Pseudogymnoascus spp. were effective in two trials, while Trichoderma and Ctenomyces spp. showed weak disease suppressive effects. In parallel, we characterized the fungal microbiome of the rhizosphere, phyllosphere, and endosphere from healthy and diseased tomato plants using ITS-rRNA sequencing. The fungal community differed significantly between the two soil origins, but P. infestans did not significantly influence fungal microbiota composition. Notably, 70\% of our antagonistic fungi from the culture collection were detected in the tomato microbiome. This work identified isolates of Chaetomium subaffine, Clonostachys sp., and Pseudogymnoascus sp. as potential biocontrol candidates promoting plant health. The findings highlight the importance of combined functional screening and microbiome profiling for identifying fungal antagonists.}, + author = {Orwa, Philemon and Kuhl-Nagel, Theresa and Meinhold-Ernst, Rosa and Seyer, Arne and Jehle, Johannes A and Mwirichia, Romano and Linkies, Ada}, + copyright = {cc by}, + doi = {10.1371/journal.pone.0335007}, + issn = {1932-6203}, + journal = {PloS one}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {January}, + number = {10}, + pages = {e0335007}, + title = {Chaetomium, {Chlonostachys}, and {Pseudogymnoascus} isolates from tomato tissues significantly suppress {Phytophthora} infestans in tomato}, + url = {https://europepmc.org/articles/PMC12551835}, + urldate = {2025-12-26}, + volume = {20}, + year = {2025} +} + @article{osca_complete_2022, abstract = {The complete nucleotide sequence of the mitochondrial (mt) genome of the demersal zebra seabream \textit{Diplodus cervinus} (Lowe, 1838) was determined for the first time. The double stranded circular molecule is 16,559 base pairs (bp) in length and encodes for the typical 37 metazoan mitochondrial genes, and 2 non-coding regions (D-loop and L-origin). The gene arrangement of the \textit{D. cervinus} mt genome follows the usual one for fishes. The nucleotide sequences of the mt protein coding and ribosomal genes of \textit{D. cervinus} mt genome were aligned with orthologous sequences from representatives of the Sparidae family and phylogenetic relationships were inferred. Maximum likelihood analyses placed \textit{D. cervinus} as a sister species of \textit{Diplodus sargus} (Linnaeus, 1758).}, author = {Osca, David and Caputi, Luigi and Tanduo, Valentina and Sepe, Rosa Maria and Liberti, Assunta and Tiralongo, Francesco and Venuti, Iolanda and Ceruso, Marina and Crocetta, Fabio and Sordino, Paolo and Pepe, Tiziana}, @@ -16514,9 +17401,9 @@ @article{oselusi_cheminformatic_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, language = {eng}, month = {June}, - note = {Publisher: MDPI AG}, number = {13}, pages = {3970}, + publisher = {MDPI AG}, title = {Cheminformatic {Characterization} of {Natural} {Antimicrobial} {Products} for the {Development} of {New} {Lead} {Compounds}}, url = {https://doi.org/10.3390/molecules26133970}, volume = {26}, @@ -16532,7 +17419,7 @@ @article{ostenfeld_hybrid_2024 keywords = {{\textgreater}UseGalaxy.eu, Campylobacter, Flagella, Fletchervirus, Phage, Receptor binding protein, flagellotropic phage, phage receptor, phage resistance}, language = {English}, month = {February}, - note = {Publisher: Frontiers}, + publisher = {Frontiers}, title = {A hybrid receptor binding protein enables phage {F341} infection of {Campylobacter} by binding to flagella and lipooligosaccharides}, url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2024.1358909/full}, urldate = {2024-03-30}, @@ -16571,11 +17458,10 @@ @article{ou_differences_2024 note = {Company: Cold Spring Harbor Laboratory Press Distributor: Cold Spring Harbor Laboratory Press Institution: Cold Spring Harbor Laboratory Press -Label: Cold Spring Harbor Laboratory Press -Publisher: Cold Spring Harbor Lab}, +Label: Cold Spring Harbor Laboratory Press}, number = {8}, pages = {1140--1153}, - pmid = {39251347}, + publisher = {Cold Spring Harbor Lab}, title = {Differences in activity and stability drive transposable element variation in tropical and temperate maize}, url = {https://genome.cshlp.org/content/34/8/1140}, urldate = {2024-11-17}, @@ -16665,8 +17551,8 @@ @article{pachanon_genomic_2024 keywords = {{\textgreater}UseGalaxy.eu, Carbapenem resistance, Colistin resistance, Klebsiella pneumoniae, Plasmidmediated resistance, whole genome analysis}, language = {English}, month = {May}, - note = {Publisher: Frontiers}, pages = {1386496}, + publisher = {Frontiers}, title = {Genomic characterization of carbapenem and colistin-resistant {Klebsiella} pneumoniae isolates from humans and dogs}, url = {https://www.frontiersin.org/articles/10.3389/fvets.2024.1386496}, urldate = {2024-06-07}, @@ -16700,9 +17586,9 @@ @article{page-karjian_fibropapillomatosis_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, language = {eng}, month = {October}, - note = {Publisher: MDPI AG}, number = {11}, pages = {3076}, + publisher = {MDPI AG}, title = {Fibropapillomatosis and {Chelonid} {Alphaherpesvirus} 5 {Infection} in {Kemp}'s {Ridley} {Sea} {Turtles} ({Lepidochelys} kempii)}, url = {https://doi.org/10.3390/ani11113076}, volume = {11}, @@ -16718,10 +17604,9 @@ @article{paiva_ld-transpeptidation_2025 keywords = {{\textgreater}UseGalaxy.eu}, language = {English}, month = {April}, - note = {Publisher: Elsevier}, number = {4}, pages = {112227}, - pmid = {40224013}, + publisher = {Elsevier}, title = {The l,d-transpeptidation pathway is inhibited by antibiotics of the β-lactam class in {Clostridioides} difficile}, url = {https://www.cell.com/iscience/abstract/S2589-0042(25)00488-2}, urldate = {2025-05-29}, @@ -16739,10 +17624,10 @@ @article{palacios-rodriguez_antimicrobial_2024 keywords = {\textit{Bacillus amyloliquefaciens} BS4, {\textgreater}NanoGalaxy, {\textgreater}UseGalaxy.eu, antimicrobial activity, broad-spectrum metabolites, culture conditions}, language = {en}, month = {April}, - note = {Number: 4 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 4}, number = {4}, pages = {304}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Antimicrobial {Activity} of {Bacillus} amyloliquefaciens {BS4} against {Gram}-{Negative} {Pathogenic} {Bacteria}}, url = {https://www.mdpi.com/2079-6382/13/4/304}, urldate = {2024-04-08}, @@ -16811,8 +17696,8 @@ @article{pallares-vega_temperature_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, language = {eng}, month = {July}, - note = {Publisher: Frontiers Media SA}, pages = {656250}, + publisher = {Frontiers Media SA}, title = {Temperature and {Nutrient} {Limitations} {Decrease} {Transfer} of {Conjugative} {IncP}-1 {Plasmid} {pKJK5} to {Wild} {Escherichia} coli {Strains}}, url = {https://doi.org/10.3389/fmicb.2021.656250}, volume = {12}, @@ -16846,9 +17731,9 @@ @article{panagiotopoulou_quorum_2025 keywords = {{\textgreater}UseGalaxy.eu, Adaptation, Physiological, Iron, Pseudomonas aeruginosa, Quorum Sensing, RNA, Bacterial, RNA, Small Untranslated}, language = {en}, month = {April}, - note = {Publisher: John Wiley \& Sons, Ltd}, number = {2}, pages = {e70090}, + publisher = {John Wiley \& Sons, Ltd}, title = {The {Quorum} {Sensing} {Regulated} {sRNA} {Lrs1} {Is} {Involved} in the {Adaptation} to {Low} {Iron} in {Pseudomonas} aeruginosa}, url = {https://enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/1758-2229.70090}, urldate = {2025-05-29}, @@ -16866,10 +17751,10 @@ @article{pannhorst_non-classical_2023 keywords = {{\textgreater}UseGalaxy.eu, African Swine Fever, African Swine Fever Virus, Craniocerebral Trauma, High-throughput screening, Virus–host interactions}, language = {en}, month = {August}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {10342}, + publisher = {Nature Publishing Group}, title = {The non-classical major histocompatibility complex {II} protein {SLA}-{DM} is crucial for {African} swine fever virus replication}, url = {https://www.nature.com/articles/s41598-023-36788-9}, urldate = {2023-08-24}, @@ -16884,9 +17769,9 @@ @article{panzitt_fxr_2025 journal = {Science Translational Medicine}, keywords = {{\textgreater}UseGalaxy.eu}, month = {August}, - note = {Publisher: American Association for the Advancement of Science}, number = {811}, pages = {eadn4558}, + publisher = {American Association for the Advancement of Science}, title = {{FXR} adapts hepatic mitochondrial function to increased substrate oxidation in patients with obesity}, url = {https://www.science.org/doi/full/10.1126/scitranslmed.adn4558}, urldate = {2025-09-03}, @@ -17021,8 +17906,8 @@ @article{paula_complete_2024 keywords = {{\textgreater}UseGalaxy.eu}, language = {en}, month = {November}, - note = {Publisher: PeerJ Inc.}, pages = {e18255}, + publisher = {PeerJ Inc.}, title = {The complete mitochondrial {DNA} of the carnivorous sponge {Lycopodina} hypogea is putatively complemented by {microDNAs}}, url = {https://peerj.com/articles/18255}, urldate = {2025-09-03}, @@ -17067,7 +17952,7 @@ @article{pelletier_standardized_2021 doi = {10.3389/fmars.2021.689280}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {July}, - note = {Publisher: Frontiers Media SA}, + publisher = {Frontiers Media SA}, title = {A {Standardized} {Workflow} {Based} on the {STAVIRO} {Unbaited} {Underwater} {Video} {System} for {Monitoring} {Fish} and {Habitat} {Essential} {Biodiversity} {Variables} in {Coastal} {Areas}}, url = {https://doi.org/10.3389/fmars.2021.689280}, volume = {8}, @@ -17083,7 +17968,6 @@ @article{pelos_fast_2023 keywords = {{\textgreater}UseGalaxy.eu, NCI-H460, NSCLC, drug resistance, epigenetic drugs, senescence}, language = {eng}, month = {November}, - pmid = {37947765}, title = {Fast proliferating and slowly migrating non-small cell lung cancer cells are vulnerable to decitabine and retinoic acid combinatorial treatment}, year = {2023} } @@ -17098,9 +17982,9 @@ @article{penaranda_dna_2025 keywords = {{\textgreater}UseGalaxy.eu, Biochemistry, Biological techniques, Biotechnology, Molecular biology}, language = {en}, month = {August}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {30879}, + publisher = {Nature Publishing Group}, title = {{DNA} aptamer {AptERA} 2 targets {ERA} from {Staphylococcus} aureus and limits {GTP} hydrolysis}, url = {https://www.nature.com/articles/s41598-025-15180-9}, urldate = {2025-09-03}, @@ -17133,10 +18017,10 @@ @article{perez-schindler_characterization_2022 keywords = {{\textgreater}UseGalaxy.eu, Cell biology, Genetics, Molecular biology, Molecular medicine, Non-alcoholic Fatty Liver Disease}, language = {en}, month = {July}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {11477}, + publisher = {Nature Publishing Group}, title = {Characterization of regulatory transcriptional mechanisms in hepatocyte lipotoxicity}, url = {https://www.nature.com/articles/s41598-022-15731-4}, urldate = {2023-08-06}, @@ -17149,7 +18033,7 @@ @article{perez-schindler_discovery_2021 doi = {10.1101/2021.03.24.436772}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {March}, - note = {Publisher: Cold Spring Harbor Laboratory}, + publisher = {Cold Spring Harbor Laboratory}, title = {Discovery of lipotoxicity-sensitive transcription factors in non-alcoholic steatohepatitis}, url = {https://doi.org/10.1101/2021.03.24.436772}, year = {2021} @@ -17164,9 +18048,9 @@ @article{perez-schindler_rna-bound_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, language = {eng}, month = {August}, - note = {Publisher: Proceedings of the National Academy of Sciences}, number = {36}, pages = {e2105951118}, + publisher = {Proceedings of the National Academy of Sciences}, title = {{RNA}-bound {PGC}-1\${\textbackslash}upalpha\$ controls gene expression in liquid-like nuclear condensates}, url = {https://doi.org/10.1073/pnas.2105951118}, volume = {118}, @@ -17187,6 +18071,7 @@ @article{perez-sisques_deficiency_2024 @article{perez-sisques_intellectual_2024, abstract = {The histone lysine demethylase KDM5B is implicated in recessive intellectual disability disorders, and heterozygous, protein-truncating variants in KDM5B are associated with reduced cognitive function in the population. The KDM5 family of lysine demethylases has developmental and homeostatic functions in the brain, some of which appear to be independent of lysine demethylase activity. To determine the functions of KDM5B in hippocampus-dependent learning and memory, we first studied male and female mice homozygous for a Kdm5bΔARID allele that lacks demethylase activity. Kdm5bΔARID/ΔARID mice exhibited hyperactivity and long-term memory deficits in hippocampus-dependent learning tasks. The expression of immediate early, activity-dependent genes was downregulated in these mice and hyperactivated upon a learning stimulus compared with wild-type (WT) mice. A number of other learning-associated genes were also significantly dysregulated in the Kdm5bΔARID/ΔARID hippocampus. Next, we knocked down Kdm5b specifically in the adult, WT mouse hippocampus with shRNA. Kdm5b knockdown resulted in spontaneous seizures, hyperactivity, and hippocampus-dependent long-term memory and long-term potentiation deficits. These findings identify KDM5B as a critical regulator of gene expression and synaptic plasticity in the adult hippocampus and suggest that at least some of the cognitive phenotypes associated with KDM5B gene variants are caused by direct effects on memory consolidation mechanisms.}, author = {Pérez-Sisqués, Leticia and Bhatt, Shail U. and Matuleviciute, Rugile and Gileadi, Talia E. and Kramar, Eniko and Graham, Andrew and Garcia, Franklin G. and Keiser, Ashley and Matheos, Dina P. and Cain, James A. and Pittman, Alan M. and Andreae, Laura C. and Fernandes, Cathy and Wood, Marcelo A. and Giese, K. Peter and Basson, M. Albert}, + chapter = {Research Articles}, copyright = {Copyright © 2024 Perez-Sisques et al.. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license, which permits unrestricted use, distribution and reproduction in any medium provided that the original work is properly attributed.}, doi = {10.1523/JNEUROSCI.1544-23.2024}, issn = {0270-6474, 1529-2401}, @@ -17194,11 +18079,9 @@ @article{perez-sisques_intellectual_2024 keywords = {{\textgreater}UseGalaxy.eu, Hippocampus, Intellectual Disability, Jumonji Domain-Containing Histone Demethylases, KDM5B, Memory Consolidation, Memory, Long-Term, chromatin, hippocampus, histone lysine demethylase, learning, memory, mouse}, language = {en}, month = {May}, - note = {Publisher: Society for Neuroscience -Section: Research Articles}, number = {19}, pages = {e1544232024}, - pmid = {38575342}, + publisher = {Society for Neuroscience}, title = {The {Intellectual} {Disability} {Risk} {Gene} {Kdm5b} {Regulates} {Long}-{Term} {Memory} {Consolidation} in the {Hippocampus}}, url = {https://www.jneurosci.org/content/44/19/e1544232024}, urldate = {2024-05-17}, @@ -17216,9 +18099,9 @@ @article{perez_investigating_2025 keywords = {{\textgreater}UseGalaxy.eu, Cancer, Cancer genomics, Proteomics}, language = {en}, month = {January}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {813}, + publisher = {Nature Publishing Group}, title = {Investigating proteogenomic divergence in patient-derived xenograft models of ovarian cancer}, url = {https://www.nature.com/articles/s41598-024-84874-3}, urldate = {2025-01-08}, @@ -17279,8 +18162,6 @@ @article{pessoa_rodrigues_histone_2021 month = {October}, number = {1}, pages = {6212}, - pmcid = {PMC8551339}, - pmid = {34707105}, title = {Histone {H4} lysine 16 acetylation controls central carbon metabolism and diet-induced obesity in mice}, volume = {12}, year = {2021} @@ -17295,9 +18176,9 @@ @article{peters_metabolic_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, language = {eng}, month = {September}, - note = {Publisher: Springer Science and Business Media LLC}, number = {1}, pages = {18822}, + publisher = {Springer Science and Business Media LLC}, title = {Metabolic drift in the aging nervous system is reflected in human cerebrospinal fluid}, url = {https://doi.org/10.1038/s41598-021-97491-1}, volume = {11}, @@ -17333,10 +18214,10 @@ @article{pfaffle_14-day_2024 keywords = {\textit{Escherichia coli}, {\textgreater}UseGalaxy.eu, BITC, Gastrointestinal Microbiome, Nasturtium, Tropaeolum, antimicrobial, gut microbiome, human beta defensin 1, metabolome, nasturtium}, language = {en}, month = {January}, - note = {Number: 3 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 3}, number = {3}, pages = {373}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {A 14-{Day} {Double}-{Blind}, {Randomized}, {Controlled} {Crossover} {Intervention} {Study} with {Anti}-{Bacterial} {Benzyl} {Isothiocyanate} from {Nasturtium} ({Tropaeolum} majus) on {Human} {Gut} {Microbiome} and {Host} {Defense}}, url = {https://www.mdpi.com/2072-6643/16/3/373}, urldate = {2024-05-17}, @@ -17353,10 +18234,10 @@ @article{pham_epigenetic_2024 keywords = {{\textgreater}UseGalaxy.eu, CBX7, Cerebral Cavernous Malformation, Epigenesis, Genetic, Hemangioma, Cavernous, Central Nervous System, KLF2, Polycomb Repressive Complex 1, WNT9, Zebrafish, Zebrafish Proteins, endoMT}, language = {eng}, month = {October}, - note = {Num Pages: 29 -Publisher: Springer Nature}, + note = {Num Pages: 29}, number = {11}, pages = {1--29}, + publisher = {Springer Nature}, title = {Epigenetic regulation by polycomb repressive complex 1 promotes cerebral cavernous malformations}, url = {https://www.embopress.org/doi/full/10.1038/s44321-024-00152-9}, urldate = {2024-10-20}, @@ -17370,8 +18251,8 @@ @article{phan_transcriptome_2021 journal = {Scientific Reports}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {November}, - note = {Publisher: Springer Science and Business Media LLC}, number = {1}, + publisher = {Springer Science and Business Media LLC}, title = {The transcriptome of {Balamuthia} mandrillaris trophozoites for structure-guided drug design}, url = {https://doi.org/10.1038/s41598-021-99903-8}, volume = {11}, @@ -17388,10 +18269,10 @@ @article{phillip_molecular_2023 keywords = {\textit{S. epidermidis}, \textit{S. haemolyticus}, {\textgreater}UseGalaxy.eu, genes for AMR, icaC virulence genes}, language = {en}, month = {February}, - note = {Number: 2 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 2}, number = {2}, pages = {180}, + publisher = {Multidisciplinary Digital Publishing Institute}, shorttitle = {Molecular {Characterizations} of the {Coagulase}-{Negative} {Staphylococci} {Species} {Causing} {Urinary} {Tract} {Infection} in {Tanzania}}, title = {Molecular {Characterizations} of the {Coagulase}-{Negative} {Staphylococci} {Species} {Causing} {Urinary} {Tract} {Infection} in {Tanzania}: {A} {Laboratory}-{Based} {Cross}-{Sectional} {Study}}, url = {https://www.mdpi.com/2076-0817/12/2/180}, @@ -17423,9 +18304,9 @@ @article{pick_complete_2024 journal = {Microbiology Resource Announcements}, keywords = {{\textgreater}UseGalaxy.eu}, month = {March}, - note = {Publisher: American Society for Microbiology}, number = {0}, pages = {e01216--23}, + publisher = {American Society for Microbiology}, title = {Complete genome sequence of {Escherichia} coli {MP1}}, url = {https://journals.asm.org/doi/full/10.1128/mra.01216-23}, urldate = {2024-03-17}, @@ -17495,10 +18376,10 @@ @article{pilliol_methanobrevibacter_2024 keywords = {\textit{Archaea}, \textit{Methanobrevibacter massiliense}, \textit{Pyramidobacter piscolens}, \textit{Synergistetes}, {\textgreater}UseGalaxy.eu, dental pulp, hydrogen-free culture, methanogen}, language = {en}, month = {January}, - note = {Number: 1 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 1}, number = {1}, pages = {215}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Methanobrevibacter massiliense and {Pyramidobacter} piscolens {Co}-{Culture} {Illustrates} {Transkingdom} {Symbiosis}}, url = {https://www.mdpi.com/2076-2607/12/1/215}, urldate = {2024-04-28}, @@ -17516,8 +18397,6 @@ @article{pimentel_description_2023 month = {December}, number = {4}, pages = {e51}, - pmcid = {PMC10788360}, - pmid = {38224718}, title = {Description of eight new mitochondrial genomes for the genus {Neoarius} and phylogenetic considerations for the family {Ariidae} ({Siluriformes})}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10788360/}, urldate = {2024-01-20}, @@ -17550,7 +18429,7 @@ @article{pinter_maxquant_2022 journal = {Journal of Proteome Research}, keywords = {+IsGalaxy, {\textgreater}UseGalaxy.eu}, month = {May}, - note = {Publisher: American Chemical Society}, + publisher = {American Chemical Society}, title = {{MaxQuant} and {MSstats} in {Galaxy} {Enable} {Reproducible} {Cloud}-{Based} {Analysis} of {Quantitative} {Proteomics} {Experiments} for {Everyone}}, url = {https://doi.org/10.1021/acs.jproteome.2c00051}, urldate = {2022-05-04}, @@ -17567,10 +18446,10 @@ @article{pinto_rescue_2024 keywords = {\textit{Mycobacterium bovis}, {\textgreater}UseGalaxy.eu, animal tuberculosis, computational biology, mixed infection, whole genome amplification, whole genome sequencing}, language = {en}, month = {January}, - note = {Number: 7 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 7}, number = {7}, pages = {3869}, + publisher = {Multidisciplinary Digital Publishing Institute}, shorttitle = {Rescue of {Mycobacterium} bovis {DNA} {Obtained} from {Cultured} {Samples} during {Official} {Surveillance} of {Animal} {TB}}, title = {Rescue of {Mycobacterium} bovis {DNA} {Obtained} from {Cultured} {Samples} during {Official} {Surveillance} of {Animal} {TB}: {Key} {Steps} for {Robust} {Whole} {Genome} {Sequence} {Data} {Generation}}, url = {https://www.mdpi.com/1422-0067/25/7/3869}, @@ -17589,9 +18468,9 @@ @article{pirnay_personalized_2024 keywords = {{\textgreater}UseGalaxy.eu, Anti-Bacterial Agents, Antimicrobial resistance, Bacterial Infections, Bacterial genetics, Bacterial infection, Bacteriophages, Phage Therapy}, language = {en}, month = {June}, - note = {Publisher: Nature Publishing Group}, number = {6}, pages = {1434--1453}, + publisher = {Nature Publishing Group}, shorttitle = {Personalized bacteriophage therapy outcomes for 100 consecutive cases}, title = {Personalized bacteriophage therapy outcomes for 100 consecutive cases: a multicentre, multinational, retrospective observational study}, url = {https://www.nature.com/articles/s41564-024-01705-x}, @@ -17649,6 +18528,26 @@ @article{pitt_biodiversity_2025 year = {2025} } +@article{plata_suarez_unlocking_2025, + abstract = {Phage therapy has emerged as a promising alternative for combating infections caused by drug-resistant pathogens. Among these, Enterococcus faecalis remains a significant public health concern due to its persistence in clinical settings and frequent involvement in healthcare-associated infections (HAIs). In this study, we report the characterization of the lytic bacteriophage vB\_EfaS\_LOK1, isolated from urban sewage using E. faecalis strain IIH-74.4 as the host. Transmission electron microscopy revealed morphological features consistent with the phages formerly classified within the Siphoviridae family. The phage exhibited high thermal and pH stability, remaining viable up to 70 °C and within a pH range of 4-11. It displayed a latent period of 20 min and a burst size of 72 PFU/cell. Notably, vB\_EfaS\_LOK1 exhibited a narrow host range, lysing only the strain used for their isolation. Genomic analysis revealed a 41.2 kb double-stranded DNA genome devoid of known virulence or antibiotic resistance genes. Phylogenomic analysis classified the phage within the genus Efquatrovirus (Caudoviricetes), suggesting it represents a newly isolated bacteriophage species. Functional annotation identified genes related to DNA replication, host interaction, and bacterial lysis, including endolysins and holins with putative antimicrobial properties. Long-term stability assays demonstrated that tryptic soy broth (TSB) with CaCl2/MgCl2 at 4 °C maintained viability for at least 90 days. Collectively, these findings support the potential of vB\_EfaS\_LOK1 as a potential candidate for the development of phage-based therapies targeting E. faecalis.}, + author = {Plata Suarez, Laura Marcela and Del Valle Balbuena, Salvador and Becerra Mejía, Isamar Leticia and Loera Piedra, Alejandra Aidee and Domínguez Espinoza, Cristina and Ángeles González, Arantxa Monserrat and Contreras Rodríguez, Araceli and Aquino Andrade, Alejandra and Martínez Díaz, Sergio Francisco and Aguilera Arreola, Ma Guadalupe}, + copyright = {cc by}, + doi = {10.3390/microorganisms13102414}, + issn = {2076-2607}, + journal = {Microorganisms}, + keywords = {{\textgreater}UseGalaxy.eu, Antibiotic Resistance, Bacteriophages, Enterococcus Faecalis Phage, Phage Therapy, Phylogenomic Analysis, Whole Genome Sequencing}, + language = {eng}, + month = {October}, + number = {10}, + pages = {2414}, + shorttitle = {Unlocking the {Potential} of \<i\>{vB}\</i\>\_\<i\>{EfaS}\</i\>\_\<i\>{LOK1}\</i\>}, + title = {Unlocking the {Potential} of \<i\>{vB}\</i\>\_\<i\>{EfaS}\</i\>\_\<i\>{LOK1}\</i\>: {A} {Newly} {Isolated} {Bacteriophage} {Against} \<i\>{Enterococcus} faecalis\</i\>}, + url = {https://europepmc.org/articles/PMC12566377}, + urldate = {2025-12-26}, + volume = {13}, + year = {2025} +} + @article{plaza_genomic_2023, author = {Plaza, David Fernando and Zerebinski, Julia and Broumou, Ioanna and Lautenbach, Maximilian Julius and Ngasala, Billy and Sundling, Christopher and Färnert, Anna}, doi = {10.1016/j.crmeth.2023.100574}, @@ -17657,8 +18556,8 @@ @article{plaza_genomic_2023 keywords = {{\textgreater}UseGalaxy.eu, CP: Biotechnology, CP: Microbiology, Malaria, Falciparum, Plasmodium, antigen discovery, circumsporozoite protein, genomic surveillance, glutamate-rich protein, long-read sequencing, malaria epidemiology, merozoite surface protein 1, merozoite surface protein 2}, language = {English}, month = {August}, - note = {Publisher: Elsevier}, number = {0}, + publisher = {Elsevier}, title = {A genomic platform for surveillance and antigen discovery in {Plasmodium} spp. using long-read amplicon sequencing}, url = {https://www.cell.com/cell-reports-methods/abstract/S2667-2375(23)00218-7}, urldate = {2023-09-14}, @@ -17672,7 +18571,7 @@ @article{plaza_protocol_2025 doi = {10.1016/j.xpro.2025.104093}, issn = {2666-1667}, journal = {STAR protocols}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Bioinformatics, Genomics, Microbiology, Molecular biology, Sequencing}, month = {September}, number = {4}, pages = {104093}, @@ -17689,8 +18588,8 @@ @article{plazas_avila_introduccion_2023 keywords = {{\textgreater}UseGalaxy.eu}, language = {Español}, month = {June}, - note = {Accepted: 2023-06-14T08:58:35Z -Publisher: Universitat Politècnica de València}, + note = {Accepted: 2023-06-14T08:58:35Z}, + publisher = {Universitat Politècnica de València}, shorttitle = {Introducción alas nuevas tecnologías}, title = {Introducción alas nuevas tecnologías: {MinION}, secuenciación en tiempo real}, url = {https://riunet.upv.es/handle/10251/194202}, @@ -17724,9 +18623,9 @@ @article{potgieter_metanovo_2023 keywords = {{\textgreater}UseGalaxy.eu, BLAST algorithm, Database searching, Metagenomics, Microbiome, Microbiota, Open source software, Proteomes, Sequence databases, Tandem Mass Spectrometry, Taxonomy}, language = {en}, month = {June}, - note = {Publisher: Public Library of Science}, number = {6}, pages = {e1011163}, + publisher = {Public Library of Science}, shorttitle = {{MetaNovo}}, title = {{MetaNovo}: {An} open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets}, url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011163}, @@ -17740,7 +18639,7 @@ @article{poulose_vprbp_2021 doi = {10.1101/2021.02.28.433236}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {February}, - note = {Publisher: Cold Spring Harbor Laboratory}, + publisher = {Cold Spring Harbor Laboratory}, title = {{VPRBP} functions downstream of the androgen receptor and {OGT} to restrict p53 activation in prostate cancer}, url = {https://doi.org/10.1101/2021.02.28.433236}, year = {2021} @@ -17849,9 +18748,9 @@ @article{punyawatthananukool_prostaglandin_2024 keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, Cancer, Chronic inflammation, Dinoprostone, Energy Metabolism, Immune evasion, Receptors, Prostaglandin E, EP2 Subtype, Receptors, Prostaglandin E, EP4 Subtype, Ribosomes, Signal Transduction, Tumor Microenvironment, Tumour immunology}, language = {en}, month = {November}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {9464}, + publisher = {Nature Publishing Group}, title = {Prostaglandin {E2}-{EP2}/{EP4} signaling induces immunosuppression in human cancer by impairing bioenergetics and ribosome biogenesis in immune cells}, url = {https://www.nature.com/articles/s41467-024-53706-3}, urldate = {2024-11-07}, @@ -17868,9 +18767,9 @@ @article{pustam_comparative_2023 keywords = {{\textgreater}UseGalaxy.eu, Bacterial pathogens, Caribbean, Genomics, Klebsiella Infections, Klebsiella pneumoniae, Mobile genetic elements, Pathogenesis, Secretion systems, Virulence factors}, language = {en}, month = {October}, - note = {Publisher: Public Library of Science}, number = {7}, pages = {e0283583}, + publisher = {Public Library of Science}, title = {Comparative genomics and virulome analysis reveal unique features associated with clinical strains of {Klebsiella} pneumoniae and {Klebsiella} quasipneumoniae from {Trinidad}, {West} {Indies}}, url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0283583}, urldate = {2023-07-13}, @@ -17908,8 +18807,8 @@ @article{pyles_altered_2024 keywords = {{\textgreater}UseGalaxy.eu, BIAFAC, Traumatic Brain Injury, fecal microbiome, metatranscriptome, microbiome}, language = {English}, month = {March}, - note = {Publisher: Frontiers}, pages = {1341808}, + publisher = {Frontiers}, title = {The altered {TBI} fecal microbiome is stable and functionally distinct}, url = {https://www.frontiersin.org/articles/10.3389/fnmol.2024.1341808}, urldate = {2024-05-17}, @@ -17935,15 +18834,15 @@ @article{pyoria_intra-host_2024 @article{qi_secreted_2020, abstract = {{\textless}p{\textgreater}Multicellular organisms coordinate tissue specific response to environmental information via both cell-autonomous and non-autonomous mechanisms. In addition to secreted ligands, secreted small RNAs have recently been reported to regulate gene expression across tissue boundaries. Here we show that the conserved poly-U specific endoribonuclease ENDU-2 is secreted from the soma and taken-up by the germline to ensure germline immortality at elevated temperature in C. elegans. ENDU-2 binds to mature mRNAs and negatively regulates mRNA abundance both in the soma and the germline. While ENDU-2 promotes RNA decay in the soma directly via its endoribonuclease activity, ENDU-2 prevents misexpression of soma-specific genes in the germline and preserves germline immortality independent of its RNA-cleavage activity. In summary, our results suggest that the secreted RNase ENDU-2 transmits environmental information across tissue boundaries and contributes to maintenance of stem cell immortality probably via retaining a stem cell specific program of gene expression.{\textless}/p{\textgreater}}, author = {Qi, Wenjing and Gromoff, Erika D. v and Xu, Fan and Zhao, Qian and Yang, Wei and Pfeifer, Dietmar and Maier, Wolfgang and Long, Lijiang and Baumeister, Ralf}, + chapter = {New Results}, copyright = {© 2020, Posted by Cold Spring Harbor Laboratory. The copyright holder for this pre-print is the author. All rights reserved. The material may not be redistributed, re-used or adapted without the author's permission.}, doi = {10.1101/2020.12.04.408260}, journal = {bioRxiv}, keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, language = {en}, month = {December}, - note = {Publisher: Cold Spring Harbor Laboratory -Section: New Results}, pages = {2020.12.04.408260}, + publisher = {Cold Spring Harbor Laboratory}, title = {A secreted endoribonuclease {ENDU}-2 from the soma protects germline immortality in {C}. elegans}, url = {https://www.biorxiv.org/content/10.1101/2020.12.04.408260v2}, urldate = {2020-12-30}, @@ -17983,6 +18882,25 @@ @article{qiu_smcyp71d373_2024 year = {2024} } +@article{quinto_genomic_2025, + abstract = {Background/Objectives: Streptococcus uberis is a Gram-positive bacterium and a major cause of bovine mastitis. The use of antimicrobial treatments raises concerns about resistance. This study aimed to characterize S. uberis isolates from one of the ten largest milk-producing regions in Europe. Methods: Thirty-six isolates from 36 cows with mastitis were identified using MALDI-TOF and VITEK®MS. Susceptibility to 9 antibiotics (penicillin G, ampicillin, tetracycline, erythromycin, clindamycin, cefotaxime, ceftriaxone, levofloxacin, and moxifloxacin) was determined with VITEK®2. Whole-genome sequencing was performed using MinION Mk1C. Results: Alleles were identified for 7 loci: arcC, ddl, gki, recP, tdk, tpi, and yqiL. Only 10 isolates had alleles for all the loci. The loci with the highest number of alleles were ddl and tdk (33/36 strains), while arcC had the fewest (19/36). Four isolates were assigned to known sequence types (ST6, ST307, and ST184), and novel alleles were detected in 32 of the 36 isolates. Twelve isolates showed phenotypic resistance to one or more of the following antibiotics: tetracycline, erythromycin, clindamycin, and ceftriaxone. The lnu was the most frequently detected resistance gene (27 out of 102 total gene appearances). A total of 19 virulence factors were identified. All strains were predicted to be capable of infecting human hosts. Conclusions: Streptococcus uberis is a potential reservoir of antimicrobial resistance genes. The use of antimicrobials to treat bovine mastitis has reduced the susceptibility of this microorganism to several antibiotics, underscoring the importance of monitoring antimicrobial use in veterinary practice. The results also highlight the high genetic diversity of the isolates, suggesting a strong capacity to adapt to different environmental conditions.}, + author = {Quinto, Emiliano J and Redondo Del Río, Paz and de Mateo Silleras, Beatriz and Prieto, Alberto and López-Lorenzo, Gonzalo and Franco, Carlos M and Vázquez, Beatriz I}, + copyright = {cc by}, + doi = {10.3390/antibiotics14111059}, + issn = {2079-6382}, + journal = {Antibiotics (Basel, Switzerland)}, + keywords = {{\textgreater}UseGalaxy.eu, Antimicrobial resistance, Bovine Mastitis, Streptococcus Uberis, virulence factors}, + language = {eng}, + month = {October}, + number = {11}, + pages = {1059}, + title = {Genomic {Characterization} and {Antimicrobial} {Resistance} {Profile} of \<i\>{Streptococcus} uberis\</i\> {Strains} {Isolated} from {Cows} with {Mastitis} from {Northwestern} {Spain}}, + url = {https://europepmc.org/articles/PMC12649216}, + urldate = {2025-12-26}, + volume = {14}, + year = {2025} +} + @mastersthesis{rabbas_surveillance_2024, abstract = {The discovery of antibiotics has radically changed the treatment of bacterial infections, making the increasing antibiotic resistance one of the top ten greatest threats to the global health. The main focus of antibiotic resistance research has, until recently, been focused on clinical settings and human and veterinary aspects. It has become more evident that the environment plays a vital role in the evolution, dissemination and prevalence of antibiotic resistant bacteria and genes. Aquatic ecosystems are a known mixing ground for clinical and environmental bacteria and can be a source and reservoir for resistance genes. The transfer of resistance between environmental and clinically important bacteria occurs, and surveillance of the environment is therefore important to better understand this flow of resistance. @@ -18002,9 +18920,9 @@ @article{ragot_edna_2022 author = {Ragot, Rose and Villemur, Richard}, journal = {Environmental monitoring and assessment}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, - note = {Publisher: Springer}, number = {2}, pages = {1--13}, + publisher = {Springer}, title = {{eDNA} profiling of mammals, birds, and fish of surface waters by mitochondrial metagenomics: application for source tracking of fecal contamination in surface waters}, volume = {194}, year = {2022} @@ -18017,9 +18935,9 @@ @article{rahman_mobilisation_2024 issn = {2057-5858}, journal = {Microbial Genomics}, keywords = {{\textgreater}UseGalaxy.eu}, - note = {Publisher: Microbiology Society,}, number = {2}, pages = {001188}, + publisher = {Microbiology Society,}, title = {Mobilisation and analyses of publicly available {SARS}-{CoV}-2 data for pandemic responses}, url = {https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001188}, urldate = {2024-02-16}, @@ -18027,17 +18945,6 @@ @article{rahman_mobilisation_2024 year = {2024} } -@article{rajczewski_rigorous_2021, - abstract = {The Coronavirus Disease 2019 (COVID-19) global pandemic has had a profound, lasting impact on the world’s population. A key aspect to providing care for those with COVID-19 and checking its further spread is early and accurate diagnosis of infection, which has been generally done via methods for amplifying and detecting viral RNA molecules. Detection and quantitation of peptides using targeted mass spectrometry-based strategies has been proposed as an alternative diagnostic tool due to direct detection of molecular indicators from non-invasively collected samples as well as the potential for high-throughput analysis in a clinical setting; many studies have revealed the presence of viral peptides within easily accessed patient samples. However, evidence suggests that some viral peptides could serve as better indicators of COVID-19 infection status than others, due to potential misidentification of peptides derived from human host proteins, poor spectral quality, high limits of detection etc. In this study we have compiled a list of 639 peptides identified from Sudden Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) samples, including from in vitro and clinical sources. These datasets were rigorously analyzed using automated, Galaxy-based workflows containing tools such as PepQuery, BLAST-P, and the Multi-omic Visualization Platform as well as the open-source tools MetaTryp and Proteomics Data Viewer (PDV). Using PepQuery for confirming peptide spectrum matches, we were able to narrow down the 639 peptide possibilities to 87 peptides which were most robustly detected and specific to the SARS-CoV-2 virus. The specificity of these sequences to coronavirus taxa was confirmed using Unipept and BLAST-P. Applying stringent statistical scoring thresholds, combined with manual verification of peptide spectrum match quality, 4 peptides derived from the nucleocapsid phosphoprotein and membrane protein were found to be most robustly detected across all cell culture and clinical samples, including those collected non-invasively. We propose that these peptides would be of the most value for clinical proteomics applications seeking to detect COVID-19 from a variety of sample types. We also contend that samples taken from the upper respiratory tract and oral cavity have the highest potential for diagnosis of SARS-CoV-2 infection from easily collected patient samples using mass spectrometry-based proteomics assays.}, - author = {Rajczewski, Andrew and Mehta, Subina and Nguyen, Dinh Duy An and Grüning, Björn and Johnson, James and McGowan, Thomas and Griffin, Timothy and Jagtap, Pratik}, - doi = {10.1101/2021.02.09.21251427}, - journal = {medRxiv}, - keywords = {{\textgreater}UseGalaxy.eu}, - title = {A rigorous evaluation of optimal peptide targets for {MS}-based clinical diagnostics of {Coronavirus} {Disease} 2019 ({COVID}-19)}, - url = {http://europepmc.org/abstract/PPR/PPR282374}, - year = {2021} -} - @article{rajczewski_rigorous_2021, abstract = {The Coronavirus Disease 2019 (COVID-19) global pandemic has had a profound, lasting impact on the world's population. A key aspect to providing care for those with COVID-19 and checking its further spread is early and accurate diagnosis of infection, which has been generally done via methods for amplifying and detecting viral RNA molecules. Detection and quantitation of peptides using targeted mass spectrometry-based strategies has been proposed as an alternative diagnostic tool due to direct detection of molecular indicators from non-invasively collected samples as well as the potential for high-throughput analysis in a clinical setting; many studies have revealed the presence of viral peptides within easily accessed patient samples. However, evidence suggests that some viral peptides could serve as better indicators of COVID-19 infection status than others, due to potential misidentification of peptides derived from human host proteins, poor spectral quality, high limits of detection etc.}, author = {Rajczewski, Andrew T. and Mehta, Subina and Nguyen, Dinh Duy An and Grüning, Björn and Johnson, James E. and McGowan, Thomas and Griffin, Timothy J. and Jagtap, Pratik D.}, @@ -18056,6 +18963,88 @@ @article{rajczewski_rigorous_2021 year = {2021} } +@article{rajczewski_rigorous_2021, + abstract = {The Coronavirus Disease 2019 (COVID-19) global pandemic has had a profound, lasting impact on the world’s population. A key aspect to providing care for those with COVID-19 and checking its further spread is early and accurate diagnosis of infection, which has been generally done via methods for amplifying and detecting viral RNA molecules. Detection and quantitation of peptides using targeted mass spectrometry-based strategies has been proposed as an alternative diagnostic tool due to direct detection of molecular indicators from non-invasively collected samples as well as the potential for high-throughput analysis in a clinical setting; many studies have revealed the presence of viral peptides within easily accessed patient samples. However, evidence suggests that some viral peptides could serve as better indicators of COVID-19 infection status than others, due to potential misidentification of peptides derived from human host proteins, poor spectral quality, high limits of detection etc. In this study we have compiled a list of 639 peptides identified from Sudden Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) samples, including from in vitro and clinical sources. These datasets were rigorously analyzed using automated, Galaxy-based workflows containing tools such as PepQuery, BLAST-P, and the Multi-omic Visualization Platform as well as the open-source tools MetaTryp and Proteomics Data Viewer (PDV). Using PepQuery for confirming peptide spectrum matches, we were able to narrow down the 639 peptide possibilities to 87 peptides which were most robustly detected and specific to the SARS-CoV-2 virus. The specificity of these sequences to coronavirus taxa was confirmed using Unipept and BLAST-P. Applying stringent statistical scoring thresholds, combined with manual verification of peptide spectrum match quality, 4 peptides derived from the nucleocapsid phosphoprotein and membrane protein were found to be most robustly detected across all cell culture and clinical samples, including those collected non-invasively. We propose that these peptides would be of the most value for clinical proteomics applications seeking to detect COVID-19 from a variety of sample types. We also contend that samples taken from the upper respiratory tract and oral cavity have the highest potential for diagnosis of SARS-CoV-2 infection from easily collected patient samples using mass spectrometry-based proteomics assays.}, + author = {Rajczewski, Andrew and Mehta, Subina and Nguyen, Dinh Duy An and Grüning, Björn and Johnson, James and McGowan, Thomas and Griffin, Timothy and Jagtap, Pratik}, + doi = {10.1101/2021.02.09.21251427}, + journal = {medRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {A rigorous evaluation of optimal peptide targets for {MS}-based clinical diagnostics of {Coronavirus} {Disease} 2019 ({COVID}-19)}, + url = {http://europepmc.org/abstract/PPR/PPR282374}, + year = {2021} +} + +@article{ramirez_diverse_2025, + abstract = {Spiroplasma +(class +Mollicutes +) is a diverse wall-less bacterial genus whose members are strictly dependent on eukaryotic hosts (mostly arthropods and plants), with which they engage in pathogenic to mutualistic interactions. +Spiroplasma +are generally fastidious to culture +in vitro +, especially those that are vertically transmitted by their hosts, which include flies in the genus +Drosophila +. +Drosophila +has been invaded by at least three independent clades of +Spiroplasma +: Poulsonii (the best studied, contains reproductive manipulators and defensive mutualists associated with two major clades of +Drosophila +and has amongst the highest substitution rates within bacteria), Citri (restricted to the +repleta +group of +Drosophila +) and Ixodetis. We report the first genome drafts of +Drosophila +-associated Citri clade +Spiroplasma +: strain +s +Moj from +Drosophila mojavensis +, strain +s +Ald-Tx from +Drosophila aldrichi +from Texas (newly discovered; also associated with +Drosophila mulleri +) and strain +s +Hy2 from +Drosophila hydei +(the only +Drosophila +species known to naturally also harbour a Poulsonii clade strain, thereby providing an arena for horizontal gene transfer). Compared to their Poulsonii clade counterparts, we infer that the three Citri clade strains have the following: (1) equal or worse DNA repair abilities; (b) more limited metabolic capacities, which may underlie their comparatively lower titres and transmission efficiency; and (c) similar content of toxin domains, including at least one ribosome-inactivating protein, which is implicated in the Poulsonii-conferred defence against natural enemies. As a byproduct of our phylogenomic analyses and exhaustive search for certain toxin domains in public databases, we document the toxin repertoire in close relatives of +Drosophila +-associated +Spiroplasma +, and in a very divergent newly discovered lineage (i.e. ‘clade X’). Phylogenies of toxin-encoding genes or domains imply substantial exchanges between closely and distantly related strains. Surprisingly, despite encoding several toxin genes and achieving relatively high prevalences in certain natural populations ( +s +Ald-Tx in this study; +s +Moj in prior work), fitness assays of +s +Moj (this study) and +s +Ald-Tx (prior work) in the context of wasp parasitism fail to detect a beneficial effect to their hosts. Thus, how Citri clade strains persist in their +Drosophila +host populations remains elusive.}, + author = {Ramirez, Paulino and Martinez Montoya, Humberto and Aramayo, Rodolfo and Mateos, Mariana}, + copyright = {http://creativecommons.org/licenses/by/4.0/}, + doi = {10.1099/mgen.0.001408}, + issn = {2057-5858}, + journal = {Microbial Genomics}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {June}, + number = {6}, + title = {Diverse toxin repertoire but limited metabolic capacities inferred from the draft genome assemblies of three {Spiroplasma} ({Citri} clade) strains associated with {Drosophila}}, + url = {https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001408}, + urldate = {2026-01-11}, + volume = {11}, + year = {2025} +} + @article{ramos_mobilome_2024, abstract = {Staphylococcus aureus thrives at animal-human-environment interfaces. A large-scale work from our group indicated that antimicrobial resistance (AMR) in commensal S. aureus strains from wild ungulates is associated with agricultural land cover and livestock farming, raising the hypothesis that AMR genes in wildlife strains may originate from different hosts, namely via exchange of mobile genetic elements (MGE). In this work, we generate the largest available dataset of S. aureus draft genomes from wild ungulates in Portugal and explore their mobilome, which can determine important traits such as AMR, virulence, and host specificity, to understand MGE exchange. Core genome multi-locus sequence typing based on 98 newly generated draft genomes and 101 publicly available genomes from Portugal demonstrated that the genomic relatedness of S. aureus from wild ungulates assigned to livestock-associated sequence types (ST) is greater compared to wild ungulate isolates assigned to human-associated STs. Screening of host specificity determinants disclosed the unexpected presence in wildlife of the immune evasion cluster encoded in φSa3 prophage, described as a human-specific virulence determinant. Additionally, two plasmids, pAVX and pETB, previously associated with avian species and humans, respectively, and the Tn553 transposon were detected. Both pETB and Tn553 encode penicillin resistance through blaZ. Pangenome analysis of wild ungulate isolates shows a core genome fraction of 2133 genes, with isolates assigned to ST72 and ST3224 being distinguished from the remaining by MGEs, although there is no reported role of these in adaptation to wildlife. AMR related gene clusters found in the shell genome are directly linked to resistance against penicillin, macrolides, fosfomycin, and aminoglycosides, and they represent mobile ARGs. Altogether, our findings support epidemiological interactions of human and non-human hosts at interfaces, with MGE exchange, including AMR determinants, associated with putative indirect movements of S. aureus among human and wildlife hosts that might be bridged by livestock.}, author = {Ramos, Beatriz and Cunha, Mónica V.}, @@ -18077,7 +19066,7 @@ @article{ran_mitochondrial_2025 doi = {10.1002/ece3.72282}, issn = {2045-7758}, journal = {Ecology and evolution}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Camaenidae, Codon usage bias, Phylogenetic analysis}, month = {October}, number = {10}, pages = {e72282}, @@ -18115,8 +19104,8 @@ @article{ranchou-peyruse_microbial_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, language = {eng}, month = {October}, - note = {Publisher: Frontiers Media SA}, pages = {688929}, + publisher = {Frontiers Media SA}, title = {Microbial {Diversity} {Under} the {Influence} of {Natural} {Gas} {Storage} in a {Deep} {Aquifer}}, url = {https://doi.org/10.3389/fmicb.2021.688929}, volume = {12}, @@ -18201,9 +19190,9 @@ @article{rasche_galactic_2020 keywords = {+Education, +Galactic, +IsGalaxy, +RefPublic, +Shared, +Tools, +Visualization, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au, Software}, language = {en}, month = {June}, - note = {Publisher: Oxford Academic}, number = {6}, pages = {giaa065}, + publisher = {Oxford Academic}, shorttitle = {Galactic {Circos}}, title = {Galactic {Circos}: {User}-friendly {Circos} plots within the {Galaxy} platform}, url = {https://academic.oup.com/gigascience/article/9/6/giaa065/5856406}, @@ -18215,15 +19204,15 @@ @article{rasche_galactic_2020 @article{rasche_training_2020, abstract = {{\textless}p{\textgreater}Background: Hands-on training, whether it is in Bioinformatics or other scientific domains, requires significant resources and knowledge to setup and run. Trainers must have access to infrastructure that can support the sudden spike in usage, with classes of 30 or more trainees simultaneously running resource-intensive tools. For efficient classes, the jobs must run quickly, without queuing delays, lest they disrupt the timetable set out for the class. Often times this is achieved via running on a private server where there is no contention for the queue, and therefore no or minimal waiting time. However, this requires the teacher or trainer to have the technical knowledge to manage compute infrastructure, in addition to their didactic responsibilities. This presents significant burdens to potential training events, in terms of infrastructure cost, person-hours of preparation, technical knowledge, and available staff to manage such events. Findings: Galaxy Europe has developed Training Infrastructure as a Service (TIaaS) which we provide to the scientific commnuity as a service built on top of the Galaxy Platform. Training event organisers request a training and Galaxy administrators can allocate private queues specifically for the training. Trainees are transparently placed in a private queue where their jobs run without delay. Trainers access the dashboard of the TIaaS Service and can remotely follow the progress of their trainees without in-person interactions. Conclusions: TIaaS on Galaxy Europe provides reusable and fast infrastructure for Galaxy training. The instructor dashboard provides visibility into class progress, making in-person trainings more efficient and remote training possible. In the past 24 months, \$\>110\$ trainings with over 3000 trainees have used this infrastructure for training, across scientific domains, all enjoying the accessibility and reproducibility of Galaxy for training the next generation of bioinformaticians. TIaaS itself is an extension to Galaxy which can be deployed by any Galaxy administrator to provide similar benefits for their users. https://galaxyproject.eu/tiaas{\textless}/p{\textgreater}}, author = {Rasche, Helena and Gruening, Bjoern Andreas}, + chapter = {New Results}, copyright = {© 2020, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/}, doi = {10.1101/2020.08.23.263509}, journal = {bioRxiv}, keywords = {+Education, +Galactic, +IsGalaxy, {\textgreater}UseGalaxy.eu}, language = {en}, month = {August}, - note = {Publisher: Cold Spring Harbor Laboratory -Section: New Results}, pages = {2020.08.23.263509}, + publisher = {Cold Spring Harbor Laboratory}, title = {Training {Infrastructure} as a {Service}}, url = {https://www.biorxiv.org/content/10.1101/2020.08.23.263509v1}, urldate = {2020-08-25}, @@ -18287,9 +19276,9 @@ @article{rashid_shotgun_2025 keywords = {{\textgreater}UseGalaxy.eu, Cattle Diseases, Endometritis, Infertility, Metagenomics, Microbial Interactions, Microbiota, Uterus}, language = {en}, month = {May}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {18274}, + publisher = {Nature Publishing Group}, title = {Shotgun metagenomic composition, microbial interactions and functional insights into the uterine microbiome of postpartum dairy cows with clinical and subclinical endometritis}, url = {https://www.nature.com/articles/s41598-025-03265-4}, urldate = {2025-05-28}, @@ -18377,15 +19366,15 @@ @article{rauschmeier_bhlhe40_2022 @article{rauschmeier_cell-intrinsic_2021, abstract = {{\textless}h3{\textgreater}ABSTRACT{\textless}/h3{\textgreater} {\textless}p{\textgreater}The generation of high-affinity antibodies against pathogens and vaccines requires the germinal center (GC) reaction – a process that relies on a complex interplay between specialized effector subsets of B and CD4 T lymphocytes – GC B cells and T follicular helper (T$_{\textrm{FH}}$) cells. Intriguingly, several key positive regulators of the GC reaction are common for both cell types. Here, we report that the transcription factor Bhlhe40 is a crucial cell-intrinsic negative regulator affecting both the B and T cell sides of the GC reaction. In activated CD4 T cells, Bhlhe40 was required to restrain proliferation thus limiting the number of T$_{\textrm{FH}}$ cells. In B cells, Bhlhe40 executed its function in the first days after immunization by selectively restricting the generation of the earliest GC B cells but not of early memory B cells or plasmablasts. Conditional Bhlhe40 inactivation confirmed cell-autonomous functions of Bhlhe40 in both GC B and T$_{\textrm{FH}}$ cells, while the GC phenotype was further enhanced upon loss of Bhlhe40 in both cell types. This negative regulation of the GC reaction by Bhlhe40 was of crucial importance, as Bhlhe40-deficient mice with progressing age succumbed to a B cell lymphoma characterized by accumulation of monoclonal GC B-like cells and polyclonal T$_{\textrm{FH}}$ cells in various tissues.{\textless}/p{\textgreater}}, author = {Rauschmeier, René and Reinhardt, Annika and Gustafsson, Charlotte and Glaros, Vassilis and Artemov, Artem V. and Taneja, Reshma and Adameyko, Igor and Månsson, Robert and Busslinger, Meinrad and Kreslavsky, Taras}, + chapter = {New Results}, copyright = {© 2021, Posted by Cold Spring Harbor Laboratory. The copyright holder for this pre-print is the author. All rights reserved. The material may not be redistributed, re-used or adapted without the author's permission.}, doi = {10.1101/2021.03.12.435122}, journal = {bioRxiv}, keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, language = {en}, month = {March}, - note = {Publisher: Cold Spring Harbor Laboratory -Section: New Results}, pages = {2021.03.12.435122}, + publisher = {Cold Spring Harbor Laboratory}, title = {Cell-intrinsic functions of the transcription factor {Bhlhe40} in activated {B} cells and {T} follicular helper cells restrain the germinal center reaction and prevent lymphomagenesis}, url = {https://www.biorxiv.org/content/10.1101/2021.03.12.435122v1}, urldate = {2021-07-21}, @@ -18435,8 +19424,8 @@ @article{raymond_targeting_2025 keywords = {{\textgreater}UseGalaxy.eu, Cadherins, Gonadal Steroid Hormones, Melanoma, Molecular Targeted Therapy, Transcription}, language = {en}, month = {June}, - note = {Publisher: Nature Publishing Group}, pages = {1--9}, + publisher = {Nature Publishing Group}, title = {Targeting {GRPR} for sex hormone-dependent cancer after loss of {E}-cadherin}, url = {https://www.nature.com/articles/s41586-025-09111-x}, urldate = {2025-06-17}, @@ -18496,8 +19485,8 @@ @article{rehm_analyse_2023 keywords = {{\textgreater}UseGalaxy.eu}, language = {de}, month = {April}, - note = {Accepted: 2023-04-13T10:45:38Z -Publisher: Universität Tübingen}, + note = {Accepted: 2023-04-13T10:45:38Z}, + publisher = {Universität Tübingen}, title = {Analyse des {Replikationszyklus} von nicht-melanozytären {Hautkrebs}-assoziierten beta-humanen {Papillomviren} in humanen {Keratinozyten}}, url = {https://publikationen.uni-tuebingen.de/xmlui/handle/10900/139172}, urldate = {2024-11-17}, @@ -18510,9 +19499,9 @@ @article{rehm_splice_2025 journal = {Journal of Virology}, keywords = {{\textgreater}UseGalaxy.eu, Betapapillomavirus, Cell Transformation, Viral, Keratinocytes, Oncogene Proteins, Viral, RNA Splice Sites}, month = {January}, - note = {Publisher: American Society for Microbiology}, number = {0}, pages = {e01640--24}, + publisher = {American Society for Microbiology}, title = {A splice donor in {E6} influences keratinocyte immortalization by beta-{HPV49}}, url = {https://journals.asm.org/doi/full/10.1128/jvi.01640-24}, urldate = {2025-02-16}, @@ -18614,7 +19603,7 @@ @article{richter_genome_2024 keywords = {{\textgreater}UseGalaxy.eu, Apple blotch, D. coronariae, Malus, Short reads, genome sequence, long reads, mating types}, language = {English}, month = {October}, - note = {Publisher: Frontiers}, + publisher = {Frontiers}, title = {Genome sequence of a {European} {Diplocarpon} coronariae strain and in silico structure of the mating-type locus}, url = {https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1437132/full}, urldate = {2024-10-28}, @@ -18630,9 +19619,9 @@ @article{richter_genomic_2024 journal = {Environmental Science \& Technology}, keywords = {{\textgreater}UseGalaxy.eu, Escherichia coli, beta-Lactamases}, month = {August}, - note = {Publisher: American Chemical Society}, number = {32}, pages = {14421--14438}, + publisher = {American Chemical Society}, shorttitle = {Genomic {Evaluation} of {Multidrug}-{Resistant} {Extended}-{Spectrum} β-{Lactamase} ({ESBL})-{Producing} {Escherichia} coli from {Irrigation} {Water} and {Fresh} {Produce} in {South} {Africa}}, title = {Genomic {Evaluation} of {Multidrug}-{Resistant} {Extended}-{Spectrum} β-{Lactamase} ({ESBL})-{Producing} {Escherichia} coli from {Irrigation} {Water} and {Fresh} {Produce} in {South} {Africa}: {A} {Cross}-{Sectional} {Analysis}}, url = {https://doi.org/10.1021/acs.est.4c02431}, @@ -18650,9 +19639,9 @@ @article{riediger_analysis_2020 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Photosynthesis, Sequence Analysis, RNA}, language = {eng}, month = {December}, - note = {Publisher: Oxford University Press (OUP)}, number = {2}, pages = {248--269}, + publisher = {Oxford University Press (OUP)}, title = {Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing ({Grad}-seq)}, url = {https://doi.org/10.1093/plcell/koaa017}, volume = {33}, @@ -18669,9 +19658,9 @@ @article{riesle_activator-blocker_2023 keywords = {{\textgreater}UseGalaxy.eu, Development, Differential equations, Gastrulation, Gene expression profiling, Histones, Transcriptional regulatory elements, Zebrafish}, language = {en}, month = {September}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {5677}, + publisher = {Nature Publishing Group}, title = {Activator-blocker model of transcriptional regulation by pioneer-like factors}, url = {https://www.nature.com/articles/s41467-023-41507-z}, urldate = {2024-07-09}, @@ -18689,10 +19678,10 @@ @article{ristinmaa_resin_2023 keywords = {{\textgreater}UseGalaxy.eu, Bacteria, Environmental microbiology, Metagenomics, Microbiome}, language = {en}, month = {December}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {8171}, + publisher = {Nature Publishing Group}, title = {Resin acids play key roles in shaping microbial communities during degradation of spruce bark}, url = {https://www.nature.com/articles/s41467-023-43867-y}, urldate = {2023-12-28}, @@ -18757,7 +19746,7 @@ @article{rocha_escherichia_2025 doi = {10.3201/eid3110.241279}, issn = {1080-6040}, journal = {Emerging infectious diseases}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, APEC, Bacteria, Bacterial infections, Brazil, Escherichia Coli, Expec, High-risk, Parrots, St131-h22, Zoonoses, Zoonotic Lineage}, month = {October}, number = {10}, pages = {2025--2028}, @@ -18839,6 +19828,29 @@ @article{rodriguez-outeirino_mir-106b_2022 year = {2022} } +@article{rogg_arp23-dependent_2025, + abstract = {Proteinuric kidney disease substantially affects renal tubules through incompletely understood mechanisms. We identify elongation of primary cilia in distal renal tubules in the context of glomerular nephropathy. In renal biopsies and mouse models, tubular injury correlates with ciliary elongation, tubule dilation, and disruption of the cortical actin cytoskeleton. In vitro studies implicate biophysical cues of the glomerular filtrate and subsequent dysregulation of the actin cytoskeleton as contributing factors, confirmed by conditional deletion of N-WASP and Arp2/3 in vivo and in vitro. Electron and fluorescence microscopy revealed enlarged ciliary pockets, basal body mislocalization, and intracellular cilia formation in +Arp3 +knockout conditions. Transcriptome analysis identifies the essential role of cilia in maintaining adaptive tubular cell states, while persistent activation leads to disease progression through extracellular matrix remodeling, exemplified by Tenascin-C. Our findings establish cilia as central mediators of tubular adaptation to injury and identify the Arp2/3-dependent actin cytoskeleton as a critical regulator, providing essential insights into the pathogenesis of chronic kidney disease. + +, +Proteinuria causes ciliary elongation and actin cytoskeleton remodeling, revealing a key mechanism in kidney disease progression.}, + author = {Rogg, Manuel and Weißer, Lisa and Maier, Jasmin I. and Sigle, August and Helmstädter, Martin and Stigler, Marlene and Sammarco, Alena and Gräwe, Katja and Andreev, Grigor and Kark, Charlotte and Ramakrishnan, Suresh K. and Özel, Cem and Butt, Linus and Arnold, Frederic and Bechtel-Walz, Wibke and Schilling, Oliver and Tanriver, Yakup and Brinkkötter, Paul and Grabbert, Markus and Simons, Matias and Werner, Martin and Kretz, Oliver and Benzing, Thomas and Huber, Tobias B. and Schell, Christoph}, + doi = {10.1126/sciadv.ady1623}, + issn = {2375-2548}, + journal = {Science Advances}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {November}, + number = {48}, + pages = {eady1623}, + title = {Arp2/3-dependent regulation of ciliogenesis governs adaptive distal tubular epithelial cell states in kidney disease}, + url = {https://www.science.org/doi/10.1126/sciadv.ady1623}, + urldate = {2025-12-01}, + volume = {11}, + year = {2025} +} + @article{rogg_srgap1_2021, abstract = {{\textless}h4{\textgreater}Background{\textless}/h4{\textgreater}Previous research demonstrated that small Rho GTPases, modulators of the actin cytoskeleton, are drivers of podocyte foot-process effacement in glomerular diseases, such as FSGS. However, a comprehensive understanding of the regulatory networks of small Rho GTPases in podocytes is lacking.{\textless}h4{\textgreater}Methods{\textless}/h4{\textgreater}We conducted an analysis of podocyte transcriptome and proteome datasets for Rho GTPases; mapped \textit{in vivo}, podocyte-specific Rho GTPase affinity networks; and examined conditional knockout mice and murine disease models targeting \textit{Srgap1}. To evaluate podocyte foot-process morphology, we used super-resolution microscopy and electron microscopy; \textit{in situ} proximity ligation assays were used to determine the subcellular localization of the small GTPase-activating protein SRGAP1. We performed functional analysis of CRISPR/Cas9-generated \textit{SRGAP1} knockout podocytes in two-dimensional and three-dimensional cultures and quantitative interaction proteomics.{\textless}h4{\textgreater}Results{\textless}/h4{\textgreater}We demonstrated SRGAP1 localization to podocyte foot processes \textit{in vivo} and to cellular protrusions \textit{in vitro}. \textit{Srgap1$^{\textrm{fl/fl}}$*Six2Cre} but not \textit{Srgap1$^{\textrm{fl/fl}}$*hNPHS2Cre} knockout mice developed an FSGS-like phenotype at adulthood. Podocyte-specific deletion of \textit{Srgap1} by \textit{hNPHS2Cre} resulted in increased susceptibility to doxorubicin-induced nephropathy. Detailed analysis demonstrated significant effacement of podocyte foot processes. Furthermore, \textit{SRGAP1}-knockout podocytes showed excessive protrusion formation and disinhibition of the small Rho GTPase machinery \textit{in vitro}. Evaluation of a SRGAP1-dependent interactome revealed the involvement of SRGAP1 with protrusive and contractile actin networks. Analysis of glomerular biopsy specimens translated these findings toward human disease by displaying a pronounced redistribution of SRGAP1 in FSGS.{\textless}h4{\textgreater}Conclusions{\textless}/h4{\textgreater}SRGAP1, a podocyte-specific RhoGAP, controls podocyte foot-process architecture by limiting the activity of protrusive, branched actin networks. Therefore, elucidating the complex regulatory small Rho GTPase affinity network points to novel targets for potentially precise intervention in glomerular diseases.}, author = {Rogg, Manuel and Maier, Jasmin I. and Dotzauer, Robert and Artelt, Nadine and Kretz, Oliver and Helmstädter, Martin and Abed, Ahmed and Sammarco, Alena and Sigle, August and Sellung, Dominik and Dinse, Patrick and Reiche, Karoline and Yasuda-Yamahara, Mako and Biniossek, Martin L. and Walz, Gerd and Werner, Martin and Endlich, Nicole and Schilling, Oliver and Huber, Tobias B. and Schell, Christoph}, @@ -18848,9 +19860,9 @@ @article{rogg_srgap1_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, language = {eng}, month = {January}, - note = {Publisher: American Society of Nephrology (ASN)}, number = {3}, pages = {563--579}, + publisher = {American Society of Nephrology (ASN)}, title = {{SRGAP1} {Controls} {Small} {Rho} {GTPases} {To} {Regulate} {Podocyte} {Foot} {Process} {Maintenance}}, url = {https://doi.org/10.1681/asn.2020081126}, volume = {32}, @@ -18867,10 +19879,10 @@ @article{rogg_yaptazarhgap29rhoa_2023 keywords = {{\textgreater}UseGalaxy.eu, ARHGAP29, EPB41L5, YAP/TAZ, Yurt, glomerular kidney disease, mechanotransduction, podocyte}, language = {en}, month = {January}, - note = {Number: 13 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 13}, number = {13}, pages = {1795}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {A {YAP}/{TAZ}–{ARHGAP29}–{RhoA} {Signaling} {Axis} {Regulates} {Podocyte} {Protrusions} and {Integrin} {Adhesions}}, url = {https://www.mdpi.com/2073-4409/12/13/1795}, urldate = {2024-07-09}, @@ -18884,7 +19896,7 @@ @article{rohrbach_microplastic_2025 doi = {10.1093/femsec/fiaf085}, issn = {0168-6496}, journal = {FEMS microbiology ecology}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Community Assembly Mechanisms, Metabarcoding, Microplastics, Plastisphere, pathogens, terrestrial ecosystems}, month = {September}, number = {10}, pages = {fiaf085}, @@ -18941,6 +19953,35 @@ @article{roncoroni_sars-cov-2_2021 year = {2021} } +@article{ronspies_crispr-casmediated_2025, + abstract = {The genome of +Arabidopsis thaliana +consists of 10 chromosomes. By inducing CRISPR-Cas–mediated breaks at subcentromeric and subtelomeric sequences, we fused entire chromosome arms, obtaining two eight-chromosome lines. In one line, both arms of chromosome 3 were fused to chromosome 1. In another line, the arms were transferred to chromosomes 1 and 5. Both chromosome number–reduced lines were fertile. Phenotypic and transcriptional analyses revealed no differences compared with wild-type plants. After crossing with the wild type, the progeny showed reduced fertility. The meiotic recombination patterns of the transferred chromosome arms were substantially changed. Directed chromosome number changes in plants may enable new breeding strategies, redefining linkage groups and establishing genetic barriers. Moreover, our data indicate that plants are highly robust to engineered karyotype changes. + +, +Editor’s summary + +Restructuring chromosomes alters inheritance patterns of genetic information. In plants, chromosomal rearrangements can reproductively isolate engineered plants from wild relatives or can change the inheritance of desirable agronomic traits. Rönspies +et al +. used the model plant +Arabidopsis thaliana +as a testbed to implement CRISPR-Cas technology to fuse chromosomes together (see the Perspective by Zhang and Dawe). The researchers generated plants with eight chromosomes instead of 10, which appeared to be phenotypically normal and were self-fertile. Altered recombination patterns illustrated the changes to genetic inheritance rules. This work opens avenues for large-scale chromosomal changes in plants and provides insights into the plasticity of plant genomes. —Madeleine Seale}, + author = {Rönspies, Michelle and Khosravi, Solmaz and Helia, Ondřej and Valisi, Alessandro and Fajkus, Jiří and Fojtová, Miloslava and Houben, Andreas and Puchta, Holger}, + doi = {10.1126/science.adz8505}, + issn = {0036-8075, 1095-9203}, + journal = {Science}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {November}, + number = {6775}, + pages = {843--848}, + title = {{CRISPR}-{Cas}–mediated heritable chromosome fusions in \textit{{Arabidopsis}}}, + url = {https://www.science.org/doi/10.1126/science.adz8505}, + urldate = {2025-11-24}, + volume = {390}, + year = {2025} +} + @article{roquis_genomic_2021, abstract = {Transposable elements (TEs) have long been known to be major contributors to plant evolution, adaptation and crop domestication. Stress-induced TE mobilization is of particular interest because it may result in novel gene regulatory pathways responding to stresses and thereby contribute to stress adaptation. Here, we investigated the genomic impacts of stress induced TE mobilization in wild type Arabidopsis plants. We find that the heat-stress responsive ONSEN TE displays an insertion site preference that is associated with specific chromatin states, especially those rich in H2A.Z histone variant and H3K27me3 histone mark. In order to better understand how novel ONSEN insertions affect the plant's response to heat stress, we carried out an in-depth transcriptomic analysis. We find that in addition to simple gene knockouts, ONSEN can produce a plethora of gene expression changes such as: constitutive activation of gene expression, alternative splicing, acquisition of heat-responsiveness, exonisation and genesis of novel non-coding and antisense RNAs. This report shows how the mobilization of a single TE-family can lead to a rapid rise of its copy number increasing the host's genome size and contribute to a broad range of transcriptomic novelty on which natural selection can then act.}, author = {Roquis, David and Robertson, Marta and Yu, Liang and Thieme, Michael and Julkowska, Magdalena and Bucher, Etienne}, @@ -18950,9 +19991,9 @@ @article{roquis_genomic_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Retroelements, Transcriptome}, language = {eng}, month = {September}, - note = {Publisher: Oxford University Press (OUP)}, number = {18}, pages = {10431--10447}, + publisher = {Oxford University Press (OUP)}, title = {Genomic impact of stress-induced transposable element mobility in {Arabidopsis}}, url = {https://doi.org/10.1093/nar/gkab828}, volume = {49}, @@ -18976,6 +20017,24 @@ @article{rossitto_trim28-dependent_2022 year = {2022} } +@article{rothschild-rodriguez_klebphacol_2025, + abstract = {The growing threat of multidrug-resistant Klebsiella pneumoniae, coupled with its role in gut colonisation, has intensified the search for new treatments, including bacteriophage therapy. Despite increasing documentation of Klebsiella-targeting phages, clinical applications remain limited, with key phage–bacteria interactions still poorly understood. A major obstacle is fragmented access to well-characterised phage–bacteria pairings, restricting the collective advancement of therapeutic and mechanistic insights. To address this gap, we created the Klebsiella Phage Collection (KlebPhaCol), an open resource comprising 52 phages and 74 Klebsiella isolates, characterised at phenotypic and genomic levels. These phages span six families—including a novel family, Felixviridae, associated with the human gut—and target 20 sequence types (including ST258, ST11, and ST14) and 19 capsular-locus types (including KL1 and KL2), across 6 Klebsiella species. Freely accessible at www.klebphacol.org, KlebPhaCol invites the scientific community to both use and contribute to this resource, fostering collaborative research and a deeper understanding of Klebsiella-phage interactions beyond therapeutic use.Multidrug-resistant Klebsiella pneumoniae is a critical global health challenge. Bacteriophages (phages) could offer new therapies, but progress has been slowed by fragmented resources. KlebPhaCol addresses this gap as the first open, community-driven Klebsiella phage collection. It brings together physical samples (52 phages and 74 Klebsiella isolates) alongside extensive genomic, phenotypic, and host-range data, all freely accessible via www.klebphacol.org. The collection includes globally relevant clones, spans six phage families, and revealed a new gut-associated phage family, Felixviridae. Crucially, KlebPhaCol is designed to grow: researchers worldwide can deposit new strains and phages or add fresh analyses to existing ones, creating a sustainable platform for therapeutic development and fundamental microbiology.}, + author = {Rothschild-Rodriguez, Daniela and Lambon, Kai S and Kushwaha, Simran Krishnakant and Garushyants, Sofya K and Ertelt, Moritz and Latka, Agnieszka and Costa, Ana Rita and Mantzouratou, Anna and King, Claire and Boeckaerts, Dimitri and Sheridan, Elizabeth and Koonin, Eugene V and Merrick, Francesca and Drobniewski, Francis and De Angelis, Ilaria and Saeed, Kordo and Martin, Macy and Sutton, J Mark and Wand, Matthew E and Andrew, Michael and Hedges, Morgen and Brouns, Stan J J and Haas, Pieter-Jan and Lawson, Sophie T and Fordham, Stephen M E and Lee, Yan-Jiun and Wu, Yi and Briers, Yves and Braun, Peter and Weigele, Peter R and Nobrega, Franklin L}, + doi = {10.1093/nar/gkaf1122}, + issn = {1362-4962}, + journal = {Nucleic Acids Research}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {November}, + number = {21}, + pages = {gkaf1122}, + shorttitle = {{KlebPhaCol}}, + title = {{KlebPhaCol}: a community-driven resource for {Klebsiella} research identified a novel phage family}, + url = {https://doi.org/10.1093/nar/gkaf1122}, + urldate = {2025-12-26}, + volume = {53}, + year = {2025} +} + @article{roux_dna_2023, abstract = {Unintegrated HIV DNA represents between 20\% and 35\% of the total viral DNA in infected patients. Only the linear forms (unintegrated linear DNAs [ULDs]) can be substrates for integration and for the completion of a full viral cycle. In quiescent cells, these ULDs may be responsible for pre-integrative latency. However, their detection remains difficult due to the lack of specificity and sensitivity of existing techniques. We developed an ultra-sensitive, specific, and high-throughput technology for ULD quantification called DUSQ (DNA ultra-sensitive quantification) combining linker-mediated PCR and next-generation sequencing (NGS) using molecular barcodes. Studying cells with different activity levels, we determined that the ULD half-life goes up to 11 days in resting CD4+ T cells. Finally, we were able to quantify ULDs in samples from patients infected with HIV-1, providing a proof of concept for the use of DUSQ in vivo to track pre-integrative latency. DUSQ can be adapted to the detection of other rare DNA molecules.}, author = {Roux, Hélène Marie and Figueiredo, Suzanne and Sareoua, Lucas and Salmona, Maud and Hamroune, Juliette and Adoux, Lucie and Migraine, Julie and Hance, Allan and Clavel, François and Cheynier, Rémi and Dutrieux, Jacques}, @@ -19002,11 +20061,10 @@ @article{roy_computational_2023 journal = {Journal of Biomolecular Structure and Dynamics}, keywords = {{\textgreater}UseGalaxy.eu, CAZymes, Fusarium wilt, MD simulation, computational proteomics, polysaccharide degradation}, month = {July}, - note = {Publisher: Taylor \& Francis -\_eprint: https://doi.org/10.1080/07391102.2022.2067236}, + note = {\_eprint: https://doi.org/10.1080/07391102.2022.2067236}, number = {10}, pages = {4344--4360}, - pmid = {35470778}, + publisher = {Taylor \& Francis}, title = {Computational identification and characterization of vascular wilt pathogen ({Fusarium} oxysporum f. sp. lycopersici) {CAZymes} in tomato xylem sap}, url = {https://doi.org/10.1080/07391102.2022.2067236}, urldate = {2024-11-17}, @@ -19094,9 +20152,9 @@ @article{russo_excrete_2024 keywords = {{\textgreater}UseGalaxy.eu, Bacterial Proteins, Bacterial secretion, Proteomic analysis, Proteomics, Workflow}, language = {en}, month = {September}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {1--13}, + publisher = {Nature Publishing Group}, title = {{EXCRETE} workflow enables deep proteomics of the microbial extracellular environment}, url = {https://www.nature.com/articles/s42003-024-06910-2}, urldate = {2024-10-20}, @@ -19204,9 +20262,9 @@ @article{saddiqa_discovery_2024 keywords = {{\textgreater}UseGalaxy.eu, Cancer, Computational biology and bioinformatics, Oncology, Receptors, Estrogen, Triple Negative Breast Neoplasms}, language = {en}, month = {September}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {20840}, + publisher = {Nature Publishing Group}, title = {On discovery of novel hub genes for {ER}+ and {TN} breast cancer types through {RNA} seq data analyses and classification models}, url = {https://www.nature.com/articles/s41598-024-69721-9}, urldate = {2024-10-20}, @@ -19220,9 +20278,9 @@ @article{sadler_complete_2025 journal = {Microbiology Resource Announcements}, keywords = {{\textgreater}UseGalaxy.eu}, month = {August}, - note = {Publisher: American Society for Microbiology}, number = {0}, pages = {e00158--25}, + publisher = {American Society for Microbiology}, title = {Complete genome sequences of 34 {Arctic} marine bacteria}, url = {https://journals.asm.org/doi/full/10.1128/mra.00158-25}, urldate = {2025-09-03}, @@ -19236,9 +20294,9 @@ @article{sadler_genomic_2025 journal = {mBio}, keywords = {{\textgreater}UseGalaxy.eu}, month = {August}, - note = {Publisher: American Society for Microbiology}, number = {0}, pages = {e01555--25}, + publisher = {American Society for Microbiology}, title = {Genomic diversity and adaptation in {Arctic} marine bacteria}, url = {https://journals.asm.org/doi/10.1128/mbio.01555-25}, urldate = {2025-09-03}, @@ -19264,6 +20322,23 @@ @article{sageman-furnas_detailing_2024 year = {2024} } +@article{saguti_variations_2025, + abstract = {Little is known about virome changes in raw and drinking water over time, and differences between raw water sources and treatment technologies. This study used metagenomics to assess viruses prevalent in raw and drinking water samples over 1 year from six Swedish drinking water treatment plants (DWTPs) with varying treatment barriers and with different raw water sources. Sequences homologous to known viruses in the raw water samples were detected by amplification and next-generation sequencing and classified into 152 different virus species belonging to 76 virus families/orders. The majority were small bacteriophages. Other viral genomes were homologous to viruses infecting plants, invertebrates, vertebrates, mammals and giant viruses infecting amoeba or algae. Several virus species were simultaneously found in both raw and drinking water, indicating passage through the purification barriers, although reduced by 1-3 log10 after treatment. Most viruses detected in water samples after ultrafiltration were small viruses, and other barriers appeared more effective at removing smaller viruses. To avoid detecting viruses possibly replicating within DWTPs, viruses were separated according to the possibility that the host could be found in the water sources or not. These results underscore the importance of monitoring both raw and drinking water for small viruses, especially when viral contamination of the source water is at risk, to ensure drinking water quality.}, + author = {Saguti, Fredy and Wang, Hao and Churqui, Marianela Patzi and Tunovic, Timur and Holmer, Linda and Pettersson, Ämma and Schleich, Caroline and Pott, Britt-Marie and Bergstedt, Olof and Nyström, Kristina and Norder, Heléne}, + doi = {10.1111/1758-2229.70222}, + issn = {1758-2229}, + journal = {Environmental Microbiology Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Bacteriophages, Drinking Water, Genome, Viral, High-Throughput Nucleotide Sequencing, Metagenomics, Sweden, Virome, Viruses, Water Microbiology, Water Purification, drinking water treatment plant, metagenomics, virome}, + language = {eng}, + month = {December}, + number = {6}, + pages = {e70222}, + shorttitle = {Variations of the {Virome} in {Raw} and {Treated} {Water}}, + title = {Variations of the {Virome} in {Raw} and {Treated} {Water}: {A} {One}-{Year} {Follow}-{Up} at {Six} {Different} {Drinking} {Water} {Treatment} {Plants}}, + volume = {17}, + year = {2025} +} + @article{sajulga_survey_2020, abstract = {To gain a thorough appreciation of microbiome dynamics, researchers characterize the functional relevance of expressed microbial genes or proteins. This can be accomplished through metaproteomics, which characterizes the protein expression of microbiomes. Several software tools exist for analyzing microbiomes at the functional level by measuring their combined proteome-level response to environmental perturbations. In this survey, we explore the performance of six available tools, to enable researchers to make informed decisions regarding software choice based on their research goals. Tandem mass spectrometry-based proteomic data obtained from dental caries plaque samples grown with and without sucrose in paired biofilm reactors were used as representative data for this evaluation. Microbial peptides from one sample pair were identified by the X! tandem search algorithm via SearchGUI and subjected to functional analysis using software tools including eggNOG-mapper, MEGAN5, MetaGOmics, MetaProteomeAnalyzer (MPA), ProPHAnE, and Unipept to generate functional annotation through Gene Ontology (GO) terms. Among these software tools, notable differences in functional annotation were detected after comparing differentially expressed protein functional groups. Based on the generated GO terms of these tools we performed a peptide-level comparison to evaluate the quality of their functional annotations. A BLAST analysis against the NCBI non-redundant database revealed that the sensitivity and specificity of functional annotation varied between tools. For example, eggNOG-mapper mapped to the most number of GO terms, while Unipept generated more accurate GO terms. Based on our evaluation, metaproteomics researchers can choose the software according to their analytical needs and developers can use the resulting feedback to further optimize their algorithms. To make more of these tools accessible via scalable metaproteomics workflows, eggNOG-mapper and Unipept 4.0 were incorporated into the Galaxy platform.}, author = {Sajulga, Ray and Easterly, Caleb and Riffle, Michael and Mesuere, Bart and Muth, Thilo and Mehta, Subina and Kumar, Praveen and Johnson, James and Gruening, Bjoern Andreas and Schiebenhoefer, Henning and Kolmeder, Carolin A. and Fuchs, Stephan and Nunn, Brook L. and Rudney, Joel and Griffin, Timothy J. and Jagtap, Pratik D.}, @@ -19273,9 +20348,9 @@ @article{sajulga_survey_2020 keywords = {+Methods, +RefPublic, +Stellar, +Tools, +UseLocal, {\textgreater}Galaxy-P, {\textgreater}UseGalaxy.eu, BLAST algorithm, Computer software, Database searching, Functional analysis, Gene ontologies, Microbiome, Software tools, Taxonomy}, language = {en}, month = {November}, - note = {Publisher: Public Library of Science}, number = {11}, pages = {e0241503}, + publisher = {Public Library of Science}, title = {Survey of metaproteomics software tools for functional microbiome analysis}, url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0241503}, urldate = {2020-11-11}, @@ -19305,8 +20380,6 @@ @article{sakamoto_detection_2023 month = {June}, number = {6}, pages = {642--646}, - pmcid = {PMC10315552}, - pmid = {37183016}, title = {Detection of domestic cat hepadnavirus by next-generation sequencing and epidemiological survey in {Japan}}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10315552/}, urldate = {2023-10-07}, @@ -19324,10 +20397,10 @@ @article{salapa_hnrnp_2024 keywords = {{\textgreater}UseGalaxy.eu, CLIP-seq, Multiple sclerosis, RNA metabolism}, language = {en}, month = {January}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {356}, + publisher = {Nature Publishing Group}, title = {{hnRNP} {A1} dysfunction alters {RNA} splicing and drives neurodegeneration in multiple sclerosis ({MS})}, url = {https://www.nature.com/articles/s41467-023-44658-1}, urldate = {2024-01-11}, @@ -19385,9 +20458,9 @@ @article{salinas_genetic_2025 journal = {Microbiology Spectrum}, keywords = {{\textgreater}UseGalaxy.eu}, month = {August}, - note = {Publisher: American Society for Microbiology}, number = {0}, pages = {e00596--25}, + publisher = {American Society for Microbiology}, title = {Genetic variability of {Shiga} toxin-producing {Escherichia} coli strains isolated from {Paraguayan} cattle}, url = {https://journals.asm.org/doi/10.1128/spectrum.00596-25}, urldate = {2025-09-03}, @@ -19395,6 +20468,26 @@ @article{salinas_genetic_2025 year = {2025} } +@article{samanic_characterisation_2025, + abstract = {This study examines the genomic composition and resistance potential of eight putative plasmid-derived contig assemblies reconstructed from marine Enterobacterales isolated in the central Adriatic Sea. Using a combination of Illumina-based whole genome sequencing, de novo assembly, and a multi-tool bioinformatics pipeline, we annotated antimicrobial resistance genes (ARGs), insertion sequences (ISs), and plasmid replicon types. Clinically significant resistance markers such as blaKPC, blaTEM, aacA4, tetA, and folP were identified, frequently co-localised with mobile genetic elements including IS110, IS4, and IS1182. The plasmid-associated contigs were assigned to MOBP and MOBQ types and contained replicon markers (IncP6, IncA/C2) characteristic of broad-host-range plasmids. Our findings provide valuable insight into the plasmidome of environmental Enterobacterales, emphasising the role of coastal pollution in shaping the distribution and potential mobility of antimicrobial resistance genes. This supports the One Health framework by linking environmental reservoirs to clinically relevant resistance mechanisms.}, + author = {Šamanić, Ivica and Dželalija, Mia and Bellulovich, Ema and Kalinić, Hrvoje and Jozić, Slaven and Ordulj, Marin and Udiković-Kolić, Nikolina and Maravić, Ana}, + copyright = {cc by}, + doi = {10.3390/ijms262210910}, + issn = {1422-0067}, + journal = {International journal of molecular sciences}, + keywords = {{\textgreater}UseGalaxy.eu, Adriatic Sea, Coastal Enterobacterales, Mobile genetic elements, One Health, Plasmid-associated Resistance, Replicon Typing}, + language = {eng}, + month = {November}, + number = {22}, + pages = {10910}, + shorttitle = {Characterisation of {Plasmid}-{Associated} {Antimicrobial} {Resistance} {Genes} in {Coastal} {Marine} \<i\>{Enterobacterales}\</i\> from the {Central} {Adriatic} {Sea}}, + title = {Characterisation of {Plasmid}-{Associated} {Antimicrobial} {Resistance} {Genes} in {Coastal} {Marine} \<i\>{Enterobacterales}\</i\> from the {Central} {Adriatic} {Sea}: {De} {Novo} {Assembly} and {Bioinformatic} {Profiling}}, + url = {https://europepmc.org/articles/PMC12652098}, + urldate = {2025-12-26}, + volume = {26}, + year = {2025} +} + @article{sanchez-leon_heteroresistance_2023, abstract = {Heteroresistance to colistin can be defined as the presence of resistant subpopulations in an isolate that is susceptible to this antibiotic. Colistin resistance in Gram-negative bacteria is more frequently related to chromosomal mutations and insertions. This work aimed to study heteroresistance in nine clinical isolates of Klebsiella pneumoniae producing OXA-48 and to describe genomic changes in mutants with acquired resistance in vitro. Antimicrobial susceptibility was determined by broth microdilution (BMD) and heteroresistance by population analysis profiling (PAP). The proteins related to colistin resistance were analyzed for the presence of mutations. Additionally, PCR of the mgrB gene was performed to identify the presence of insertions. In the nine parental isolates, the PAP method showed colistin heteroresistance of colonies growing on plates with concentrations of up to 64 mg/L, corresponding to stable mutant subpopulations. The MICs of some mutants from the PAP plate containing 4×MIC of colistin had absolute values of ≤2 mg/L that were higher than the parental MICs and were defined as persistent variants. PCR of the mgrB gene identified an insertion sequence that inactivated the gene in 21 mutants. Other substitutions in the investigated mutants were found in PhoP, PhoQ, PmrB, PmrC, CrrA and CrrB proteins. Colistin heteroresistance in K. pneumoniae isolates was attributed mainly to insertions in the mgrB gene and point mutations in colistin resistance proteins. The results of this study will improve understanding regarding the mechanisms of colistin resistance in mutants of K. pneumoniae producing OXA-48.}, author = {Sánchez-León, Irene and García-Martínez, Teresa and Diene, Seydina M. and Pérez-Nadales, Elena and Martínez-Martínez, Luis and Rolain, Jean-Marc}, @@ -19405,10 +20498,10 @@ @article{sanchez-leon_heteroresistance_2023 keywords = {\textit{Klebsiella pneumoniae} producing OXA-48, \textit{mgr}B, {\textgreater}UseGalaxy.eu, heteroresistance to colistin}, language = {en}, month = {July}, - note = {Number: 7 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 7}, number = {7}, pages = {1111}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Heteroresistance to {Colistin} in {Clinical} {Isolates} of {Klebsiella} pneumoniae {Producing} {OXA}-48}, url = {https://www.mdpi.com/2079-6382/12/7/1111}, urldate = {2023-07-31}, @@ -19422,8 +20515,8 @@ @article{sanchez-leon_heterorresistencia_2024 copyright = {https://creativecommons.org/licenses/by-nc-nd/4.0/}, keywords = {{\textgreater}UseGalaxy.eu}, language = {spa}, - note = {Accepted: 2024-10-29T12:08:23Z -Publisher: Universidad de Córdoba, UCOPress}, + note = {Accepted: 2024-10-29T12:08:23Z}, + publisher = {Universidad de Córdoba, UCOPress}, title = {Heterorresistencia a colistina en aislados clínicos de {Klebsiella} pneumoniae con fenotipo de resistencia silvestre o productores de la carbapenemasa {OXA}-48}, url = {http://helvia.uco.es/xmlui/handle/10396/29757}, urldate = {2024-11-17}, @@ -19455,9 +20548,9 @@ @article{sanchez_pathwaymatcher_2019 keywords = {+Tools, {\textgreater}UseGalaxy.eu, Gene Regulatory Networks, Signal Transduction, Software}, language = {en}, month = {August}, - note = {Publisher: Oxford Academic}, number = {8}, pages = {giz088}, + publisher = {Oxford Academic}, shorttitle = {{PathwayMatcher}}, title = {{PathwayMatcher}: proteoform-centric network construction enables fine-granularity multiomics pathway mapping}, url = {https://academic.oup.com/gigascience/article/8/8/giz088/5541632}, @@ -19483,6 +20576,22 @@ @article{sandybayev_next_2022 year = {2022} } +@article{sang_smart_2025, + abstract = {This research presents an innovative smart community interactive art therapy platform that integrates multimodal computer graphics with resilient artificial intelligence adaptation mechanisms to address the growing challenges of home-based elderly care. The platform employs a four-layered hierarchical architecture encompassing perception, network, platform, and application layers to deliver personalized therapeutic interventions. The system utilizes multimodal data fusion algorithms to process visual, auditory, and haptic inputs while implementing adaptive learning mechanisms that continuously optimize user experiences based on individual preferences and capabilities. Experimental validation demonstrates superior performance with response times averaging 387 ms under 100 concurrent users, therapeutic recommendation accuracy of 87.3\%, and user satisfaction scores of 4.2/5.0 across multiple evaluation dimensions. The resilient adaptation mechanisms achieved 99.7\% service availability and 34\% improvement in CPU utilization compared to conventional systems. Long-term usage tracking revealed sustained engagement patterns with minimal dropout rates over 6-month evaluation periods. The platform successfully addresses key limitations of traditional elderly care models by providing comprehensive support that encompasses cognitive stimulation, emotional well-being, and social connection while maintaining cost-effectiveness and scalability for large-scale deployment in smart community environments.}, + author = {Sang, DianDian and Miao, Ling and Wu, Qitao}, + doi = {10.1038/s41598-025-27129-z}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Adaptive systems, Aged, Algorithms, Art Therapy, Artificial Intelligence, Computer Graphics, Elderly care, Female, Home Care Services, Humans, Interactive art therapy, Male, Multimodal computer graphics, Resilient artificial intelligence, Smart community}, + language = {eng}, + month = {December}, + number = {1}, + pages = {43057}, + title = {A smart community interactive art therapy platform based on multimodal computer graphics and resilient artificial intelligence for home-based elderly care}, + volume = {15}, + year = {2025} +} + @article{santos_wastewater_2025, abstract = {This study investigates viral composition in wastewater through metagenomic analysis, evaluating the performance of four bioinformatic tools—Genome Detective, CZ.ID, INSaFLU-TELEVIR and Trimmomatic + Kraken2—on samples collected from four sites in each of two wastewater treatment plants (WWTPs) in Lisbon, Portugal in April 2019. From each site, we collected and processed separately three replicates and one pool of nucleic acids extracted from the replicates. A total of 32 samples were processed using sequence-independent single-primer amplification (SISPA) and sequenced on an Illumina MiSeq platform. Across the 128 sample–tool combinations, viral read counts varied widely, from 3 to 288,464. There was a lack of consistency between replicates and their pools in terms of viral abundance and diversity, revealing the heterogeneity of the wastewater matrix and the variability in sequencing effort. There was also a difference between software tools highlighting the impact of tool selection on community profiling. A positive correlation between crAssphage and human pathogens was found, supporting crAssphage as a proxy for public health surveillance. A custom Python pipeline automated viral identification report processing, taxonomic assignments and diversity calculations, streamlining analysis and ensuring reproducibility. These findings emphasize the importance of sequencing depth, software tool selection and standardized pipelines in advancing wastewater-based epidemiology.}, author = {Santos, André F. B. and Nunes, Mónica and Filipa-Silva, Andreia and Pimentel, Victor and Pingarilho, Marta and Abrantes, Patrícia and Miranda, Mafalda N. S. and Crespo, Maria Teresa Barreto and Abecasis, Ana B. and Parreira, Ricardo and Seabra, Sofia G.}, @@ -19493,10 +20602,10 @@ @article{santos_wastewater_2025 keywords = {{\textgreater}UseGalaxy.eu, Computational Biology, Metagenomics, Virome, Viruses, Wastewater, environmental surveillance, metagenomic analysis, next generation sequencing, wastewater}, language = {en}, month = {May}, - note = {Number: 5 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 5}, number = {5}, pages = {707}, + publisher = {Multidisciplinary Digital Publishing Institute}, shorttitle = {Wastewater {Metavirome} {Diversity}}, title = {Wastewater {Metavirome} {Diversity}: {Exploring} {Replicate} {Inconsistencies} and {Bioinformatic} {Tool} {Disparities}}, url = {https://www.mdpi.com/1660-4601/22/5/707}, @@ -19527,9 +20636,9 @@ @article{saragih_potential_2022 keywords = {{\textgreater}UseGalaxy.eu}, language = {en}, month = {May}, - note = {Publisher: IOP Publishing}, number = {1}, pages = {012007}, + publisher = {IOP Publishing}, title = {The potential of bacterial key species as a tool for monitoring peatland quality}, url = {https://doi.org/10.1088/1755-1315/1025/1/012007}, urldate = {2022-09-24}, @@ -19545,8 +20654,8 @@ @article{sarkar_insights_2024 keywords = {{\textgreater}ChemicalToolbox, Harmine, Principal Component Analysis (PCA), beta-carboline alkaloid, isothermal calorimetry, molecular docking, molecular dynamics, ribonucleic acids RNAs, spectroscopy}, language = {English}, month = {July}, - note = {Publisher: Elsevier}, number = {0}, + publisher = {Elsevier}, shorttitle = {Insights on the comparative affinity of ribonucleic acids with plant-based beta carboline alkaloid, harmine}, title = {Insights on the comparative affinity of ribonucleic acids with plant-based beta carboline alkaloid, harmine: {Spectroscopic}, calorimetric and computational evaluation}, url = {https://www.cell.com/heliyon/abstract/S2405-8440(24)10214-9}, @@ -19586,6 +20695,25 @@ @misc{sarker_genetic_2024 year = {2024} } +@article{sarker_zoonotic_2025, + abstract = {This study investigated the prevalence of methicillin-resistant Staphylococcus aureus (MRSA), their antimicrobial resistance, virulence determinants, and potential zoonotic potential between pets, owners, and veterinary professionals. From July 2022 to June 2024, 213 human and 191 animal samples (nasal, pus, and wound swabs) were collected from two veterinary hospitals. Staphylococcus aureus was isolated using conventional cultural method and subsequently confirmed through Gram staining, biochemical tests, and PCR targeting the nuc gene. Methicillin resistance was confirmed using the cefoxitin disk diffusion method and PCR for the mecA gene. Antimicrobial susceptibility testing was performed using the disc diffusion method against 15 antibiotics. Additionally, whole genome sequencing (WGS) was conducted on selected MRSA isolates from pets and their owners to study clonal transmission and virulence factors. The prevalence of MRSA in humans was 15.0\%, in cats was 5.8\% and in dogs was 13.5\%. The MRSA isolates exhibited resistance to penicillin (94.9\%), azithromycin (82\%), and ciprofloxacin (53.9\%), in addition to their intrinsic resistance to cefoxitin. Multidrug resistance was observed in 94.9\% of MRSA isolates, though all were sensitive to amikacin, clindamycin, linezolid, and vancomycin. Notably, six dogs and cats, along with their respective owners, tested positive for MRSA. WGS analysis of these six pairs (12 isolates) showed four sequence types (ST), with ST6 being the most common (66.7\%). There were also four spa types identified, with t304 being the predominant (58.3\%). Within four pairs, identical ST-spa patterns were observed, except for the pair C52-P52 and D88-P88. Two pairs of isolates, C134-P134 and C185-P185, showed clonality based on whole genome and core genome SNP analysis, and other genetic parameters, suggesting clonal transmission between the pets and their respective owners. Virulence profiling revealed the presence of hemolysins, Panton-Valentine Leukocidin, and toxic shock syndrome toxin genes in selected isolates. The detection of diverse MRSA lineages, including human lineages ST80, ST88 and ST6-t304 in pets, indicates their zoonotic potential, and emphasizes the necessity for targeted MRSA surveillance and effective infection control measures. A collaborative One Health approach is therefore imperative to address the spread of MRSA between pets and their owners, thereby mitigating associated risks. The detection of diverse MRSA lineages, including human lineages ST80, ST88, and ST6-t304 in pets, underscores their zoonotic potential and emphasizes the necessity for targeted MRSA surveillance and effective infection control measures. A collaborative One Health approach is therefore imperative to address the spread of MRSA between pets and their owners, thereby mitigating associated risks.}, + author = {Sarker, Himangsu and Hassan, Jayedul and Rahman, A K M Anisur and Korber, Darren R and Alam, Md Mahbub}, + copyright = {cc by-nc-nd}, + doi = {10.1038/s41598-025-02638-z}, + issn = {2045-2322}, + journal = {Scientific reports}, + keywords = {{\textgreater}UseGalaxy.eu, MRSA, One Health, Owners, Pets, Zoonotic Potential}, + language = {eng}, + month = {October}, + number = {1}, + pages = {37002}, + title = {Zoonotic potential of methicillin-resistant {Staphylococcus} aureus isolated from pets and their owners in {Bangladesh}}, + url = {https://europepmc.org/articles/PMC12550073}, + urldate = {2025-12-26}, + volume = {15}, + year = {2025} +} + @article{sauriol_modeling_2020, abstract = {Cancer cell lines are amongst the most important pre-clinical models. In the context of epithelial ovarian cancer, a highly heterogeneous disease with diverse subtypes, it is paramount to study a wide panel of models in order to draw a representative picture of the disease. As this lethal gynaecological malignancy has seen little improvement in overall survival in the last decade, it is all the more pressing to support future research with robust and diverse study models. Here, we describe ten novel spontaneously immortalized patient-derived ovarian cancer cell lines, detailing their respective mutational profiles and gene/biomarker expression patterns, as well as their in vitro and in vivo growth characteristics. Eight of the cell lines were classified as high-grade serous, while two were determined to be of the rarer mucinous and clear cell subtypes, respectively. Each of the ten cell lines presents a panel of characteristics reflective of diverse clinically relevant phenomena, including chemotherapeutic resistance, metastatic potential, and subtype-associated mutations and gene/protein expression profiles. Importantly, four cell lines formed subcutaneous tumors in mice, a key characteristic for pre-clinical drug testing. Our work thus contributes significantly to the available models for the study of ovarian cancer, supplying additional tools to better understand this complex disease.}, author = {Sauriol, Alexandre and Simeone, Kayla and Portelance, Lise and Meunier, Liliane and Leclerc-Desaulniers, Kim and de Ladurantaye, Manon and Chergui, Meriem and Kendall-Dupont, Jennifer and Rahimi, Kurosh and Carmona, Euridice and Provencher, Diane M. and Mes-Masson, Anne-Marie}, @@ -19595,10 +20723,10 @@ @article{sauriol_modeling_2020 keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, biomarkers, carboplatin, cell lines, clear cell, epithelial ovarian cancer, gene expression, high-grade serous, mucinous, mutation profile, xenograft}, language = {en}, month = {August}, - note = {Number: 8 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 8}, number = {8}, pages = {2222}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Modeling the {Diversity} of {Epithelial} {Ovarian} {Cancer} through {Ten} {Novel} {Well} {Characterized} {Cell} {Lines} {Covering} {Multiple} {Subtypes} of the {Disease}}, url = {https://www.mdpi.com/2072-6694/12/8/2222}, urldate = {2021-04-09}, @@ -19611,10 +20739,10 @@ @phdthesis{schafer_algorithms_2024 author = {Schäfer, Richard A.}, copyright = {info:eu-repo/semantics/openAccess}, doi = {10.18419/opus-14990}, + isbn = {978-1-903881-60-6}, keywords = {{\textgreater}UseGalaxy.eu}, language = {en}, note = {Accepted: 2024-10-01T08:49:19Z -ISBN: 9781903881606 Journal Abbreviation: Algorithmen zur globalen Abbildung von RNA-RNA Interaktomen}, title = {Algorithms for the global mapping of {RNA}-{RNA} interactomes}, type = {{doctoralThesis}}, @@ -19645,9 +20773,9 @@ @article{schafer_practical_2024 issn = {2057-5858}, journal = {Microbial Genomics}, keywords = {{\textgreater}UseGalaxy.eu, Algorithms, Genome, Bacterial}, - note = {Publisher: Microbiology Society,}, number = {1}, pages = {001173}, + publisher = {Microbiology Society,}, title = {A practical guide and {Galaxy} workflow to avoid inter-plasmidic repeat collapse and false gene loss in {Unicycler}’s hybrid assemblies}, url = {https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001173}, urldate = {2025-01-05}, @@ -19663,10 +20791,9 @@ @article{schene_misidentification_2024 keywords = {{\textgreater}UseGalaxy.eu}, language = {English}, month = {March}, - note = {Publisher: Elsevier}, number = {3}, pages = {315--316}, - pmid = {38335964}, + publisher = {Elsevier}, title = {Misidentification of neural cell identity in liver-derived organoid systems}, url = {https://www.cell.com/stem-cell-reports/abstract/S2213-6711(24)00009-2}, urldate = {2024-10-20}, @@ -19684,10 +20811,10 @@ @article{schildhauer_glycation_2023 keywords = {{\textgreater}UseGalaxy.eu, Glioblastoma, Glioma, astrocytes, glioblastoma, glioma, glycation, methylglyoxal, polysialylation, sialyltransferases}, language = {en}, month = {January}, - note = {Number: 23 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 23}, number = {23}, pages = {2758}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Glycation {Interferes} with the {Expression} of {Sialyltransferases} and {Leads} to {Increased} {Polysialylation} in {Glioblastoma} {Cells}}, url = {https://www.mdpi.com/2073-4409/12/23/2758}, urldate = {2024-11-17}, @@ -19805,10 +20932,10 @@ @article{schneider_crispr-cas9_2023 keywords = {\textit{KMT2A}-rearranged, {\textgreater}UseGalaxy.eu, ARID4B, BMPR2, CRISPR-Cas Systems, CRISPR-Cas9, MBD3, Precursor Cell Lymphoblastic Leukemia-Lymphoma, epigenome, infant, kinome, leukemia}, language = {en}, month = {January}, - note = {Number: 17 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 17}, number = {17}, pages = {13207}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {{CRISPR}-{Cas9} {Library} {Screening} {Identifies} {Novel} {Molecular} {Vulnerabilities} in {KMT2A}-{Rearranged} {Acute} {Lymphoblastic} {Leukemia}}, url = {https://www.mdpi.com/1422-0067/24/17/13207}, urldate = {2024-11-17}, @@ -19843,10 +20970,10 @@ @article{schoof_mouse_2023 keywords = {{\textgreater}UseGalaxy.eu, Cancer models, Oncogenesis}, language = {en}, month = {November}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {7717}, + publisher = {Nature Publishing Group}, title = {Mouse models of pediatric high-grade gliomas with {MYCN} amplification reveal intratumoral heterogeneity and lineage signatures}, url = {https://www.nature.com/articles/s41467-023-43564-w}, urldate = {2023-11-28}, @@ -19862,9 +20989,8 @@ @article{schroder_eomes_2024 keywords = {{\textgreater}UseGalaxy.eu, Eomes, SWI/SNF complex, Tbx factors, cell fate decision, chromatin accessibility, enhancer regulation, epigenetic remodeling, gastrulation}, language = {English}, month = {December}, - note = {Publisher: Elsevier}, number = {0}, - pmid = {39662466}, + publisher = {Elsevier}, title = {{EOMES} establishes mesoderm and endoderm differentiation potential through {SWI}/{SNF}-mediated global enhancer remodeling}, url = {https://www.cell.com/developmental-cell/abstract/S1534-5807(24)00696-8}, urldate = {2025-03-09}, @@ -19880,9 +21006,8 @@ @article{schule_eomes_2023 keywords = {{\textgreater}UseGalaxy.eu, Brachyury, Eomes, T-box transcription factors, chromatin accessibility, endoderm, lineage specification, mesoderm, mouse gastrulation, transcriptional control}, language = {English}, month = {August}, - note = {Publisher: Elsevier}, number = {0}, - pmid = {37633271}, + publisher = {Elsevier}, title = {Eomes restricts {Brachyury} functions at the onset of mouse gastrulation}, url = {https://www.cell.com/developmental-cell/abstract/S1534-5807(23)00396-9}, urldate = {2023-08-28}, @@ -19930,10 +21055,10 @@ @article{schwabenland_neonatal_2023 keywords = {{\textgreater}UseGalaxy.eu, Development of the nervous system, Neuroimmunology}, language = {en}, month = {May}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {2721}, + publisher = {Nature Publishing Group}, title = {Neonatal immune challenge poses a sex-specific risk for epigenetic microglial reprogramming and behavioral impairment}, url = {https://www.nature.com/articles/s41467-023-38373-0}, urldate = {2023-05-16}, @@ -19965,9 +21090,9 @@ @article{seah_maternal_2025 keywords = {{\textgreater}UseGalaxy.eu, Embryonic induction, Meiosis, Transcription}, language = {en}, month = {February}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {1939}, + publisher = {Nature Publishing Group}, title = {Maternal {PRDM10} activates essential genes for oocyte-to-embryo transition}, url = {https://www.nature.com/articles/s41467-025-56991-8}, urldate = {2025-02-27}, @@ -20056,10 +21181,10 @@ @article{semenzato_genomic_2023 keywords = {{\textgreater}UseGalaxy.eu, Arthrobacter, Oils, Volatile, Origanum, Plants, Medicinal, endophytes, essential oil, genome, plant microbiota, volatile organic compounds}, language = {en}, month = {January}, - note = {Number: 5 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 5}, number = {5}, pages = {4845}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Genomic, {Molecular}, and {Phenotypic} {Characterization} of {Arthrobacter} sp. {OVS8}, an {Endophytic} {Bacterium} {Isolated} from and {Contributing} to the {Bioactive} {Compound} {Content} of the {Essential} {Oil} of the {Medicinal} {Plant} {Origanum} vulgare {L}.}, url = {https://www.mdpi.com/1422-0067/24/5/4845}, urldate = {2023-03-15}, @@ -20107,9 +21232,9 @@ @article{senft_biologists_2023 keywords = {{\textgreater}UseGalaxy.eu, Artificial light, Fluorescence, Fluorescence imaging, Fluorescence microscopy, Image analysis, Light, Light microscopy, Open source software}, language = {en}, month = {June}, - note = {Publisher: Public Library of Science}, number = {6}, pages = {e3002167}, + publisher = {Public Library of Science}, title = {A biologist’s guide to planning and performing quantitative bioimaging experiments}, url = {https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002167}, urldate = {2023-07-02}, @@ -20117,6 +21242,25 @@ @article{senft_biologists_2023 year = {2023} } +@article{serrano-solano_fostering_2021, + abstract = {The COVID-19 pandemic is shifting teaching to an online setting all over the world. The Galaxy framework facilitates the online learning process and makes it accessible by providing a library of high-quality community-curated training materials, enabling easy access to data and tools, and facilitates sharing achievements and progress between students and instructors. By combining Galaxy with robust communication channels, effective instruction can be designed inclusively, regardless of the students’ environments.}, + author = {Serrano-Solano, Beatriz and Föll, Melanie C. and Gallardo-Alba, Cristóbal and Erxleben, Anika and Rasche, Helena and Hiltemann, Saskia and Fahrner, Matthias and Dunning, Mark J. and Schulz, Marcel H. and Scholtz, Beáta and Clements, Dave and Nekrutenko, Anton and Batut, Bérénice and Grüning, Björn A.}, + doi = {10.1371/journal.pcbi.1008923}, + issn = {1553-7358}, + journal = {PLOS Computational Biology}, + keywords = {+Education, +Galactic, +IsGalaxy, +Project, {\textgreater}UseGalaxy.eu, Bioinformatics, Computer software, Computer-Assisted Instruction, Education, Galaxies, Genome analysis, Human learning, Instructors, Workshops}, + language = {en}, + month = {May}, + number = {5}, + pages = {e1008923}, + publisher = {Public Library of Science}, + title = {Fostering accessible online education using {Galaxy} as an e-learning platform}, + url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008923}, + urldate = {2021-05-13}, + volume = {17}, + year = {2021} +} + @article{sethi_ezsinglecell_2024, abstract = {ezSingleCell is an interactive and easy-to-use application for analysing various single-cell and spatial omics data types without requiring prior programing knowledge. It combines the best-performing publicly available methods for in-depth data analysis, integration, and interactive data visualization. ezSingleCell consists of five modules, each designed to be a comprehensive workflow for one data type or task. In addition, ezSingleCell allows crosstalk between different modules within a unified interface. Acceptable input data can be in a variety of formats while the output consists of publication ready figures and tables. In-depth manuals and video tutorials are available to guide users on the analysis workflows and parameter adjustments to suit their study aims. ezSingleCell’s streamlined interface can analyse a standard scRNA-seq dataset of 3000 cells in less than five minutes. ezSingleCell is available in two forms: an installation-free web application (https://immunesinglecell.org/ezsc/) or a software package with a shinyApp interface (https://github.com/JinmiaoChenLab/ezSingleCell2) for offline analysis.}, author = {Sethi, Raman and Ang, Kok Siong and Li, Mengwei and Long, Yahui and Ling, Jingjing and Chen, Jinmiao}, @@ -20127,9 +21271,9 @@ @article{sethi_ezsinglecell_2024 keywords = {{\textgreater}UseGalaxy.eu, Bioinformatics, Computational platforms and environments, Data processing, Programming language, Software}, language = {en}, month = {July}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {5600}, + publisher = {Nature Publishing Group}, shorttitle = {{ezSingleCell}}, title = {{ezSingleCell}: an integrated one-stop single-cell and spatial omics analysis platform for bench scientists}, url = {https://www.nature.com/articles/s41467-024-48188-2}, @@ -20141,6 +21285,7 @@ @article{sethi_ezsinglecell_2024 @article{shaforost_experience_2023, abstract = {Objective. To review the main stages of Klebsiella pneumoniae genome sequencing using the Illumina short-read method and describe the peculiarities of sample library preparation and analysis of the obtained data. Materials and methods. Deoxyribonucleic acid (DNA) for high-throughput sequencing was isolated from Klebsiella pneumoniae cultures. Sample preparation was performed according to the manufacturer’s instructions for the Nextera XT DNA Library Prep kit. Sequencing was performed on an Illumina MiSeq platform using a 2x151 cartridge. Genome assembly to the contigs was performed using the SPAdes Genome Assembler application on the Illumina BaseSpace Sequence Hub service and a set of programs in a Linux environment. The quality of genome assembly was assessed using the QUAST service. Results. Genome sequencing of K. pneumoniae culture samples was performed, followed by an evaluation of the quality of the launch, assembly of the genome, and determination of its main parameters. Conclusion. The main steps of K. pneumoniae genome sequencing have been considered using the short-read method on the Illumina platform. The main parameters for assessing the quality of sample preparation, launch and genome assembly are described.}, author = {Shaforost, A. S. and Ziatskov, A. A. and Voropaev, E. V. and Osipkina, O. V. and Voropaeva, A. V. and Bonda, N. A. and Stoma, I. O.}, + chapter = {NEW TECHNOLOGIES}, copyright = {Authors who publish with this journal agree to the following terms: Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a  Creative Commons Attribution License CC BY-NC-ND 4.0  that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal. Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal. Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See  The Effect of Open Access ).}, doi = {10.51523/2708-6011.2023-20-1-19}, issn = {2708-6011}, @@ -20148,8 +21293,7 @@ @article{shaforost_experience_2023 keywords = {{\textgreater}UseGalaxy.eu}, language = {ru}, month = {March}, - note = {Number: 1 -Section: NEW TECHNOLOGIES}, + note = {Number: 1}, number = {1}, pages = {152--159}, title = {Experience of {Klebsiella} pneumoniae genome sequencing using the short read method on the {Illumina} platform}, @@ -20220,10 +21364,10 @@ @article{sharaf_bridging_2023 keywords = {{\textgreater}UseGalaxy.eu, Agricultural genetics, Communication and replication, Developing world, Education, Plant genetics}, language = {en}, month = {September}, - note = {Number: 9 -Publisher: Nature Publishing Group}, + note = {Number: 9}, number = {9}, pages = {1348--1354}, + publisher = {Nature Publishing Group}, title = {Bridging the gap in {African} biodiversity genomics and bioinformatics}, url = {https://www.nature.com/articles/s41587-023-01933-2}, urldate = {2023-09-17}, @@ -20231,6 +21375,25 @@ @article{sharaf_bridging_2023 year = {2023} } +@article{sharifian_genetic_2025, + abstract = {BackgroundLeishmaniasis is a major public health concern, with a high annual incidence and extensive geographical distribution. This parasitic disease is transmitted through the bite of specific species of sand flies and is caused by flagellated protozoa. Leishmania major is one of the main causes of cutaneous leishmaniasis (CL) in Iran, with diverse clinical manifestations. This research seeks to explore the impact of genetic diversity on clinical differences by investigating variations in chromosomal count and analyzing single nucleotide polymorphisms (SNPs) and insertions/deletions (Indels).Materials and methodsThe whole genome of the Iranian Leishmania major strain MRHO/IR/75/ER has been sequenced using next-generation sequencing. Data alignment to the reference genome, variant calling, and SNP, Indel, and chromosomal variation identification were carried out using bioinformatics tools.ResultsThe findings indicated notable karyotypic variations in the Iranian Leishmania major strain, specifically demonstrating monosomy on chromosome 2 and trisomy on chromosomes 5, 13, 28, and 31. The analysis of SNPs and INDELs revealed 144,509 genetic variants, with 99\% situated within coding regions. Significant changes were observed in MRPA, HSP70.4, GP63, and CPA, which may affect drug resistance and pathogenicity.ConclusionThis research clarifies the genetic diversity of L. major and its consequences for disease development and resistance to treatment. Further functional studies are essential to validate these genetic discoveries and their implications for clinical practice.}, + author = {Sharifian, Hanieh and Khalafiyan, Anis and Fadaie, Mahmood and Khanahmad, Hossein and Shahmoradi, Zabihollah and Zaker, Erfan and Mousavi, Parisa and Pourmoshir, Nadia and Zolfaghari, Azadeh}, + copyright = {cc by-nc-sa}, + doi = {10.4103/abr.abr_172_25}, + issn = {2277-9175}, + journal = {Advanced biomedical research}, + keywords = {{\textgreater}UseGalaxy.eu, Cutaneous Leishmaniasis, Leishmania Major, Variant Calling, Whole Genome Sequencing}, + language = {eng}, + month = {January}, + pages = {112}, + shorttitle = {Genetic {Diversity} and {Chromosomal} {Variations} in the {Iranian} \<i\>{Leishmania} major\</i\> {Strain}}, + title = {Genetic {Diversity} and {Chromosomal} {Variations} in the {Iranian} \<i\>{Leishmania} major\</i\> {Strain}: {Insights} into {Pathogenicity} and {Drug} {Resistance}}, + url = {https://europepmc.org/articles/PMC12543250}, + urldate = {2025-12-26}, + volume = {14}, + year = {2025} +} + @article{sharma_cytokinesis_2025, abstract = {The polarized architecture of neurons is intricately associated with modulation of microtubule dynamics. Over the years several microtubule-associated-factors that modulate neuronal polarity have been identified. However, the precise details of how microtubule arrangement and stability is established in axon and dendrites is not clearly understood. To uncover relevant factors involved in the biological pathways governing microtubule regulation in neuron, we conducted a suppressor screen using the neuronal ectopic extension phenotype caused due to loss of kinesin-13 family microtubule depolymerizing protein KLP-7 in C. elegans . Interestingly, apart from eleven variants of α ( mec-12 ) and β ( mec-7 ) tubulins, we isolated a variant of cytokinesis associated protein, W02B8.2/citk-1, the kinase-less worm orthologue of mammalian citron-rho interacting kinase (CIT). Little is known about the role of CITK in microtubule regulation in post-mitotic neurons. In this study, we found that the kinase-less worm orthologues of CIT, citk-1 and citk-2 redundantly modulate microtubule stability in the axon-like anterior process and maintain the population of plus-end-out microtubules in the dendrite-like posterior process of the PLM mechanosensory neurons in a cell autonomous manner. In the absence of citk-1 , PLM neurons exhibit variable morphological defects including defects in migration, growth, and guidance. Moreover, the neuronal and microtubule phenotypes of loss of both citk-1 and citk-2 were phenocopied by the mutant animals of aspm-1, the worm homolog of abnormal spindle-like microcephaly-associated protein (ASPM), suggesting a genetic association, similar to their association in dividing mammalian cells. These observations suggest that the cytokinesis associated citron kinase and ASPM-1 have non-mitotic roles in C. elegans mechanosensory neurons in the regulation of microtubules.}, author = {Sharma, Sunanda and Ponniah, Keerthana and Ghosh-Roy, Anindya}, @@ -20269,8 +21432,6 @@ @article{sharma_pan-cancer_2019 journal = {Nature Communications}, keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, month = {June}, - pmcid = {PMC6562042}, - pmid = {31189880}, title = {A pan-cancer analysis of synonymous mutations}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6562042/}, urldate = {2019-07-25}, @@ -20286,9 +21447,9 @@ @article{sheikh_volatile_2023 journal = {Microbiology Spectrum}, keywords = {{\textgreater}UseGalaxy.eu, Pythium, Volatile Organic Compounds, Zingiber officinale}, month = {August}, - note = {Publisher: American Society for Microbiology}, number = {0}, pages = {e01510--23}, + publisher = {American Society for Microbiology}, title = {Volatile {Organic} {Compounds} {Emitted} by the {Biocontrol} {Agent} {Pythium} oligandrum {Contribute} to {Ginger} {Plant} {Growth} and {Disease} {Resistance}}, url = {https://journals.asm.org/doi/10.1128/spectrum.01510-23}, urldate = {2023-08-09}, @@ -20302,7 +21463,7 @@ @article{sherwood_transcriptional_2025 doi = {10.1093/aob/mcaf104}, issn = {0305-7364}, journal = {Annals of Botany}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Barley, Gene Expression Profiling, Gene Expression Regulation, Plant, Gene Regulatory Networks, Hordeum, Plant Roots, Stress, Physiological, Transcriptome, Water, aerenchyma, flooding, root transcriptomics, waterlogging}, month = {June}, pages = {mcaf104}, title = {Transcriptional signatures associated with waterlogging stress responses and aerenchyma formation in barley root tissue}, @@ -20345,9 +21506,9 @@ @article{shi_recapitulating_2022 journal = {Cellular and Molecular Gastroenterology and Hepatology}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Necroptosis, Organoids}, language = {eng}, - note = {Publisher: Elsevier BV}, number = {2}, pages = {541--564}, + publisher = {Elsevier BV}, title = {Recapitulating {Cholangiopathy}-{Associated} {Necroptotic} {Cell} {Death} {In} {Vitro} {Using} {Human} {Cholangiocyte} {Organoids}}, url = {https://doi.org/10.1016/j.jcmgh.2021.10.009}, volume = {13}, @@ -20362,7 +21523,7 @@ @article{shiekh_suliman_taxonomic_2025 keywords = {{\textgreater}UseGalaxy.eu, Bacillus, Bacillus cereus, bacterial taxonomy, biological control, phylotaxonomy}, language = {English}, month = {February}, - note = {Publisher: Frontiers}, + publisher = {Frontiers}, title = {Taxonomic refinement of {Bacillus} thuringiensis}, url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2025.1518307/full}, urldate = {2025-02-23}, @@ -20378,11 +21539,10 @@ @article{shinge_inspired_2025 journal = {Journal of Biomolecular Structure and Dynamics}, keywords = {{\textgreater}UseGalaxy.eu, Garuga pinnata, NMDA receptors, amentoflavone, molecular docking, molecular dynamics simulation}, month = {April}, - note = {Publisher: Taylor \& Francis -\_eprint: https://doi.org/10.1080/07391102.2025.2477776}, + note = {\_eprint: https://doi.org/10.1080/07391102.2025.2477776}, number = {0}, pages = {1--15}, - pmid = {40166865}, + publisher = {Taylor \& Francis}, title = {Inspired by molecular dynamic simulation, exploring chemical constituents of alcoholic extract of {Garuga} pinnata computationally as inhibitors of {GluN2B}-containing {NMDA} receptors}, url = {https://doi.org/10.1080/07391102.2025.2477776}, urldate = {2025-04-21}, @@ -20398,9 +21558,9 @@ @article{shipman_combined_2024 journal = {Phytopathology®}, keywords = {{\textgreater}UseGalaxy.eu, Fusarium oxysporum f. sp. cubense, Fusarium oxysporum species complex, Fusarium wilt, banana, secreted in xylem (SIX)}, month = {June}, - note = {Publisher: Scientific Societies}, number = {6}, pages = {1305--1319}, + publisher = {Scientific Societies}, title = {Combined {Use} of {Phenotype}-{Based} and {Genome}-{Informed} {Approaches} {Identified} a {Unique} {Fusarium} oxysporum f. sp. cubense {Isolate} in {Hawaii}}, url = {https://apsjournals.apsnet.org/doi/abs/10.1094/PHYTO-07-23-0257-R}, urldate = {2024-11-17}, @@ -20433,10 +21593,10 @@ @article{siatra_return_2023 keywords = {{\textgreater}UseGalaxy.eu, Cell biology, Stem cells}, language = {en}, month = {March}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {1--15}, + publisher = {Nature Publishing Group}, title = {Return of the {Tbx5}; lineage-tracing reveals ventricular cardiomyocyte-like precursors in the injured adult mammalian heart}, url = {https://www.nature.com/articles/s41536-023-00280-9}, urldate = {2023-03-15}, @@ -20470,10 +21630,10 @@ @article{silva_comparative_2024 keywords = {\textit{Blattabacterium}, \textit{Blattella germanica}, {\textgreater}UseGalaxy.eu, Fat Body, Symbiosis, Transcriptome, antimicrobial peptides, cuticle, fat body, metabolite transporters, peptidoglycan-recognition proteins, transcriptome, tyrosine metabolism, uricolytic pathway}, language = {en}, month = {January}, - note = {Number: 8 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 8}, number = {8}, pages = {4228}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Comparative {Transcriptomics} of {Fat} {Bodies} between {Symbiotic} and {Quasi}-{Aposymbiotic} {Adult} {Females} of {Blattella} germanica with {Emphasis} on the {Metabolic} {Integration} with {Its} {Endosymbiont} {Blattabacterium} and {Its} {Immune} {System}}, url = {https://www.mdpi.com/1422-0067/25/8/4228}, urldate = {2024-05-17}, @@ -20542,9 +21702,9 @@ @article{simonis_persistent_2025 journal = {Molecular Systems Biology}, keywords = {{\textgreater}UseGalaxy.eu, COVID-19, COVID-19 Vaccines, Epigenesis, Genetic, Epigenetic Memory, G-quadruplex, H3K27ac, Immunologic Memory, Macrophages, SARS-CoV-2, SARS-Cov-2 mRNA Vaccination, Trained Innate Immunity}, month = {March}, - note = {Num Pages: 20 -Publisher: John Wiley \& Sons, Ltd}, + note = {Num Pages: 20}, pages = {1--20}, + publisher = {John Wiley \& Sons, Ltd}, title = {Persistent epigenetic memory of {SARS}-{CoV}-2 {mRNA} vaccination in monocyte-derived macrophages}, url = {https://www.embopress.org/doi/full/10.1038/s44320-025-00093-6}, urldate = {2025-03-29}, @@ -20579,11 +21739,10 @@ @article{singh_gaur_galaxy_2023 journal = {Expert Opinion on Drug Discovery}, keywords = {{\textgreater}UseGalaxy.eu, Data-driven, MPDS, drug discovery, galaxy, integrated methods, open-source, workflow management system}, month = {June}, - note = {Publisher: Taylor \& Francis -\_eprint: https://doi.org/10.1080/17460441.2023.2205122}, + note = {\_eprint: https://doi.org/10.1080/17460441.2023.2205122}, number = {6}, pages = {579--590}, - pmid = {37089036}, + publisher = {Taylor \& Francis}, title = {Galaxy for open-source computational drug discovery solutions}, url = {https://doi.org/10.1080/17460441.2023.2205122}, urldate = {2024-11-17}, @@ -20650,10 +21809,10 @@ @article{skalon_expression_2024 keywords = {\textit{Fasciola hepatica} life cycle, {\textgreater}UseGalaxy.eu, RNA-seq analysis, long non-coding RNA, transposable elements}, language = {en}, month = {August}, - note = {Number: 4 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 4}, number = {4}, pages = {39}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Expression of {Transposable} {Elements} throughout the {Fasciola} hepatica {Trematode} {Life} {Cycle}}, url = {https://www.mdpi.com/2311-553X/10/4/39}, urldate = {2024-10-20}, @@ -20690,6 +21849,27 @@ @article{sliti_whole_2025 year = {2025} } +@article{slowakiewicz_viruses_2023, + abstract = {Travertines, which precipitate from high temperature water saturated with calcium carbonate, are generally considered to be dominated by physico-chemical and microbial precipitates. Here, as an additional influence on organomineral formation, metagenomic data and microscopic analyses clearly demonstrate that highly diverse viral, bacterial and archaeal communities occur in the biofilms associated with several modern classic travertine sites in Europe and Asia, along with virus-like particles. Metagenomic analysis reveals that bacteriophages (bacterial viruses) containing icosahedral capsids and belonging to the Siphoviridae, Myoviridae and Podoviridae families are the most abundant of all viral strains, although the bacteriophage distribution does vary across the sampling sites. Icosahedral shapes of capsids are also the most frequently observed under the microscope, occurring as non-mineralized through to mineralized viruses and virus-like particles. Viruses are initially mineralized by Ca-Si amorphous precipitates with subordinate Mg and Al contents; these then alter to nanospheroids composed of Ca carbonate with minor silicate 80–300 nm in diameter. Understanding the roles of bacteriophages in modern carbonate-saturated settings and related organomineralization processes is critical for their broader inclusion in the geological record and ecosystem models.}, + author = {Słowakiewicz, Mirosław and Perri, Edoardo and Tagliasacchi, Ezher and Działak, Paweł and Borkowski, Andrzej and Gradziński, Michał and Kele, Sándor and Tucker, Maurice E.}, + copyright = {2023 The Author(s)}, + doi = {10.1038/s41598-023-38873-5}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Bacteriophages, Biogeochemistry, Podoviridae, Siphoviridae, Viruses}, + language = {en}, + month = {July}, + note = {Number: 1}, + number = {1}, + pages = {11663}, + publisher = {Nature Publishing Group}, + title = {Viruses participate in the organomineralization of travertines}, + url = {https://www.nature.com/articles/s41598-023-38873-5}, + urldate = {2023-07-22}, + volume = {13}, + year = {2023} +} + @article{smith_autocrine_2020, abstract = {Although accumulation of myeloid-derived suppressor cells (MDSC) is a hallmark of cancer, the underlying mechanism of this accumulation within the tumor microenvironment remains incompletely understood. We report here that TNFα-RIP1-mediated necroptosis regulates accumulation of MDSCs. In tumor-bearing mice, pharmacologic inhibition of DNMT with the DNA methyltransferease inhibitor decitabine (DAC) decreased MDSC accumulation and increased activation of antigen-specific cytotoxic T lymphocytes. DAC-induced decreases in MDSC accumulation correlated with increased expression of the myeloid cell lineage-specific transcription factor IRF8 in MDSCs. However, DAC also suppressed MDSC-like cell accumulation in IRF8-deficient mice, indicating that DNA methylation may regulate MDSC survival through an IRF8-independent mechanism. Instead, DAC decreased MDSC accumulation by increasing cell death via disrupting DNA methylation of RIP1-dependent targets of necroptosis. Genome-wide DNA bisulfite sequencing revealed that the \textit{Tnf} promoter was hypermethylated in tumor-induced MDSCs \textit{in vivo}. DAC treatment dramatically increased TNFα levels in MDSC \textit{in vitro}, and neutralizing TNFα significantly increased MDSC accumulation and tumor growth in tumor-bearing mice \textit{in vivo}. Recombinant TNFα induced MDSC cell death in a dose- and RIP1-dependent manner. IL6 was abundantly expressed in MDSCs in tumor-bearing mice and patients with human colorectal cancer. \textit{In vitro}, IL6 treatment of MDSC-like cells activated STAT3, increased expression of DNMT1 and DNMT3b, and enhanced survival. Overall, our findings reveal that MDSCs establish a STAT3-DNMT epigenetic axis, regulated by autocrine IL6, to silence TNFα expression. This results in decreased TNFα-induced and RIP1-dependent necroptosis to sustain survival and accumulation. SIGNIFICANCE: These findings demonstrate that targeting IL6 expression or function represent potentially effective approaches to suppress MDSC survival and accumulation in the tumor microenvironment.}, author = {Smith, Alyssa D and Lu, Chunwan and Payne, Daniela and Paschall, Amy V and Klement, John D and Redd, Priscilla S and Ibrahim, Mohammed L and Ibrahim, Mohammed L and Yang, Dafeng and Han, Qimei and Liu, Zhuoqi and Shi, Huidong and Hartney, Thomas J and Nayak-Kapoor, Asha and Liu, Kebin}, @@ -20716,9 +21896,9 @@ @article{soares_hierarchical_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Mitosis, Neural Stem Cells}, language = {eng}, month = {June}, - note = {Publisher: Cold Spring Harbor Laboratory}, number = {13-14}, pages = {1020--1034}, + publisher = {Cold Spring Harbor Laboratory}, title = {Hierarchical reactivation of transcription during mitosis-to-{G1} transition by {Brn2} and {Ascl1} in neural stem cells}, url = {https://doi.org/10.1101/gad.348174.120}, volume = {35}, @@ -20750,10 +21930,10 @@ @article{soleau_first_2024 keywords = {{\textgreater}UseGalaxy.eu, Escherichia coli Infections, Genome, Bacterial, Phylogeny, Shiga-Toxigenic Escherichia coli, Shiga-toxin-producing \textit{Escherichia coli} (STEC), Whole Genome Sequencing, characterization, emerging pathogen, first isolation, serotype O80:H2, whole-genome sequencing}, language = {en}, month = {January}, - note = {Number: 10 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 10}, number = {10}, pages = {5428}, + publisher = {Multidisciplinary Digital Publishing Institute}, shorttitle = {First {Isolation} of the {Heteropathotype} {Shiga} {Toxin}-{Producing} and {Extra}-{Intestinal} {Pathogenic} ({STEC}-{ExPEC}) {E}. coli {O80}}, title = {First {Isolation} of the {Heteropathotype} {Shiga} {Toxin}-{Producing} and {Extra}-{Intestinal} {Pathogenic} ({STEC}-{ExPEC}) {E}. coli {O80}:{H2} in {French} {Healthy} {Cattle}: {Genomic} {Characterization} and {Phylogenetic} {Position}}, url = {https://www.mdpi.com/1422-0067/25/10/5428}, @@ -20803,10 +21983,10 @@ @article{soriano-sexto_identification_2022 keywords = {{\textgreater}UseGalaxy.eu, Maple Syrup Urine Disease, Metabolism, Inborn Errors, allelic expression imbalance, differential gene expression, inherited metabolic disorders, multi-omics, targeted transcriptomics}, language = {en}, month = {January}, - note = {Number: 21 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 21}, number = {21}, pages = {12850}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Identification of {Clinical} {Variants} beyond the {Exome} in {Inborn} {Errors} of {Metabolism}}, url = {https://www.mdpi.com/1422-0067/23/21/12850}, urldate = {2022-11-06}, @@ -20822,7 +22002,7 @@ @article{soumia_unravelling_2025 keywords = {{\textgreater}UseGalaxy.eu, Thrips parvispinus, Thrips tabaci, invasive pest, mitochondrial genome, phylogeny}, language = {English}, month = {February}, - note = {Publisher: Frontiers}, + publisher = {Frontiers}, shorttitle = {Unravelling the complete mitochondrial genomes of {Thrips} tabaci {Lindeman} and {Thrips} parvispinus {Karny} ({Thysanoptera}}, title = {Unravelling the complete mitochondrial genomes of {Thrips} tabaci {Lindeman} and {Thrips} parvispinus {Karny} ({Thysanoptera}: {Thripidae}) and their phylogenetic implications}, url = {https://www.frontiersin.org/journals/insect-science/articles/10.3389/finsc.2025.1536160/full}, @@ -20842,20 +22022,6 @@ @phdthesis{souza_effect_2024 year = {2024} } -@article{souza_new_2025, - author = {Souza, Júlia W. and Henriques, Lethícia R. and Carlson, Roger M. and Botelho, Bruna B. F. and Carvalho, João Victor R. P. and Santos, João Pedro N. and Aguiar, Eric R. G. R. and Agarkova, Irina V. and Van Etten, James L. and Dunigan, David D. and Rodrigues, Rodrigo A. L.}, - issn = {1999-4915}, - journal = {Viruses}, - keywords = {{\textgreater}UseGalaxy.eu}, - language = {eng}, - month = {August}, - number = {8}, - title = {New {Isolates} of {Betachloroviruses} {Shed} {Light} on the {Diversity} and {Biological} {Complexity} of an {Unexplored} {Group} of {Giant} {Algal} {Viruses}}, - url = {http://europepmc.org/abstract/PMC/PMC12390592}, - volume = {17}, - year = {2025} -} - @article{souza_new_2025, abstract = {Satellite DNAs (satDNAs) play a crucial role in understanding chromosomal evolution and the differentiation of sex chromosomes across diverse taxa, particularly when high karyotypic diversity occurs. The Physalaemus cuvieri–Physalaemus ephippifer species complex comprises at least seven divergent lineages, each exhibiting specific karyotypic signatures. The group composed of Ph. ephippifer, Lineage 1B of ‘Ph. cuvieri’ (L1B), and a lineage resulting from their secondary contact is especially intriguing due to varying degrees of sex chromosome heteromorphism. In this study, we characterized the satellitome of Ph. ephippifer in order to identify novel satDNAs that may provide insights into chromosomal evolution, particularly concerning sex chromosomes. We identified 62 satDNAs in Ph. ephippifer, collectively accounting for approximately 10\% of the genome. Notably, nine satDNA families were shared with species from distantly related clades, raising questions about their potential roles in anurans genomes. Among the seven satDNAs mapped via fluorescent in situ hybridization, PepSat3 emerged as a strong candidate for the centromeric sequence in this group. Additionally, PepSat11 and PepSat24 provided evidence supporting a translocation involving both arms of the W chromosome in Ph. ephippifer. Furthermore, a syntenic block composed of PepSat3, PcP190, and PepSat11 suggested an inversion event during the divergence of Ph. ephippifer and L1B. The variation in signal patterns of satDNAs associated with nucleolar organizer regions (NORs) highlights the complexity of NOR evolution in this species complex, which exhibits substantial diversity in this genomic region. Additionally, our findings for PepSat30-350 emphasize the importance of validating the sex-biased abundance of satDNAs.}, author = {Souza, Lucas H. B. and Ferro, Juan M. and Milanez, Helena M. and Haddad, Célio F. B. and Lourenço, Luciana B.}, @@ -20866,10 +22032,10 @@ @article{souza_new_2025 keywords = {{\textgreater}UseGalaxy.eu, Anura, DNA, Satellite, Evolution, Molecular, Sex Chromosomes, chromosomal homologies, chromosomal rearrangements, nucleolar organizer region, repetitive elements, satellitome}, language = {en}, month = {June}, - note = {Number: 6 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 6}, number = {6}, pages = {876}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {New {Insights} into the {Sex} {Chromosome} {Evolution} of the {Common} {Barker} {Frog} {Species} {Complex} ({Anura}, {Leptodactylidae}) {Inferred} from {Its} {Satellite} {DNA} {Content}}, url = {https://www.mdpi.com/2218-273X/15/6/876}, urldate = {2025-06-20}, @@ -20877,6 +22043,20 @@ @article{souza_new_2025 year = {2025} } +@article{souza_new_2025, + author = {Souza, Júlia W. and Henriques, Lethícia R. and Carlson, Roger M. and Botelho, Bruna B. F. and Carvalho, João Victor R. P. and Santos, João Pedro N. and Aguiar, Eric R. G. R. and Agarkova, Irina V. and Van Etten, James L. and Dunigan, David D. and Rodrigues, Rodrigo A. L.}, + issn = {1999-4915}, + journal = {Viruses}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {August}, + number = {8}, + title = {New {Isolates} of {Betachloroviruses} {Shed} {Light} on the {Diversity} and {Biological} {Complexity} of an {Unexplored} {Group} of {Giant} {Algal} {Viruses}}, + url = {http://europepmc.org/abstract/PMC/PMC12390592}, + volume = {17}, + year = {2025} +} + @mastersthesis{soyland_mapping_2024, abstract = {The last few decades have seen a massive use of antibiotics worldwide, in all from human health care and veterinary use to agriculture and aquaculture. This has led to a rise in emergence of antibiotic resistant bacteria (ARB), where bacteria harbouring genes for extended-spectrum β-lactamases (ESBL) and carbapenem resistance are of particular concern. Infectious diseases caused by these bacteria can be very challenging to treat, and a staggering number of deaths every year result directly or indirectly from antibiotic resistance. With no measurements taken to stop the ARB spread, this problem will only keep on growing. @@ -20941,10 +22121,10 @@ @article{spano_comparative_2023 keywords = {{\textgreater}UseGalaxy.eu, artichoke ecotype, artichoke transcriptome, bioactive compounds, lignin, peroxidase, virus sanitation}, language = {en}, month = {January}, - note = {Number: 8 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 8}, number = {8}, pages = {1600}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Comparative {Analysis} of {Bioactive} {Compounds} in {Two} {Globe} {Artichoke} {Ecotypes} {Sanitized} and {Non}-{Sanitized} from {Viral} {Infections}}, url = {https://www.mdpi.com/2223-7747/12/8/1600}, urldate = {2023-07-31}, @@ -20981,10 +22161,10 @@ @article{spano_spotlight_2024 keywords = {{\textgreater}UseGalaxy.eu, RNAseq analysis, anti-inflammatory effects, antioxidant and antimicrobial effects, artichoke, polyphenol extracts, supercritical fluid extraction, virus infection, virus sanitation protocol}, language = {en}, month = {July}, - note = {Number: 7 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 7}, number = {7}, pages = {852}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Spotlight on {Secondary} {Metabolites} {Produced} by an {Early}-{Flowering} {Apulian} {Artichoke} {Ecotype} {Sanitized} from {Virus} {Infection} by {Meristem}-{Tip}-{Culture} and {Thermotherapy}}, url = {https://www.mdpi.com/2076-3921/13/7/852}, urldate = {2024-11-17}, @@ -21002,9 +22182,9 @@ @article{spradling_mitochondrial_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Genome, Mitochondrial}, language = {eng}, month = {July}, - note = {Publisher: Public Library of Science (PLoS)}, number = {7}, pages = {e0254138}, + publisher = {Public Library of Science (PLoS)}, title = {Mitochondrial genome of {Geomydoecus} aurei, a pocket-gopher louse}, url = {https://doi.org/10.1371/journal.pone.0254138}, volume = {16}, @@ -21038,9 +22218,9 @@ @article{staehle_lysine-specific_2025 keywords = {{\textgreater}UseGalaxy.eu, Epigenetics, Haematopoietic stem cells, Myelopoiesis, Transcriptomics}, language = {en}, month = {August}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {619}, + publisher = {Nature Publishing Group}, title = {Lysine-specific demethylase 1 regulates hematopoietic stem cell expansion and myeloid cell differentiation}, url = {https://www.nature.com/articles/s41419-025-07951-z}, urldate = {2025-08-20}, @@ -21058,9 +22238,9 @@ @article{stafiniak_stabilizing_2025 keywords = {\textit{Reynoutria}, {\textgreater}UseGalaxy.eu, housekeeping genes, invasive species, qRT-PCR normalization, reference-gene validation}, language = {en}, month = {January}, - note = {Publisher: Multidisciplinary Digital Publishing Institute}, number = {17}, pages = {8265}, + publisher = {Multidisciplinary Digital Publishing Institute}, shorttitle = {Stabilizing the {Baseline}}, title = {Stabilizing the {Baseline}: {Reference} {Gene} {Evaluation} in {Three} {Invasive} {Reynoutria} {Species}}, url = {https://www.mdpi.com/1422-0067/26/17/8265}, @@ -21069,12 +22249,31 @@ @article{stafiniak_stabilizing_2025 year = {2025} } +@article{stefanovska_fibroblast_2025, + abstract = {During aging, peripheral nerves undergo structural and cellular changes that trigger loss of function, impair quality of life, and increase disease risk. During peripheral nerve aging there are cellular and molecular changes, such as increased extracellular matrix deposition. The mechanisms behind these aging-induced alterations remain unclear. Here, we profile mouse sciatic nerves using single nucleus transcriptomics and unravel changes in macrophage subtypes during nerve aging. Phagocytic macrophage numbers increase at the onset of aging, followed by higher numbers of chronic inflammatory macrophages. Based on ligand-receptor analysis, we predict that increased fibroblast growth factor (FGF) signaling from adipocytes activates a chondrocyte-like neural fibroblast state during peripheral nerve aging. Finally, we show that FGF2 induces the co-expression of the chondrocyte markers SOX9 and FOXC2 in senescent human perineurial fibroblast, that can be blocked with FGF1. In conclusion, our findings reveal some of the molecular mechanisms of peripheral nerve aging by FGF-regulated induction of a chondrocyte-like fibroblast state.}, + author = {Stefanovska, Dragana and Sassu, Eliza and Tekman, Mehmet and Naghsh Nilchi, Amirhossein and Haider, Severin and Domisch, Claudia and Hossfeld, Madelon and Perez-Feliz, Stefanie and Miarka, Lauritz and Schneider-Warme, Franziska and Arnold, Sebastian J and Prinz, Marco and Grüning, Björn and Preissl, Sebastian and Hortells, Luis}, + copyright = {cc by}, + doi = {10.1038/s41467-025-65297-8}, + issn = {2041-1723}, + journal = {Nature communications}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {November}, + number = {1}, + pages = {10020}, + title = {Fibroblast growth factor signaling induces a chondrocyte-like state of peripheral nerve fibroblast during aging}, + url = {https://europepmc.org/articles/PMC12618493}, + urldate = {2025-12-26}, + volume = {16}, + year = {2025} +} + @article{stein_single-cell_2021, author = {Stein, Catarina M. and Weiskirchen, Ralf and Damm, Frederik and Strzelecka, Paulina M.}, doi = {10.1002/jcb.30134}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {August}, - note = {Publisher: Wiley}, + publisher = {Wiley}, title = {Single-cell omics: {Overview}, analysis, and application in biomedical science}, url = {https://doi.org/10.1002/jcb.30134}, year = {2021} @@ -21088,8 +22287,8 @@ @article{stephen_jr_comparative_2022 journal = {PeerJ}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, language = {eng}, - note = {Publisher: PeerJ Inc.}, pages = {e12632}, + publisher = {PeerJ Inc.}, title = {Comparative genomics of the black rot pathogen {Xanthomonas} campestris pv. campestris and non-pathogenic co-inhabitant {Xanthomonas} melonis from {Trinidad} reveal unique pathogenicity determinants and secretion system profiles}, url = {http://europepmc.org/abstract/MED/35036136}, volume = {9}, @@ -21106,8 +22305,8 @@ @article{sterling_revision_2025 keywords = {{\textgreater}UseGalaxy.eu}, language = {en}, month = {March}, - note = {Publisher: Pensoft Publishers}, pages = {297--368}, + publisher = {Pensoft Publishers}, title = {A revision of the hitherto neglected genus {Topiris} {Walker}, 1863 ({Lepidoptera}, {Xyloryctidae}) with taxonomic notes on the genus {Athrypsiastis} {Meyrick}, 1910}, url = {https://zookeys.pensoft.net/article/119155/}, urldate = {2025-03-09}, @@ -21144,10 +22343,10 @@ @article{stojkovic_targeted_2024 keywords = {{\textgreater}UseGalaxy.eu, Ferroptosis, Multiple Sclerosis, PBMCs, ferroptosis, gene expression, multiple sclerosis, severity, targeted RNAseq}, language = {en}, month = {January}, - note = {Number: 5 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 5}, number = {5}, pages = {3016}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Targeted {RNAseq} {Revealed} the {Gene} {Expression} {Signature} of {Ferroptosis}-{Related} {Processes} {Associated} with {Disease} {Severity} in {Patients} with {Multiple} {Sclerosis}}, url = {https://www.mdpi.com/1422-0067/25/5/3016}, urldate = {2024-05-17}, @@ -21202,16 +22401,16 @@ @article{storms_influenza_2024 @article{strateva_analysis_2023, abstract = {Abstract The present study aimed to explore the genotypic and phenotypic characteristics of biofilm formation in Bulgarian nosocomial Stenotrophomonas maltophilia isolates (n = 221) during the period 2011–2022, by screening for the presence of biofilm-associated genes (BAG) (spgM, rmlA and rpfF), their mutational variability, and assessment of the adherent growth on a polystyrene surface. The methodology included: PCR amplification, whole-genome sequencing (WGS) and crystal violet microtiter plate assay for biofilm quantification. The overall incidence of BAG was: spgM 98.6\%, rmlA 86\%, and rpfF 66.5\%. The most prevalent genotype was spgM+/rmlA+/rpfF+ (56.1\%), followed by spgM+/rmlA+/rpfF- (28.5\%), and spgM+/rmlA-/rpfF+ (9.5\%), with their significant predominance in lower respiratory tract isolates compared to those with other origin (P {\textless} 0.001). All strains examined were characterized as strong biofilm producers (OD550 from 0.224 ± 0.049 to 2.065 ± 0.023) with a single exception that showed a weak biofilm-forming ability (0.177 ± 0.024). No significant differences were observed in the biofilm formation according to the isolation source, as well as among COVID-19 and non-COVID-19 isolates (1.256 ± 0.028 vs. 1.348 ± 0.128, respectively). Also, no correlation was found between the biofilm amounts and the corresponding genotypes. WGS showed that the rmlA accumulated a larger number of variants (0.0086 per base) compared to the other BAG, suggesting no critical role of its product to the biofilm formation. Additionally, two of the isolates were found to harbour class 1 integrons (7-kb and 2.6-kb sized, respectively) containing sul1 in their 3′ conservative ends, which confers sulfonamide resistance. To the best of our knowledge, this is the first study on S. maltophilia biofilm formation in Bulgaria, which also identifies novel sequence types (ST819, ST820 and ST826). It demonstrates the complex nature of this adaptive mechanism in the multifactorial pathogenesis of biofilm-associated infections.}, author = {Strateva, Tanya and Trifonova, Angelina and Sirakov, Ivo and Borisova, Dayana and Stancheva, Mikaela and Keuleyan, Emma and Setchanova, Lena and Peykov, Slavil}, + chapter = {Acta Microbiologica et Immunologica Hungarica}, doi = {10.1556/030.2023.01920}, issn = {1217-8950, 1588-2640}, journal = {Acta Microbiologica et Immunologica Hungarica}, keywords = {{\textgreater}UseGalaxy.eu, PCR screening, Stenotrophomonas maltophilia, biofilm formation, biofilm-associated genes, phenotypic characteristics, whole-genome sequencing}, language = {en}, month = {January}, - note = {Publisher: Akadémiai Kiadó -Section: Acta Microbiologica et Immunologica Hungarica}, number = {1}, pages = {11--21}, + publisher = {Akadémiai Kiadó}, shorttitle = {Analysis of biofilm formation in nosocomial {Stenotrophomonas} maltophilia isolates collected in {Bulgaria}}, title = {Analysis of biofilm formation in nosocomial {Stenotrophomonas} maltophilia isolates collected in {Bulgaria}: {An} 11-year study (2011–2022)}, url = {https://akjournals.com/view/journals/030/70/1/article-p11.xml}, @@ -21223,15 +22422,15 @@ @article{strateva_analysis_2023 @article{strateva_first_2024, abstract = {Abstract Cefiderocol (CFDC) is a first-in-class siderophore cephalosporin with potent activity against multidrug-resistant Gram-negative bacteria including carbapenem-resistant Acinetobacter baumannii. The present study aimed to explore the CFDC resistance mechanisms of an extensively drug-resistant A. baumannii isolate from Bulgaria. The A. baumannii Aba52 strain (designated Aba52) was obtained in 2018 from a blood sample of a critically ill patient. The methodology included antimicrobial susceptibility testing, whole-genome sequencing (WGS), reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR), multilocus sequence typing, and phylogenomic analysis. The isolate demonstrated high-level resistance to CFDC (MIC = 64 mg L−1), resistance to carbapenems, aminoglycosides, fluoroquinolones, sulfamethoxazole-trimethoprim, and tigecycline, as well as susceptibility only to colistin. WGS-based resistome analysis revealed the existence of blaOXA-23, blaOXA-66 and blaADC-73. Seven non-conservative missense mutations affecting iron transport-related genes were detected: exbD4 (p.Ser61Pro), tonB2 (p.Ala268Val), bauA (p.Thr61Ala), ftsI (p.Ala515Val), piuA (p.Gly216Val), and feoB (p.Ser429Pro and p.Thr595Ala). A variety of virulence factors associated with adherence, biofilm formation, enzyme production, immune invasion, iron uptake, quorum sensing, and two-component regulatory systems were identified, suggesting a significant pathogenic potential of Aba52. The performed RT-qPCR analysis showed diminished (0.17) and absent expression of the pirA and piuA genes, respectively, encoding TonB-dependent siderophore receptors. Aba52 belonged to the widespread high-risk sequence type ST2 (Pasteur scheme). To the best of our knowledge, this is the first documented case of CFDC-resistant A. baumannii in Bulgaria even though, CFDC has never been applied in our country. The emerging resistance highlights the crucial need for nationwide surveillance targeting the implementation of novel antibiotics.}, author = {Strateva, Tanya and Peykov, Slavil}, + chapter = {Acta Microbiologica et Immunologica Hungarica}, doi = {10.1556/030.2024.02201}, issn = {1217-8950, 1588-2640}, journal = {Acta Microbiologica et Immunologica Hungarica}, keywords = {{\textgreater}UseGalaxy.eu}, language = {en}, month = {January}, - note = {Publisher: Akadémiai Kiadó -Section: Acta Microbiologica et Immunologica Hungarica}, number = {aop}, + publisher = {Akadémiai Kiadó}, title = {First detection of a cefiderocol-resistant and extensively drug-resistant {Acinetobacter} baumannii clinical isolate in {Bulgaria}}, url = {https://akjournals.com/view/journals/030/aop/article-10.1556-030.2024.02201/article-10.1556-030.2024.02201.xml}, urldate = {2024-01-27}, @@ -21249,10 +22448,10 @@ @article{strateva_first_2025 keywords = {\textit{Enterococcus faecalis}, \textit{optrA}, {\textgreater}UseGalaxy.eu, G2576T mutation, ST1102, hospital-adapted ST6 lineage, linezolid resistance, pAR0780 plasmid, whole-genome sequencing}, language = {en}, month = {January}, - note = {Number: 1 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 1}, number = {1}, pages = {195}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {First {Detection} and {Genomic} {Characterization} of {Linezolid}-{Resistant} {Enterococcus} faecalis {Clinical} {Isolates} in {Bulgaria}}, url = {https://www.mdpi.com/2076-2607/13/1/195}, urldate = {2025-02-11}, @@ -21270,10 +22469,10 @@ @article{strateva_genomic_2024 keywords = {\textit{Pseudomonas aeruginosa}, {\textgreater}UseGalaxy.eu, Anti-Bacterial Agents, Drug Resistance, Multiple, Bacterial, Intensive Care Units, Microbial Sensitivity Tests, Pseudomonas Infections, Pseudomonas aeruginosa, VEB-9 extended-spectrum β-lactamase, beta-Lactamases, carbapenem resistance, exotoxin U, extensive drug resistance, high-risk clone ST357, phylogenomic analysis, whole-genome sequencing}, language = {en}, month = {September}, - note = {Number: 9 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 9}, number = {9}, pages = {719}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Genomic {Insights} into {Vietnamese} {Extended}-{Spectrum} β-{Lactamase}-9-{Producing} {Extensively} {Drug}-{Resistant} {Pseudomonas} aeruginosa {Isolates} {Belonging} to the {High}-{Risk} {Clone} {ST357} {Obtained} from {Bulgarian} {Intensive} {Care} {Unit} {Patients}}, url = {https://www.mdpi.com/2076-0817/13/9/719}, urldate = {2024-08-29}, @@ -21284,15 +22483,15 @@ @article{strateva_genomic_2024 @article{strateva_genotypic_2023, abstract = {Abstract The present study aimed to explore the virulence characteristics in 221 Bulgarian nosocomial Stenotrophomonas maltophilia isolates (2011–2022) via screening for the presence of virulence genes, their mutational variability, and the corresponding enzyme activity. PCR amplification, enzymatic assays, whole-genome sequencing (WGS), and biofilm quantification on a polystyrene plate were performed. The incidence of virulence determinants was as follows: stmPr1 (encoding for the major extracellular protease StmPr1) 87.3\%, stmPr2 (minor extracellular protease StmPr2) 99.1\%, Smlt3773 locus (outer membrane esterase) 98.2\%, plcN1 (non-hemolytic phospholipase C) 99.1\%, and smf-1 (type-1 fimbriae, biofilm-related gene) 96.4\%. The 1621-bp allele of stmPr1 was most frequently found (61.1\%), followed by the combined allelic variant (17.6\%), stmPr1-negative genotype (12.7\%), and 868-bp allele (8.6\%). Protease, esterase, and lecithinase activity was observed in 95\%, 98.2\%, and 17.2\% of the isolates, respectively. The WGS-subjected isolates (n = 9) formed two groups. Five isolates possessed only the 1621-bp variant of stmPr1, higher biofilm formation ability (Optical Density at λ = 550 nm (OD550): 1.253–1.789), as well as a low number of mutations in the protease genes and smf-1. Three other isolates had only the 868-bp variant, weaker biofilm production (OD550: 0.788–1.108), and higher number of mutations within these genes. The only weak biofilm producer (OD550 = 0.177) had no stmPr1 alleles. In conclusion, the similar PCR detection rates did not allow differentiation of the isolates. In contrast, WGS permitted stmPr1 alleles-based differentiation. To the best of our knowledge, this is the first Bulgarian study presenting genotypic and phenotypic insights into virulence factors of S. maltophilia isolates.}, author = {Strateva, Tanya and Trifonova, Angelina and Stratev, Alexander and Peykov, Slavil}, + chapter = {Acta Microbiologica et Immunologica Hungarica}, doi = {10.1556/030.2023.02059}, issn = {1217-8950, 1588-2640}, journal = {Acta Microbiologica et Immunologica Hungarica}, keywords = {{\textgreater}UseGalaxy.eu}, language = {en}, month = {July}, - note = {Publisher: Akadémiai Kiadó -Section: Acta Microbiologica et Immunologica Hungarica}, number = {aop}, + publisher = {Akadémiai Kiadó}, title = {Genotypic and phenotypic insights into virulence factors of nosocomial {Stenotrophomonas} maltophilia isolates collected in {Bulgaria} (2011–2022)}, url = {https://akjournals.com/view/journals/030/aop/article-10.1556-030.2023.02059/article-10.1556-030.2023.02059.xml}, urldate = {2023-07-31}, @@ -21310,10 +22509,10 @@ @article{strateva_phenotypic_2023 keywords = {\textit{Acinetobacter baumannii}, {\textgreater}UseGalaxy.eu, antimicrobial resistance genes, carbapenem resistance, extensive drug resistance, resistome analysis, whole-genome sequencing}, language = {en}, month = {April}, - note = {Number: 4 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 4}, number = {4}, pages = {875}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Phenotypic and {Molecular} {Characteristics} of {Carbapenem}-{Resistant} {Acinetobacter} baumannii {Isolates} from {Bulgarian} {Intensive} {Care} {Unit} {Patients}}, url = {https://www.mdpi.com/2076-2607/11/4/875}, urldate = {2024-11-17}, @@ -21365,9 +22564,9 @@ @article{subramani_genetic_2023 journal = {Applied and Environmental Microbiology}, keywords = {{\textgreater}UseGalaxy.eu, Enteritis, Enterotoxigenic Escherichia coli, Escherichia coli Infections}, month = {October}, - note = {Publisher: American Society for Microbiology}, number = {10}, pages = {e00559--23}, + publisher = {American Society for Microbiology}, title = {Genetic background of neomycin resistance in clinical {Escherichia} coli isolated from {Danish} pig farms}, url = {https://journals.asm.org/doi/full/10.1128/aem.00559-23}, urldate = {2024-11-17}, @@ -21402,9 +22601,9 @@ @article{subramoney_sars-cov-2_2023 keywords = {{\textgreater}UseGalaxy.eu, Antibodies, Microbial mutation, Mutation, Mutation detection, Respiratory infections, SARS CoV 2, Single nucleotide polymorphisms, Substitution mutation}, language = {en}, month = {May}, - note = {Publisher: Public Library of Science}, number = {5}, pages = {e0286373}, + publisher = {Public Library of Science}, title = {{SARS}-{CoV}-2 spike protein diversity at an intra-host level, among {SARS}-{CoV}-2 infected individuals in {South} {Africa}, 2020 to 2022}, url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0286373}, urldate = {2023-06-03}, @@ -21421,9 +22620,9 @@ @article{sun_complete_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, language = {eng}, month = {July}, - note = {Publisher: Informa UK Limited}, number = {8}, pages = {2209--2211}, + publisher = {Informa UK Limited}, title = {The complete mitochondrial genome of the wild silkmoth {Antheraea} yamamai from {Heilongjiang}, {China} ({Lepidoptera}: {Saturniidae})}, url = {https://doi.org/10.1080/23802359.2021.1945975}, volume = {6}, @@ -21453,9 +22652,9 @@ @article{sun_stencil_2022 journal = {PLOS Computational Biology}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {February}, - note = {Publisher: Public Library of Science (PLoS)}, number = {2}, pages = {e1009859}, + publisher = {Public Library of Science (PLoS)}, title = {{STENCIL}: {A} web templating engine for visualizing and sharing life science datasets}, url = {https://doi.org/10.1371/journal.pcbi.1009859}, volume = {18}, @@ -21483,10 +22682,10 @@ @article{suresh_comparative_2025 doi = {10.1099/mgen.0.001511}, issn = {2057-5858}, journal = {Microbial Genomics}, - keywords = {{\textgreater}UseGalaxy.eu}, - note = {Publisher: Microbiology Society,}, + keywords = {{\textgreater}UseGalaxy.eu, Antimicrobial resistance, Comparative genomics, Novel Species, Pan-genome Analysis, Parvimonas Micra, Phylogenetic analysis, virulence factors}, number = {9}, pages = {001511}, + publisher = {Microbiology Society,}, title = {Comparative genome analysis of human pathogen {Parvimonas} micra revealed strain {JM503A} as potential novel species in the genus {Parvimonas} and high intra-species functional diversity}, url = {https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001511}, urldate = {2025-10-03}, @@ -21519,7 +22718,7 @@ @incollection{suzuki_genomic_2023 booktitle = {Nanopore {Sequencing}: {Methods} and {Protocols}}, doi = {10.1007/978-1-0716-2996-3_16}, editor = {Arakawa, Kazuharu}, - isbn = {978-1-07-162996-3}, + isbn = {978-1-0716-2996-3}, keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au, Antimicrobial resistance, Chromosome, ESKAPE pathogens, Mobile genetic element, Mycobacteria, Phage, Plasmid, Virulence}, language = {en}, pages = {227--246}, @@ -21552,8 +22751,8 @@ @article{sweatman_setd1a-dependent_2025 keywords = {{\textgreater}UseGalaxy.eu, Cancer therapeutic resistance, Histone-Lysine N-Methyltransferase, Methylation, Neoplasms, Poly(ADP-ribose) Polymerase Inhibitors}, language = {en}, month = {February}, - note = {Publisher: Nature Publishing Group}, pages = {1--13}, + publisher = {Nature Publishing Group}, title = {{SETD1A}-dependent {EME1} transcription drives {PARPi} sensitivity in {HR} deficient tumour cells}, url = {https://www.nature.com/articles/s41416-025-02963-0}, urldate = {2025-02-28}, @@ -21587,10 +22786,10 @@ @article{tabarelli_chasing_2022 keywords = {\textit{Malus} × \textit{domestica}, \textit{TCP} gene family, {\textgreater}UseGalaxy.eu, Arabidopsis, GDDH13v1.1 genome assembly, Malus}, language = {en}, month = {October}, - note = {Number: 10 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 10}, number = {10}, pages = {1696}, + publisher = {Multidisciplinary Digital Publishing Institute}, shorttitle = {Chasing {Consistency}}, title = {Chasing {Consistency}: {An} {Update} of the {TCP} {Gene} {Family} of {Malus} × {Domestica}}, url = {https://www.mdpi.com/2073-4425/13/10/1696}, @@ -21627,10 +22826,10 @@ @article{talubo_qsar-based_2025 keywords = {{\textgreater}UseGalaxy.eu, QSAR, drug repurposing, hepatocellular carcinoma, pyrimidine metabolism}, language = {en}, month = {January}, - note = {Number: 5 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 5}, number = {5}, pages = {903}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {{QSAR}-{Based} {Drug} {Repurposing} and {RNA}-{Seq} {Metabolic} {Networks} {Highlight} {Treatment} {Opportunities} for {Hepatocellular} {Carcinoma} {Through} {Pyrimidine} {Starvation}}, url = {https://www.mdpi.com/2072-6694/17/5/903}, urldate = {2025-05-29}, @@ -21664,10 +22863,10 @@ @article{tang_denser_2025 keywords = {{\textgreater}UseGalaxy.eu, Mollusca, Tellinoidea, mitogenome, phylogeny}, language = {en}, month = {May}, - note = {Number: 5 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 5}, number = {5}, pages = {303}, + publisher = {Multidisciplinary Digital Publishing Institute}, shorttitle = {Denser {Mitogenomic} {Sampling} for {Exploring} the {Phylogeny} of {Tellinoidea} ({Mollusca}}, title = {Denser {Mitogenomic} {Sampling} for {Exploring} the {Phylogeny} of {Tellinoidea} ({Mollusca}: {Bivalvia})}, url = {https://www.mdpi.com/1424-2818/17/5/303}, @@ -21685,9 +22884,9 @@ @article{tangaro_laniakea_2020 keywords = {+Cloud, +Galactic, +IsGalaxy, +RefPublic, {\textgreater}GVL-Unspecified, {\textgreater}Laniakea, {\textgreater}PhenoMeNal, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au, Software, Workflow}, language = {en}, month = {April}, - note = {Publisher: Oxford Academic}, number = {4}, pages = {giaa033}, + publisher = {Oxford Academic}, shorttitle = {Laniakea}, title = {Laniakea: an open solution to provide {Galaxy} “on-demand” instances over heterogeneous cloud infrastructures}, url = {https://academic.oup.com/gigascience/article/9/4/giaa033/5816668}, @@ -21696,15 +22895,33 @@ @article{tangaro_laniakea_2020 year = {2020} } +@article{tangermann_saturation_2025, + abstract = {Variants of uncertain significance represent the biggest challenge for genomics-based precision oncology. Activated fibroblast growth factor receptors (FGFRs) frequently drive tumorigenesis by different genetic aberrations. However, it remains unknown which of the many point mutations affecting FGFR1, FGFR2, FGFR3 or FGFR4 in cancer are druggable, that is, activating signaling while not mediating FGFR inhibitor resistance. Here we implemented a saturation mutational scanning platform to screen all 11,520 possible point mutations covering the kinase domains of FGFR1–4. Pooled positive selection screens identified 474 activating and 738 mutations mediating resistance to the FGFR inhibitors pemigatinib and futibatinib, together revealing 301 druggable FGFR mutations analogous to a strong PS3/BS3 evidence level. The screens also identified loss-of-function mutations and an association of gain-of-function mutations with hydrophobic changes. The functional screens identified 97\% of acquired resistance mutations in clinical trials. Our comprehensive catalog of every druggable mutation in the FGFR kinase domains is readily available for clinical decision support.}, + author = {Tangermann, Carla and Ghosh, Avantika and Ziegler, Martin and Facchinetti, Francesco and Stappenbeck, Jannis and Carus Sahin, Yagmur Oyku and Riester, Marisa and Viardot, Luise Carmina and Zundel, Tobias and Friboulet, Luc and Hollebecque, Antoine and Naveja, José J. and Wanninger, Angela and Hess, Maria Elena and Brummer, Tilman and Boerries, Melanie and Loges, Sonja and Loriot, Yohann and Illert, Anna L. and Diederichs, Sven}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s41588-025-02431-8}, + issn = {1546-1718}, + journal = {Nature Genetics}, + keywords = {{\textgreater}UseGalaxy.eu, Mutagenesis, Oncogenes, Targeted therapies}, + language = {en}, + month = {December}, + pages = {1--12}, + publisher = {Nature Publishing Group}, + title = {Saturation mutagenesis identifies activating and resistance-inducing {FGFR} kinase domain mutations}, + url = {https://www.nature.com/articles/s41588-025-02431-8}, + urldate = {2025-12-10}, + year = {2025} +} + @article{tapia_nanopore_2024, author = {Tapia, Stephanie and Orellana, Joseph and Duran, Yerson and Rodriguez, Jose and Angulo, Derly and Dominguez-Mendoza, Luz and Grabiel, Sandra and Silva, Jose and Caballero, Romina and Zapata, Katherine and Gómez, Muriel and Tataje-Lavanda, Luis and Velazco, Rodolfo}, doi = {10.1128/mra.00190-24}, journal = {Microbiology Resource Announcements}, keywords = {{\textgreater}NanoGalaxy, {\textgreater}UseGalaxy.eu}, month = {August}, - note = {Publisher: American Society for Microbiology}, number = {0}, pages = {e00190--24}, + publisher = {American Society for Microbiology}, title = {Nanopore sequencing of {IPNV} vp2 gene in {Peruvian} {Andean} trout ({Oncorhynchus} mykiss) cultures}, url = {https://journals.asm.org/doi/full/10.1128/mra.00190-24}, urldate = {2024-08-24}, @@ -21805,7 +23022,7 @@ @article{tekman_single-cell_2020 doi = {10.1093/gigascience/giaa102}, issn = {2047-217X}, journal = {GigaScience}, - keywords = {+Education, +Galactic, +IsGalaxy, +Project, +RefPublic, +Tools, {\textgreater}Human Cell Atlas, {\textgreater}Live EU, {\textgreater}SingleCell, Ecosystem, Software}, + keywords = {+Education, +Galactic, +IsGalaxy, +Project, +RefPublic, +Tools, {\textgreater}Human Cell Atlas, {\textgreater}Live EU, {\textgreater}SingleCell, {\textgreater}UseGalaxy.eu, Ecosystem, Software}, language = {eng}, month = {October}, number = {10}, @@ -21827,9 +23044,9 @@ @article{teng_tgf-_2025 keywords = {{\textgreater}UseGalaxy.eu, Cancer, Growth factor signalling}, language = {en}, month = {May}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {1--14}, + publisher = {Nature Publishing Group}, title = {{TGF}-β signaling redirects {Sox11} gene regulatory activity to promote partial {EMT} and collective invasion of oncogenically transformed intestinal organoids}, url = {https://www.nature.com/articles/s41389-025-00560-7}, urldate = {2025-05-23}, @@ -21845,8 +23062,8 @@ @article{tensen_dark_2024 journal = {African Journal of Wildlife Research}, keywords = {{\textgreater}UseGalaxy.eu}, month = {September}, - note = {Publisher: Southern African Wildlife Management Association}, number = {1}, + publisher = {Southern African Wildlife Management Association}, shorttitle = {Dark {Mystery} {Solved}}, title = {Dark {Mystery} {Solved}: {A} {Captive} {Black} {Leopard} from {South} {Africa} is of {Asian} {Descent}}, url = {https://bioone.org/journals/african-journal-of-wildlife-research/volume-54/issue-1/056.054.0101/Dark-Mystery-Solved--A-Captive-Black-Leopard-from-South/10.3957/056.054.0101.full}, @@ -21865,8 +23082,8 @@ @article{tetzlaff_small_2024 keywords = {{\textgreater}UseGalaxy.eu, Genome, Mitochondrial, RNA, Small Untranslated, Toxoplasma gondii, mitochondria, mitogenome, polysomes, rRNA, rribosome}, language = {eng}, month = {February}, - note = {Publisher: eLife Sciences Publications, Ltd}, pages = {e95407}, + publisher = {eLife Sciences Publications, Ltd}, title = {Small {RNAs} from mitochondrial genome recombination sites are incorporated into {T}. gondii mitoribosomes}, url = {https://doi.org/10.7554/eLife.95407}, urldate = {2024-05-17}, @@ -21880,8 +23097,8 @@ @article{teznerova_ago-hook_2023 keywords = {{\textgreater}UseGalaxy.eu, ⛔ No DOI found}, language = {cs\_CZ}, month = {September}, - note = {Accepted: 2024-09-12T06:33:52Z -Publisher: Univerzita Karlova, Přírodovědecká fakulta}, + note = {Accepted: 2024-09-12T06:33:52Z}, + publisher = {Univerzita Karlova, Přírodovědecká fakulta}, title = {{AGO}-hook domény v metylaci {DNA} řízené malými {RNA} u {Arabidopsis} thaliana}, url = {https://dspace.cuni.cz/handle/20.500.11956/185345}, urldate = {2024-11-17}, @@ -21915,10 +23132,10 @@ @article{thangameeran_examining_2024 keywords = {{\textgreater}UseGalaxy.eu, Cerebral Hemorrhage, Disease Models, Animal, Rats, Sprague-Dawley, Transcriptome, gene expression, intracerebral hemorrhage, neuroinflammation, severe intracerebral hemorrhage, transcriptomics}, language = {en}, month = {June}, - note = {Number: 6 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 6}, number = {6}, pages = {678}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Examining {Transcriptomic} {Alterations} in {Rat} {Models} of {Intracerebral} {Hemorrhage} and {Severe} {Intracerebral} {Hemorrhage}}, url = {https://www.mdpi.com/2218-273X/14/6/678}, urldate = {2024-09-02}, @@ -21926,17 +23143,6 @@ @article{thangameeran_examining_2024 year = {2024} } -@article{thanki_aequatus_2016, - abstract = {{\textless}h4{\textgreater}Background{\textless}/h4{\textgreater} Phylogenetic information inferred from the study of homologous genes helps us to understand the evolution of genes and gene families, including the identification of ancestral gene duplication events as well as regions under positive or purifying selection within lineages. Gene family and orthogroup characterisation enables the identification of syntenic blocks, which can then be visualised with various tools. Unfortunately, currently available tools display only an overview of syntenic regions as a whole, limited to the gene level, and none provide further details about structural changes within genes, such as the conservation of ancestral exon boundaries amongst multiple genomes. {\textless}h4{\textgreater}Findings{\textless}/h4{\textgreater} We present Aequatus, a standalone web-based tool that provides an in-depth view of gene structure across gene families, with various options to render and filter visualisations. It relies on pre-calculated alignment and gene feature information typically held in, but not limited to, the Ensembl Compara and Core databases. We also offer Aequatus.js, a reusable JavaScript module that fulfils the visualisation aspects of Aequatus, available within the Galaxy web platform as a visualisation plugin, which can be used to visualise gene trees generated by the GeneSeqToFamily workflow. {\textless}h4{\textgreater}Availability{\textless}/h4{\textgreater} Aequatus is an open-source tool freely available to download under the MIT license at https://github.com/TGAC/Aequatus . A demo server is available at http://aequatus.earlham.ac.uk/ . A publicly available instance of the GeneSeqToFamily workflow to generate gene tree information and visualise it using Aequatus is available on the Galaxy EU server at https://usegalaxy.eu . {\textless}h4{\textgreater}Contacts{\textless}/h4{\textgreater} Anil.Thanki@earlham.ac.uk and Robert.Davey@earlham.ac.uk}, - author = {Thanki, Anil and Soranzo, Nicola and Herrero, Javier and Haerty, Wilfried and Davey, Robert}, - doi = {10.1101/055632}, - journal = {bioRxiv}, - keywords = {{\textgreater}UseGalaxy.eu}, - title = {Aequatus: {An} open-source homology browser}, - url = {http://europepmc.org/abstract/PPR/PPR9505}, - year = {2016} -} - @article{thanki_aequatus_2018, abstract = {Background. Phylogenetic information inferred from the study of homologous genes helps us to understand the evolution of genes and gene families, inclu}, author = {Thanki, Anil S. and Soranzo, Nicola and Herrero, Javier and Haerty, Wilfried and Davey, Robert P.}, @@ -21995,9 +23201,9 @@ @article{thompson_draft_2023 keywords = {{\textgreater}UseGalaxy.eu}, language = {eng}, month = {December}, - note = {Publisher: American Society for Microbiology}, number = {1}, pages = {e00470--23}, + publisher = {American Society for Microbiology}, title = {Draft genome sequence of {Amycolatopsis} camponoti {RTGN1}, a bacterial endophyte isolated from {Alnus} glutinosa root nodules}, url = {https://journals.asm.org/doi/full/10.1128/mra.00470-23}, urldate = {2024-05-17}, @@ -22005,15 +23211,15 @@ @article{thompson_draft_2023 year = {2023} } -@article{thompson_draft_2023, +@article{thompson_draft_2023-1, author = {Thompson, Ryan Michael and Fox, Edward M. and Montero-Calasanz, Maria del Carmen}, doi = {10.1128/mra.00486-23}, journal = {Microbiology Resource Announcements}, keywords = {{\textgreater}UseGalaxy.eu}, month = {December}, - note = {Publisher: American Society for Microbiology}, number = {2}, pages = {e00486--23}, + publisher = {American Society for Microbiology}, title = {Draft genome sequence of {Streptomyces} poriferorum {RTGN2}, a bacterial endophyte isolated from {Alnus} glutinosa root nodules}, url = {https://journals.asm.org/doi/full/10.1128/mra.00486-23}, urldate = {2024-05-17}, @@ -22027,9 +23233,9 @@ @article{thompson_draft_2024 journal = {Microbiology Resource Announcements}, keywords = {{\textgreater}UseGalaxy.eu}, month = {January}, - note = {Publisher: American Society for Microbiology}, number = {2}, pages = {e01132--23}, + publisher = {American Society for Microbiology}, title = {Draft genome sequences of five {Mycobacterium} strains, isolated from {Alnus} glutinosa root nodules}, url = {https://journals.asm.org/doi/full/10.1128/mra.01132-23}, urldate = {2024-05-17}, @@ -22037,15 +23243,15 @@ @article{thompson_draft_2024 year = {2024} } -@article{thompson_draft_2024-1, +@article{thompson_draft_2024, author = {Thompson, Ryan Michael and Fox, Edward M. and Montero-Calasanz, Maria del Carmen}, doi = {10.1128/mra.01131-23}, journal = {Microbiology Resource Announcements}, keywords = {{\textgreater}UseGalaxy.eu}, month = {February}, - note = {Publisher: American Society for Microbiology}, number = {3}, pages = {e01131--23}, + publisher = {American Society for Microbiology}, title = {Draft genome sequences of two {Micromonospora} strains isolated from the root nodules of {Alnus} glutinosa}, url = {https://journals.asm.org/doi/full/10.1128/mra.01131-23}, urldate = {2024-11-17}, @@ -22063,9 +23269,9 @@ @article{thompson_pollution_2025 keywords = {{\textgreater}UseGalaxy.eu, Alnus, Environmental microbiology, Microbial communities, Microbial ecology, Microbiota, Root Nodules, Plant}, language = {en}, month = {July}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {23373}, + publisher = {Nature Publishing Group}, shorttitle = {From pollution to reforestation}, title = {From pollution to reforestation: the hidden microbiome of {Alnus} glutinosa nodules over 30 years}, url = {https://www.nature.com/articles/s41598-025-07006-5}, @@ -22074,6 +23280,24 @@ @article{thompson_pollution_2025 year = {2025} } +@article{thongbunrod_fungal_2026, + abstract = {This study investigated fungal isolates enriched under strictly anaerobic conditions from buffalo (Bubalus bubalis) rumen fluid for their potential in lignocellulosic biomass conversion. Two isolates, B031 and E033, were obtained using serial dilution in Hungate tubes with cellobiose as a carbon source. Their characterization included morphological examination, ITS-5.8 S-LSU sequencing, substrate utilization profiling, and lignocellulosic degradation assays. Phylogenetic analysis indicated that B031 is related to uncultured Basidiomycota-affiliated fungi, while E033 is closely affiliated with the yeast-like fungus Trichosporon asahii. Although these taxa are not obligate anaerobic fungi, both isolates exhibited stable growth and sustained lignocellulosic degradation under oxygen-deprived conditions across successive anaerobic subcultures. Isolate B031 demonstrated greater versatility, achieving 60\% microcrystalline cellulose (MCC), 66\% lignin, and 58\% rice straw degradation within 7 days, whereas E033 reached 55\% MCC, 58\% lignin, and 33\% rice straw degradation. Given that rice straw is a major lignocellulosic residue in Thailand, these fungi have significant potential to enhance biogas conversion. Based on annual production of 23 million tons of rice straw, B031 could yield 3.93 billion Nm³ CH₄ (39.13 TWh primary energy; 13.70 TWh electricity), while E033 yielded 2.24 billion Nm³ CH₄ (22.26 TWh primary energy; 7.79 TWh electricity). These results highlight the importance of strain selection based on functional anaerobic degradation capacity rather than taxonomic affiliation alone and support the potential application of these isolates as bioaugmentation agents in anaerobic digestion systems. Further genomic and functional studies are recommended to refine their taxonomic classification and assess their practical application in sustainable biogas production.}, + author = {Thongbunrod, Nitiya and Chaiprasert, Pawinee}, + doi = {10.1007/s12155-025-10954-5}, + issn = {1939-1242}, + journal = {BioEnergy Research}, + keywords = {{\textgreater}UseGalaxy.eu, Anaerobic conditions, Biogas production, Fungal isolates, Lignocellulosic degradation, Rice straw}, + language = {en}, + month = {January}, + number = {1}, + pages = {19}, + title = {Fungal {Isolates} {Enriched} {Under} {Anaerobic} {Conditions} from {Buffalo} {Rumen} {Fluid} for {Lignocellulosic} {Rice} {Straw} {Conversion} and {Biogas} {Production} {Potential}}, + url = {https://doi.org/10.1007/s12155-025-10954-5}, + urldate = {2026-01-17}, + volume = {19}, + year = {2026} +} + @article{thongbunrod_potential_2024, abstract = {Anaerobic lignocellulosic microbial consortia are known to be prodigiously efficient at converting lignocellulosic biomass to methane. In this study, the efficacy of anaerobic fungal consortia (AFC) from five different inocula, including Bubalus bubalis rumen fluid (RU), in degrading filter paper, microcrystalline cellulose, and rice straw (RS), was screened. The AFC from RU performed best in lignocellulosic material degradation and methane production; thus, RU was selected for further experiments. Consecutive batch subculturing (CBS) was performed in RU to enrich and stabilize the dominant and key microorganisms categorized as anaerobic fungi, using the addition of antibacterial agents to suppress the growth of untargeted bacteria. After the CBS, subculture E19 proved the most efficient, with RS degradation of 84\% and a methane yield of 310 mL/g VSadded, representing 1.83- and 2.25-fold increases compared to the initial seed, respectively. The microbial community of E19 consisted of anaerobic fungi (uncultured Neocallimastigales, Anaeromyces sp., Orpinomyces sp., and Feramyces sp.) coexisting with anaerobic bacteria (streptomycin resistant Proteiniphilum acetatigenes), and methanogens. The E19 consortium was able to use various carbon sources (87.5\%) and contained potential genes encoding enzymes involved in RS degradation. The microbial community of E19 was highly stable, making it a promising inoculum for biomass degradation, especially for anaerobic digestion to produce biogas.}, author = {Thongbunrod, Nitiya and Chaiprasert, Pawinee}, @@ -22092,6 +23316,25 @@ @article{thongbunrod_potential_2024 year = {2024} } +@article{thuy-boun_metaproteomics_2021, + abstract = {In this Letter, we reanalyze published mass spectrometry data sets of clinical samples with a focus on determining the coinfection status of individuals infected with SARS-CoV-2 coronavirus. We demonstrate the use of ComPIL 2.0 software along with a metaproteomics workflow within the Galaxy platform to detect cohabitating potential pathogens in COVID-19 patients using mass spectrometry-based analysis. From a sample collected from gargling solutions, we detected Streptococcus pneumoniae (opportunistic and multidrug-resistant pathogen) and Lactobacillus rhamnosus (a probiotic component) along with SARS-Cov-2. We could also detect Pseudomonas sps. Bc-h from COVID-19 positive samples and Acinetobacter ursingii and Pseudomonas monteilii from COVID-19 negative samples collected from oro- and nasopharyngeal samples. We believe that the early detection and characterization of coinfections by using metaproteomics from COVID-19 patients will potentially impact the diagnosis and treatment of patients affected by SARS-CoV-2 infection.}, + author = {Thuy-Boun, Peter S. and Mehta, Subina and Gruening, Bjoern and McGowan, Thomas and Nguyen, An and Rajczewski, Andrew T. and Johnson, James. E and Griffin, Timothy J. and Wolan, Dennis W. and Jagtap, Pratik D.}, + doi = {10.1021/acs.jproteome.0c00822}, + issn = {1535-3893}, + journal = {Journal of Proteome Research}, + keywords = {+Methods, {\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {January}, + number = {2}, + pages = {1451--1454}, + publisher = {American Chemical Society}, + title = {Metaproteomics {Analysis} of {SARS}-{CoV}-2-{Infected} {Patient} {Samples} {Reveals} {Presence} of {Potential} {Coinfecting} {Microorganisms}}, + url = {https://doi.org/10.1021/acs.jproteome.0c00822}, + urldate = {2021-01-06}, + volume = {20}, + year = {2021} +} + @article{tiwari_innate_2024, abstract = {{\textless}h2{\textgreater}Summary{\textless}/h2{\textgreater}{\textless}p{\textgreater}The reduced ability of the central nervous system to regenerate with increasing age limits functional recovery following demyelinating injury. Previous work has shown that myelin debris can overwhelm the metabolic capacity of microglia, thereby impeding tissue regeneration in aging, but the underlying mechanisms are unknown. In a model of demyelination, we found that a substantial number of genes that were not effectively activated in aged myeloid cells displayed epigenetic modifications associated with restricted chromatin accessibility. Ablation of two class I histone deacetylases in microglia was sufficient to restore the capacity of aged mice to remyelinate lesioned tissue. We used Bacillus Calmette-Guerin (BCG), a live-attenuated vaccine, to train the innate immune system and detected epigenetic reprogramming of brain-resident myeloid cells and functional restoration of myelin debris clearance and lesion recovery. Our results provide insight into aging-associated decline in myeloid function and how this decay can be prevented by innate immune reprogramming.{\textless}/p{\textgreater}}, author = {Tiwari, Vini and Prajapati, Bharat and Asare, Yaw and Damkou, Alkmini and Ji, Hao and Liu, Lu and Naser, Nawraa and Gouna, Garyfallia and Leszczyńska, Katarzyna B. and Mieczkowski, Jakub and Dichgans, Martin and Wang, Qing and Kawaguchi, Riki and Shi, Zechuan and Swarup, Vivek and Geschwind, Daniel H. and Prinz, Marco and Gokce, Ozgun and Simons, Mikael}, @@ -22101,10 +23344,9 @@ @article{tiwari_innate_2024 keywords = {{\textgreater}UseGalaxy.eu}, language = {English}, month = {September}, - note = {Publisher: Elsevier}, number = {9}, pages = {2173--2190.e8}, - pmid = {39053462}, + publisher = {Elsevier}, title = {Innate immune training restores pro-reparative myeloid functions to promote remyelination in the aged central nervous system}, url = {https://www.cell.com/immunity/abstract/S1074-7613(24)00348-0}, urldate = {2024-10-20}, @@ -22112,6 +23354,27 @@ @article{tiwari_innate_2024 year = {2024} } +@article{tomasello_erga-bge_2025, + abstract = {The +Xanthium orientale +subsp. +italicum +(Asterales: Asteraceae: Asteroideae) reference genome offers a valuable resource for understanding the genetic basis of invasiveness and fitness differences among congeneric species. The entirety of the genome sequence was assembled into 18 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 2.26 Gb, composed of 46 contigs and 32 scaffolds, with contig and scaffold N50 values of 98.8 Mb and 124 Mb, respectively.}, + author = {Tomasello, Salvatore and Manzo, Eleonora and Monteiro, Rita and Böhne, Astrid and Marcussen, Thomas and Struck, Torsten H and Oomen, Rebekah A and {Genoscope Sequencing Team} and Moussy, Alice and Cruaud, Corinne and Labadie, Karine and Demirdjian, Lola and N’dar, Adama and Wincker, Patrick and Oliveira, Pedro H and Aury, Jean-Marc and Barrera Enriquez, Vianey Paola and Haggerty, Leanne and Martin, Fergal and Brown, Tom}, + doi = {10.12688/openreseurope.21891.1}, + issn = {2732-5121}, + journal = {Open Research Europe}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {November}, + pages = {367}, + title = {{ERGA}-{BGE} genome of {Xanthium} orientale subsp. italicum ({Moretti}) {Greuter}. {A} plant of {American} origin, now widespread and, in some cases, invasive in {Europe}}, + url = {https://open-research-europe.ec.europa.eu/articles/5-367/v1}, + urldate = {2025-11-30}, + volume = {5}, + year = {2025} +} + @patent{toni_truly_2019, address = {EP}, author = {Toni, Cathomen and Alexandra, Haas Simone and Markus, Hildenbeutel and Claudio, Mussolino and Melanie, Börries and Geoffroy, Andrieux}, @@ -22166,9 +23429,9 @@ @article{tosar_ri-sec-seq_2021 journal = {Bio-protocol}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, language = {eng}, - note = {Publisher: Bio-Protocol, LLC}, number = {4}, pages = {e3918}, + publisher = {Bio-Protocol, LLC}, title = {{RI}-{SEC}-seq: {Comprehensive} {Profiling} of {Nonvesicular} {Extracellular} {RNAs} with {Different} {Stabilities}}, url = {https://doi.org/10.21769/bioprotoc.3918}, volume = {11}, @@ -22185,10 +23448,10 @@ @article{toth_divergence_2024 keywords = {{\textgreater}UseGalaxy.eu, carrot, hybrid assembly, phylogeny, virulence factors}, language = {en}, month = {May}, - note = {Number: 5 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 5}, number = {5}, pages = {1016}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Divergence within the {Taxon} ‘{Candidatus} {Phytoplasma} asteris’ {Confirmed} by {Comparative} {Genome} {Analysis} of {Carrot} {Strains}}, url = {https://www.mdpi.com/2076-2607/12/5/1016}, urldate = {2024-06-07}, @@ -22206,10 +23469,10 @@ @article{toth_genomic_2024 keywords = {\textit{Escherichia coli}, \textit{bla}$_{\textrm{CTX-M-15}}$, \textit{bla}$_{\textrm{CTX-M-27}}$, {\textgreater}UseGalaxy.eu, C1-M27, C2/H30RX, ST131, long-read sequencing, whole genome sequencing (WGS)}, language = {en}, month = {April}, - note = {Number: 4 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 4}, number = {4}, pages = {363}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Genomic {Epidemiology} of {C2}/{H30Rx} and {C1}-{M27} {Subclades} of {Escherichia} coli {ST131} {Isolates} from {Clinical} {Blood} {Samples} in {Hungary}}, url = {https://www.mdpi.com/2079-6382/13/4/363}, urldate = {2024-05-17}, @@ -22244,8 +23507,6 @@ @article{tregear_micro-rna-regulated_2022 month = {March}, number = {5}, pages = {685}, - pmcid = {PMC8912876}, - pmid = {35270155}, title = {Micro-{RNA}-{Regulated} {SQUAMOSA}-{PROMOTER} {BINDING} {PROTEIN}-{LIKE} ({SPL}) {Gene} {Expression} and {Cytokinin} {Accumulation} {Distinguish} {Early}-{Developing} {Male} and {Female} {Inflorescences} in {Oil} {Palm} ({Elaeis} guineensis)}, url = {http://europepmc.org/abstract/MED/35270155}, volume = {11}, @@ -22260,11 +23521,10 @@ @article{trifonova_combination_2023 journal = {Infectious Diseases}, keywords = {{\textgreater}UseGalaxy.eu, COVID-19, M gene, SARS-CoV-2, mutation, prolonged infection}, month = {July}, - note = {Publisher: Taylor \& Francis -\_eprint: https://doi.org/10.1080/23744235.2023.2238077}, + note = {\_eprint: https://doi.org/10.1080/23744235.2023.2238077}, number = {0}, pages = {1--5}, - pmid = {37493404}, + publisher = {Taylor \& Francis}, title = {Combination of two rare mutations in the {SARS}-{CoV}-2 {M} gene in patients with severe and prolonged {COVID}-19}, url = {https://doi.org/10.1080/23744235.2023.2238077}, urldate = {2023-07-31}, @@ -22289,6 +23549,25 @@ @article{trifonova_expansion_2025 year = {2025} } +@article{triggiano_clinical_2025, + abstract = {Chryseobacterium spp. are Gram-negative, opportunistic pathogens antibiotic-resistant commonly found in the environment. The aim of this study was to investigate potential sources of Chryseobacterium infections in healthcare settings by comparing clinical and environmental isolates using phenotypic and genotypic analyses. Between June and July 2023, six cases of infection with Chryseobacterium spp. were identified in a hospital in Apulia, southern Italy. Environmental sampling (air, surfaces and water) was performed in parallel with routine clinical investigations. Isolates were subjected to antibiotic susceptibility testing and genotypic analysis using Sanger and Next-Generation Sequencing. Five cases of Chryseobacterium spp. infection were recorded in the Gastroenterology Department (Pavilion A) and one in the Vertebral Surgery Department (Pavilion B). C. indologenes was identified in blood and tracheal aspirate samples using MALDI-TOF MS. Environmental analysis carried out in the pavilions A and B isolated C. indologenes from sink tap in Pavilion B. Subsequently, genome sequencing revealed that Chryseobacterium strains misidentified as C. indologenes were more closely related to C. arthrosphaerae. Genetic analysis confirmed the cluster hypothesis involving four patients from the pavilion A, while no genetic link was found between the environmental and clinical strains. Innovative molecular methods in clinical and environmental investigations have allowed more accurate identification of the etiologic agent and possibly tracing the source of infection in the nosocomial setting. Control measures, such as patient isolation and room disinfection, have prevented the spread of infection.}, + author = {Triggiano, Francesco and Caggiano, Giuseppina and Capozzi, Loredana and Castellana, Stefano and Diella, Giusy and Furio, Alessandro and Cantalice, Michele Alberto and Manicone, Anna Lucia and Savino, Antonella Francesca and Mosca, Adriana and De Carlo, Carmela and Sparapano, Eleonora and Dalfino, Lidia and Saracino, Annalisa and Di Gennaro, Francesco and Principi, Maria Beatrice and Parisi, Antonio and Montagna, Maria Teresa and Tafuri, Silvio and De Giglio, Osvalda}, + copyright = {cc by-nc-nd}, + doi = {10.1038/s41598-025-24632-1}, + issn = {2045-2322}, + journal = {Scientific reports}, + keywords = {{\textgreater}UseGalaxy.eu, C. Indologenes, Chryseobacterium Spp., Environmental Surveillance, Genome sequencing, Hospital Infections, bacteremia}, + language = {eng}, + month = {November}, + number = {1}, + pages = {39814}, + title = {Clinical and environmental investigation of six cases of {Chryseobacterium} arthrosphaerae infections in a {Southern} {Italian} hospital}, + url = {https://europepmc.org/articles/PMC12615676}, + urldate = {2025-12-26}, + volume = {15}, + year = {2025} +} + @article{trinh-minh_effect_2024, abstract = {Objective.S100A4 is a DAMP protein. S100A4 is overexpressed in patients with systemic sclerosis (SSc), andlevels correlate with organ involvement and disease activity. S100A4−/−mice are protected fromfibrosis. The aim ofthis study was to assess the antifibrotic effects of anti-S100A4 monoclonal antibody (mAb) in murine models of SScand in precision cut skin slices of patients with SSc.Methods.The effects of anti-S100A4 mAbs were evaluated in a bleomycin-induced skinfibrosis model and inTsk-1 mice with a therapeutic dosing regimen. In addition, the effects of anti-S100A4 mAbs on precision cut SSc skinslices were analyzed by RNA sequencing.Results.Inhibition of S100A4 was effective in the treatment of pre-established bleomycin-induced skinfibrosis andin regression of pre-establishedfibrosis with reduced dermal thickening, myofibroblast counts, and collagen accumu-lation. Transcriptional profiling demonstrated targeting of multiple profibrotic and proinflammatory processes relevantto the pathogenesis of SSc on targeted S100A4 inhibition in a bleomycin-induced skinfibrosis model. Moreover, tar-geted S100A4 inhibition also modulated inflammation- andfibrosis-relevant gene sets in precision cut SSc skin slicesin an ex vivo trial approach. Selected downstream targets of S100A4, such as AMP-activated protein kinase,calsequestrin-1, and phosphorylated STAT3, were validated on the protein level, and STAT3 inhibition was shown toprevent the profibrotic effects of S100A4 onfibroblasts in human skin.Conclusion.Inhibition of S100A4 confers dual targeting of inflammatory andfibrotic pathways in complementarymouse models offibrosis and in SSc skin. These effects support the further development of anti-S100A4 mAbs asdisease-modifying targeted therapies for SSc.}, author = {Trinh-Minh, Thuong and Györfi, Andrea Hermina and Tomcik, Michal and Tran-Manh, Cuong and Zhou, Xiang and Dickel, Nicholas and Tümerdem, Bilgesu Safak and Kreuter, Alexander and Burmann, Sven Niklas and Borchert, Signe Vedel and Hussain, Rizwan Iqbal and Hallén, Jonas and Klingelhöfer, Jörg and Kunz, Meik and Distler, Jörg H.W.}, @@ -22344,9 +23623,9 @@ @article{tsai_biogenesis_2022 journal = {Science Advances}, keywords = {{\textgreater}UseGalaxy.eu}, month = {August}, - note = {Publisher: American Association for the Advancement of Science}, number = {32}, pages = {eabm0699}, + publisher = {American Association for the Advancement of Science}, title = {Biogenesis of {C}. elegans spermatogenesis small {RNAs} is initiated by a zc3h12a-like ribonuclease}, url = {https://www.science.org/doi/full/10.1126/sciadv.abm0699}, urldate = {2022-09-24}, @@ -22364,9 +23643,9 @@ @article{tsangaras_crossing_2025 keywords = {{\textgreater}UseGalaxy.eu, Endogenous Retroviruses, Evolution, Genomics, Leukemia Virus, Gibbon Ape}, language = {en}, month = {March}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {9790}, + publisher = {Nature Publishing Group}, shorttitle = {Crossing {Wallace}’s line}, title = {Crossing {Wallace}’s line: an evolutionarily young gibbon ape leukemia virus like endogenous retrovirus identified from the {Philippine} flying lemur ({Cynocephalus} volans)}, url = {https://www.nature.com/articles/s41598-025-94582-1}, @@ -22384,15 +23663,35 @@ @article{tu_molecular_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, language = {eng}, month = {March}, - note = {Publisher: MDPI AG}, number = {3}, pages = {667}, + publisher = {MDPI AG}, title = {Molecular {Physiological} {Characterization} of a {High} {Heat} {Resistant} {Spore} {Forming} {Bacillus} subtilis {Food} {Isolate}}, url = {https://doi.org/10.3390/microorganisms9030667}, volume = {9}, year = {2021} } +@article{ueira-vieira_deep_2025, + abstract = {Characterizing the complex web of ecological interactions is a central challenge in molecular ecology. Shotgun metagenomics of environmental samples offers a powerful, high-resolution approach, yet its potential for simultaneously generating multiple genomic resources from different trophic levels remains underexplored. This study serves as a proof-of-concept, using deep sequencing of a single, complex sample—the larval food of the stingless bee Tetragonisca angustula—to demonstrate the method's capacity to recover genomic information across varying template abundances. We successfully assembled three genomes of different completeness levels: a near-complete bacterial genome (Acetilactobacillus jinshanensis, 2,097,977 bp with 0.002\% ambiguous bases), a draft mitochondrial genome (T. angustula, 15,498–15,549 bp), and a fragmented chloroplast genome (Lactuca sativa, 130,532 bp with 23.47\% ambiguous bases). The assembly quality gradient, observed from complete to fragmented, directly reflects the relative abundance of each DNA template in the environmental sample, demonstrating the method's sensitivity and ecological informativeness. Beyond these genomic resources, the data provided a comprehensive biodiversity profile, revealing DNA from seven major taxonomic groups, including 209 bacterial genera, 123 plant families, and 55 insect taxa. Additionally, genomic comparisons using Average Nucleotide Identity (ANI) and digital DNA–DNA Hybridization (dDDH) analyses suggest that the dominant bacterial strain represents a putative novel species within the genus Acetilactobacillus. This approach simultaneously provided insights into host genetics, food sources, and microbial communities, illustrating the potential of single metagenomic datasets to generate multiple valuable genomic resources for molecular ecology research.}, + author = {Ueira-Vieira, Carlos and Santos, Ana Carolina Costa and Araújo, Thayane Nogueira and Augusto, Solange Cristina and de Avila, Natanael Borges and Bonetti, Ana Maria and dos Santos, Anderson Rodrigues}, + copyright = {© 2025 The Author(s). Ecology and Evolution published by British Ecological Society and John Wiley \& Sons Ltd.}, + doi = {10.1002/ece3.72546}, + issn = {2045-7758}, + journal = {Ecology and Evolution}, + keywords = {{\textgreater}UseGalaxy.eu, NGS, genome assembly, genomic resources, pollinator, proof-of-concept, stingless bee}, + language = {en}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.72546}, + number = {12}, + pages = {e72546}, + shorttitle = {A {Deep} {Metagenomic} {Snapshot} as a {Proof}-of-{Concept} for {Resource} {Generation}}, + title = {A {Deep} {Metagenomic} {Snapshot} as a {Proof}-of-{Concept} for {Resource} {Generation}: {Simultaneous} {Assembly} of {Host}, {Food}, and {Microbiome} {Genomes} {From} {Stingless} {Bee} {Larval} {Food}}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.72546}, + urldate = {2025-12-26}, + volume = {15}, + year = {2025} +} + @article{uellendahl-werth_benchmark_2020, abstract = {RNA-Sequencing (RNA-Seq) of peripheral blood can be a valuable source of information for investigating the status and mechanism of diseases. However, blood contains 50–80\% unwanted hemoglobin (Hb) transcripts. Lexogen’s QuantSeq mRNA-Seq-Kit for Illumina RNA-Seq features a ‘Globin Block’ (GB) module that depletes Hb cDNAs during library preparation. Here, we aimed to assess GB’s effectiveness and checked for technical biases attributable to GB. Using whole blood total RNA samples of 91 healthy individuals, we sequenced 91 pairs of GB and non-blocked samples (noGB) on Illumina HiSeq2500 and 8 pairs of GB/noGB technical replicates on HiSeq4000. GB reduced the fraction of Hb transcripts from 43\% (s.d. 14\%) to 8.0\% (s.d. 4.3\%). From GB samples we detected 1,397 more expressed genes at approximately 11 million reads per RNA-isolate. Enrichment and differential expression analyses did not reveal significant differences for GB and noGB samples with respect to molecular function. In contrast to results from studies that have examined the performance of GB during RNA isolation, we were able to assign GB to corresponding noGB samples (from multiple sequencing runs on HiSeq2500) with at least 89.8\% accuracy from the complete correlation matrix of all GB/GB, noGB/noGB and GB/noGB pairs. However, the use of different sequencers (HiSeq2500 vs HiSeq4000) impaired assignment of technical replicates, whereas assignment of GB to corresponding noGB samples worked perfectly when sequencing on one lane on HiSeq4000. Lexogen’s GB RNA-Seq module is a valuable addition during mRNA-Seq library preparation which works even with low amounts of input total RNA (50 ng per sample). GB facilitated the detection of low abundant transcripts and yielded more non-hemoglobin reads, while preserving biological information. We observed that differences in sequencing run and platform have a far greater effect on technical variation than the use of GB.}, author = {Uellendahl-Werth, Florian and Wolfien, Markus and Franke, Andre and Wolkenhauer, Olaf and Ellinghaus, David}, @@ -22403,10 +23702,10 @@ @article{uellendahl-werth_benchmark_2020 keywords = {+Methods, +Shared, +Stellar, +UsePublic, {\textgreater}UseGalaxy.eu}, language = {en}, month = {March}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {1--10}, + publisher = {Nature Publishing Group}, title = {A benchmark of hemoglobin blocking during library preparation for {mRNA}-{Sequencing} of human blood samples}, url = {https://www.nature.com/articles/s41598-020-62637-0}, urldate = {2020-04-09}, @@ -22440,10 +23739,10 @@ @article{uluar_mitogenomics_2025 keywords = {{\textgreater}UseGalaxy.eu}, language = {en}, month = {July}, - note = {Number: 3 -Publisher: Hacettepe University}, + note = {Number: 3}, number = {3}, pages = {81--96}, + publisher = {Hacettepe University}, shorttitle = {Mitogenomics of {Psorodonotus} ebneri {Brunner} von {Wattenwyl}, 1861 ({Orthoptera}}, title = {Mitogenomics of {Psorodonotus} ebneri {Brunner} von {Wattenwyl}, 1861 ({Orthoptera}: {Tettigoniidae}): {Selection} profile and patterns of intraspecific and interspecific divergence}, url = {https://dergipark.org.tr/en/pub/hjbc/issue/92227/1661824}, @@ -22474,9 +23773,9 @@ @article{umpeleva_identification_2024 keywords = {{\textgreater}UseGalaxy.eu, Diarylquinolines, Mycobacterium tuberculosis, Tuberculosis, Multidrug-Resistant}, language = {eng}, month = {February}, - note = {Publisher: American Society for Microbiology}, number = {3}, pages = {e03749--23}, + publisher = {American Society for Microbiology}, title = {Identification of genetic determinants of bedaquiline resistance in {Mycobacterium} tuberculosis in {Ural} region, {Russia}}, url = {https://journals.asm.org/doi/full/10.1128/spectrum.03749-23}, urldate = {2024-05-17}, @@ -22595,8 +23894,8 @@ @article{valer_pi3k_2025 journal = {eLife}, keywords = {{\textgreater}UseGalaxy.eu, Class I Phosphatidylinositol 3-Kinases, Inflammation, Ossification, Heterotopic, Phosphoinositide-3 Kinase Inhibitors, fibrodysplasia ossificans progressiva, heterotopic bone, mesenchymal progenitors, rare diseases}, month = {June}, - note = {Publisher: eLife Sciences Publications, Ltd}, pages = {RP91779}, + publisher = {eLife Sciences Publications, Ltd}, title = {{PI3Kα} inhibition blocks osteochondroprogenitor specification and the hyper-inflammatory response to prevent heterotopic ossification}, url = {https://doi.org/10.7554/eLife.91779}, urldate = {2025-07-12}, @@ -22645,10 +23944,10 @@ @article{valsecchi_rna_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, language = {en}, month = {January}, - note = {Number: 7840 -Publisher: Nature Publishing Group}, + note = {Number: 7840}, number = {7840}, pages = {137--142}, + publisher = {Nature Publishing Group}, title = {{RNA} nucleation by {MSL2} induces selective {X} chromosome compartmentalization}, url = {https://www.nature.com/articles/s41586-020-2935-z}, urldate = {2021-05-11}, @@ -22773,7 +24072,7 @@ @article{velasquez_emerging_2025 keywords = {{\textgreater}UseGalaxy.eu, biological cycle, diagnostics, emerging pests, mitogenome, taxonomy}, language = {English}, month = {June}, - note = {Publisher: Frontiers}, + publisher = {Frontiers}, shorttitle = {An emerging {Platynota} sp. ({Lepidoptera}}, title = {An emerging {Platynota} sp. ({Lepidoptera}: {Tortricidae}) infesting blueberry ({Vaccinium} corymbosum) in the central coast of {Peru}}, url = {https://www.frontiersin.org/journals/insect-science/articles/10.3389/finsc.2025.1593907/full}, @@ -22842,7 +24141,7 @@ @article{verma_identification_2022 doi = {10.21203/rs.3.rs-1253773/v1}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {February}, - note = {Publisher: Research Square Platform LLC}, + publisher = {Research Square Platform LLC}, title = {Identification {Of} {Taxa} and {Functional} {Pathway} {Information} {Of} {Mycobacterium} tuberculosis {Microbiome} {And} {High} {Throughput} {Simulation} {Studies} {With} {Mycobacteriophage}}, url = {https://doi.org/10.21203/rs.3.rs-1253773/v1}, year = {2022} @@ -22853,10 +24152,10 @@ @inproceedings{verma_identification_2023 author = {Verma, Divya and Murthy, I. A. Shylesh and Bagchi, Preenon}, doi = {10.2991/978-94-6463-164-7_16}, isbn = {978-94-6463-164-7}, + issn = {2468-5739}, keywords = {{\textgreater}UseGalaxy.eu}, language = {en}, month = {June}, - note = {ISSN: 2468-5739}, pages = {221--238}, publisher = {Atlantis Press}, title = {Identification of {Taxa} and {Functional} {Pathway} {Information} of {Mycobacterium} tuberculosis {Microbiome} and {High} {Throughput} {Simulation} {Studies} with {Mycobacteriophage}}, @@ -22909,10 +24208,10 @@ @article{vieira_da_cruz_pyridylpiperazine_2024 keywords = {{\textgreater}UseGalaxy.eu, AcrAB-TolC, Anti-Bacterial Agents, Antibiotic Efflux Pump, Antimicrobial Resistance, Cryo-EM, Efflux Pump Inhibitor, Escherichia coli Proteins}, language = {eng}, month = {January}, - note = {Num Pages: 111 -Publisher: Springer Nature}, + note = {Num Pages: 111}, number = {1}, pages = {93--111}, + publisher = {Springer Nature}, title = {Pyridylpiperazine efflux pump inhibitor boosts in vivo antibiotic efficacy against {K}. pneumoniae}, url = {https://www.embopress.org/doi/full/10.1038/s44321-023-00007-9}, urldate = {2024-05-17}, @@ -22930,10 +24229,10 @@ @article{vieira_polymyxin_2024 keywords = {\textit{Salmonella} spp., {\textgreater}UseGalaxy.eu, antimicrobial resistance, colistin, polymyxin}, language = {en}, month = {February}, - note = {Number: 2 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 2}, number = {2}, pages = {110}, + publisher = {Multidisciplinary Digital Publishing Institute}, shorttitle = {Polymyxin {Resistance} in {Salmonella}}, title = {Polymyxin {Resistance} in {Salmonella}: {Exploring} {Mutations} and {Genetic} {Determinants} of {Non}-{Human} {Isolates}}, url = {https://www.mdpi.com/2079-6382/13/2/110}, @@ -22942,6 +24241,26 @@ @article{vieira_polymyxin_2024 year = {2024} } +@article{vijayanathan_auxin_2025, + abstract = {The critically important YUCCA (YUC) gene family is highly conserved and specific to the plant kingdom, primarily responsible for the final and rate-limiting step for indole-3-acetic acid (IAA) biosynthesis. IAA is an essential phytohormone, involved in virtually all aspects of plant growth and development. In addition, IAA is involved in fine-tuning plant responses to biotic and abiotic interactions and stresses. While the YUC gene family has significantly expanded throughout the plant kingdom, a detailed analysis of the evolutionary patterns driving this diversification has not been performed. Here, we present a comprehensive phylogenetic analysis of the YUC family, combining YUCs from species representing key evolutionary plant lineages. The evolutionary history of YUCs is complex and suggests multiple recruitment events via horizontal gene transfer from bacteria. We identify and hierarchically classify the YUC family into an early diverging grade, five distinct classes and 41 subclasses. Angiosperm YUC diversity and expansion are explained in the context of protein sequence conservation, as well as spatial and gene expression patterns. The presented YUC gene landscape offers new perspectives on the distribution and evolutionary trends of this crucial family, which facilitates further YUC characterization within plant development and response to environmental change.}, + author = {Vijayanathan, Mallika and Faryad, Amna and Abeywickrama, Thanusha D and Christensen, Joachim Møller and Jakobsen Neilson, Elizabeth H}, + copyright = {cc by-nc-nd}, + doi = {10.1111/tpj.70563}, + issn = {1365-313X}, + journal = {The Plant journal}, + keywords = {{\textgreater}UseGalaxy.eu, Evolution, Flavin‐containing Monooxygenase, Fmo, Yucca, auxin}, + language = {eng}, + month = {November}, + number = {4}, + pages = {e70563}, + shorttitle = {The auxin gatekeepers}, + title = {The auxin gatekeepers: {Evolution} and diversification of the {YUCCA} family}, + url = {https://europepmc.org/articles/PMC12659883}, + urldate = {2025-12-26}, + volume = {124}, + year = {2025} +} + @article{vijaykrishna_expanding_2022, abstract = {Summary: Properly and effectively managing reference datasets is an important task for many bioinformatics analyses. Refgenie is a reference asset management system that allows users to easily organize, retrieve and share such datasets. Here, we describe the integration of refgenie into the Galaxy platform. Server administrators are able to configure Galaxy to make use of reference datasets made available on a refgenie instance. In addition, a Galaxy Data Manager tool has been developed to provide a graphical interface to refgenie's remote reference retrieval functionality. A large collection of reference datasets has also been made available using the CVMFS (CernVM File System) repository from GalaxyProject.org, with mirrors across the USA, Canada, Europe and Australia, enabling easy use outside of Galaxy. Availability and implementation: The ability of Galaxy to use refgenie assets was added to the core Galaxy framework in version 22.01, which is available from https://github.com/galaxyproject/galaxy under the Academic Free License version 3.0. The refgenie Data Manager tool can be installed via the Galaxy ToolShed, with source code managed at https://github.com/BlankenbergLab/galaxy-tools-blankenberg/tree/main/data\_managers/data\_manager\_refgenie\_pull and released using an MIT license. Access to existing data is also available through CVMFS, with instructions at https://galaxyproject.org/admin/reference-data-repo/. No new data were generated or analyzed in support of this research.}, @@ -22953,8 +24272,6 @@ @article{vijaykrishna_expanding_2022 language = {eng}, number = {1}, pages = {vbac030}, - pmcid = {PMC9155181}, - pmid = {35669346}, title = {Expanding the {Galaxy}'s reference data}, url = {http://europepmc.org/abstract/MED/35669346}, volume = {2}, @@ -22979,15 +24296,39 @@ @article{vila-luna_draft_2025 year = {2025} } +@article{vila_taboada_erga-bge_2026, + abstract = {The reference genome of +Erebia palarica +(Chapman’s ringlet; Lepidoptera: Nymphalidae, Satyrinae) provides valuable insights into evolutionary and conservation genomics. On one hand, it paves the way to unravel the speciation processes, reproductive barriers, and potential hybridisation between +E. palarica +and its closely related sister species, +Erebia meolans +. On the other hand, this genomic resource will be key for the genetic monitoring of this narrowly endemic species, restricted to the Cantabrian Mountains (NW Spain), facilitating the use of genomic data to estimate population genetic parameters. The genome of a female individual was assembled into 13 phased contiguous autosomes, two sex chromosomes (W and Z), and one mitochondrial genome. This chromosome-level assembly encompasses 0.51 Gb and has no gaps, making this a telomere-to-telomere (T2T) genome assembly. The assembly is composed of 15 contigs with an N50 value of 36.4 Mb.}, + author = {Vila Taboada, Marta and Torrado-Blanco, Laura and Ryrholm, Nils and Romero-Pedreira, David and Conejero, María and Böhne, Astrid and Monteiro, Rita and Marcussen, Thomas and A. Oomen, Rebekah and H. Struck, Torsten and Aguilera, Laura and Gut, Marta and Câmara Ferreira, Francisco and Cruz, Fernando and Gómez-Garrido, Jèssica and S. Alioto, Tyler and Haggerty, Leanne and Martin, Fergal and Bortoluzzi, Chiara}, + doi = {10.12688/openreseurope.20717.1}, + issn = {2732-5121}, + journal = {Open Research Europe}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {January}, + pages = {9}, + shorttitle = {{ERGA}-{BGE} genome of {Erebia} palarica {Chapman}, 1905}, + title = {{ERGA}-{BGE} genome of {Erebia} palarica {Chapman}, 1905: a montane butterfly endemic to {North}-{West} {Spain}}, + url = {https://open-research-europe.ec.europa.eu/articles/6-9/v1}, + urldate = {2026-01-09}, + volume = {6}, + year = {2026} +} + @article{viljoen_rabies-related_2023, author = {Viljoen, Natalie and Ismail, Arshad and Weyer, Jacqueline and Markotter, Wanda}, doi = {10.1128/MRA.00621-23}, journal = {Microbiology Resource Announcements}, keywords = {{\textgreater}UseGalaxy.eu}, month = {October}, - note = {Publisher: American Society for Microbiology}, number = {11}, pages = {e00621--23}, + publisher = {American Society for Microbiology}, title = {A rabies-related lyssavirus from a {Nycticeinops} schlieffeni bat with neurological signs, {South} {Africa}}, url = {https://journals.asm.org/doi/full/10.1128/mra.00621-23}, urldate = {2023-12-28}, @@ -23058,9 +24399,9 @@ @article{virgili_paedomorphic_2025 keywords = {{\textgreater}UseGalaxy.eu}, language = {en}, month = {July}, - note = {Publisher: CSIRO PUBLISHING}, number = {7}, pages = {NULL--NULL}, + publisher = {CSIRO PUBLISHING}, shorttitle = {Paedomorphic adaptations in a new {Heterostigma} species}, title = {Paedomorphic adaptations in a new {Heterostigma} species: a novel strategy for ascidians to live in soft-bottom habitats}, url = {https://www.publish.csiro.au/is/IS24103}, @@ -23079,10 +24420,10 @@ @article{vitali_employing_2023 keywords = {{\textgreater}UseGalaxy.eu, VOCs, biosynthesis pathways, endophyte, medicinal plants}, language = {en}, month = {July}, - note = {Number: 7 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 7}, number = {7}, pages = {1179}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Employing {Genome} {Mining} to {Unveil} a {Potential} {Contribution} of {Endophytic} {Bacteria} to {Antimicrobial} {Compounds} in the {Origanum} vulgare {L}. {Essential} {Oil}}, url = {https://www.mdpi.com/2079-6382/12/7/1179}, urldate = {2023-07-31}, @@ -23097,12 +24438,12 @@ @article{viushkov_influence_2025 doi = {10.3390/ijms26188837}, issn = {1422-0067}, journal = {International Journal of Molecular Sciences}, - keywords = {{\textgreater}UseGalaxy.eu, CRISPR-Sirius, RAD21, auxin-inducible degron, chromatin dynamics, cohesin, double-strand breaks repair, live-cell imaging}, + keywords = {{\textgreater}UseGalaxy.eu, Auxin-inducible Degron, CRISPR-Sirius, Chromatin Dynamics, Cohesin, Crispr-sirius, Double-strand Breaks Repair, Live-cell Imaging, RAD21, Rad21, auxin-inducible degron, chromatin dynamics, cohesin, double-strand breaks repair, live-cell imaging}, language = {en}, month = {January}, - note = {Publisher: Multidisciplinary Digital Publishing Institute}, number = {18}, pages = {8837}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {The {Influence} of {Cohesin} on the {Short}-{Scale} {Dynamics} of {Intact} and {Damaged} {Chromatin} in {Different} {Phases} of the {Cell} {Cycle}}, url = {https://www.mdpi.com/1422-0067/26/18/8837}, urldate = {2025-09-15}, @@ -23115,8 +24456,8 @@ @article{voelker_high-quality_2021 doi = {10.46471/gigabyte.28}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {August}, - note = {Publisher: GigaScience Press}, pages = {1--15}, + publisher = {GigaScience Press}, title = {A high-quality draft genome for {Melaleuca} alternifolia (tea tree): a new platform for evolutionary genomics of myrtaceous terpene-rich species}, url = {https://doi.org/10.46471/gigabyte.28}, volume = {2021}, @@ -23160,7 +24501,7 @@ @article{voigt_genetic_2025 doi = {10.7554/elife.106239}, issn = {2050-084X}, journal = {eLife}, - keywords = {{\textgreater}UseGalaxy.eu, Anthozoa, Biomineralization, Porifera}, + keywords = {{\textgreater}UseGalaxy.eu, Anthozoa, Biomineralization, Calcareous Sponges, Convergent Evolution, Corals, Evolutionary Biology, Gene duplication, Porifera, Sycon Ciliatum}, language = {eng}, month = {September}, pages = {RP106239}, @@ -23191,8 +24532,8 @@ @article{volkova_radiosensitivity_2021 doi = {10.1016/j.scitotenv.2021.146206}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {July}, - note = {Publisher: Elsevier BV}, pages = {146206}, + publisher = {Elsevier BV}, title = {Radiosensitivity of herbaceous plants to chronic radiation exposure: {Field} study in the {Chernobyl} exclusion zone}, url = {https://doi.org/10.1016/j.scitotenv.2021.146206}, volume = {777}, @@ -23264,10 +24605,10 @@ @article{voronezhskaya_multi-omics_2023 keywords = {\textit{Fabaceae}, {\textgreater}UseGalaxy.eu, abiotic stress, low doses, metabolomics, proteomics, transcriptomics}, language = {en}, month = {January}, - note = {Number: 12 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 12}, number = {12}, pages = {2318}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Multi-{Omics} {Analysis} of {Vicia} cracca {Responses} to {Chronic} {Radiation} {Exposure} in the {Chernobyl} {Exclusion} {Zone}}, url = {https://www.mdpi.com/2223-7747/12/12/2318}, urldate = {2023-07-31}, @@ -23324,8 +24665,8 @@ @phdthesis{wadhawan_investigating_2022 keywords = {{\textgreater}UseGalaxy.eu}, language = {en-US-GB}, month = {December}, - note = {Accepted: 2023-06-12T16:00:04Z -Publisher: Imperial College London}, + note = {Accepted: 2023-06-12T16:00:04Z}, + school = {Imperial College London}, title = {Investigating the determinants of {Enterococcus} faecalis virulence in {Drosophila} melanogaster}, url = {http://spiral.imperial.ac.uk/handle/10044/1/104869}, urldate = {2023-07-31}, @@ -23342,10 +24683,10 @@ @article{wahlberg_genome_2025 keywords = {{\textgreater}UseGalaxy.eu, Thysanoptera, genome skimming, high-throughput sequencing, mitochondrial genome, phylogeny, species delimitation}, language = {en}, month = {April}, - note = {Number: 4 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 4}, number = {4}, pages = {226}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Genome {Skimming} of {Thysanoptera} ({Arthropoda}, {Insecta}) and {Its} {Taxonomic} and {Systematic} {Applications}}, url = {https://www.mdpi.com/1424-2818/17/4/226}, urldate = {2025-03-29}, @@ -23353,6 +24694,23 @@ @article{wahlberg_genome_2025 year = {2025} } +@article{wambreuse_carotenoid-based_2025, + abstract = {Sea cucumbers are marine deuterostomes possessing a complex innate immune system composed of a wide diversity of immune cells—coelomocytes—making them compelling models for exploring the evolution of immunity. This study investigates the functional specialisation of coelomocytes within the two main echinoderm body fluids, namely, the perivisceral fluid (PF) from the perivisceral cavity and the hydrovascular fluid (HF) from the hydrovascular–ambulacral system. Given their distribution restricted to the HF, haemocyte-like cells (HELs) are particularly investigated. In echinoderms, haemocytes have been described as reddish cells containing haemoglobin and thus presenting a function in oxygen transport. Using an integrative approach that combines cell morphological analyses, pigment profiling, and multi-omics technologies, we demonstrate in the sea cucumber Holothuria forskali that HELs harbour exceptionally high concentrations of carotenoids, primarily canthaxanthin and astaxanthin, potent antioxidant molecules responsible for their pigmentation. Transcriptomics and proteomics analyses reveal that HELs express candidate genes involved in the carotenoid metabolism pathway as well as catalase, an antioxidant enzyme. Additionally, spectral flow cytometry assays reveal that HELs do not produce reactive oxygen species (ROS) in contrast to most coelomocyte types, reinforcing the hypothesis of their antioxidant function. HELs also contribute to the formation of large red bodies (i.e., coelomocyte aggregates) and increase in concentration following lipopolysaccharide injections, indicating an active role in immunity. Given these results, we hypothesise that these cells act after the culmination of the immune response, forming an antioxidant shell around the cellular aggregates to mitigate oxidative stress from ROS produced while encapsulating pathogens, thus protecting the host tissues. The discovery of carotenoid-carrying coelomocytes constitutes the first report of pigmented coelomocytes in sea cucumbers (except respiratory pigments), challenging the long-standing assumption that these cells contain haemoglobin. Therefore, we propose renaming haemocytes into carotenocytes, at least in this species. However, we believe that this newly described coelomocyte type has been misidentified as haemoglobin-containing cells in many previous studies and may be present in many other holothuroid species. Our findings thus establish a new paradigm in the study of coelomocytes in echinoderms, as well as in the function of the hydrovascular system, which is unique to this phylum.}, + author = {Wambreuse, Noé and Bossiroy, Estelle and David, Frank and Vanwinge, Céline and Fievez, Laurence and Bureau, Fabrice and Gabriele, Sylvain and Karasiewicz, Tania and Mascolo, Cyril and Wattiez, Ruddy and Eeckhaut, Igor and Caulier, Guillaume and Delroisse, Jérôme}, + doi = {10.3389/fimmu.2025.1668167}, + issn = {1664-3224}, + journal = {Frontiers in Immunology}, + keywords = {{\textgreater}UseGalaxy.eu, Echinodermata, antioxidant, deuterostome, gene expression, haemocyte, hydrovascular system, immune cell, reactive oxygen species}, + language = {English}, + month = {November}, + publisher = {Frontiers}, + title = {Carotenoid-based immune response in sea cucumbers relies on newly identified coelomocytes—the carotenocytes}, + url = {https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2025.1668167/full}, + urldate = {2025-12-26}, + volume = {16}, + year = {2025} +} + @misc{wambreuse_morpho-functional_2023, abstract = {Holothuria scabra is one of the most valuable species of sea cucumber owing to its exploitation as a seafood product. This study aims to describe the main molecular and cellular actors in the immunology of the holothuroid H. scabra. First of all, a detailed description of the immune cells – the cœlomocytes – is provided, highlighting five main cell types including phagocytes, small round cells (SRCs), spherulocytes, fusiform cells, and crystal cells, with a further five subtypes identified using transmission electron microscopy. Cœlomocyte aggregates were also described morphologically, yielding two main types, one comprising three successive maturation stages. A comparison of the concentration and proportion of cell populations was carried out between the two main body fluids, namely the hydrovascular fluid of the Polian vesicle (HF) and the perivisceral fluid of the general cavity (PF), and no clear relation could be revealed. Next, the cœlomocyte immune response was studied 24 hours after a lipopolysaccharide (LPS) injection. Firstly, the fluctuation in cell populations was assessed, and despite a high inter-individual variability, it shows a decrease in the phagocyte proportion and an increase in the SRC proportion. Secondly, the differential gene expression of PF cœlomocytes was studied by de novo RNA-sequencing between LPS-injected and control-injected individuals: 945 genes were differentially expressed, including 673 up-regulated and 272 down-regulated in the LPS-injected individuals. Among these genes, 80 had a presumed function in immunity based on their annotation, covering a wide range of immune mechanisms. Overall, this study reveals a complex immune system at both molecular and cellular levels and constitutes a baseline reference on H. scabra immunity, which may be useful for the development of sustainable aquaculture and provides valuable data for comparative immunology.}, address = {Rochester, NY}, @@ -23387,6 +24745,30 @@ @article{wambreuse_morpho-functional_2025 year = {2025} } +@article{wan_immunogenic_2025, + abstract = {This work utilized an ORFeome phage display platform to systematically identify antigenic +epitopes produced by Streptococcus equi subspecies equi (S. equi), an important equine pathogen and the causative agent of horses strangles. Three +major S. equi surface proteins were identified: a novel proline-rich repeat domain protein, a serine +peptidase, and the M-like protein SeM. The proline-rich repeat protein and serine +peptidase were confirmed to be immunogenic in horses with strangles, and their sequences +were shown to be conserved in global S. equi genomes, in contrast to their diversity in S. equi subsp. zooepidemicus. With the well-characterized S. equi immunogenic protein SeM, this paper identified an immunogenic region outside of the +reported critical IgG-binding region. This work provides novel insights to the understanding +of the S. equi immunogenic proteins and provides peptide regions that could serve as vaccine candidates +against S. equi or as diagnostic markers to specifically identify S. equi infections.}, + author = {Wan, Joshua and Weldon, Evan and Ganser, Gabriella and Morris, Ellen Ruth A. and Hughes, Emma V. and Bordin, Angela I. and Heine, Philip Alexander and Hust, Michael and Cohen, Noah D. and Gill, Jason J. and Liu, Mei}, + copyright = {Copyright © 2025 Wan et al.}, + doi = {10.1128/msphere.00626-25}, + journal = {mSphere}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {EN}, + month = {December}, + publisher = {American Society for Microbiology1752 N St., N.W., Washington, DC}, + title = {Immunogenic {Streptococcus} equi cell surface proteins identified by {ORFeome} phage display}, + url = {https://journals.asm.org/doi/10.1128/msphere.00626-25}, + urldate = {2025-12-26}, + year = {2025} +} + @phdthesis{wang_application_2024, abstract = {VEZF1 is a highly conserved vertebrate transcription factor that has ubiquitous expression in vertebrates. VEZF1 is essential for the barrier activity of the chicken ẞ globin HS4 insulator, where it prevents de novo DNA methylation. Knock-out of VEZF1 results in lethal haemorrhaging and edema in murine embryos, indicating a role for VEZF1 in the maintenance of vascular integrity. @@ -23405,13 +24787,29 @@ @phdthesis{wang_application_2024 year = {2024} } +@article{wang_detection_2025, + abstract = {Theories and simulations predict that intense space-time curvature near black holes bends the trajectories of light and matter, driving disk and jet precession under relativistic torques. However, direct observational evidence of disk-jet coprecession remains elusive. Here, we report the most compelling case to date: a tidal disruption event (TDE) exhibiting unprecedented 19.6-day quasi-periodic variations in both x-rays and radio, with x-ray amplitudes exceeding an order of magnitude. The nearly synchronized x-ray and radio variations suggest a shared mechanism regulating the emission regions. We demonstrate that a disk-jet Lense-Thirring precession model successfully reproduces these variations while requiring a low-spin black hole. This study uncovers previously uncharted short-term radio variability in TDEs, highlights the transformative potential of high-cadence radio monitoring, and offers profound insights into disk-jet physics.}, + author = {Wang, Yanan and Lin, Zikun and Wu, Linhui and Lei, Wei-Hua and Wei, Shuyuan and Zhang, Shuang-Nan and Ji, Long and Del Palacio, Santiago and Baldi, Ranieri D. and Huang, Yang and Liu, Ji-Feng and Zhang, Bing and Yang, Aiyuan and Chen, Ru-Rong and Zhang, Yangwei and Wang, Ai-Ling and Yang, Lei and Charalampopoulos, Panos and Williams-Baldwin, David R. A. and Yao, Zhu-Heng and Xie, Fu-Guo and Bu, Defu and Feng, Hua and Cao, Xinwu and Wu, Hongzhou and Li, Wenxiong and Qiao, Erlin and Leloudas, Giorgos and Anderson, Joseph P. and Shu, Xinwen and Pasham, Dheeraj R. and Zou, Hu and Nicholl, Matt and Wevers, Thomas and Müller-Bravo, Tomás E. and Wang, Jing and Wei, Jian-Yan and Qiu, Yu-Lei and Guo, Wei-Jian and Gutiérrez, Claudia P. and Gromadzki, Mariusz and Inserra, Cosimo and Makrygianni, Lydia and Onori, Francesca and Petrushevska, Tanja and Altamirano, Diego and Galbany, Lluís and Peréz-Torres, Miguel and Chen, Ting-Wan}, + doi = {10.1126/sciadv.ady9068}, + issn = {2375-2548}, + journal = {Science Advances}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {December}, + number = {50}, + pages = {eady9068}, + title = {Detection of disk-jet coprecession in a tidal disruption event}, + volume = {11}, + year = {2025} +} + @article{wang_exploring_2025, abstract = {Perlidae represents one of the most diverse and ecologically important groups within the order Plecoptera. However, the phylogenetic relationships within Perlidae remain unresolved due to morphological plasticity and the limited availability of molecular data. Here we sequenced and assembled the mitogenome of \<i\>Hemacroneuria ovalis\</i\> and \<i\>Hesperoperla pacifica\</i\>. By comparing with other published Acroneuriinae mitogenomes, we found that minimal length variation in protein-coding genes (PCGs), transfer RNA genes (tRNAs), and ribosomal RNA genes (rRNAs), whereas the control region (CR) exhibits considerable length divergence. Meanwhile, the mitogenome of Acroneuriinae species is relatively conserved in nucleotide composition and codon usage. The nucleotide diversity (Pi) and Ka/Ks values indicated that the \<i\>ND6\</i\> gene evolves at a faster rate than the \<i\>COI\</i\> gene, and all 13 PCGs are under purifying selection. We also identified gene rearrangement in these two mitogenomes, representing the first report of such events in the order Plecoptera. Phylogenetic results support the monophyly of the tribes Claasseniini, Neoperlini, and Kiotinini, as well as the subfamily Perlinae. Trees from the PCG and PCG12 datasets exhibited more congruent and well accepted topologies. Although both Acroneuriini and Perlini failed to demonstrate monophyly, the phylogenetic relationships among the five families of Perlidae were still reconstructed as (((Perlini + Neoperlini) + Claasseniini) + Kiotinini) + Acroneuriini.}, author = {Wang, Ying and Niu, Yannan and Qin, Baoni and Cao, Jinjun and Li, Weihai and Murányi, Dávid}, doi = {10.1002/ece3.72309}, issn = {2045-7758}, journal = {Ecology and evolution}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Mitochondrial genome, Phylogeny, Stonefly, gene rearrangement}, month = {October}, number = {10}, pages = {e72309}, @@ -23431,10 +24829,10 @@ @article{wang_genome_2024 keywords = {\textit{Arsenophonus} sp., \textit{Peregrinus maidis}, {\textgreater}UseGalaxy.eu, genome assembly, hemiptera}, language = {en}, month = {February}, - note = {Number: 2 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 2}, number = {2}, pages = {113}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {The {Genome} of {Arsenophonus} sp. and {Its} {Potential} {Contribution} in the {Corn} {Planthopper}, {Peregrinus} maidis}, url = {https://www.mdpi.com/2075-4450/15/2/113}, urldate = {2024-05-17}, @@ -23452,10 +24850,10 @@ @article{wang_growth_2024 keywords = {{\textgreater}UseGalaxy.eu, CAZymes, Cellulases, Hypocreales, XYR1/XlnR/XLR-1, cellulose, transcriptional regulation}, language = {en}, month = {February}, - note = {Number: 2 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 2}, number = {2}, pages = {148}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Growth, {Enzymatic}, and {Transcriptomic} {Analysis} of xyr1 {Deletion} {Reveals} a {Major} {Regulator} of {Plant} {Biomass}-{Degrading} {Enzymes} in {Trichoderma} harzianum}, url = {https://www.mdpi.com/2218-273X/14/2/148}, urldate = {2024-05-17}, @@ -23484,8 +24882,8 @@ @article{wang_systems-level_2023 keywords = {{\textgreater}UseGalaxy.eu, Epigenetics, RNA modification}, language = {en}, month = {August}, - note = {Publisher: Nature Publishing Group}, pages = {1--28}, + publisher = {Nature Publishing Group}, title = {A systems-level mass spectrometry-based technique for accurate and sensitive quantification of the {RNA} cap epitranscriptome}, url = {https://www.nature.com/articles/s41596-023-00857-0}, urldate = {2023-08-15}, @@ -23514,8 +24912,6 @@ @article{waterhouse_elixir_2024 keywords = {{\textgreater}UseGalaxy.eu, Biodiversity}, month = {May}, pages = {ELIXIR--499}, - pmcid = {PMC11179050}, - pmid = {38882711}, shorttitle = {The {ELIXIR} {Biodiversity} {Community}}, title = {The {ELIXIR} {Biodiversity} {Community}: {Understanding} short- and long-term changes in biodiversity}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11179050/}, @@ -23534,10 +24930,10 @@ @article{watson_modification_2024 keywords = {{\textgreater}UseGalaxy.eu, G2 Phase, Mitosis, RNA sequencing, bioinformatics, cell cycle, mitosis, phase assignment}, language = {en}, month = {January}, - note = {Number: 9 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 9}, number = {9}, pages = {4589}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Modification of {Seurat} v4 for the {Development} of a {Phase} {Assignment} {Tool} {Able} to {Distinguish} between {G2} and {Mitotic} {Cells}}, url = {https://www.mdpi.com/1422-0067/25/9/4589}, urldate = {2024-05-17}, @@ -23587,7 +24983,7 @@ @article{weigang_within-host_2021 journal = {medRxiv}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {May}, - note = {Publisher: Cold Spring Harbor Laboratory}, + publisher = {Cold Spring Harbor Laboratory}, title = {Within-host evolution of {SARS}-{CoV}-2 in an immunosuppressed {COVID}-19 patient: a source of immune escape variants}, url = {https://doi.org/10.1101/2021.04.30.21256244}, year = {2021} @@ -23600,7 +24996,7 @@ @incollection{wein_analysis_2023 booktitle = {Computational {Epigenomics} and {Epitranscriptomics}}, doi = {10.1007/978-1-0716-2962-8_15}, editor = {Oliveira, Pedro H.}, - isbn = {978-1-07-162962-8}, + isbn = {978-1-0716-2962-8}, keywords = {{\textgreater}UseGalaxy.eu, Mass spectrometry, OpenMS, RNA, Transcriptomics}, language = {en}, pages = {225--239}, @@ -23700,7 +25096,7 @@ @article{werner_mitochondrial_2022 author = {Werner, Erica and Gokhale, Avanti and Ackert, Molly and Xu, Chongchong and Wen, Zhexing and Roberts, Anne M and Roberts, Blaine R and Vrailas-Mortimer, Alysia R and Crocker, Amanda J and Faundez, Victor}, journal = {bioRxiv}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, - note = {Publisher: Cold Spring Harbor Laboratory}, + publisher = {Cold Spring Harbor Laboratory}, title = {The {Mitochondrial} {RNA} {Granule} is {Necessary} for {Parkinsonism}-{Associated} {Metal} {Toxicity}}, year = {2022} } @@ -23781,8 +25177,8 @@ @article{whitmore_inadvertent_2023 keywords = {{\textgreater}NanoGalaxy, {\textgreater}UseGalaxy.eu, DNA, Ecological genetics, Environmental, Science, Sequencing, Zoology, technology and society}, language = {en}, month = {May}, - note = {Publisher: Nature Publishing Group}, pages = {1--16}, + publisher = {Nature Publishing Group}, title = {Inadvertent human genomic bycatch and intentional capture raise beneficial applications and ethical concerns with environmental {DNA}}, url = {https://www.nature.com/articles/s41559-023-02056-2}, urldate = {2023-05-18}, @@ -23834,8 +25230,8 @@ @article{wicaksono_hairpin_2025 keywords = {{\textgreater}UseGalaxy.eu, Malpighiales, RNAi, gene regulation, ncRNA, small RNA}, language = {en}, month = {January}, - note = {Publisher: De Gruyter Open Access}, number = {1}, + publisher = {De Gruyter Open Access}, shorttitle = {Hairpin in a haystack}, title = {Hairpin in a haystack: {In} silico identification and characterization of plant-conserved {microRNA} in {Rafflesiaceae}}, url = {https://www.degruyter.com/document/doi/10.1515/biol-2022-1033/html}, @@ -23853,8 +25249,8 @@ @article{wichers_common_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, language = {eng}, month = {April}, - note = {Publisher: eLife Sciences Publications, Ltd}, pages = {e69040}, + publisher = {eLife Sciences Publications, Ltd}, title = {Common virulence gene expression in adult first-time infected malaria patients and severe cases}, url = {https://doi.org/10.7554/elife.69040}, volume = {10}, @@ -23870,9 +25266,9 @@ @article{wight_anthropogenic_2024 keywords = {{\textgreater}UseGalaxy.eu, Anti-Infective Agents, Escherichia coli Infections}, language = {eng}, month = {February}, - note = {Publisher: American Society for Microbiology}, number = {3}, pages = {e01809--23}, + publisher = {American Society for Microbiology}, title = {Anthropogenic contamination sources drive differences in antimicrobial-resistant {Escherichia} coli in three urban lakes}, url = {https://journals.asm.org/doi/full/10.1128/aem.01809-23}, urldate = {2024-06-07}, @@ -23902,8 +25298,6 @@ @article{williams_discovery_2023 month = {May}, number = {5}, pages = {mgen000996}, - pmcid = {PMC10272871}, - pmid = {37166955}, title = {Discovery and biosynthetic assessment of '{Streptomyces} ortus' sp. nov. isolated from a deep-sea sponge}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10272871/}, urldate = {2023-07-31}, @@ -23921,8 +25315,8 @@ @article{willnow_nuclear_2024 keywords = {{\textgreater}UseGalaxy.eu, Cell proliferation, Differentiation}, language = {en}, month = {June}, - note = {Publisher: Nature Publishing Group}, pages = {1--9}, + publisher = {Nature Publishing Group}, title = {Nuclear position and local acetyl-{CoA} production regulate chromatin state}, url = {https://www.nature.com/articles/s41586-024-07471-4}, urldate = {2024-06-08}, @@ -23953,7 +25347,7 @@ @article{winkler_contrast_2020 keywords = {+RefPublic, {\textgreater}UseGalaxy.eu}, language = {en}, month = {May}, - note = {Publisher: ChemRxiv}, + publisher = {ChemRxiv}, title = {Contrast {Optimization} of {Mass} {Spectrometry} {Imaging} ({MSI}) {Data} {Visualization} by {Threshold} {Intensity} {Quantization} ({TrIQ})}, url = {https://chemrxiv.org/articles/preprint/Contrast_Optimization_of_Mass_Spectrometry_Imaging_MSI_Data_Visualization_by_Threshold_Intensity_Quantization_TrIQ_/12312251}, urldate = {2020-08-13}, @@ -23967,7 +25361,7 @@ @article{winkler_gene_2021 journal = {Research Square}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {July}, - note = {Publisher: Research Square Platform LLC}, + publisher = {Research Square Platform LLC}, title = {Gene {Homologies} {Identified} between {Trypanosoma} cruzi {Antigen} 36 and {Mammalian} {TRIM21} {Genes} {Using} {Bioinformatics} {Analysis}}, url = {https://doi.org/10.21203/rs.3.rs-553828/v2}, year = {2021} @@ -24001,10 +25395,10 @@ @article{winkler_molecular_2025 keywords = {\textit{Trypanosoma brucei}, \textit{Trypanosoma cruzi}, {\textgreater}UseGalaxy.eu, Chagas disease, Microtubule-Associated Proteins, Protozoan Proteins, Trypanosoma cruzi, antigen 36, genetic diversity, microtubule associated protein, molecular bioinformatics}, language = {en}, month = {May}, - note = {Number: 5 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 5}, number = {5}, pages = {476}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Molecular and {Genetic} {Analysis} of the {Increased} {Number} of {Genes} for {Trypanosoma} cruzi {Microtubule} {Associated} {Proteins} in the {Class} {Kinetoplastida}}, url = {https://www.mdpi.com/2076-0817/14/5/476}, urldate = {2025-05-29}, @@ -24035,7 +25429,7 @@ @article{wirth_chlorella_2020 journal = {Frontiers in Bioengineering and Biotechnology}, keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Metagenomics, algal-bacterial interactions, green algae, phycosphere, wastewater}, language = {English}, - note = {Publisher: Frontiers}, + publisher = {Frontiers}, shorttitle = {Chlorella vulgaris and {Its} {Phycosphere} in {Wastewater}}, title = {Chlorella vulgaris and {Its} {Phycosphere} in {Wastewater}: {Microalgae}-{Bacteria} {Interactions} {During} {Nutrient} {Removal}}, url = {https://www.frontiersin.org/articles/10.3389/fbioe.2020.557572/full}, @@ -24052,7 +25446,7 @@ @article{wirth_gene_2024 journal = {American Journal of Physiology-Heart and Circulatory Physiology}, keywords = {{\textgreater}UseGalaxy.eu, endothelial cells, heart, heart failure, transcription factor, transcriptome}, month = {July}, - note = {Publisher: American Physiological Society}, + publisher = {American Physiological Society}, title = {Gene expression networks in endothelial cellsfrom failing human hearts}, url = {https://journals.physiology.org/doi/abs/10.1152/ajpheart.00425.2024}, urldate = {2024-07-21}, @@ -24069,10 +25463,10 @@ @article{witmer_epigenetic_2020 keywords = {+Methods, +UseMain, +UsePublic, {\textgreater}UseGalaxy.eu}, language = {en}, month = {April}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {6354}, + publisher = {Nature Publishing Group}, title = {An epigenetic map of malaria parasite development from host to vector}, url = {https://www.nature.com/articles/s41598-020-63121-5}, urldate = {2020-05-20}, @@ -24162,15 +25556,15 @@ @article{wolf_characterization_2021 @article{wolf_comparative_2021, abstract = {{\textless}h3{\textgreater}Abstract{\textless}/h3{\textgreater} {\textless}h3{\textgreater}Background{\textless}/h3{\textgreater} {\textless}p{\textgreater}Visual outcome of patients with neovascular age-related macular degeneration has significantly improved during the last years following the introduction of anti-vascular endothelial growth factor (VEGF) therapy. However, about one third of patients show persistent exudation and decreasing visual acuity despite recurrent anti-VEGF treatment, which implies a role of other, still unknown proangiogenic mediators.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Methods{\textless}/h3{\textgreater} {\textless}p{\textgreater}The present study applied transcriptional profiling of human and mouse (C57BL/6J wildtype) choroidal neovascularization (CNV) membranes each with reference to healthy control tissue to identify yet unrecognized mediators of CNV formation. Key factors were further investigated by immunohistochemistry as well as by intravitreal inhibition experiments and multiplex protein assays in the laser-induced CNV mouse model.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Results{\textless}/h3{\textgreater} {\textless}p{\textgreater}Transcriptional profiles of CNV membranes were characterized by enhanced activation of blood vessel development, cytoskeletal organization, and cytokine production, with angiogenesis and wound healing processes predominating in humans and activation of immune processes in mice. Besides several species-specific factors, 95 phylogenetically conserved CNV-associated genes were detected, among which fibroblast growth factor inducible-14 (FN14), a member of the tumor necrosis factor (TNF) receptor family, was identified as a key player of CNV formation. Blocking the pathway by intravitreal injection of a FN14 decoy receptor modulated the cytokine profile - most notably IL-6 - and led to a significant reduction of CNV size \textit{in vivo}.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Conclusions{\textless}/h3{\textgreater} {\textless}p{\textgreater}This study characterizes the transcriptome of human and mouse CNV membranes in an unprejudiced manner and identifies FN14 as a phylogenetically conserved mediator of CNV formation and a promising new therapeutic target for neovascular AMD.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Funding{\textless}/h3{\textgreater} {\textless}p{\textgreater}This study was funded by the Helmut-Ecker-Stiftung and the Volker-Homann-Stiftung.{\textless}/p{\textgreater}}, author = {Wolf, Julian and Schlecht, Anja and Rosmus, Dennis-Dominik and Boneva, Stefaniya and Agostini, Hansjürgen and Schlunck, Günther and Wieghofer, Peter and Lange, Clemens}, + chapter = {New Results}, copyright = {© 2021, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/}, doi = {10.1101/2021.05.10.443381}, journal = {bioRxiv}, keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, language = {en}, month = {May}, - note = {Publisher: Cold Spring Harbor Laboratory -Section: New Results}, pages = {2021.05.10.443381}, + publisher = {Cold Spring Harbor Laboratory}, title = {Comparative transcriptome analysis of human and murine choroidal neovascularization identifies fibroblast growth factor inducible-14 as phylogenetically conserved mediator of neovascular age-related macular degeneration}, url = {https://www.biorxiv.org/content/10.1101/2021.05.10.443381v1}, urldate = {2021-07-27}, @@ -24183,9 +25577,9 @@ @article{wolf_comparative_2022 journal = {Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {April}, - note = {Publisher: Elsevier BV}, number = {4}, pages = {166340}, + publisher = {Elsevier BV}, title = {Comparative transcriptome analysis of human and murine choroidal neovascularization identifies fibroblast growth factor inducible-14 as phylogenetically conserved mediator of neovascular age-related macular degeneration}, url = {https://doi.org/10.1016/j.bbadis.2022.166340}, volume = {1868}, @@ -24240,8 +25634,8 @@ @article{wolf_human_2022 journal = {Genomics}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {February}, - note = {Publisher: Elsevier BV}, pages = {110286}, + publisher = {Elsevier BV}, title = {The {Human} {Eye} {Transcriptome} {Atlas}: {A} searchable comparative transcriptome database for healthy and diseased human eye tissue}, url = {https://doi.org/10.1016/j.ygeno.2022.110286}, year = {2022} @@ -24267,8 +25661,6 @@ @article{wolf_proteotranscriptomic_2025 language = {eng}, month = {May}, pages = {1571702}, - pmcid = {PMC12088971}, - pmid = {40395327}, title = {A proteotranscriptomic approach to dissect the molecular landscape of human retinoblastoma}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12088971/}, urldate = {2025-05-28}, @@ -24286,10 +25678,10 @@ @article{wolf_transcriptional_2020 keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Gene Expression Regulation, Neoplastic}, language = {en}, month = {October}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {17022}, + publisher = {Nature Publishing Group}, title = {Transcriptional characterization of conjunctival melanoma identifies the cellular tumor microenvironment and prognostic gene signatures}, url = {https://www.nature.com/articles/s41598-020-72864-0}, urldate = {2021-05-15}, @@ -24324,10 +25716,10 @@ @article{wolf_transcriptional_2023 keywords = {{\textgreater}UseGalaxy.eu, Conjunctival Neoplasms, EMZL, Lymphoma, B-Cell, Marginal Zone, RNA sequencing, cellular tumor microenvironment, conjunctival lymphoma, formalin-fixation and paraffin-embedding (FFPE), prognosis, recurrence}, language = {en}, month = {January}, - note = {Number: 1 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 1}, number = {1}, pages = {115}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Transcriptional {Profiling} {Identifies} {Prognostic} {Gene} {Signatures} for {Conjunctival} {Extranodal} {Marginal} {Zone} {Lymphoma}}, url = {https://www.mdpi.com/2218-273X/13/1/115}, urldate = {2023-03-15}, @@ -24354,6 +25746,25 @@ @article{wolff_galaxy_2018 year = {2018} } +@article{wolff_galaxy_2020, + abstract = {Abstract. The Galaxy HiCExplorer provides a web service at https://hicexplorer.usegalaxy.eu. It enables the integrative analysis of chromosome conformation by}, + author = {Wolff, Joachim and Rabbani, Leily and Gilsbach, Ralf and Richard, Gautier and Manke, Thomas and Backofen, Rolf and Grüning, Björn A.}, + doi = {10.1093/nar/gkaa220}, + issn = {0305-1048}, + journal = {Nucleic Acids Research}, + keywords = {+Galactic, +IsGalaxy, +Tools, +Visualization, {\textgreater}HiCExplorer, {\textgreater}UseGalaxy.eu, Software}, + language = {en}, + month = {April}, + number = {W1}, + pages = {W177--W184}, + shorttitle = {Galaxy {HiCExplorer} 3}, + title = {Galaxy {HiCExplorer} 3: a web server for reproducible {Hi}-{C}, capture {Hi}-{C} and single-cell {Hi}-{C} data analysis, quality control and visualization}, + url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaa220/5821269}, + urldate = {2020-05-26}, + volume = {48}, + year = {2020} +} + @incollection{wolfien_single-cell_2021, author = {Wolfien, Markus and David, Robert and Galow, Anne-Marie}, doi = {10.36255/exonpublications.bioinformatics.2021.ch2}, @@ -24398,6 +25809,23 @@ @article{wolkowicz_utility_2017 year = {2017} } +@article{woller_no_2026, + abstract = {Magnetotactic bacteria produce membrane-bound organelles known as magnetosomes, which consist of chains of magnetite crystals and function as sensors for orientation within the Earth’s magnetic field. Magnetosome biosynthesis is a complex, multistep process that depends on iron availability and suboxic conditions. However, the expression of the ca. 30 core magnetosome biosynthetic genes has previously been described as constitutive and largely unaffected by environmental conditions.A recent study by Pang et al., published in this journal, reported the identification of a transcriptional regulator, NsrRMg, which was proposed to activate magnetosome biosynthesis in Magnetospirillum gryphiswaldense in response to the endogenous signaling molecule nitric oxide (NO). Furthermore, the study suggested that NO also regulates a putative, previously unrecognized nitrification pathway that presumably supports endogenous NO production via denitrification, even in the absence of extracellular nitrate.Here, we present results of genetic and transcriptional analyses demonstrating that, contrary to the findings of Pang et al., NsrRMg is not required for magnetosome biosynthesis. We also refute the existence of the proposed nitrification pathway and conclude that there is no compelling evidence supporting a role of NsrRMg as a key regulator of magnetosome formation in M. gryphiswaldense.}, + author = {Woller, Alexandra and Uebe, René and Schüler, Dirk}, + doi = {10.1093/nar/gkaf1422}, + issn = {1362-4962}, + journal = {Nucleic Acids Research}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {January}, + number = {1}, + pages = {gkaf1422}, + title = {No evidence for the putative nitric oxide sensor {NsrR} as a key regulator of magnetosome formation in {Magnetospirillum} gryphiswaldense}, + url = {https://doi.org/10.1093/nar/gkaf1422}, + urldate = {2026-01-11}, + volume = {54}, + year = {2026} +} + @article{wright*_structure_2018, abstract = {Many years of research in RNA biology have soundly established the importance of RNA-based regulation far beyond most early traditional presumptions. Importantly, the advances in “wet” laboratory techniques have produced unprecedented amounts of data that require efficient and precise computational analysis schemes and algorithms. Hence, many in silico methods that attempt topological and functional classification of novel putative RNA-based regulators are available. In this review, we technically outline thermodynamics-based standard RNA secondary structure and RNA-RNA interaction prediction approaches that have proven valuable to the RNA research community in the past and present. For these, we highlight their usability with a special focus on prokaryotic organisms and also briefly mention recent advances in whole-genome interactomics and how this may influence the field of predictive RNA research.}, author = {Wright*, Patrick R. and Mann*, Martin and Backofen*, Rolf}, @@ -24442,9 +25870,9 @@ @article{wu_comparative_2025 keywords = {{\textgreater}UseGalaxy.eu}, language = {en}, month = {April}, - note = {Publisher: John Wiley \& Sons, Ltd}, number = {4}, pages = {e71224}, + publisher = {John Wiley \& Sons, Ltd}, shorttitle = {Comparative {Genomic} and {Mitochondrial} {Phylogenetic} {Relationships} of {Ovulidae} ({Mollusca}}, title = {Comparative {Genomic} and {Mitochondrial} {Phylogenetic} {Relationships} of {Ovulidae} ({Mollusca}: {Gastropoda}) {Along} the {Chinese} {Coast}}, url = {https://onlinelibrary.wiley.com/doi/10.1002/ece3.71224}, @@ -24463,10 +25891,10 @@ @article{wu_differential_2025 keywords = {\textit{RT}-qPCR, {\textgreater}UseGalaxy.eu, high-temperature stress, mitochondrial genome expression, selection pressure, skink}, language = {en}, month = {January}, - note = {Number: 7 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 7}, number = {7}, pages = {999}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Differential {Mitochondrial} {Genome} {Expression} of {Four} {Skink} {Species} {Under} {High}-{Temperature} {Stress} and {Selection} {Pressure} {Analyses} in {Scincidae}}, url = {https://www.mdpi.com/2076-2615/15/7/999}, urldate = {2025-05-29}, @@ -24482,7 +25910,7 @@ @article{wu_genome_2025 keywords = {{\textgreater}UseGalaxy.eu, Salmonella, colistin-resistant, mcr-1.1, multidrug resistance, whole-genome sequence}, language = {English}, month = {January}, - note = {Publisher: Frontiers}, + publisher = {Frontiers}, title = {Genome analysis of colistin-resistant {Salmonella} isolates from human sources in {Guizhou} of southwestern {China}, 2019–2023}, url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2025.1498995/full}, urldate = {2025-02-16}, @@ -24500,9 +25928,9 @@ @article{wurzbacher_planctoellipticum_2024 keywords = {{\textgreater}UseGalaxy.eu, Bacterial genomics, Bacterial physiology, Fatty Acids, Wastewater}, language = {en}, month = {March}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {5741}, + publisher = {Nature Publishing Group}, title = {Planctoellipticum variicoloris gen. nov., sp. nov., a novel member of the family {Planctomycetaceae} isolated from wastewater of the aeration lagoon of a sugar processing plant in {Northern} {Germany}}, url = {https://www.nature.com/articles/s41598-024-56373-y}, urldate = {2024-04-28}, @@ -24535,8 +25963,8 @@ @article{wynne_apoe_2023 keywords = {{\textgreater}UseGalaxy.eu, APOE, Apolipoprotein E4, Mitochondria, alzheimer's disease, mitochondria}, language = {eng}, month = {May}, - note = {Publisher: eLife Sciences Publications, Ltd}, pages = {e85779}, + publisher = {eLife Sciences Publications, Ltd}, title = {{APOE} expression and secretion are modulated by mitochondrial dysfunction}, url = {https://doi.org/10.7554/eLife.85779}, urldate = {2024-07-22}, @@ -24561,13 +25989,59 @@ @article{xavier_diversity_2025 year = {2025} } +@article{xie_benchmarking_2025, + abstract = {CRISPR/Cas9 has facilitated yeast functional genomics by generating a large number +of precise genetic variants in a very short period of time. This enabled the interrogation +of reconstituted natural genetic variants across different genetic backgrounds or +entirely synthetic mutations to discover novel or improved functions. However, Cas9 +only targets a limited genomic sequence space due to its preference for G-rich PAM +sequences. In this study, we close this gap by developing a CRISPR/Cas12a-based system +to engineer user-defined genetic variants targeting T-rich PAM sequences. Our system +adopts a homology-integrated design and the most PAM-relaxed Cas12a characterized +in yeast to date. These features collectively enabled the creation of genetic variant +libraries and multiplex edited strains. This genome editing tool can be used together +with Cas9-based tools to interrogate a greater genomic sequence space.}, + author = {Xie, Weiyu and Cai, Zhenkun and Bao, Zehua}, + copyright = {Copyright © 2025 Xie et al.}, + doi = {10.1128/aem.01618-25}, + journal = {Applied and Environmental Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {EN}, + month = {December}, + publisher = {American Society for Microbiology1752 N St., N.W., Washington, DC}, + title = {Benchmarking the {PAM} compatibility of {Cas12a} variants for high-throughput yeast genetic variant engineering}, + url = {https://journals.asm.org/doi/10.1128/aem.01618-25}, + urldate = {2025-12-26}, + year = {2025} +} + +@article{xu_characterization_2025, + abstract = {To enhance our understanding of the phylogenetics and evolutionary processes within Dacinae, we sequenced and analyzed four complete mitogenomes for the first time, specifically Acroceratitis separata, Acrotaeniostola quadrivittata, Gastrozona parviseta, and Paragastrozona vulgaris, which represent Gastrozonini species. Our results indicated that these four mitogenomes, including A. separata, A. quadrivittata, G. parviseta, and P. vulgaris, comprised 37 mitochondrial genes and an A+T-control region, with a total length of 16,603 bp, 16,112 bp, 16,691 bp, and 16,594 bp, revealing a notably high AT content reaching 77.4\%, 78.4\%, 75.1\%, and 75.1\%, respectively. Our phylogenetic analyses using Bayesian inference and Maximum Likelihood methods under site-homogeneous models consistently demonstrated their superiority over the site-heterogeneous mixture model CAT + GTR, given the currently accepted phylogenetic framework. Apart from a few species demonstrating unstable placements, the inferred phylogenetic relationships among the three tribes were strongly supported as monophyletic groups, with the topology represented as ((Ceratitidini + Gastrozonini) + Dacini), and most branches displaying moderate-to-high support values, of which four newly sequenced mitogenomes and A. dissimilis robustly formed a single clade representing Gastrozonini. This study substantially augments the existing mitogenome data, thereby providing more profound insight into the evolutionary history and higher-level phylogenetic structure within the Dacinae.}, + author = {Xu, Deliang and Ding, Shuangmei and Zeng, Xiaojie and Du, Lele}, + copyright = {cc by}, + doi = {10.3390/ani15223301}, + issn = {2076-2615}, + journal = {Animals}, + keywords = {{\textgreater}UseGalaxy.eu, Gastrozonini, Mitochondrial genome, Phylobayes, True Fruit Flies}, + language = {eng}, + month = {November}, + number = {22}, + pages = {3301}, + shorttitle = {Characterization of the {Complete} {Mitogenomes} of {Four} {Dacinae} {Species} ({Diptera}}, + title = {Characterization of the {Complete} {Mitogenomes} of {Four} {Dacinae} {Species} ({Diptera}: {Tephritidae}) with {Phylogenetic} {Analysis}}, + url = {https://europepmc.org/articles/PMC12649545}, + urldate = {2025-12-26}, + volume = {15}, + year = {2025} +} + @article{xu_mitogenomic_2025, abstract = {Mitochondrial genomes are powerful tools for taxonomic delimitation and species identification, yet they remain scarce for Chironomidae (Diptera). In this study, we assembled and annotated 63 new mitochondrial genomes, encompassing 63 species within 39 genera in Orthocladiinae \<i\>sensu lato\</i\> (including Prodiamesinae and Orthocladiinae) and Chironominae by whole-genome sequencing, marking the first report of mitochondrial genome data for the Xiaomyini. Comparative analyses revealed structural variation, including transfer RNA gene rearrangements, along with strong nucleotide composition bias, codon usage patterns, and gene-specific selection pressure differences. Distinct evolutionary dynamics were detected among protein-coding genes, ribosomal RNAs, transfer RNAs, and the control region. Heterogeneity analyses and phylogenetic analyses showed that amino acid datasets perform better for basal branch of Orthocladiinae relationships, although the resolution within non-basal branches of Orthocladiinae remains limited. By substantially increasing both the number and taxonomic breadth of mitochondrial genomes in Chironomidae, this study delivers a vital foundation for future multi-marker phylogenetic reconstruction, taxonomic revision, and rapid species identification, with direct applications to biodiversity conservation and freshwater ecosystem monitoring.}, author = {Xu, Hai-Feng and Xiao, Xiu-Ru and Zhang, Zhi-Chao and Li, Yu-Fan and Lin, Xiao-Long}, doi = {10.3390/biology14091178}, issn = {2079-7737}, journal = {Biology}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Mitogenome, Ngs, Rearrangement}, month = {September}, number = {9}, pages = {1178}, @@ -24587,10 +26061,10 @@ @article{xu_reprogramming_2023 keywords = {{\textgreater}UseGalaxy.eu, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Cell biology, Cell signalling, Genetics}, language = {en}, month = {July}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {1--16}, + publisher = {Nature Publishing Group}, title = {Reprogramming of the transcriptome after heat stress mediates heat hormesis in {Caenorhabditis} elegans}, url = {https://www.nature.com/articles/s41467-023-39882-8}, urldate = {2023-07-18}, @@ -24598,6 +26072,25 @@ @article{xu_reprogramming_2023 year = {2023} } +@article{yaghoubi_khanghahi_transcriptomic_2025, + abstract = {This study investigates the efficacy of plant growth-promoting bacteria (PGPB) in improving stress tolerance in plants by analyzing the molecular and biochemical bases in durum wheat grain. An experiment was conducted where soil and seeds were inoculated with PGPB, under drought and salinity stress. 16 S rRNA sequencing indicated no change in grain bacterial communities in response to biofertilizers and stress. However, a genome-wide analysis identified 153 up-regulated and 33 down-regulated plant genes in response to PGPB, predominantly enriched in stress-related biological processes. These genes specifically encode for proteins involved in metabolite interconversion enzyme, chaperone, protein modifying enzyme, and transporters, which are functionally related groups assisting protein folding in the cell under stress conditions. Moreover, pathway analysis confirmed related changes at the metabolite and enzyme activity levels. In this regard, PGPB-treated plants exhibited heightened activity of both enzymatic and non-enzymatic (e.g., thioredoxins, peroxiredoxins, etc.) antioxidants under stress, showcasing significant enhancements ranging from + 27\% to + 283\% and + 36\% to + 266\%, respectively. Further elucidation of biochemical pathways revealed alterations in the activation of non-antioxidant enzymes in PGPB-treated plants, exemplified by increased activities of glutamate synthase (40-44\%) and decreased activities of protein-tyrosine-phosphatase (29-31\%) under both stresses, as well as elevated activities of anthocyanidin reductase (91\%) and lipoxygenases (18\%) specifically under drought. Overall, the present research highlighted the potential of beneficial bacteria in improving plant stress tolerance, especially under drought, through shifting transcriptome expression of plant genes and employing multiple protective strategies which can complement each other.Supplementary informationThe online version contains supplementary material available at 10.1007/s12298-025-01686-z.}, + author = {Yaghoubi Khanghahi, Mohammad and AbdElgawad, Hamada and Curci, Maddalena and Garrigues, Romain and Korany, Shereen Magdy and Alsherif, Emad A and Verbruggen, Erik and Spagnuolo, Matteo and Addesso, Rosangela and Sofo, Adriano and Beemster, Gerrit T S and Crecchio, Carmine}, + copyright = {cc by}, + doi = {10.1007/s12298-025-01686-z}, + issn = {0974-0430}, + journal = {Physiology and molecular biology of plants}, + keywords = {{\textgreater}UseGalaxy.eu, Durum Wheat Grain, Endophytic Bacterial Community, Plant Growth-promoting Bacteria, Stress, Transcriptomics}, + language = {eng}, + month = {December}, + number = {12}, + pages = {2121--2143}, + title = {Transcriptomic, biochemical, and microbiome assessments into drought and salinity tolerance in durum wheat mediated by plant growth-promoting bacteria}, + url = {https://europepmc.org/articles/PMC12715099}, + urldate = {2025-12-26}, + volume = {31}, + year = {2025} +} + @article{yan_diet-like_2023, abstract = {Direct interspecies electron transfer (DIET) has been demonstrated to be an efficient type of mutualism in methanogenesis. However, few studies have reported its presence in mixed microbial communities and its trigger mechanism in the natural environment and engineered systems. Here, we reported DIET-like mutualism of Geobacter and methanogens in the planktonic microbiome for the first time in anaerobic electrochemical digestion (AED) fed with propionate, potentially triggered by excessive cathodic hydrogen (56 times higher than the lowest) under the electrochemical condition. In contrast with model prediction without DIET, the highest current density and hydrogen and methane production were concurrently observed at −0.2 V where an abundance of Geobacter (49\%) and extracellular electron transfer genes were identified in the planktonic microbiome via metagenomic analysis. Metagenomic assembly genomes annotated to Geobacter anodireducens were identified alongside two methanogens, Methanothrix harundinacea and Methanosarcina mazei, which were previously identified to participate in DIET. This discovery revealed that DIET-like mutualism could be triggered without external conductive materials, highlighting its potentially ubiquitous presence. Such mutualism simultaneously boosted methane and hydrogen production, thereby demonstrating the potential of AED in engineering applications.}, author = {Yan, Yuqing and Zhang, Jiayao and Tian, Lili and Yan, Xuejun and Du, Lin and Leininger, Aaron and Zhang, Mou and Li, Nan and Ren, Zhiyong Jason and Wang, Xin}, @@ -24622,11 +26115,10 @@ @article{yang_complete_2025 journal = {Mitochondrial DNA Part B}, keywords = {{\textgreater}UseGalaxy.eu, Alpheus brevicristatus, Mitochondrial genome, phylogenetic analysis, snapping shrimp}, month = {July}, - note = {Publisher: Taylor \& Francis -\_eprint: https://doi.org/10.1080/23802359.2025.2487072}, + note = {\_eprint: https://doi.org/10.1080/23802359.2025.2487072}, number = {7}, pages = {554--557}, - pmid = {40503060}, + publisher = {Taylor \& Francis}, title = {The complete mitochondrial genome of the snapping shrimp, {Alpheus} brevicristatus {De} {Haan}, 1844 ({Crustacea}, {Decapoda}, {Alpheidae})}, url = {https://doi.org/10.1080/23802359.2025.2487072}, urldate = {2025-07-12}, @@ -24644,9 +26136,9 @@ @article{yang_opposing_2025 keywords = {{\textgreater}UseGalaxy.eu, Long Interspersed Nucleotide Elements, Molecular Chaperones, Nuclear Pore Complex Proteins, Protein quality control, Transposition}, language = {en}, month = {July}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {6327}, + publisher = {Nature Publishing Group}, title = {Opposing roles of pseudokinases {NRBP1} and {NRBP2} in regulating {L1} retrotransposition}, url = {https://www.nature.com/articles/s41467-025-61626-z}, urldate = {2025-09-03}, @@ -24737,7 +26229,7 @@ @article{yol_high-density_2021 doi = {10.3389/fpls.2021.679659}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {June}, - note = {Publisher: Frontiers Media SA}, + publisher = {Frontiers Media SA}, title = {A {High}-{Density} {SNP} {Genetic} {Map} {Construction} {Using} {ddRAD}-{Seq} and {Mapping} of {Capsule} {Shattering} {Trait} in {Sesame}}, url = {https://doi.org/10.3389/fpls.2021.679659}, volume = {12}, @@ -24754,8 +26246,8 @@ @article{yong_complete_2024 keywords = {{\textgreater}UseGalaxy.eu}, language = {en}, month = {July}, - note = {Publisher: Senckenberg Gesellschaft für Naturforschung}, pages = {515--526}, + publisher = {Senckenberg Gesellschaft für Naturforschung}, shorttitle = {Complete mitochondrial genomes of {Bactrocera} ({Bulladacus}) cinnabaria and {B}. ({Bactrocera}) propinqua ({Diptera}}, title = {Complete mitochondrial genomes of {Bactrocera} ({Bulladacus}) cinnabaria and {B}. ({Bactrocera}) propinqua ({Diptera}: {Tephritidae}) and their phylogenetic relationships with other congeners}, url = {https://arthropod-systematics.arphahub.com/article/115954/}, @@ -24817,10 +26309,10 @@ @article{yousif_sars-cov-2_2023 keywords = {{\textgreater}UseGalaxy.eu, COVID-19, Epidemiology, Genomics, SARS-CoV-2, Wastewater}, language = {en}, month = {October}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {6325}, + publisher = {Nature Publishing Group}, title = {{SARS}-{CoV}-2 genomic surveillance in wastewater as a model for monitoring evolution of endemic viruses}, url = {https://www.nature.com/articles/s41467-023-41369-5}, urldate = {2023-10-12}, @@ -24925,9 +26417,9 @@ @article{yu_usp1246_2024 journal = {EMBO reports}, keywords = {{\textgreater}UseGalaxy.eu, DUB, ESCRT, Endosomal Sorting Complexes Required for Transport, Integrin, Integrin beta1, Lysosomes, Proteolysis, USP12/USP46, Ubiquitination}, month = {November}, - note = {Num Pages: 32 -Publisher: John Wiley \& Sons, Ltd}, + note = {Num Pages: 32}, pages = {1--32}, + publisher = {John Wiley \& Sons, Ltd}, title = {The {USP12}/46 deubiquitinases protect integrins from {ESCRT}-mediated lysosomal degradation}, url = {https://www.embopress.org/doi/full/10.1038/s44319-024-00300-9}, urldate = {2024-11-10}, @@ -24944,10 +26436,10 @@ @article{yuan_ezh2_2022 keywords = {{\textgreater}UseGalaxy.eu, Epigenetics, Inflammasome, Long Noncoding, RNA}, language = {en}, month = {October}, - note = {Number: 10 -Publisher: Nature Publishing Group}, + note = {Number: 10}, number = {10}, pages = {2009--2023}, + publisher = {Nature Publishing Group}, title = {Ezh2 competes with p53 to license {lncRNA} {Neat1} transcription for inflammasome activation}, url = {https://www.nature.com/articles/s41418-022-00992-3}, urldate = {2022-12-03}, @@ -24979,11 +26471,10 @@ @article{zafar_identification_2024 issn = {0739-1102}, journal = {Journal of Biomolecular Structure and Dynamics}, keywords = {{\textgreater}UseGalaxy.eu, Frankliniella occidentalis, odorant-binding proteins, p-anisaldehyde, semiochemicals, verbenone}, - note = {Publisher: Taylor \& Francis -\_eprint: https://doi.org/10.1080/07391102.2024.2317990}, + note = {\_eprint: https://doi.org/10.1080/07391102.2024.2317990}, number = {0}, pages = {1--16}, - pmid = {38415377}, + publisher = {Taylor \& Francis}, title = {Identification of the odorant binding proteins of {Western} {Flower} {Thrips} ({Frankliniella} occidentalis), characterization and binding analysis of {FoccOBP3} with molecular modelling, molecular dynamics simulations and a confirmatory field trial}, url = {https://doi.org/10.1080/07391102.2024.2317990}, urldate = {2024-05-17}, @@ -25001,9 +26492,9 @@ @article{zakir_cohesive_2025 keywords = {{\textgreater}UseGalaxy.eu, Breast Neoplasms, Breast cancer, Cancer, Receptor, erbB-2, Triple Negative Breast Neoplasms}, language = {en}, month = {July}, - note = {Publisher: Nature Publishing Group}, number = {1}, pages = {23675}, + publisher = {Nature Publishing Group}, title = {Cohesive data analysis for the identification of prognostic hub genes and significant pathways associated with {HER2} + and {TN} breast cancer types}, url = {https://www.nature.com/articles/s41598-025-94084-0}, urldate = {2025-07-12}, @@ -25087,9 +26578,9 @@ @article{zavala-alvarado_transcriptional_2020 keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Bacterial pathogens, Gene expression, Gene prediction, Hydrogen peroxide, Leptospira, Leptospira interrogans, Non-coding RNA, Operons}, language = {en}, month = {October}, - note = {Publisher: Public Library of Science}, number = {10}, pages = {e1008904}, + publisher = {Public Library of Science}, title = {The transcriptional response of pathogenic {Leptospira} to peroxide reveals new defenses against infection-related oxidative stress}, url = {https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1008904}, urldate = {2021-05-15}, @@ -25106,9 +26597,9 @@ @article{zebua_bacterial_2022 keywords = {{\textgreater}UseGalaxy.eu}, language = {en}, month = {May}, - note = {Publisher: IOP Publishing}, number = {1}, pages = {012023}, + publisher = {IOP Publishing}, title = {Bacterial key species candidates for biomonitoring peatland burnt in the {Giam} {Siak} {Kecil}-{Bukit} {Batu} biosphere reserve, {Riau}}, url = {https://doi.org/10.1088/1755-1315/1025/1/012023}, urldate = {2022-09-24}, @@ -25123,8 +26614,8 @@ @article{zehr_patterns_2023 keywords = {{\textgreater}UseGalaxy.eu, ⛔ No DOI found}, language = {eng}, month = {May}, - note = {Accepted: 2023-09-03T14:54:54Z -Publisher: Temple University. Libraries}, + note = {Accepted: 2023-09-03T14:54:54Z}, + publisher = {Temple University. Libraries}, title = {{PATTERNS} {OF} {NATURAL} {SELECTION} {ASSOCIATED} {WITH} {TROPISM} {SHIFTS} {IN} {ANIMAL} {CORONAVIRUS} {GENOMES}}, url = {https://scholarshare.temple.edu/handle/20.500.12613/8932}, urldate = {2024-11-17}, @@ -25140,9 +26631,9 @@ @article{zehr_positive_2024 keywords = {{\textgreater}UseGalaxy.eu, Evolution, Molecular, Genome, Viral, Phylogeny, Recombination, Genetic, Selection, Genetic}, language = {eng}, month = {October}, - note = {Publisher: American Society for Microbiology}, number = {0}, pages = {e00867--24}, + publisher = {American Society for Microbiology}, title = {Positive selection, genetic recombination, and intra-host evolution in novel equine coronavirus genomes and other members of the {Embecovirus} subgenus}, url = {https://journals.asm.org/doi/full/10.1128/spectrum.00867-24}, urldate = {2024-10-20}, @@ -25186,10 +26677,10 @@ @article{zhan_comparison_2024 keywords = {\textit{RT}-qPCR, {\textgreater}UseGalaxy.eu, Genome, Mitochondrial, Lizards, latitudinal pattern, low-temperature stress, mitochondrial genome expression, skink}, language = {en}, month = {January}, - note = {Number: 19 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 19}, number = {19}, pages = {10637}, + publisher = {Multidisciplinary Digital Publishing Institute}, title = {Comparison of {Mitochondrial} {Genome} {Expression} {Differences} among {Four} {Skink} {Species} {Distributed} at {Different} {Latitudes} under {Low}-{Temperature} {Stress}}, url = {https://www.mdpi.com/1422-0067/25/19/10637}, urldate = {2024-11-17}, @@ -25207,10 +26698,10 @@ @article{zhang_complete_2024 keywords = {\textit{Nedyopus patrioticus}, {\textgreater}UseGalaxy.eu, color polymorphism, mitochondrial genomes, phylogenetic analysis}, language = {en}, month = {March}, - note = {Number: 3 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 3}, number = {3}, pages = {2514--2527}, + publisher = {Multidisciplinary Digital Publishing Institute}, shorttitle = {Complete {Mitochondrial} {Genomes} of {Nedyopus} patrioticus}, title = {Complete {Mitochondrial} {Genomes} of {Nedyopus} patrioticus: {New} {Insights} into the {Color} {Polymorphism} of {Millipedes}}, url = {https://www.mdpi.com/1467-3045/46/3/159}, @@ -25227,9 +26718,9 @@ @article{zhang_deciphering_2024 journal = {The EMBO Journal}, keywords = {{\textgreater}UseGalaxy.eu, Arabidopsis, Arabidopsis Proteins, Cell-specific Transcriptomic and Epigenetic Profiling, Gene Expression Regulation, Plant, Plant Roots, Root, Stem Cells, Stem Cells Organizer, WOX5}, month = {November}, - note = {Num Pages: 23 -Publisher: John Wiley \& Sons, Ltd}, + note = {Num Pages: 23}, pages = {1--23}, + publisher = {John Wiley \& Sons, Ltd}, title = {Deciphering the molecular logic of {WOX5} function in the root stem cell organizer}, url = {https://www.embopress.org/doi/full/10.1038/s44318-024-00302-2}, urldate = {2024-11-21}, @@ -25246,10 +26737,10 @@ @article{zhang_first_2024 keywords = {\textit{L. scaber}, {\textgreater}UseGalaxy.eu, Arthropods, Diplopoda, Genome, Mitochondrial, genomic features, mitochondrial genome, phylogenetic analysis}, language = {en}, month = {February}, - note = {Number: 2 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 2}, number = {2}, pages = {254}, + publisher = {Multidisciplinary Digital Publishing Institute}, shorttitle = {The {First} {Complete} {Mitochondrial} {Genome} of the {Genus} {Litostrophus}}, title = {The {First} {Complete} {Mitochondrial} {Genome} of the {Genus} {Litostrophus}: {Insights} into the {Rearrangement} and {Evolution} of {Mitochondrial} {Genomes} in {Diplopoda}}, url = {https://www.mdpi.com/2073-4425/15/2/254}, @@ -25268,9 +26759,9 @@ @article{zhang_irf4_2025 keywords = {{\textgreater}UseGalaxy.eu, NK cells, Tumour immunology}, language = {en}, month = {July}, - note = {Publisher: Nature Publishing Group}, number = {7}, pages = {1062--1073}, + publisher = {Nature Publishing Group}, title = {{IRF4} expression by {NK} precursors predetermines exhaustion of {NK} cells during tumor metastasis}, url = {https://www.nature.com/articles/s41590-025-02176-w}, urldate = {2025-07-12}, @@ -25313,10 +26804,10 @@ @article{zhang_replication_2022 keywords = {{\textgreater}UseGalaxy.eu, Adult Stem Cells, Cancer epigenetics, Cancer stem cells, Histone-Lysine N-Methyltransferase, Mechanisms of disease}, language = {en}, month = {November}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {6907}, + publisher = {Nature Publishing Group}, title = {Replication collisions induced by de-repressed {S}-phase transcription are connected with malignant transformation of adult stem cells}, url = {https://www.nature.com/articles/s41467-022-34577-y}, urldate = {2022-12-03}, @@ -25334,10 +26825,10 @@ @article{zhao_nodulating_2024 keywords = {\textit{Aeschynomene indica} rhizobia, {\textgreater}UseGalaxy.eu, comparative genome, evolution, nitrogen fixation gene cluster, photosynthesis gene cluster, phylogenetic analysis}, language = {en}, month = {June}, - note = {Number: 6 -Publisher: Multidisciplinary Digital Publishing Institute}, + note = {Number: 6}, number = {6}, pages = {1295}, + publisher = {Multidisciplinary Digital Publishing Institute}, shorttitle = {Nodulating {Aeschynomene} indica without {Nod} {Factor} {Synthesis} {Genes}}, title = {Nodulating {Aeschynomene} indica without {Nod} {Factor} {Synthesis} {Genes}: {In} {Silico} {Analysis} of {Evolutionary} {Relationship}}, url = {https://www.mdpi.com/2073-4395/14/6/1295}, @@ -25371,7 +26862,7 @@ @article{zhong_distinct_2025 doi = {10.1186/s13059-025-03741-0}, issn = {1474-7596}, journal = {Genome biology}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Central dogma, Chromatin Interaction, Data-independent Acquisition, Gene Expression, Gene-body Methylation, Genome Assembly, Long Reads, Mim-trnaseq, Protein expression, Ribosome-associated Expression, Rnaseq}, month = {September}, number = {1}, pages = {319}, @@ -25417,10 +26908,9 @@ @article{zhu_bas_2024 keywords = {{\textgreater}UseGalaxy.eu, Arabidopsis, Arabidopsis Proteins, BAS-chromatin-remodeling complexes, BZR1, Brassinosteroid, SWI/SNF, chromatin accessibility, growth and development, phytohormone}, language = {English}, month = {April}, - note = {Publisher: Elsevier}, number = {7}, pages = {924--939.e6}, - pmid = {38359831}, + publisher = {Elsevier}, title = {The {BAS} chromatin remodeler determines brassinosteroid-induced transcriptional activation and plant growth in {Arabidopsis}}, url = {https://www.cell.com/developmental-cell/abstract/S1534-5807(24)00041-8}, urldate = {2024-05-17}, @@ -25437,9 +26927,9 @@ @article{zhuang_time-_2021 keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Macrophages, Monocytes}, language = {eng}, month = {June}, - note = {Publisher: S. Karger AG}, number = {2}, pages = {1--14}, + publisher = {S. Karger AG}, title = {Time- and {Stimulus}-{Dependent} {Characteristics} of {Innate} {Immune} {Cells} in {Organ}-{Cultured} {Human} {Corneal} {Tissue}}, url = {https://doi.org/10.1159/000516669}, volume = {14}, @@ -25456,8 +26946,8 @@ @article{zilbauer_roadmap_2023 keywords = {{\textgreater}UseGalaxy.eu, Biotechnology, Gastrointestinal system}, language = {en}, month = {May}, - note = {Publisher: Nature Publishing Group}, pages = {1--18}, + publisher = {Nature Publishing Group}, title = {A {Roadmap} for the {Human} {Gut} {Cell} {Atlas}}, url = {https://www.nature.com/articles/s41575-023-00784-1}, urldate = {2023-06-03}, @@ -25474,10 +26964,10 @@ @article{zinati_deciphering_2023 keywords = {{\textgreater}UseGalaxy.eu, Computational biology and bioinformatics, Cucumis sativus, Molecular biology}, language = {en}, month = {August}, - note = {Number: 1 -Publisher: Nature Publishing Group}, + note = {Number: 1}, number = {1}, pages = {12942}, + publisher = {Nature Publishing Group}, title = {Deciphering the molecular basis of abiotic stress response in cucumber ({Cucumis} sativus {L}.) using {RNA}-{Seq} meta-analysis, systems biology, and machine learning approaches}, url = {https://www.nature.com/articles/s41598-023-40189-3}, urldate = {2023-08-13}, @@ -25512,8 +27002,8 @@ @article{zubaer_comparative_2025 journal = {Canadian Journal of Microbiology}, keywords = {{\textgreater}UseGalaxy.eu}, month = {January}, - note = {Publisher: NRC Research Press}, pages = {1--13}, + publisher = {NRC Research Press}, title = {Comparative mitogenomics of {Leptographium} procerum, {Leptographium} terebrantis, and {Leptographium} wingfieldii, an invasive fungal species in {Canadian} forests}, url = {https://cdnsciencepub.com/doi/abs/10.1139/cjm-2024-0179}, urldate = {2025-09-03},