diff --git a/papers/main-pints.bib b/papers/main-pints.bib index 2eae4a542..6be778972 100644 --- a/papers/main-pints.bib +++ b/papers/main-pints.bib @@ -1,10 +1,10 @@ @article{Clerx2019Pints, title={Probabilistic Inference on Noisy Time Series ({PINTS})}, author={Clerx, Michael and Robinson, Martin and Lambert, Ben and Lei, Chon Lok and Ghosh, Sanmitra and Mirams, Gary R and Gavaghan, David J}, + year={2019}, journal={Journal of Open Research Software}, volume={7}, number={1}, pages={23}, - year={2019}, doi={10.5334/jors.252} } diff --git a/papers/used-pints.bib b/papers/used-pints.bib index 4e5b75920..c7ca8e815 100644 --- a/papers/used-pints.bib +++ b/papers/used-pints.bib @@ -1,49 +1,572 @@ +@article{Augustin2022ModelSelection, + title={Treatment response prediction: Is model selection unreliable?}, + author={Augustin, David and Wang, Ken and Walz, Antje-Christine and Lambert, Ben and Clerx, Michael and Robinson, Martin and Gavaghan, David}, + year={2022}, + journal={bioRxiv}, + publisher={Cold Spring Harbor Laboratory}, + doi={10.1101/2022.03.19.483454} +} +@article{Augustin2023FilterInference, + title={Filter inference: A scalable nonlinear mixed effects inference approach for snapshot time series data}, + author={Augustin, David and Lambert, Ben and Wang, Ken and Walz, Antje-Christine and Robinson, Martin and Gavaghan, David}, + year={2023}, + journal={PLOS Computational Biology}, + publisher={Public Library of Science San Francisco, CA USA}, + volume={19}, + number={5}, + pages={e1011135}, + doi={10.1371/journal.pcbi.1011135} +} +@article{Augustin2023PrecisionDosing, + title={Simulating clinical trials for model-informed precision dosing: using warfarin treatment as a use case}, + author={Augustin, David and Lambert, Ben and Robinson, Martin and Wang, Ken and Gavaghan, David}, + year={2023}, + journal={Frontiers in pharmacology}, + publisher={Frontiers Media SA}, + volume={14}, + pages={1270443}, + doi={10.3389/fphar.2023.1270443} +} +@article{Augustin2024Chi, + title={Chi: A Python package for treatment response modelling}, + author={Augustin, David}, + year={2024}, + journal={Journal of Open Source Software}, + volume={9}, + number={94}, + pages={5925}, + doi={10.21105/joss.05925} +} +@article{Barral2022AnalyticV, + title={A parameter representing missing charge should be considered when calibrating action potential models}, + author={Barral, Yann-Stanislas HM and Shuttleworth, Joseph G and Clerx, Michael and Whittaker, Dominic G and Wang, Ken and Polonchuk, Liudmila and Gavaghan, David J and Mirams, Gary R}, + year={2022}, + journal={Frontiers in Physiology}, + publisher={Frontiers Media SA}, + volume={13}, + pages={879035}, + doi={10.3389/fphys.2022.879035} +} +@inproceedings{Barral2022Normalisation, + title={Normalisation of Action Potential Data Recorded with Sharp Electrodes Maximises Its Utility for Model Development}, + author={Barral, Yann-Stanislas H M and Polonchuk, Liudmila and Mirams, Gary R and Clerx, Michael and Page, Guy and Sweat, Katrina and Abi-Gerges, Najah and Wang, Ken and Gavaghan, David J}, + year={2022}, + booktitle={2022 Computing in Cardiology (CinC)}, + volume={498}, + pages={1--4}, + doi={10.22489/CinC.2022.356} +} +@article{Beekman2025Lymphopenia, + title={Radiation-Induced Lymphopenia: In Silico Replications of Preclinical Studies Suggest Importance of Dose to Lymphoid Organs}, + author={Beekman, Chris and Carrasco-Rojas, Natalia and Withrow, Julia and Dawson, Robert and Bolch, Wesley E. and Paganetti, Harald}, + year={2025}, + journal={International Journal of Radiation Oncology*Biology*Physics}, + volume={123}, + number={2}, + pages={550--562}, + doi={10.1016/j.ijrobp.2025.03.080} +} +@article{Booth2025Covid, + title={Preventing SARS-CoV-2 superspreading events with antiviral intranasal sprays}, + author={Booth, George and Hadjichrysanthou, Christoforos and Rice, Keira L and Frallicciardi, Jacopo and Magyarics, Zolt{\'a}n and de Wolf, Frank and Goudsmit, Jaap and Beukenhorst, Anna L and Anderson, Roy}, + year={2025}, + journal={Journal of Theoretical Biology}, + publisher={Elsevier}, + pages={112237}, + doi={10.1016/j.jtbi.2025.112237} +} +@article{Burton2021GeneRegulation, + title={Inferring kinetic parameters of oscillatory gene regulation from single cell time-series data}, + author={Burton, Joshua and Manning, Cerys S and Rattray, Magnus and Papalopulu, Nancy and Kursawe, Jochen}, + year={2021}, + journal={Journal of The Royal Society Interface}, + publisher={The Royal Society}, + volume={18}, + number={182}, + pages={20210393}, + doi={10.1098/rsif.2021.0393} +} +@article{Celora2022CyclicHypoxia, + title={A DNA-structured mathematical model of cell-cycle progression in cyclic hypoxia}, + author={Celora, Giulia L and Bader, Samuel B and Hammond, Ester M and Maini, Philip K and Pitt-Francis, Joe M and Byrne, Helen M}, + year={2022}, + journal={Journal of Theoretical Biology}, + publisher={Elsevier}, + volume={545}, + pages={111104}, + doi={10.1016/j.jtbi.2022.111104} +} +@inproceedings{Clerx2022Sensitivities, + title={Derivative-based Inference for Cell and Channel Electrophysiology Models}, + author={Clerx, Michael and Augustin, David and Dale-Evans, Alister R and Mirams, Gary R}, + year={2022}, + booktitle={2022 Computing in Cardiology (CinC)}, + volume={498}, + pages={1--4}, + doi={10.22489/CinC.2022.287}, + keywords={Sensitivity;Computational modeling;Current measurement;Differential equations;Ions;Mathematical models;Data models} +} +@article{Clerx2019FourWays, + title={Four Ways to Fit an Ion Channel Model}, + author={Clerx, Michael and Beattie, Kylie A and Gavaghan, David J and Mirams, Gary R}, + year={2019}, + journal={Biophyical Journal}, + doi={10.1016/j.bpj.2019.08.001} +} +@article{Crawshaw2025OcularPKPD, + title={Modeling the Ocular Pharmacokinetics and Pharmacodynamics of Ranibizumab for Improved Understanding and Data Collection Strategies in Ocular Diseases}, + author={Crawshaw, Jessica R and Gaffney, Eamonn A and Gertz, Michael and Maini, Philip K and Caruso, Antonello}, + year={2025}, + journal={Investigative Ophthalmology \& Visual Science}, + publisher={The Association for Research in Vision and Ophthalmology}, + volume={66}, + number={6}, + pages={20--20}, + doi={10.1167/iovs.66.6.20} +} +@article{Creswell2020Misspecification, + title={Using flexible noise models to avoid noise model misspecification in inference of differential equation time series models}, + author={Creswell, Richard and Lambert, Ben and Lei, Chon Lok and Robinson, Martin and Gavaghan, David}, + year={2020}, + journal={arXiv preprint arXiv:2011.04854}, + doi={10.48550/arXiv.2011.04854} +} +@article{Creswell2024Solvers, + title={Understanding the impact of numerical solvers on inference for differential equation models}, + author={Creswell, Richard and Shepherd, Katherine M and Lambert, Ben and Mirams, Gary R and Lei, Chon Lok and Tavener, Simon and Robinson, Martin and Gavaghan, David J}, + year={2024}, + journal={Journal of the Royal Society Interface}, + publisher={The Royal Society}, + volume={21}, + number={212}, + pages={20230369}, + doi={10.1098/rsif.2023.0369} +} +@article{DaleEvans2021VoltammetricPerspective, + title={A voltammetric perspective of multi-electron and proton transfer in protein redox chemistry: insights from computational analysis of Escherichia coli HypD Fourier transformed alternating current voltammetry}, + author={Dale-Evans, Alister R and Robinson, Martin J and Lloyd-Laney, Henry O and Gavaghan, David J and Bond, Alan M and Parkin, Alison}, + year={2021}, + journal={Frontiers in Chemistry}, + publisher={Frontiers Media SA}, + volume={9}, + pages={672831}, + doi={10.3389/fchem.2021.672831} +} +@article{Farm2023HergBinding, + title={Importance of modelling hERG binding in predicting drug-induced action potential prolongations for drug safety assessment}, + author={Farm, Hui Jia and Clerx, Michael and Cooper, Fergus and Polonchuk, Liudmila and Wang, Ken and Gavaghan, David J and Lei, Chon Lok}, + year={2023}, + journal={Frontiers in pharmacology}, + publisher={Frontiers Media SA}, + volume={14}, + pages={1110555}, + doi={10.3389/fphar.2023.1110555} +} +@article{Gallagher2024Software, + title={Ten simple rules for training scientists to make better software}, + author={Gallagher, Kit and Creswell, Richard and Lambert, Ben and Robinson, Martin and Lok Lei, Chon and Mirams, Gary R and Gavaghan, David J}, + year={2024}, + journal={PLOS Computational Biology}, + publisher={Public Library of Science San Francisco, CA USA}, + volume={20}, + number={9}, + pages={e1012410}, + doi={10.1371/journal.pcbi.1012410} +} +@article{Ghosh2025LearningRt, + title={Assessing the performance of compartmental and renewal models for learning $R_t$ using spatially heterogeneous epidemic simulations on real geographies}, + author={Ghosh, Matthew and Qi, Yunli and Evans, Abbie and Reed, Tom and Herriott, Lara and Bouros, Ioana and Lambert, Ben and Gavaghan, David J and Shepherd, Katherine M and Creswell, Richard and others}, + year={2025}, + journal={arXiv preprint arXiv:2503.04648}, + doi={10.48550/arXiv.2503.04648} +} +@article{Gundry2021VoltammetryReview, + title={Recent advances and future perspectives for automated parameterisation, Bayesian inference and machine learning in voltammetry}, + author={Gundry, Luke and Guo, Si-Xuan and Kennedy, Gareth and Keith, Jonathan and Robinson, Martin and Gavaghan, David and Bond, Alan M and Zhang, Jie}, + year={2021}, + journal={Chemical Communications}, + publisher={Royal Society of Chemistry}, + volume={57}, + number={15}, + pages={1855--1870}, + doi={10.1039/d0cc07549c} +} +@article{Gundry2021InferenceStrategies, + title={A comparison of Bayesian inference strategies for parameterisation of large amplitude AC voltammetry derived from total current and Fourier transformed versions}, + author={Gundry, Luke and Kennedy, Gareth and Keith, Jonathan and Robinson, Martin and Gavaghan, David and Bond, Alan M and Zhang, Jie}, + year={2021}, + journal={ChemElectroChem}, + publisher={Wiley Online Library}, + volume={8}, + number={12}, + pages={2238--2258}, + doi={10.1002/celc.202100391} +} +@article{Hewson2024ImpedimetricBiosensing, + title={Harnessing glycofluoroforms for impedimetric biosensing}, + author={Hewson, Alice R and Lloyd-Laney, Henry O and Keenan, Tessa and Richards, Sarah-Jane and Gibson, Matthew I and Linclau, Bruno and Signoret, Nathalie and Fascione, Martin A and Parkin, Alison}, + year={2024}, + journal={Chemical Science}, + publisher={Royal Society of Chemistry}, + volume={15}, + number={39}, + pages={16086--16095}, + doi={10.1039/d4sc04409f} +} +@article{Huang2024SchroedingerFoellmer, + title={Schr{\"o}dinger-f{\"o}llmer sampler}, + author={Huang, Jian and Jiao, Yuling and Kang, Lican and Liao, Xu and Liu, Jin and Liu, Yanyan}, + year={2024}, + journal={IEEE Transactions on Information Theory}, + publisher={Ieee}, + doi={10.1109/tit.2024.3522494} +} +@article{Huang2021SchroedingerFoellmer, + title={Schr{\"o}dinger-F{\"o}llmer sampler: sampling without ergodicity}, + author={Huang, Jian and Jiao, Yuling and Kang, Lican and Liao, Xu and Liu, Jin and Liu, Yanyan}, + year={2021}, + journal={arXiv preprint arXiv:2106.10880}, + volume={1}, + doi={10.48550/arXiv.2106.10880} +} +@article{Huang2025MiningAssociationRules, + title={Probabilistic and reinforced mining of association rules}, + author={Huang, Yongchao}, + year={2025}, + doi={10.48550/arXiv.2506.18155} +} +@article{Kemp2021R56Q, + title={Electrophysiological characterization of the hERG R56Q LQTS variant and targeted rescue by the activator RPR260243}, + author={Kemp, Jacob M and Whittaker, Dominic G and Venkateshappa, Ravichandra and Pang, ZhaoKai and Johal, Raj and Sergeev, Valentine and Tibbits, Glen F and Mirams, Gary R and Claydon, Thomas W}, + year={2021}, + journal={Journal of General Physiology}, + publisher={Rockefeller University Press}, + volume={153}, + number={10}, + pages={e202112923}, + doi={10.1085/jgp.202112923} +} +@article{Lambert2023Autocorrelation, + title={Autocorrelated measurement processes and inference for ordinary differential equation models of biological systems}, + author={Lambert, Ben and Lei, Chon Lok and Robinson, Martin and Clerx, Michael and Creswell, Richard and Ghosh, Sanmitra and Tavener, Simon and Gavaghan, David J}, + year={2023}, + journal={Journal of the Royal Society Interface}, + publisher={The Royal Society}, + volume={20}, + number={199}, + pages={20220725}, + doi={10.1098/rsif.2022.0725} +} +@article{Lei2019RapidHergI, + title={Rapid characterisation of {hERG} channel kinetics {I}: using an automated high-throughput system}, + author={Lei, {Chon Lok} and Clerx, Michael and Gavaghan, David J. and Polonchuk, Liudmila and Mirams, Gary R. and Wang, Ken}, + year={2019}, + journal={Biophysical Journal}, + publisher={Elsevier}, + doi={10.1016/j.bpj.2019.07.029} +} +@article{Lei2019RapidHergII, + title={Rapid characterisation of {hERG} channel kinetics {II}: temperature dependence}, + author={Lei, {Chon Lok} and Clerx, Michael and Beattie, Kylie A. and Melgari, Dario and Hancox, Jules C. and Gavaghan, David J. and Polonchuk, Liudmila and Wang, Ken and Mirams, Gary R.}, + year={2019}, + journal={Biophysical Journal}, + publisher={Elsevier}, + doi={10.1016/j.bpj.2019.07.030} +} +@article{Lei2020ArtefactModel, + title={Accounting for variability in ion current recordings using a mathematical model of artefacts in voltage-clamp experiments}, + author={Lei, Chon Lok and Clerx, Michael and Whittaker, Dominic G and Gavaghan, David J and de Boer, Teun P and Mirams, Gary R}, + year={2020}, + journal={Philosophical Transactions of the Royal Society A}, + publisher={The Royal Society Publishing}, + volume={378}, + number={2173}, + pages={20190348}, + doi={10.1098/rsta.2019.0348} +} +@article{Lei2020Discrepancy, + title={Considering discrepancy when calibrating a mechanistic electrophysiology model}, + author={Lei, Chon Lok and Ghosh, Sanmitra and Whittaker, Dominic G. and Aboelkassem, Yasser and Beattie, Kylie A. and Cantwell, Chris D. and Delhaas, Tammo and Houston, Charles and Novaes, Gustavo Montes and Panfilov, Alexander V. and Pathmanathan, Pras and Riabiz, Marina and dos Santos, Rodrigo Weber and Walmsley, John and Worden, Keith and Mirams, Gary R. and Wilkinson, Richard D.}, + year={2020}, + month={05}, + journal={Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences}, + volume={378}, + number={2173}, + pages={20190349}, + doi={10.1098/rsta.2019.0349} +} +@article{Lei2021NNChanelModel, + title={Neural network differential equations for ion channel modelling}, + author={Lei, Chon Lok and Mirams, Gary R}, + year={2021}, + journal={Frontiers in Physiology}, + publisher={Frontiers Media SA}, + volume={12}, + pages={708944}, + doi={10.3389/fphys.2021.708944} +} +@article{Lei2021PrintedCochleae, + title={3D printed biomimetic cochleae and machine learning co-modelling provides clinical informatics for cochlear implant patients}, + author={Lei, Iek Man and Jiang, Chen and Lei, Chon Lok and de Rijk, Simone Rosalie and Tam, Yu Chuen and Swords, Chloe and Sutcliffe, Michael PF and Malliaras, George G and Bance, Manohar and Huang, Yan Yan Shery}, + year={2021}, + journal={Nature Communications}, + publisher={Nature Publishing Group UK London}, + volume={12}, + number={1}, + pages={6260}, + doi={10.1038/s41467-021-26491-6} +} +@article{Lei2023OptimalDesign, + title={Model-driven optimal experimental design for calibrating cardiac electrophysiology models}, + author={Lei, Chon Lok and Clerx, Michael and Gavaghan, David J and Mirams, Gary R}, + year={2023}, + journal={Computer Methods and Programs in Biomedicine}, + publisher={Elsevier}, + volume={240}, + pages={107690}, + doi={10.1016/j.cmpb.2023.107690} +} +@article{Lei2024HergBinding, + title={The impact of uncertainty in hERG binding mechanism on in silico predictions of drug-induced proarrhythmic risk}, + author={Lei, Chon Lok and Whittaker, Dominic G and Mirams, Gary R}, + year={2024}, + journal={British Journal of Pharmacology}, + publisher={Wiley Online Library}, + volume={181}, + number={7}, + pages={987--1004}, + doi={10.1111/bph.16250} +} +@article{Lei2025INaArtifacts, + title={Resolving Artifacts in Voltage-Clamp Experiments with Computational Modeling: An Application to Fast Sodium Current Recordings}, + author={Lei, Chon Lok and Clark, Alexander P and Clerx, Michael and Wei, Siyu and Bloothooft, Meye and de Boer, Teun P and Christini, David J and Krogh-Madsen, Trine and Mirams, Gary R}, + year={2025}, + journal={Advanced Science}, + publisher={Wiley Online Library}, + volume={12}, + number={30}, + pages={e00691}, + doi={10.1002/advs.202500691} +} +@article{Lei2025HergProtocols, + title={A range of voltage-clamp protocol designs for rapid capture of hERG kinetics}, + author={Lei, Chon Lok and Whittaker, Dominic J and Windley, Monique J and Perry, Matthew D and Hill, Adam P and Mirams, Gary R}, + year={2025}, + journal={Wellcome Open Research}, + volume={9}, + pages={673}, + doi={10.12688/wellcomeopenres.23319.2} +} +@article{Lin2022CaChannels, + title={Nuanced interactions between AKAP79 and STIM1 with Orai1 Ca2+ channels at endoplasmic reticulum-plasma membrane junctions sustain NFAT activation}, + author={Lin, Yu-Ping and Scappini, Erica and Landaverde, Carlos and Parekh-Glitsch, Frederick and Tucker, Charles J and Mirams, Gary R and Parekh, Anant B}, + year={2022}, + journal={Molecular and Cellular Biology}, + publisher={Taylor \& Francis}, + volume={42}, + number={11}, + pages={e00175--22}, + doi={10.1128/mcb.00175-22} +} +@article{LloydLaney2020SinusoidalVoltammetry, + title={Using Purely Sinusoidal Voltammetry for Rapid Parameterization of Surface-Confined Electrochemistry}, + author={Lloyd-Laney, Henry and Robinson, Martin and Hewson, Alice R. and Firth, Jack and Zhang, Jie and Bond, Alan and Parkin, Alison and Gavaghan, David and Yates, Nick and Elton, Darell}, + year={2022}, + journal={chemRxiv}, + doi={10.26434/chemrxiv.12919367.v1} +} +@article{MartinaPerez2024Heterogeneity, + title={Spatial heterogeneity in collective electrotaxis: continuum modelling and applications to optimal control}, + author={Martina-Perez, Simon F. and Breinyn, Isaac B. and Cohen, Daniel J. and Baker, Ruth E.}, + year={2024}, + journal={bioRxiv}, + publisher={Cold Spring Harbor Laboratory}, + doi={10.1101/2024.02.28.580259} +} +@article{MartinaPerez2024OptimalControl, + title={Optimal control of collective electrotaxis in epithelial monolayers}, + author={Martina-Perez, Simon F and Breinyn, Isaac B and Cohen, Daniel J and Baker, Ruth E}, + year={2024}, + journal={Bulletin of Mathematical Biology}, + publisher={Springer}, + volume={86}, + number={8}, + pages={95}, + doi={10.1007/s11538-024-01319-8} +} +@article{Nixson2025PDEvsODE, + title={Characterising the Behaviour of a Structured PDE Model of the Cell Cycle in Contrast to a Corresponding ODE System: RE Nixson et al.}, + author={Nixson, Ruby E and Byrne, Helen M and Pitt-Francis, Joe M and Maini, Philip K}, + year={2025}, + journal={Bulletin of Mathematical Biology}, + publisher={Springer}, + volume={87}, + number={7}, + pages={93}, + doi={10.1007/s11538-025-01472-8} +} +@article{Noessler2025GrasslandTraitSim, + title={A trait-based model to describe plant community dynamics in managed grasslands ({GrasslandTraitSim.jl v1.0.0})}, + author={N{\"o}{\ss}ler, Felix and Moulin, Thibault and Buzhdygan, Oksana and Tietjen, Britta and May, Felix}, + year={2025}, + journal={Geoscientific Model Development}, + publisher={Copernicus Publications G{\"o}ttingen, Germany}, + volume={18}, + number={19}, + pages={7077--7128}, + doi={10.5194/gmd-18-7077-2025} +} +@article{Owen2025IonBench, + title={{IonBench}: A benchmark of optimisation strategies for mathematical models of ion channel currents}, + author={Owen, Matt J and Mirams, Gary R}, + year={2025}, + journal={PLOS Computational Biology}, + publisher={Public Library of Science San Francisco, CA USA}, + volume={21}, + number={8}, + pages={e1013319}, + doi={10.1371/journal.pcbi.1013319} +} +@article{PattenElliot2025ExpDesign, + title={Optimizing experimental designs for model selection of ion channel drug-binding mechanisms}, + author={Patten-Elliott, Frankie and Lei, Chon Lok and Preston, Simon P and Wilkinson, Richard D and Mirams, Gary R}, + year={2025}, + journal={Philosophical Transactions A}, + publisher={The Royal Society}, + volume={383}, + number={2292}, + pages={20240227}, + doi={10.1098/rsta.2024.0227} +} +@article{PereiraIglesias2025EpigeneticControl, + title={Epigenetic control of microglial developmental milestones from proliferative progenitors to efficient phagocytes}, + author={Pereira-Iglesias, Marta and Martinson, Duncan and Falco, Carles and Maldonado-Teixido, Joel and Gonz{\'a}lez-Dom{\'\i}nguez, Marco and Senovilla-Ganzo, Rodrigo and Beccari, Sol and Valero, Jorge and Mora-Romero, Bella and Ballasch, Ivan and Viguier, Sarah and Hane, Philipp and Boettiger, Molly and Reisz, Julie A. and El{\'\i}as-Tersa, Alba and Manso, Yasmina and Parkkinen, Laura and Aransay, Ana Mar{\'\i}a and Soria, Federico N. and D{\textquoteright}Alessandro, Angelo and Soriano, Eduardo and Thion, Morgane S. and Garel, Sonia and Greter, Melanie and Giralt, Albert and Pascual, Alberto and Garc{\'\i}a-Moreno, Fernando and Menassa, David A. and Carrillo, Jose A. and Sierra, Amanda}, + year={2025}, + journal={bioRxiv}, + publisher={Cold Spring Harbor Laboratory}, + doi={10.1101/2025.11.03.685577} +} +@article{Planden2025PyBOP, + title={PyBOP: A Python package for battery model optimisation and parameterisation}, + author={Planden, Brady and Courtier, Nicola E. and Robinson, Martin and Khetarpal, Agriya and Planella, Ferran Brosa and Howey, David A.}, + year={2025}, + journal={Journal of Open Source Software}, + publisher={The Open Journal}, + volume={10}, + number={116}, + pages={7874}, + doi={10.21105/joss.07874} +} +@article{Ranjan2025AerosolComposition, + title={Optimizing CCN predictions through inferred modal aerosol composition--a boreal forest case study}, + author={Ranjan, Rahul and Dewey, Maura and Heikkinen, Liine and Ahonen, Lauri R and Luoma, Krista and Bowen, Paul and Pet{\"a}j{\"a}, Tuukka and Ekman, Annica ML and Partridge, Daniel G and Riipinen, Ilona}, + year={2025}, + journal={Atmospheric Chemistry and Physics}, + publisher={Copernicus Publications G{\"o}ttingen, Germany}, + volume={25}, + number={23}, + pages={17275--17300}, + doi={10.5194/acp-25-17275-2025} +} @article{Robinson2018Separating, title={Separating the effects of experimental noise from inherent system variability in voltammetry: The {[Fe(CN)6]3--/4--} Process}, author={Robinson, Martin and Simonov, Alexandr N and Zhang, Jie and Bond, Alan M and Gavaghan, David}, + year={2018}, journal={Analytical chemistry}, + publisher={ACS Publications}, volume={91}, number={3}, pages={1944--1953}, - year={2018}, - publisher={ACS Publications}, doi={10.1021/acs.analchem.8b04238} } - @article{Robinson2018Parametrization, title={Integration of Heuristic and Automated Parametrization of Three Unresolved Two-Electron Surface-Confined Polyoxometalate Reduction Processes by {AC} Voltammetry}, author={Robinson, Martin and Ounnunkad, Kontad and Zhang, Jie and Gavaghan, David and Bond, Alan}, + year={2018}, journal={ChemElectroChem}, + publisher={Wiley Online Library}, volume={5}, number={23}, pages={3771--3785}, - year={2018}, - publisher={Wiley Online Library}, doi={10.1002/celc.201800950} } - -@article{Lei2019RapidHergI, - author = {Lei, {Chon Lok} and Clerx, Michael and Gavaghan, David J. and Polonchuk, Liudmila and Mirams, Gary R. and Wang, Ken}, - title = {Rapid characterisation of {hERG} channel kinetics {I}: using an automated high-throughput system}, - year = {2019}, - doi = {10.1016/j.bpj.2019.07.029}, - publisher = {Elsevier}, - journal = {Biophysical Journal} -} - -@article{Lei2019RapidHergII, - author = {Lei, {Chon Lok} and Clerx, Michael and Beattie, Kylie A. and Melgari, Dario and Hancox, Jules C. and Gavaghan, David J. and Polonchuk, Liudmila and Wang, Ken and Mirams, Gary R.}, - title = {Rapid characterisation of {hERG} channel kinetics {II}: temperature dependence}, - year = {2019}, - doi = {10.1016/j.bpj.2019.07.030}, - publisher = {Elsevier}, - journal = {Biophysical Journal} -} - -@article{Clerx2019FourWays, - title={Four Ways to Fit an Ion Channel Model}, - author={Clerx, Michael and Beattie, Kylie A and Gavaghan, David J and Mirams, Gary R}, - journal={Biophyical Journal}, - year={2019}, - doi={10.1016/j.bpj.2019.08.001} +@article{Shuttleworth2024ModelDiscrepancy, + title={Empirical quantification of predictive uncertainty due to model discrepancy by training with an ensemble of experimental designs: an application to ion channel kinetics}, + author={Shuttleworth, Joseph G and Lei, Chon Lok and Whittaker, Dominic G and Windley, Monique J and Hill, Adam P and Preston, Simon P and Mirams, Gary R}, + year={2024}, + journal={Bulletin of Mathematical Biology}, + publisher={Springer}, + volume={86}, + number={1}, + pages={2}, + doi={10.1007/s11538-023-01224-6} +} +@article{Shuttleworth2025ExperimentalDesign, + title={Evaluating the predictive accuracy of ion-channel models using data from multiple experimental designs}, + author={Shuttleworth, Joseph G and Lei, Chon Lok and Windley, Monique J and Hill, Adam P and Preston, Simon P and Mirams, Gary R}, + year={2025}, + journal={Philosophical Transactions A}, + publisher={The Royal Society}, + volume={383}, + number={2292}, + pages={20240211}, + doi={10.1098/rsta.2024.0211} +} +@article{Simitev2025CellSpecific, + title={A large population of cell-specific action potential models replicating fluorescence recordings of voltage in rabbit ventricular myocytes}, + author={Simitev, Radostin D and Gilchrist, Rebecca J and Yang, Zhechao and Myles, Rachel C and Burton, Francis L and Smith, Godfrey L}, + year={2025}, + journal={Royal Society Open Science}, + publisher={The Royal Society}, + volume={12}, + number={3}, + pages={241539}, + doi={10.1098/rsos.241539} +} +@article{Song2023HergDeepLearning, + title={Improving the hERG model fitting using a deep learning-based method}, + author={Song, Jaekyung and Kim, Yu Jin and Leem, Chae Hun}, + year={2023}, + journal={Frontiers in Physiology}, + publisher={Frontiers Media SA}, + volume={14}, + pages={1111967}, + doi={10.3389/fphys.2023.1111967} +} +@article{Wei2024BenNevis, + title={Where's {B}en {N}evis? A {2D} optimisation benchmark with 957,174 local optima based on {G}reat {B}ritain terrain data}, + author={Wei, Yuhang and Clerx, Michael and Mirams, Gary R.}, + year={2024}, + doi={10.48550/arXiv.2410.02422} +} +@article{Whittaker2020CalibrationReview, + title={Calibration of ionic and cellular cardiac electrophysiology models}, + author={Whittaker, Dominic G and Clerx, Michael and Lei, Chon Lok and Christini, David J and Mirams, Gary R}, + year={2020}, + journal={Wiley Interdisciplinary Reviews: Systems Biology and Medicine}, + publisher={Wiley Online Library}, + volume={12}, + number={4}, + pages={e1482}, + doi={10.1002/wsbm.1482} +} +@article{Whittaker2022Manifolds, + title={Ion channel model reduction using manifold boundaries}, + author={Whittaker, Dominic G and Wang, Jiahui and Shuttleworth, Joseph G and Venkateshappa, Ravichandra and Kemp, Jacob M and Claydon, Thomas W and Mirams, Gary R}, + year={2022}, + journal={Journal of the Royal Society Interface}, + publisher={The Royal Society}, + volume={19}, + number={193}, + pages={20220193}, + doi={10.1098/rsif.2022.0193} +} +@article{Whittaker2023Covid, + title={Uncertainty and error in {SARS-CoV-2} epidemiological parameters inferred from population-level epidemic models}, + author={Whittaker, Dominic G. and Herrera-Reyes, Alejandra D. and Hendrix, Maurice and Owen, Markus R. and Band, Leah R. and Mirams, Gary R. and Bolton, Kirsty J. and Preston, Simon P.}, + year={2023}, + journal={Journal of Theoretical Biology}, + volume={558}, + pages={111337}, + doi={10.1016/j.jtbi.2022.111337} }