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akoshkareva/README.md

🌱 Alena Koshkareva 🌱

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I'm a junior bioinformatician, with hands-on experience in working with biological data, scripting, and molecular biology.

🔬 Background

I hold a BSc in Biology (Biophysics) and have completed core coursework in the professional program Bioinformatics for Biologists at the Bioinformatics Institute (2024–2025). (Note: I have completed key modules but have not received a full program certificate)

📌 Looking for opportunities as a junior bioinformatician or intern to grow through real-world challenges and teamwork.

🛠️ Skills

Bioinformatics tools & workflows:
Worked with biological data formats (FASTA, FASTQ, GFF/GTF), performed sequence alignment using BLAST, multiple sequence alignment with Clustal Omega and MAFFT, and gene annotation via Ensembl and NCBI databases.
Performed variant interpretation using ClinVar and post-processing with BEDTools.
Used trimming tools like ClipKit and TrimAl to refine alignments and constructed phylogenetic trees using FastTree and IQ-TREE.
Visualized tree topologies in R using the treedataverse suite (e.g., ggtree).
Also experienced in protein structure prediction with AlphaFold and scripting data pipelines with Biopython, visualizing results using pandas, matplotlib, and seaborn.

Programming & scripting:
Python (pandas, matplotlib, Biopython), Jupyter Notebooks, Bash scripting, R (tidyverse), RStudio, Git, LaTeX.

Pinned Loading

  1. hsp70-evolution-structure hsp70-evolution-structure Public

    open-data project; status: in progress

  2. bio-nautilus bio-nautilus Public

    🐚 This repo for homework assignments, scripts, and utilities created as part of the Bioinformatics Institute course (2024-2025).

  3. HW2_Git_and_python HW2_Git_and_python Public

    Forked from Python-BI-2024-25/HW2_Git_and_python

    2nd homework of the BI Python 2024/25 course

    3

  4. akoshkareva akoshkareva Public

    Repo for GitHub profile page