Katarzyna Sikora
Staff Bioinformatician
Freiburg im Breisgau, Baden-Württemberg, Germany
Summary
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Senior🎓
Top SchoolKatarzyna Sikora is a Staff Bioinformatician with nine years of experience building and maintaining NGS workflows and delivering data-driven solutions at the Max Planck Institute for Immunobiology and Epigenetics. She specializes in R and Python development, uses Snakemake/Nextflow and workflow tools like Ruffus to productionize analyses, and builds Shiny apps to make results accessible to internal users. Her background spans RNA-seq, WGBS, variant calling and CNV analysis across projects from ancient vertebrate microassembly to cancer exomes, reflecting a strong bridge between computational rigor and wet-lab collaboration. Based in Freiburg, she champions inclusive workplace culture and women in STEM, and brings a knack for replacing ad hoc bash with maintainable Python to improve reproducibility. An experienced teacher and pipeline maintainer, she combines practical engineering with domain-focused curiosity to turn complex biological questions into reproducible analytic solutions.
9 years of coding experience
Diplom, Biology, Diplom, Biology at Universität GiessenVordiplom, Biology, Vordiplom, Biology at Uniwersytet Łódzki / University of Lodz
English, German, French, Italian, Polish
Github Skills (33)
snakemake10
chip-seq10
rna-seq10
cran10
single-cell-genomics9
seurat9
python9
bioinformatics9
genomics9
user-input8
r-language8
sequencing8
pipeline7
gene-expression6
shiny5
Programming languages (5)
Github contributions (5)
maxplanck-ie/scRNAseq_shiny_app
Nov 2018 - Aug 2020
Contributions:1 release, 2 PRs, 74 pushes in 1 year 9 months
maxplanck-ie/snakequest
May 2018 - Jun 2022
A shiny app that collects user input required for running snakepipes.
Contributions:2 releases, 38 commits, 69 PRs in 4 years
shiny-appshinyuser-input
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