Maciej Bąk, PhD

Scientific Software Engineering Expert

Maciej Bąk - Profile picture

I'm currently a freelance computational researcher. Previous affiliations include City, University of London (Department of Mathematics) as well as Swiss Institute of Bioinformatics & Universitat Basel (Biozentrum).

I am interested in computational research: workflows, optimisation techniques, reproducibility, testing and automation. High-quality scientific software engineering is my speciality. Also: mostly passionate about math/stat modelling as well as machine learning methods. In my (little) spare time I train combat systems, design and develop my very own horror game or read about mathematics and philosophy.

If you'd like to collaborate with me please check out the CORE.

scientific articles


  1. Szewczyk B., Japtok J., Held A., Dash P. B., Bak M., et al. (2025). Activation of polo-like kinase 1 expression in spinal motor neurons as shared molecular mechanisms across different types of familial ALS. Cell Reports, DOI

  2. Stein A., Kizhuttil R., Bak M., Noble R. (2024). Selective sweep probabilities in spatially expanding populations. Nature Communications (under revision), DOI

  3. Katsantoni M., Gypas F., Herrmann J C., Burri D., Bak M., et al. (2024). ZARP: A user-friendly and versatile RNA-seq analysis workflow. F1000Research, DOI

  4. Bak M., et al. (2024). Frequent co-regulation of splicing and polyadenylation by RNA-binding proteins inferred with MAPP. Nature Communications, DOI

  5. Colyer B., Bak M., Basanta D., Noble R. (2024). A seven-step guide to spatial, agent-based modelling of tumour evolution. Evolutionary Applications, DOI

  6. Bak M. (2023). Hypercomplex: abstract & fast header-only C++ template library for lattice-based cryptosystems in high-dimensional algebras. Journal of Open Source Software, DOI

  7. Bak M., Colyer B., Manojlović V., Noble R. (2023). Warlock: an automated computational workflow for simulating spatially structured tumour evolution. arXiv, DOI

  8. Bak M.*, Rozlach A. (2023). Modeling microbial communities with evolutionary game theory. Journal of Brief Ideas, URL

  9. Kwiecien K., Majewski P., Bak M., et al. (2023). Alternative splicing is not a key source of chemerin isoforms diversity. Molecular Biology Reports, DOI

  10. Ghosh S., Ataman M., Bak M., et al. (2022). CFIm-mediated alternative polyadenylation remodels cellular signaling and miRNA biogenesis. Nucleic Acid Research, DOI

  11. Bak M., Rozlach A. (2020). Moran Pycess: a Python package to simulate Moran processes driven by game theory. Journal of Open Source Software, DOI

  12. Kwiecien K., Brzoza P., Bak M., et al. (2020). The methylation status of the chemerin promoter region located from - 252 to + 258 bp regulates constitutive but not acute-phase cytokine-inducible chemerin expression levels. Scientific Reports, DOI

  13. Hasler D., Rajyalakshmi M., Bak M., et al. (2020). The Alazami Syndrome-associated protein LARP7 guides U6 small nuclear RNA modification and contributes to splicing robustness. Molecular Cell, DOI

  14. Gałan W., Bąk M., Jakubowska M. (2019). Host Taxon Predictor - A Tool for Predicting Taxon of the Host of a Newly Discovered Virus. Scientific Reports, DOI

  15. Bak M., Jazwa A., Kasper L. et al. (2015). Involvement of microRNAs in the inflammatory pathways of pulmonary sarcoidosis. Journal of Physiology and Pharmacology, URL

  16. Jazwa A., Kasper L., Bak M., et al. (2015). Differential inflammatory microRNA and cytokine expression in pulmonary sarcoidosis. Archivum Immunologiae et Therapiae Experimentalis, DOI

software repositories

Science

warlock
Snakemake workflow dedicated to deme-based oncology modeling.
MAPP
Computational method to identify binding motifs for RBPs that shape pre-mRNA processing.
bindz
Tool for predicting binding sites of RNA-binding proteins in transcripts.
ZARP
Snakemake pipeline for automated RNA-seq data processing.
Moran Pycess
Python package for simulations according to evolutionary game theory.

Others

Hypercomplex
Abstract & fast C++ template library for lattice-based cryptosystems in high-dimensional algebras.
efcomp
Collection of efficient statistical computing methods (interfacing from R/Python to Cpp).
Angry Runner
Docker recipe for a self-hosted GitHub Actions runner (CI/CD).
Angry Droid
Scientific computing platform setup for Android.
Angry Bubblef*ck
Bubble sort implemented in brainf*ck language.