Maciej Bąk, PhD

Scientific Software Engineering Expert

Maciej Bąk - Profile picture

I'm currently a postdoctoral research assistant at the Department of Mathematics, City, University of London. Previous affiliations include Swiss Institute of Bioinformatics and Biozentrum, Universitat Basel, Switzerland.

I am interested in various computational approaches to study and combat cancer. Mostly passionate about the application of math/stat modelling and machine learning methods to solve biological problems. High-quality scientific software engineering is my speciality. In my (little) spare time I train martial arts, design and develop my very own horror game or read about mathematics and philosophy.

scientific articles


  1. Bak M. (2023). Hypercomplex: abstract & fast header-only C++ template library for lattice-based cryptosystems in high-dimensional algebras. Journal of Open Source Software, 8(85), 5272

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

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

  4. Kwiecien K., Majewski P., Bak M., et al. (2023). Alternative splicing is not a key source of chemerin isoforms diversity. Mol Biol Rep, 50:2521–2529

  5. Bak M., van Nimwegen E., Schmidt R., Zavolan M., Gruber A.J. (2022). Frequent co-regulation of splicing and polyadenylation by RNA-binding proteins inferred with MAPP. bioRxiv, preprint

  6. Ghosh S., Ataman M., Bak M., et al. (2022). CFIm-mediated alternative polyadenylation remodels cellular signaling and miRNA biogenesis. Nucleic Acid Res., 50(6):3096-3114

  7. Bak M.*, Rozlach A. (2020). Moran Pycess: a Python package to simulate Moran processes driven by game theory. Journal of Open Source Software, 5(54), 2643

  8. 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. Sci. Rep., 10(1):13702

  9. 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. Mol Cell, 77(5):1014-1031.e13

  10. Gałan W., Bąk M., Jakubowska M. (2019). Host Taxon Predictor - A Tool for Predicting Taxon of the Host of a Newly Discovered Virus. Sci Rep., 9(1):3436

  11. Bak M., Jazwa A., Kasper L. et al. (2015). Involvement of microRNAs in the inflammatory pathways of pulmonary sarcoidosis. J Physiol Pharmacol., 66(5):635-42

  12. Jazwa A., Kasper L., Bak M., et al. (2015). Differential inflammatory microRNA and cytokine expression in pulmonary sarcoidosis. Arch. Immunol. Ther. Exp., (63), 139–146

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.