I’m a Zurich-based data scientist with over nine years of experience in machine learning, biomedical research, and software development. On this personal website, I share insights from my academic and industry work.

I trained in computer science and bioinformatics at the University of Warsaw’s Faculty of Mathematics, Informatics and Mechanics (MIMUW). I completed my Ph.D. as a doctoral researcher in Prof. Altuna Akalin’s group at the Bioinformatics and Omics Data Science Platform at MDC-BIMSB, where I contributed and co-developed computational tools, the BioC genomation package, and the snakemake-based PiGx BS-seq workflow for disease epigenomics. Using computational and algorithmic analyses of hundreds of NGS datasets, I investigated the origins of spurious peaks and other technical biases in ChIP-seq. My research also examined epigenomic changes in neuroblastoma and cardiovascular disease using solid tissue and liquid-biopsy samples from blood and urine. At ETH Zurich (Laboratory of Nutrition and Metabolic Epigenetics, Laboratory of Regenerative and Muscle Biology) and the Functional Genomics Center Zurich I further explored scRNA-seq analysis, including germline chimerism.

In industry and freelance collaborations, I apply machine learning and deep learning to translational challenges. My work includes prioritizing therapeutic targets for clinical trials, developing single-cell RNA-seq methods to support endometriosis prediction, detecting chemical anomalies in wastewater using sequential variational autoencoders, and identifying blood-based biomarkers for cancer and autoimmune diseases. I’ve collaborated with teams at:

I’m open for collaborations. Feel free to contact me: katwre (at) gmail.com.