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 in data analysis, disease (epi)genomics, and tool development.

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 co-developed computational methods, the BioC genomation package, and the PiGx BS-seq workflow for disease epigenomics. This included integrating multiple NGS datasets to investigate 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 have applied machine learning and deep learning to translational challenges, including prioritizing therapeutic targets for clinical trials, developing single-cell RNA-seq methods for endometriosis prediction, monitoring wastewater for chemical anomalies, and identifying blood-based biomarkers for cancer and autoimmune diseases. Some of my high profile clients include:

Research interests

Rapid advances in molecular profiling create new opportunities to study disease through genomics, epigenomics, and transcriptomics - including bulk, single-cell, and spatially resolved approaches - as well as imaging and proteomics. I integrate these data using machine learning and deep learning to address biological and clinical questions. I am committed to advancing machine learning research in biomedicine to improve clinical decision-making.

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