I’m a Zurich-based data scientist with 9+ years of experience spanning machine learning, biomedical research, and software development.

I studied computer science and bioinformatics at the University of Warsaw’s Faculty of Mathematics, Informatics and Mechanics (MIMUW) and completed a Ph.D. in computational molecular biology with Prof. Altuna Akalin’s group at the Bioinformatics and Omics Data Science Platform at MDC-BIMSB. There, I co-developed the BioC genomation package and the PiGx BS-seq snakemake-based workflow, explored phantom peaks in ChIP-seq and DNA-methylation changes in neuroblastoma and cardiovascular disease. Later, at ETH Zurich (Laboratory of Nutrition and Metabolic Epigenetics, Laboratory of Regenerative and Muscle Biology) and the Functional Genomics Center Zurich, I worked on multiple projects, including germline chimerism based on scRNA-seq.

In freelance and industry projects, I apply machine learning and deep learning to biomedical and sensor data. My work includes a PyTorch LSTM variational autoencoder for water-safety monitoring, transfer learning and classification for endometriosis biomarkers, therapeutic-target prioritization in oncology, and Enformer-based enhancer analysis in Alzheimer’s disease. I collaborate with research, clinical, and data science teams to make analyses reproducible and useful for downstream decisions. Explore more of my deep-learning projects on the Independent Projects page. I’ve collaborated with teams at:

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