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 use machine learning and deep learning to turn complex biomedical and sensor data into biologically meaningful insights. For water-safety monitoring, I built a PyTorch LSTM variational autoencoder to detect and forecast unusual patterns in high-frequency chemical measurements. In a menstrual-effluent biomarker project, I combined generative modeling and scArches-based transfer learning to analyze bulk and scRNA-seq, then evaluated classifiers for endometriosis-associated signatures. For oncology, I used positive-unlabeled learning and autoencoders to prioritize therapeutic targets from molecular and treatment data. As part of a team, I applied Enformer, a published hybrid CNN–Transformer, to multi-omics data in Alzheimer’s disease research, identifying candidate regulatory enhancers and their potential target genes. Across these projects, I work closely with research, clinical, and data science teams to make analyses reproducible and useful for downstream decisions. Explore more of my deep-learning projects, including AWS-deployed applications, 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.