Dr Mateusz Wójcik
Senior Research Fellow leading the Computational Biology Group. Specializing in single-cell multi-omics foundation models, genomic graph algorithms, and privacy-preserving clinical data pipelines.
Dr Mateusz Wójcik
Head of Computational Biology & Medical Data Group (CBMD Group)
Department of Computational Mathematics & Bio-Intelligence · Computational Biology & Medical Data Intelligence Group (CBMD Group)
Academic Biography
Dr Mateusz Wójcik is a Senior Research Fellow and Group Leader at BBQ Institute of Advanced Science & Technology. He received his Ph.D. in Computational Biology from the Faculty of Biochemistry, Biophysics and Biotechnology at the Jagiellonian University in Kraków, followed by research training at the Wellcome Sanger Institute in Cambridge, UK.
His work focuses on developing scalable machine learning models for high-dimensional biological systems, including spatial transcriptomics, protein-protein interaction networks, and clinical cohort analysis. Dr. Wójcik’s group collaborates with leading biomedical institutes across Poland and Europe.
Key Responsibilities & Leadership
- Leading bioinformatics research and medical AI applications at BBQ Institute.
- Collaborating with Warsaw Medical University clinical oncology teams.
- Principal Investigator for NCN SONATA Grant on Multi-Modal Genomic Graph Embeddings.
- Supervising interdisciplinary graduate students in computational biology.
Research Interests
- Single-Cell Transcriptomics & Spatial Multi-Omics Modeling
- Geometric Deep Learning on Genomic Knowledge Graphs
- Federated Learning & Differential Privacy for Clinical Datasets
- Structural Biology & Protein Interaction Prediction
Teaching & Courses
- Computational Genomics and Biological Data Science (BIO-601)
- Machine Learning for Healthcare and Biomedicine (CS-520)
- Algorithms in Structural Bioinformatics (BIO-405)
Selected Recent Publications
- Wójcik, M., Wiśniewski, T., et al. (2026). Graph Transformer Embeddings for Single-Cell Spatial Perturbation Mapping. Nature Computational Science.
- Wójcik, M. (2025). Privacy-Preserving Federated Genotype-Phenotype Association Studies. Genome Research.
- Wójcik, M., Kowalczyk, J. (2024). Deep Representation Learning on Epigenetic Topological Structures. Bioinformatics.
Office Hours & Student Advising
- Office hours: Wednesdays 14:00–16:00 (Room 3.25).
- Main liaison for European Bioinformatics Community (ELIXIR Poland).