Damian WÓJTOWICZ

I am an Assistant Professor at the University of Warsaw, specializing in computational molecular biology. My research focuses on developing mathematical and computational methods to decipher the molecular mechanisms underlying cancer development. Through integrative analysis of genomic and molecular information, I work to uncover how DNA damage, repair processes, and structural variations contribute to disease development, providing insights that may inform future therapeutic approaches.

My research is supported by the Polish National Agency for Academic Exchange (NAWA) via a Polish Returns grant and the National Science Centre (NCN) via a OPUS grant.

         

Open positions

I'm seeking motivated BSc, MSc, and PhD students to join my research group. Whether you're interested in developing your thesis project or exploring potential research directions, I'm here to support your academic journey. Prior experience is valued but not required; what matters most is your enthusiasm and commitment to learning.

Ready to discuss your research aspirations? Reach out with your background and interests, and let's explore how we can work together to achieve your academic goals. Join our MSc seminar series on "Biomedical data analysis." to get insights into our research interests.

Experience

Education / Degrees

Group members

Postdocs and students

• Piotr Radziński, Postdoc (Mathematics, 2025-2026)
• Marcin Wierzbiński, Ph.D. student (Computer Science, 2023-2026)
• Mikołaj Dziewiatowski, M.Sc. student (Bioinformatics, 2024-2026)
• Agnieszka Prudło, B.Sc. & M.Sc. student (Bioinformatics, 2025-2026)
• Cezary Botta, M.Sc. student (Machine Learning, 2025/2026)
• Zuzanna Milczarska, M.Sc. student (Bioinformatics, 2025/2026)
• Ignacy Makowski, M.Sc. student (Bioinformatics, 2025/2026)
• Agata Paluch, M.Sc. student (Bioinformatics, 2025/2026)
• Małgorzata Ciołek, M.Sc. student (Data Science and Business Analytics, 2025/2026)

Alumni

• Julia Sobecka, M.Sc. student (Wroclaw University of Science and Technology, Mathematics, 2024/2025)
• Bartosz Brzeziński, M.Sc. student (Mathematics, 2023/2024)
• Radosław Jurczak, M.Sc. student (Mathematics, 2023/2024)

Research

My research focuses on computational modeling of mutagenic processes in cancer, with particular emphasis on developing methods to decipher mutational signatures - the genomic footprints left by DNA damage and repair mechanisms. I co-developed sequence-dependent models that capture the non-random distribution of mutations, revealing how processes like APOBEC mutagenesis generate clustered mutations with distinct genomic dependencies. A key contribution is RepairSig, which mathematically factorizes complex mutational patterns of deficient DNA repair into their constituent components, addressing the non-additive nature of these processes. My work extends to establishing the etiology of mutational signatures through integrative analysis of multi-omics data and network-based approaches that uncover relationships between mutagenic processes and cellular pathways. Beyond cancer genomics, I investigate alternative DNA conformations including G-quadruplexes and Z-DNA, developing computational frameworks to map these structures genome-wide and understand their regulatory potential. I also study DNA topology and supercoiling dynamics, creating methods to analyze how topoisomerases regulate transcription through spatial and temporal control of DNA structure. My earlier work includes mathematical modeling of genome evolution through gene duplication and loss, and computational approaches to protein structure analysis and coevolution. Through these diverse but interconnected research areas, I aim to understand how DNA structure, damage, and repair shape genomic stability and evolution in both healthy and diseased states.

Selected publications

• D. Wójtowicz, J. Hoinka, B. Amgalan, Y.-A. Kim, T.M. Przytycka, RepairSig: Deconvolution of DNA damage and repair contributions to the mutational landscape of cancer, Cell Systems 12(10), pp. 994-1003.e4, 2021.
• D. Wójtowicz, I. Sason, X. Huang, Y.-A. Kim, M.D.M. Leiserson, T.M. Przytycka, R. Sharan, Hidden Markov models lead to higher resolution maps of mutation signature activity in cancer, Genome Medicine 11(49), pp. 1-12, 2019.
• X. Huang, D. Wójtowicz, T.M. Przytycka, Detecting presence of mutational signatures in cancer with confidence, Bioinformatics 34:2, pp. 330-337, 2018.
• F. Kouzine, D. Wójtowicz, L. Baranello, A. Yamane, S. Nelson, W. Resch, K.-R. Kieffer-Kwon, C.J. Benham, R. Casellas, T.M. Przytycka, D. Levens, Permanganate/S1 Nuclease Footprinting Reveals Non-B DNA Structures with Regulatory Potential across a Mammalian Genome, Cell Systems 4(3), pp.344-356.e7, 2017.
• F. Kouzine, D. Wójtowicz, A. Yamane, W. Resch, K.-R. Kieffer-Kwon, R. Bandle, S. Nelson, H. Nakahashi, P. Awasthi, L. Feigenbaum, H. Menoni, J. Hoeijmakers, W. Vermeulen, H. Ge, T.M. Przytycka, D. Levens, R. Casellas, Global regulation of promoter melting in naive lymphocytes, Cell 153(5), pp.988-99, 2013.
• L. Baranello, D. Wójtowicz, K. Cui, B.N. Devaiah, H.-J. Chung, K.Y. Chan-Salis, R. Guha, K. Wilson, X. Zhang, H. Zhang, J. Piotrowski, C.J. Thomas, D.S. Singer, B.F. Pugh, Y. Pommier, T.M. Przytycka, F. Kouzine, B.A. Lewis, K. Zhao, D. Levens, RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription, Cell 165(2):357-71, 2016.
• R. Salari, D. Wójtowicz, J. Zheng, D. Levens, Y. Pilpel, T.M. Przytycka, Teasing apart translational and transcriptional components of stochastic variations in eukaryotic gene expression, PLoS Computational Biology 8(8):e1002644, 2012.
• D. Wójtowicz, J. Tiuryn, Evolution of gene families based on gene duplication, loss, accumulated change, and innovation, Journal of Computational Biology 14(4), pp.479-95, 2007.

For a complete list of my publications and preprints please visit my Google Scholar profile.