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Research Interests

Main interests: computational biology and bioinformatics with the focus on algorithms, combinatorial optimization and theoretical properties of models of trees and networks.

In particular the main topics cover:

• tree reconciliation of gene tree and species tree,
• inference of a species tree or a network from gene trees,
• modelling evolutionary scenarios,
• inference of horizontal gene transfers,
• inference of genomic duplications,
• metagenomics,
• bootstrapping methods for trees and networks,
• and mathematical properties of tree/network comparison functions.

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Students and Researchers

Please contact me if you are interested in writing a bachelor, master, or Ph.D. thesis under my supervision. Some examples of completed theses are available at APD. The topics that I offer can be of algorithmic, computational, programming or theoretical nature depending on skills and background. See also journal and conference papers co-authored by my master's students: A. Betkier (ISBRA 2014), P. Tabaszewski (ACM BCB 2018) or D. Dąbkowski (JBCB).

We invite to our master seminar Bioinformatyka i analiza danych biomedycznych.

My Ph.D. students:

• Agnieszka Mykowiecka
• Jarosław Paszek (defended in 2018).

Check also our Computational Biology Group seminar.

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Grants and other resources

My current research is supported by two National Science Centre grants:

• #2017/27/B/ST6/02720 Consistent Models and Efficient Algorithms for Genomic Duplications (2018-2023)
• #2019/33/B/ST6/00737 Biologically Meaningful Inference of Phylogenetic Networks (2020-2025)

Funding is usually available for students participating in projects, e.g., stipends, travel or equipment. We have also computing servers available for performing computational experiments.

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Short Biography

My background is computer science (M.Sc. in 1999) and math (M.Sc. in 2000) both at University of Warsaw. I completed my Ph.D. in 2006 in mathematics (scope computer science) with several theoretical and algorithmic results on detecting horizontal gene transfers. A large part of the thesis is also devoted to evolutionary scenarios, i.e., DLS-trees and H-trees. From 2019, I am an Associate Professor (profesor uczelni, in Polish) at the Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw. In 2006 and 2007 I also was a Research Fellow at Max Planck Institute for Molecular Genetics in Berlin. I am a member of Polish Bioinformatics Society since 2008.

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Publications

Most of them can be found using some of the links below.

Scopus 8970815500
Google Scholar
ResearchGate
ResearchId D-3160-2013
OrcidId 0000-0002-2045-5892
PBN (PL)
Mendeley

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Teaching

Supplementary teaching materials are usually available for my students by private links, e.g., for the lectures in Introduction to Computer Science, Comparative Genomics, and Introduction to Computational Biology. Please contact me if you are interested.

More information on the master seminar Bioinformatyka i analiza danych biomedycznych.

I am avaiable for students at my office. The current office hours can be checked at USOS.

My teaching website at USOS in English | Polish.

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Software

Software packages related to my research are available at bitbucket or github