Research interests
Research interests include algorithms (theory and applications), mathematical modeling, combinatorial problems in life sciences, RNA structure (modeling, analysis, dynamics).
Bioinformatics projects
RNApolis – a virtual laboratory of RNA bioinformatics |
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| under construction projects are marked with * | |
| @ GitHub | some RNApolis projects available at GitHub |
| RNAssess | webserver for quality assessment of RNA 3D structures [ref] |
| RNAComposer | fully automated RNA structure prediction server [ref, ref, ref] |
| RNAfitme | webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures [ref] |
| RNA FRABASE | RNA FRAgments dataBASE and search engine [ref, ref] |
| RNAhugs | webserver for RNA 3D structure alignment [ref, ref] |
| RNAloops | database of RNA multiloops [ref] |
| RNAlyzer | framework for quality analysis of RNA models [ref] |
| RNApdbee | multifunctional webserver tool for RNA structure annotation [ref, ref] |
| RNAQUA | computational tool for RNA QUality Assessment [ref] |
| RNAspider | webserver to analyze entanglements in RNA 3D structures [ref] |
| RNAsolo | database of cleaned PDB-derived RNA 3D structures [ref] |
| RNAtango* | webserver for torsion-angle based similarity analysis of RNA 3D structures [ref] |
| RNAthor | webserver for the automatic normalization of RNA probing data [ref] |
| RNAtive | webserver to rank 3D RNA models and infer the native [ref] |
| RNAvista | webserver to assess RNA secondary structures with non-canonical base pairs [ref] |
| MCQ4Structures | standalone app to compute torsion angle-based similarity of molecule structures [ref] |
SpaceTetrado – computational tools for quadruplexes |
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| DrawTetrado | standalone app to draw layer diagrams representing quadruplex structures [ref] |
| ElTetrado | standalone app for identification and classification of tetrads and quadruplexes [ref] |
| ONQUADRO | database of tetrads, quadruplexes, and G4-helices [ref] |
| WebTetrado | webserver to annotate and visualize quadruplexes in nucleic acid 3D structures [ref] |
Other bioinformatics tools |
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| miRarchitect* | machine learning-based tool for rational design of artificial miRNAs [ref] |
| SMERFA* | structural, muscular and elastic RNA finder and aligner [ref] |
| Virxicon | a lexicon of viral sequences [ref] |
Research grants
| 2024-2026 | – | PAS-CAS Mobility Project within the scientific cooperation between the Polish Academy of Sciences and the Czech Academy of Sciences, Zaawansowane algorytmy wspomagające predykcję wysokiej jakości modeli 3D RNA (Advanced algorithms to support prediction of high quality 3D RNA models) – principal investigator |
| 2022-2027 | – | Grant No 2021/ABM/05/00004 from the Medical Research Agency (ABM, Poland), Development of a universal fast-response platform, based on RNA technology, ensuring the national drug and epidemiological safety – task manager, team leader |
| 2021-2025 | – | Grant No 2020/39/O/ST6/01488 (PRELUDIUM BIS 2) from the National Science Centre (NCN, Poland), Przewidywanie struktur 3D RNA z wykorzystaniem generatywnych sieci przestawnych (Predicting 3D RNA structures using Generative Adversarial Networks) – principal investigator |
| 2020-2023 | – | Grant No 2019/35/B/ST6/03074 (OPUS 18) from the National Science Centre (NCN, Poland), Eksploracja cech i modelowanie struktury kwadrupleksów (Feature exploration and modelling of quadruplex structures) – principal investigator |
| 2017-2020 | – | Grant No 2016/23/B/ST6/03931 (OPUS 12) from the National Science Centre (NCN, Poland), RNApolis – metody i algorytmy do modelowania i analizy struktury RNA (RNApolis – methods and algorithms to model and analyze the RNA structure) – principal investigator |
| 2017-2018 | – | Grant No 2016/23/N/ST6/03779 (PRELUDIUM 12) from the National Science Centre (NCN, Poland), Rozwój bioinformatycznych modeli do analizy struktur 3D RNA w przestrzeni kątowej (Development of bioinformatics models to analyze 3D RNA structures in torsion angle space) – supervisor |
| 2016-2018 | – | PAS-CNR Research Project Canaletto from the Polish Academy of Sciences, Zaprojektowanie i implementacja metod do integracji danych z
eksperymentów analizy zmienności liczby kopii (CNV) z ekspresją genów (GE) oraz sieciami interakcji białko-białko (PPI) (Design and implemntation of methods to integrate the analysis of Copy Number Variation (CNV) experiments with Gene Expression (GE) and Protein-Protein Interaction (PPI)) – principal investigator |
| 2013-2015 | – | Grant No 2012/05/B/ST6/03026 (OPUS 3) from the National Science Centre (NCN, Poland), Informatyczne modele i metody w biologii komórkowej (Computational models and methods in cell biology) – main executor |
| 2013-2015 | – | Grant No 2012/06/A/ST6/00384 (MAESTRO 3) from the National Science Centre (NCN, Poland), Automatyczne, wysokoprzepustowe modelowanie struktur przestrzennych RNA (Automated, high-throughput modeling of RNA three-dimensional structures) – executor |
| 2010-2012 | – | POIG.02.02-30-009/09, Rozwój Infrastruktury Europejskiego Centrum Bioinformatyki i Genomiki (A development of the European Centre for Bioinformatics and Genomics infrastructure) – administrative specialist |
| 2010-2012 | – | PAN-CNR Joint Research Project from the Polish Academy of Sciences, Advanced bioinformatic algorithms in molecular biology (Zaawansowane algorytmy bioinformatyczne w biologii molekularnej) – project participant |
| 2008-2011 | – | Grant No NN519314635 from the Ministry of Science and Higher Education (MNiSW, Poland), Pierwszorzędowa i przestrzenna struktura kwasów nukleinowych i białek – analiza i algorytmy (Primary and tertiary structure of nucleic acids and proteins – analysis and algorithms) – executor |
| 2005-2009 | – | EU FP6 project BIOPTRAIN (Grant agreement ID: 7597) from the European Commission, Bioinformatics Optimisation Training (Optymalizacja w bioinformatyce) – project manager |
| 2005-2009 | – | EU FP6 project COMPUVAC (Grant agreement ID: 5246) from the European Commission, Rational design and standardized evaluation of novel genetic vaccines (Racjonalne projektowanie oraz standaryzowana ewaluacja nowych szczepionek genetycznych) – executor |
| 2005-2008 | – | EU FP6 project METAFUNCTIONS (Grant agreement ID: 511784) from the European Commission, Environmental – and meta-genomics – a bioinformatic system to detect and assign functions to habitat specific gene patterns (Środowisko i metagenomy – bioinformatyczny system do odkrywania i przypisywania funkcji do uwarunkowanych środowiskowo wzorców
genomowych) – senior researcher, project manager |
| 2004-2007 | – | Grant No 3T11F00227 from the State Committee for Scientific Research (KBN, Poland), Informatyczne aspekty analizy strukturalnej biomolekuł (Computational aspects of biomolecule structure analysis) – executor |
| 2002-2004 | – | MPI-PUT ESR Training Project – ESR |
| 2001-2003 | – | Grant No 7T11F02621 from the State Committee for Scientific Research (KBN, Poland), Algorytmy wspomagające analizę liniowej i przestrzennej struktury kwasów nukleinowych i białek (Algorithms for an analysis of primary and tertiary structure of proteins and nucleic acids) – executor |