Department of Bioinformatics
Prof. Marta Kasprzak,
Dr. Piotr Łukasiak;
Dr. Agnieszka Rybarczyk;
Dr. Szymon Wąsik;
Dr. Karol Kamel;
Dr. Maciej Antczak;
Dr. Marcin Borowski;
Jakub Wiedemann, MSc;
Gutowska Kaja, MSc;
structural and functional analysis of RNAs and proteins, high-throughput sequencing, comparative modeling, systems biology, automated RNA 3D structure prediction, algorithms for spectrometry data analysis, analysis and designing nucleotide sequences.
Research topics of our Laboratory concern an analysis of problems in computational biology, construction of tools for the analysis of experimental biochemical and biophysical data, development and implementation of new algorithms for solving the examined problems. The research issues cover several phases of DNA and RNA sequencing, the analysis of NMR spectral data, the prediction of tertiary structure of RNA and proteins, the process of RNA degradation, the modeling and analysis of complex biological systems, the analysis of microarray experimental data, designing algorithms for the data analysis from mass spectrometers, creating algorithms for the analysis and designing nucleotide sequences based on graph theory.
In the Laboratory, we have constructed models and algorithms supporting DNA sequencing process in its several phases: the analysis and processing of data from sequencer, assembly and sequence alignment, and DNA mapping. We have developed and implemented tools for RNA structure prediction and the database of RNA structural data. The new way for evaluation of RNA and protein models has been also created. In the tool for prediction of tertiary protein structures, we used small protein structures (descriptors). We analyzed selected biological processes, e.g., iron homeostasis in human organism, creation and development of atherosclerosis with the use of Petri nets.
Owing to thorough analysis of biological problems and the development of methods and tools supporting the work of biochemical experts, several problems have been solved. The tools developed in our Laboratory are used by many people, also from foreign Laboratories (Bioserver http://bio.cs.put.poznan.pl/ and RNApolis http://rnapolis.pl/ ).
Current research activity:
Most important research achievements:
Actual research projects:
Selected publications:N. Szóstak, S. Wąsik, J. Błażewicz, Hypercycle, PLOS Computational Biology, 12(4), 2006 (doi: 10.1371/journal.pcbi.1004853).
M. Antczak, M. Kasprzak, P. Łukasiak, J. Błażewicz,
A. Mickiewicz, A. Rybarczyk, J. Sarzyńska, M. Figlerowicz, J. Błażewicz, AmiRNA Designer - new method of artificial miRNA design, Acta Biochimica Polonica, 63, 2016, 71-77 (doi:10.18388/abp.2015_989).
T. Prejzendanc, S. Wąsik, J. Błażewicz, Computer representations of bioinformatics models, Current Bioinformatics 11 (5), 2016, 551-560, (doi: 10.2174/1574893610666150928193510).
K. Kwarciak, M. Radom, P. Formanowicz, A multilevel ant colony optimization algorithm for classical and isothermic DNA sequencing by hybridization with multiplicity information available, Computational Biology and Chemistry, 61, 2016, 109-120 (doi: 10.1016/j.compbiolchem.2016.01.010 ).D. Formanowicz, M. Wanic-Kossakowska, E. Pawliczak, M. Radom, P. Formanowicz, Usefulness of serum interleukin-18 in predicting cardiovascular mortality in patients with chronic kidney disease - systems and clinical approach, Scientific Reports, 5, 2015, Article number: 18332 (doi: 10.1038/srep18332).
A. Rybarczyk, N. Szóstak, M. Antczak, T. Żok, M. Popenda, R.W. Adamiak, J. Błażewicz, M. Szachniuk New in silico approach to assessing RNA secondary structures with non-canonical base pairs, BMC Bioinformatics 16, 2015, 276 (doi:10.1186/s12859-015-0718-6).
P. Lukasiak, M. Antczak, T. Ratajczak, M. Szachniuk, M. Popenda, R.W. Adamiak, J. Błażewicz RNAssess - a webserver for quality assessment of RNA 3D structures, Nucleic Acids Research 43(W1), 2015, W502-W506 (doi:10.1093/nar/gkv557).
M. Szachniuk, M.C. De Cola, G. Felici, D. de Werra, J. Błażewicz. Optimal pathway reconstruction on 3D NMR maps, Discrete Applied Mathematics 182, 2015, 134-149 (doi:10.1016/j.dam.2014.04.010).