Department of Bioinformatics


 

Head:
Prof. Jacek Błażewicz

 


Staff:
Prof. Piotr Formanowicz;

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;


 
   
 

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Key words:

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.

 

Scientific profile:

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:

  • Study of a new pipeline for the analysis of sequencing data
  • Methods for alternative splicing of maize
  • Modeling and analysis of complex biological systems
  • Modeling of tertiary structure of RNA and proteins
  • Study on the RNA degradation process
  • Secondary and tertiary structure modeling
  • Quality analysis of structural models of  RNA and proteins
  • Algorithms for peptide sequencing and assembly
  • DNA computing
  • Searching for motifs in mRNA sequences
  • Modeling and simulations of early replicator systems
  • Analysis of data from mass spectrometers

 

Most important research achievements:

  • The construction and implementation of G-MSA - GPU-based, fast and accurate algorithm for multiple sequence alignment
  • The construction of the method for the prediction of tertiary RNA structure, the project and implementation of the webserwer - RNAcomposer.
  • The construction of RNA FRABASE - the database for RNA structures, and the search engine of structural modules.
  • A new solution has been proposed for the DNA mapping problem, which is the last stage of the process of reconstructing a sequenced genome. The problem has been theoretically analyzed, a new model from the graph theory has been proposed, and new approximate algorithms have been constructed and tested.
  • A new pipeline for processing data coming from Illumina sequencer has been proposed. Due to utilizing the existing methods and proposing new ones, one can verify the alternative splicing of maize.
  • In the tool for the prediction of full tertiary protein structures, we used small protein structures (descriptors). The correctness of assigning the descriptors to the sequences were examined, also the correctness of the protein structures models can be verified. A new evaluation measure was developed for the protein and RNA models.
  • Development and analysis of Petri net based models of selected complex biological processes of the human body having important medical significance.
  • Formulation and theoretical analysis of the RNA degradation problem, implementation of an algorithm reconstructing the RNA molecule on the basis of its degradation products.
  • Development of new graph-theoretical models for the signal assignment problem in NMR spectra and implementation of the algorithms for solving the examined problems.
  • Development of parallel method for multiple sequence alignment problem on GPU and method for finding of promising pairs of reads, required at the level of graph building in de novo sequencing  based on the overlap-layout-consensus approach.
  • Development and implementation of the methods for RNA structure quality evaluation in the Cartesian and torsion Space.
  • The new method for determining alternative splicing events has been implemented.
  • Identification of motifs directing mRNA into exosomes of hepatic origin.
  • Development of a new RNA secondary structure prediction method taking into account pseudo-knots and non-canonical base pairs.
  • Development of model based on differential equations of statin influence on the atherosclerosis plaque growth.
  • Defining and analysis of new labeled graphs and on their basis creation of the algorithm for oligonucleotides libraries construction.
  • Development of the algorithm for peptides assembly.
  • Review of various approaches used to model hypercycles - structures probably occurring on prebiotic Earth and design of consistent and coherent model

 

Actual research projects:

  • Study of the capabilities and limits of the use of Petri nets for modeling and analysis of complex biological systems on the basis of the exemplary process of atherosclerosis formation and development in the human body (National Science Centre) /2013-2016/.

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,
Structural alignment of protein descriptors − a combinatorial model, BMC Bioinformatics, 17, 2016, 383 (doi:10.1186/s12859-016-1237-9).

M. Biesiada M, K.J. Purzycka, M. Szachniuk, J. Błażewicz, R.W. Adamiak, Automated RNA 3D structure prediction with RNAComposer, RNA Structure Determination: Methods and Protocols (Methods in Molecular Biology 1490) Springer, Humana Press, 2016, 199-215 (doi:10.1007/978-1-4939-6433-8).

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).