Department of Bioinformatics

Prof. Jacek Błażewicz

Head of Department
jblazewicz@cs.put.poznan.pl
Phone: 61 6653100

Researchers:

Prof. Piotr Formanowicz

professor

Dr. habil. Maciej Antczak

assistant professor

Dr. Karol Kamel

assistant professor

Technical Staff:

Dr. habil. Agnieszka Rybarczyk

senior specialist chemist

Dr. habil. Piotr Łukasiak

senior specialist chemist

Dr. Marcin Borowski

biologist

Research Projects

  • Structural and functional analysis of RNAs and proteins

  • High-throughput sequencing

  • Comparative modeling

  • Systems biology

  • Algorithms for spectrometry data analysis

  • Analysis and design of nucleotide sequences

Research area

Keywords

  • Modeling computational biology problems

  • Development and implementation of new algorithms for solving examined biological problems

  • Construction of tools for analysis of experimental biochemical and biophysical data

  • Prediction of tertiary structure of proteins

  • Analysis of microarray experimental data

  • Construction of models and algorithms supporting DNA sequencing process in its several phases: 

    •  Analysis and processing of data from sequencers, e.g. study of a new pipeline for the analysis of sequencing data derived from Illumina sequencer

    • Assembly

    • Sequence alignment 

    • DNA mapping

  • Methods for alternative splicing of maize

  • Development and implementation of specialized tools as well as widely used computational servers for prediction and comprehensive analysis of 3D RNA structure

  • Creating algorithms for analysis and design of nucleotide sequences based on graph theory

  • Modeling and analysis of complex biological systems using Petri nets theory, e.g., iron homeostasis in human organism, creation and development of atherosclerosis

  • Study of the RNA degradation proces

  • DNA computing

  • Modeling and simulations of early replicator systems

  • Analysis of data from mass spectrometers

  • Our algorithms and tools are publicly available at Bioserver (http://bio.cs.put.poznan.pl), RNApolis (http://rnapolis.pl/), and the RNA-Puzzles toolkit page (https://chichaumiau.github.io/rnapuzzlestoolkit/blog/2018/07/22/rnaqua/)

Selected publications

  • Z. Miao, R.W. Adamiak, M. Antczak, M.J. Boniecki, J.M. Bujnicki, S-J. Chen, C.Y. Cheng, Y. Cheng, F-C. Chou, R. Das, N.V. Dokholyan, F. Ding, C. Geniesse, Y. Jiang, A. Joshi, A. Krokhotin, M. Magnus, O. Mailhot, F. Major, T.M. Mann, P. Piatkowski, R. Pluta, M. Popenda, J. Sarzynska, L. Sun, M. Szachniuk, S. Tian, J. Wang, A.M. Watkins, J. Wiedemann, X. Xu, J.D. Yesselman, D. Zhang, Z. Zhang, C. Zhao, P. Zhao, Y. Zhou, T. Zok, A. Zyla, R. Aiming, R.T. Batey, B.L. Golden, L. Huang, D.M. Lilley, Y. Liu, D.J. Patel, E. Westhof, RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers, RNA, 2020, 26, 982-995, DOI:10.1261/rna.075341.120.

  • M. Magnus, M. Antczak, T. Zok, J. Wiedemann, P. Lukasiak, Y. Cao, J.M. Bujnicki, E. Westhof, M. Szachniuk, Z. Miao, RNA-Puzzles toolkit: A computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools, Nucleic Acids Research, 2020, 48, 576-588, DOI:10.1093/nar/gkz1108.

  • D. Formanowicz, A. Rybarczyk, M. Radom, P. Formanowicz, A role of inflammation and immunity in essential hypertension - modeled and analyzed using Petri nets, International Journal of Molecular Sciences, 2020, 21(9), 3348, DOI: 10.3390/ijms21093348.

  • T. Zok, J. Badura, S. Swat, K. Figurski, M. Popenda, M. Antczak, New models and algorithms for RNA pseudoknot order assignment, International Journal of Applied Mathematics and Computer Science, 2020, 30(2), 315-324,  DOI: 10.34768/amcs-2020-0024.

  • J.F. Carrascoza Mayen, J. Błażewicz, Recent Results on Computational Molecular Modeling of The Origins of Life,

  • Foundations of Computing and Decision Sciences, 2020, 45, 35-46, DOI: 10.2478/fcds-2020-0003.

  • X. Chen, Y. Liang, M. Sterna, W. Wang, J. Blazewicz, Fully Polynomial Time Approximation Scheme to Maximize Early Work on Parallel Machines with Common Due Date, European Journal of Operational Research, 2020, 284, 67-74, DOI: 10.1016/j.ejor.2019.12.003.

  • X. Chen, S. Kovalev, M. Sterna, J. Błażewicz, Mirror scheduling problems with early and late work criteria, Journal of Scheduling, 2020, DOI: 10.1007/s10951-020-00636-9.

  • T. Villmann, M. Kaden, S. Wasik, M. Kudla, K. Gutowska, A. Villmann, J. Blazewicz, Searching for the Origins of Life – Detecting RNA Life Signatures Using Learning Vector Quantization, In: Vellido A., Gibert K., Angulo C., Martín Guerrero J. (eds) Advances in Self-Organizing Maps, Learning Vector Quantization, Clustering and Data Visualization. WSOM 2019. Advances in Intelligent Systems and Computing, vol 976. Springer, Cham, 2020, 324-333, DOI: 10.1007/978-3-030-19642-4_32.

  • L. Gutowski, K. Gutowska, M. Piorunska-Stolzmann, P. Formanowicz, D. Formanowicz, Systems Approach to Study Associations between OxLDL and Abdominal Aortic Aneurysms, International Journal of Molecular Sciences 2019, 20, 3909, DOI: 10.3390/ijms20163909.

  • M. Antczak, M. Zablocki, T. Zok, A. Rybarczyk, J. Blazewicz, M. Szachniuk, RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs, Bioinformatics 2019, 35, 152-155, DOI: 10.1093/bioinformatics/bty609.

  • M. Radom, M.A. Machnicka, J. Krwawicz, J.M. Bujnicki, P. Formanowicz, Petri net–based model of the human DNA base excision repair pathway, PLOS ONE 2019, 14, e0217913, DOI: 10.1371/journal.pone.0217913.

  • M. Sajek, D.M. Janecki, M.J. Smialek, B. Ginter-Matuszewska, A. Spik, S. Oczkowski, E. Ilaslan, K. Kusz-Zamelczyk, M. Kotecki, J. Blazewicz, J. Jaruzelska, PUM1 and PUM2 exhibit different modes of regulation for SIAH1 that involve cooperativity with NANOS paralogues, Cellular and Molecular Life Sciences 2019, 76, 147-161, DOI: 10.1007/s00018-018-2926-5.

  • X. Chen, Z. Wang, E. Pesch, M. Sterna, J. Blazewicz, Two-machine flow-shop scheduling to minimize total late work: revisited, Engineering Optimization 2019, 51, 1268-1278, DOI: 10.1080/0305215X.2018.1519073.

  • S. Wasik, N. Szostak, M. Kudla, M. Wachowiak, K. Krawiec, J. Blazewicz, Detecting life signatures with RNA sequence similarity measures, Journal of Theoretical Biology 2019, 463, 110-120, DOI: 10.1016/j.jtbi.2018.12.018.

  • J. Blazewicz, X. Chen, R. CT Lee, B. MT Lin, F.-Ch. Lin, E. Pesch, M. Sterna, Z. Wang, Clarification of lower bounds of two-machine flow-shop scheduling to minimize total late work, Engineering Optimization 2019, 51, 1279-1280, DOI: 10.1080/0305215X.2018.1554066.

  • J.F.C. Mayen, J. Rydzewski, N. Szostak, J. Blazewicz, W. Nowak, Prebiotic soup components trapped in montmorillonite nanoclay form new molecules: car-parrinello ab initio simulations, Life 2019, 9, DOI: 10.3390/life9020046.

  • B. Gryszczynska, M. Budzyn, D. Formanowicz, P. Formanowicz, Z. Krasinski, N. Majewska, M. Iskra, M.P. Kasprzak, Advanced oxidation protein products and carbonylated proteins levels in endovascular and open repair of an abdominal aortic aneurysm: the effect of pre-, intra-, and postoperative treatment, Journal of Biomedicine and Biotechnology 2019, 8, 7976043, DOI: 10.1155/2019/7976043.

  • D. Formanowicz, J.B. Krawczyk, B. Perek, P. Formanowicz, A control-theoretic model of atherosclerosis, International Journal of Molecular Sciences 2019, 20, 785, DOI: 10.3390/ijms20030785.

  • K. Gutowska, D. Formanowicz, P. Formanowicz, Selected aspects of tobacco-induced prothrombotic state, inflammation and oxidative stress: modeled and analyzed using petri nets, Interdisciplinary Sciences 2019, 11, 373-386, DOI: 10.1007/s12539-018-0310-7.

  • A. Kozak, T. Glowacki, P. Formanowicz, A method for constructing artificial DNA libraries based on generalized de Bruijn sequences, Discrete Applied Mathematics 2019, 259, 127-144, DOI: 10.1016/j.dam.2018.12.029.

  • M. Kroc, G. Koczyk, K.A. Kamel, K. Czepiel, O. Fedorowicz-Stronska, P. Krajewski, J. Kosinska, J. Podkowinski, P. Wilczura, W. Swiecicki, Transcriptome-derived investigation of biosyn¬thesis of quinolizidine alkaloids in narrow-leafed lupin (Lupinus angustifolius L.) highlights candidate genes linked to iucundus locus, Scientific Reports 2019, 9, 2231, DOI: 10.1038/s41598-018-37701-5.

  • J. Blazewicz, M. Kasprzak, M. Kierzynka, W. Frohmberg, A. Swiercz, P. Wojciechowski, P. Zurkowski, Graph algorithms for DNA sequencing-origins, current models and the future, European Journal of Operational Research, 2018, 264, 799-812, DOI: doi.org/10.1016/j.ejor.2016.06.043.

  • M. Kasprzak, Classification of de Bruijn-based labeled digraphs, Discrete Applied Mathematics, 2018, 234, 86-92, DOI:10.1016/j.dam.2016.10.014.

  • L. Handschuh, P. Wojciechowski, M. Kazmierczak, M. Marcinkowska-Swojak, M. Łuczak, K. Lewandowski, M. Komarnicki, J. Blazewicz, M. Figlerowicz, P. Kozlowski, NPM1 alternative transcripts are upregulated in acute myeloid and lymphoblastic leukemia and their expression level affects patient outcome, Journal of Translational Medicine, 2018, 16: 232, DOI: 10.1186/s12967-018-1608-2.

  • A. Swiercz, W. Frohmberg, M. Kierzynka, P. Wojciechowski, P. Zurkowski, J. Badura, A. Laskowski, M. Kasprzak, J. Blazewicz, GRASShopPER-An algorithm for de novo assembly based on GPU alignments,  PLOS ONE, 2018, 13(8): e0202355, DOI: 10.1371/journal.pone.0202355.

  • J. Musial, M. Guzek, P. Bouvry, J. Blazewicz, A note on the complexity of scheduling of communication-aware directed acyclic graph, Bulletin of the Polish Academy of Sciences – Technical Sciences, 2018, 66(2): 187-191, DOI: 10.24425/122099.

  • J. Blażewicz, M. Kasprzak, M. Kierzynka, W. Frohmberg, A. Swiercz, P. Wojciechowski, P. Zurkowski, Graph algorithms for DNA sequencing - origins, current models and the future,  European Journal of Operational Research, 2018, 264(3): 799-812, DOI: 10.1016/j.ejor.2016.06.043.

  • T. Zok, M. Antczak, M. Zurkowski, M. Popenda, J. Blazewicz, R.W. Adamiak, M. Szachniuk, RNApdbee 2.0: multifunctional tool for RNA structure annotation, Nucleic Acids Research, 2018,46(W1): W30-W35, DOI: 10.1093/nar/gky314.

  • J. Blazewicz, B. Moseley, E. Pesch, D. Trystram, G.C. Zhang, New challenges in scheduling theory,  Journal of Scheduling, 2018, 21(6): 581-582, DOI: 10.1007/s10951-018-0571-3.

  • M. Antczak, T. Zok, M. Osowiecki, M. Popenda, R. Adamiak, M. Szachniuk, RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures, BMC Bioinformatics, 2018, 19: 304, DOI: 10.1186/s12859-018-2317-9.

  • J. Miskiewicz, M. Szachniuk, Discovering structural motifs in miRNA precursors from Viridiplantae kingdom, Molecules, 2018, 23(6): UNSP 1367, DOI: 10.3390/molecules23061367.

  • M. Antczak, M. Popenda, T. Zok, M. Zurkowski, R.W. Adamiak, M. Szachniuk, New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation,  Bioinformatics, 2018, 34(8): 1304-1312, DOI: 10.1093/bioinformatics/btx783.

  • D. Mietchen, S. Wodak, S. Wasik, N. Szostak, C. Dessimoz, Submit a Topic Page to PLOS Computational Biology and Wikipedia,  PLOS Computational Biology, 2018, 14(5):. e1006137, DOI: 10.1371/journal.pcbi.1006137.

  • S. Wasik, M. Antczak, J. Badura, A. Laskowski, T. Sternal, A Survey on Online Judge Systems and Their Applications,  ACM Computing Surveys, 2018, 51:(1): 3, DOI: 10.1145/3143560.

  • D. Formanowicz, A. Rybarczyk, P. Formanowicz, Factors Influencing Essential Hypertension and Cardiovascular Disease Modeled and Analyzed using Stochastic Petri Nets,  Fundamenta Informaticae, 2018, 160(1-2): 143-165, DOI: 10.3233/FI-2018-1678.

  • A. Kozak, D. Formanowicz, P. Formanowicz, Structural analysis of a Petri net model of oxidative stress in atherosclerosis, IET Systems Biology, 2018, 12(3): 108-117, DOI: 10.1049/iet-syb.2017.0015.

  • T. Glowacki, A. Kozak, P. Formanowicz, Dedicated Heuristic for Peptide Assembly Problem, Current Bioinformatics, 2018, 13(2): 120-126, DOI: 10.2174/1574893612666170222092425.

  • J. Olszak, M. Radom, P. Formanowicz, Some aspects of modeling and analysis of complex biological systems using time Petri nets, Bulletin of the Polish Academy of Sciences – Technical Sciences, 2018, 66(1): 67-78, DOI: 10.24425/119060.

  • D. Formanowicz, M. Radom, A. Rybarczyk, P. Formanowicz, The role of Fenton reaction in ROS-induced toxicity underlying atherosclerosis - modeled and analyzed using a Petri net-based approach, Biosystems, 2018, 165: 71-87, DOI: 10.1016/j.biosystems.2018.01.002.

  • M. Radom, P. Formanowicz, An Algorithm for Sequencing by Hybridization Based on an Alternating DNA Chip,  Interdisciplinary Sciences – Computational Life Sciences, 2018, 10(3): 605-615, DOI: 10.1007/s12539-017-0220-0.

  • D. Formanowicz, K. Gutowska, P. Formanowicz, Theoretical studies on the engagement of interleukin 18 in the immuno-inflammatory processes underlying atherosclerosis, International Journal of Molecular Sciences, 2018, 19(11): 3476, DOI: 10.3390/ijms19113476.

  • M. Ciemny, M. Kurcinski, K. Kamel, A. Kolinski, N. Alam, O. Schueler-Furman, S. Kmiecik, Protein-peptide docking: opportunities and challenges, Drug Discovery Today, 2018, 23(8): 1530-1537, DOI: 10.1016/j.drudis.2018.05.006. 

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Polish Academy of Sciences
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