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Europejskie Centrum Bioinformatyki i Genomiki

Instytut Informatyki Politechniki Poznańskiej

Wielkopolskie Centrum Zaawansowanych Technologii

Institute of Bioorganic Chemistry,
Polish Academy of Sciences
Z. Noskowskiego 12/14
61-704 Poznań
tel centrala: (+48) 61 852 85 03
fax: (+48) 61 852 05 32
e-mail: ibch@ibch.poznan.pl

Sekretariat Dyrektora, tel: 61 852 89 19

Department of Bioinformatics

Prof. Jacek Błażewicz

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

Prof. Piotr Formanowicz

professor

Dr. habil. Maciej Antczak

assistant professor

Dr. Karol Kamel

assistant professor

Dr. habil. Agnieszka Rybarczyk

senior specialist chemist

Dr. habil. Piotr Łukasiak

senior specialist chemist

Dr. Marcin Borowski

biologist

• 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

• 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/)

• 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.