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ACHIEVEMENTS
ACHIEVEMENTS
We are proud of...
2023


  1. M. Justyna, M. Antczak, M. Szachniuk (2023) Machine learning for RNA 2D structure prediction benchmarked on experimental data, Briefings in Bioinformatics 24(3):bbad153 (doi: 110.1093/bib/bbad153).

  2. B. Adamczyk, M. Zurkowski, M. Szachniuk, T. Zok (2023) WebTetrado: a webserver to explore quadruplexes in nucleic acid 3D structures, Nucleic Acids Research 51(W1):W607-W612 (doi: 10.1093/nar/gkad346).

  3. M. Zurkowski, M. Antczak, M. Szachniuk (2023) High-quality, customizable heuristics for RNA 3D structure alignment, Bioinformatics 39(5):btad315 (doi: 10.1093/bioinformatics/btad315).

2022


  1. P. Formanowicz, M. Kasprzak, P. Wawrzyniak (2022) Labeled Graphs in Life Sciences - Two Important Applications, in: S. Zawislak, J. Rysinski (eds.), Graph-Based Modelling in Science, Technology and Art, Mechanisms and Machine Science v. 107, Springer 2022, online publication: 02 August 2021 (doi:10.1007/978-3-030-76787-7_10).

  2. T. Zok, N. Kraszewska, J. Miskiewicz, P. Pielacinska, M. Zurkowski, M. Szachniuk (2022) ONQUADRO: a database of experimentally determined quadruplex structures, Nucleic Acids Research 50(D1), D253-D258 (doi:10.1093/nar/gkab1118).

  3. F. Carrascoza, M. Antczak, Z. Miao, E. Westhof, M. Szachniuk (2022) Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions, RNA 28(2), 250-262 (doi:10.1261/rna.078685.121).

  4. A. Belter, M. Popenda, M. Sajek, T. Wozniak, M.Z. Naskret-Barciszewska, M. Szachniuk, S. Jurga, J. Barciszewski (2022) A new molecular mechanism of RNA circularization and the microRNA sponge formation, Journal of Biomolecular Structure and Dynamics 40(7):3038-3045 (doi:10.1080/07391102.2020.1844802).

  5. K. Luwanski, V. Hlushchenko, M. Popenda, T. Zok, J. Sarzynska, D. Martsich, M. Szachniuk, M. Antczak (2022) RNAspider: a webserver to analyze entanglements in RNA 3D structures, Nucleic Acids Research 50(W1):W663-W669 (doi:10.1093/nar/gkac218).

  6. B. Adamczyk, M. Antczak, M. Szachniuk (2022) RNAsolo: a repository of cleaned PDB-derived RNA 3D structures, Bioinformatics 38(14):3668-3670 (doi:10.1093/bioinformatics/btac386).

  7. M. Zurkowski, T. Zok, M. Szachniuk (2022) DrawTetrado to create layer diagrams of G4 structures, Bioinformatics 38(15):3835-3836 (doi:10.1093/bioinformatics/btac394).

  8. J. Wiedemann, J. Kaczor, M. Milostan, T. Zok, J. Blazewicz, M. Szachniuk, M. Antczak (2022) RNAloops: a database of RNA multiloops, Bioinformatics 38(17):4200-4205 (doi: 10.1093/bioinformatics/btac484).

  9. A.M. Kilpatrick, F. Rahman, A. Anjum, S. Shome, K.M.S. Andalib, S. Banik, S.F. Chowdhury, P. Coombe, Y.C. Astroz, J.M. Douglas, P. Eranti, A.D. Kiran, S. Kumar, H. Lim, V. Lorenzi, T. Lubiana, S. Mahmud, R. Puche, A. Rybarczyk, S.M. Al Sium, D. Twesigomwe, T. Zok, C.A. Orengo, I. Friedberg, J.F. Kelso, L. Welch (2022) Characterizing domain-specific open educational resources by linking ISCB Communities of Special Interest to Wikipedia, Bioinformatics 38(I1):i19-i27 (doi:10.1093/bioinformatics/btac236).

  10. J. Gumna, M. Antczak, R.W. Adamiak, J.M. Bujnicki, S.-J. Chen, F. Ding, P. Ghosh, J. Li, S. Mukherjee, C. Nithin, K. Pachulska-Wieczorek, A. Ponce-Salvatierra, M. Popenda, J. Sarzynska, T. Wirecki, D. Zhang, S. Zhang, T. Zok, E. Westhof, Z. Miao, M. Szachniuk, A. Rybarczyk (2022), Computational pipeline for reference-free comparative analysis of RNA 3D structures applied to SARS-CoV-2 UTR models, International Journal of Molecular Sciences 23(17):9630 (doi: 10.3390/ijms23179630).

2021

  1. J. Miskiewicz, J. Sarzynska, M. Szachniuk (2021) How bioinformatics resources work with G4 RNAs, Briefings in Bioinformatics 22(3):bbaa201, (doi:10.1093/bib/bbaa201).

  2. T. Zok (2021) BioCommons: a robust Java library for RNA structural bioinformatics, Bioinformatics 37(1), 2766-2767 (doi:10.1093/bioinformatics/btab069).

  3. S. Swat, A. Laskowski, J. Badura, W. Frohmberg, P. Wojciechowski, A. Swiercz, M. Kasprzak, J. Blazewicz (2021) Genome-scale de novo assembly using ALGA, Bioinformatics 37(12), 1644-1651 (doi:10.1093/bioinformatics/btab005).

  4. M. Popenda, T. Zok, J. Sarzynska, A. Korpeta, R.W. Adamiak, M. Antczak, M. Szachniuk (2021) Entanglements of structure elements revealed in RNA 3D models, Nucleic Acids Research 49(17), 9625-9632 (doi:10.1093/nar/gkab716).

2020


  1. M. Kudla, K. Gutowska, J. Synak, M. Weber, K.S. Bohnsack, P. Lukasiak, T. Villmann, J. Blazewicz, M. Szachniuk (2020) Virxicon: a lexicon of viral sequences, Bioinformatics 36(22-23), 5507–5513 (doi:10.1093/bioinformatics/btaa1066).

  2. M. Magnus, M. Antczak, T. Zok, J. Wiedemann, P. Lukasiak, Y. Cao, J.M. Bujnicki, E. Westhof, M. Szachniuk,
    Z. Miao (2020) RNA-Puzzles toolkit: A computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools, Nucleic Acids Research 48(2), 576–588
    (doi: 10.1093/nar/gkz1108).

  3. T. Zok, M. Popenda, M. Szachniuk (2020) ElTetrado: a tool for identification and classification of tetrads and quadruplexes, BMC Bioinformatics 21, 40 (doi:10.1186/s12859-020-3385-1).

  4. M. Popenda, J. Miskiewicz, J. Sarzynska, T. Zok, M. Szachniuk (2020) Topology-based classification of tetrads and quadruplex structures, Bioinformatics 36(4), 1129-1134,
    online publication: 7 October 2019 (doi:10.1093/bioinformatics/btz738).

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

  6. 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, A. Ren, R.T. Batey, B.L. Golden, L. Huang, D.M. Lilley, Y. Liu, D.J. Patel, E. Westhof (2020) RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers, RNA 26, 982-995 (doi:10.1261/rna.075341.120).

  7. J. Gumna, T. Zok, K. Figurski, K. Pachulska-Wieczorek, M. Szachniuk (2020) RNAthor - fast, accurate normalization, visualization and statistical analysis of RNA probing data resolved by capillary electrophoresis, PLoS ONE 15(10), e0239287 (doi:10.1371/journal.pone.0239287).

  8. J. Synak, A. Rybarczyk, J. Blazewicz (2020) Multi-agent approach to sequence structure simulation in the RNA World hypothesis, PLoS ONE 15(8), e0238253 (doi:10.1371/journal.pone.0238253).

  9. T.P. Lehmann, J. Miskiewicz, N. Szostak, M. Szachniuk, S. Grodecka-Gazdecka, P.P. Jagodzinski (2020) In vitro and in silico analysis of miR-125a with rs12976445 polymorphism in breast cancer patients, Applied Sciences 10(20), 7275 (doi:10.3390/app10207275).

2019


  1. M. Antczak, M. Zablocki, T. Zok, A. Rybarczyk, J. Blazewicz, M. Szachniuk (2019) RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs, Bioinformatics 35(1), 152-155 (doi:10.1093/bioinformatics/bty609).

  2. M. Szachniuk (2019) RNApolis: computational platform for RNA structure analysis, Foundations of Computing and Decision Sciences 44(2), 241-257 (doi:10.2478/fcds-2019-0012).

  3. D. Formanowicz, J. Krawczyk, B. Perek, P. Formanowicz (2019) A Control-Theoretic Model of Atherosclerosis, International Journal of Molecular Sciences 20(3), 785 (doi:10.3390/ijms20030785).

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

  5. B. Gryszczynska, M. Budzyn, D. Formanowicz, P. Formanowicz, Z. Krasinski, N. Majewska, M. Iskra, M. Kasprzak (2019) 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, BioMed Research International (18):1-9 (doi:10.1155/2019/7976043).

  6. K. Wiatr, P. Piasecki, L. Marczak, P. Wojciechowski, M. Kurkowiak, R. Ploski, M. Rydzanicz, L. Handschuh, J. Jungverdorben, O. Brustle, M. Figlerowicz, M. Figiel (2019) Altered Levels of Proteins and Phosphoproteins, in the Absence of Early Causative Transcriptional Changes, Shape the Molecular Pathogenesis in the Brain of Young Presymptomatic Ki91 SCA3/MJD Mouse, Molecular Neurobiology, vol. 56, 8168–8202 (doi:10.1007/s12035-019-01643-4).

  7. K. Switonska, W. Szlachcic, L. Handschuh, P. Wojciechowski, L. Marczak, M. Stelmaszczuk, M. Figlerowicz, M. Figiel (2019) Identification of altered developmental pathways in human juvenile HD iPSC with 71Q and 109Q using transcriptome profiling, Frontiers in Cellular Neuroscience 2018, 12:528 (doi:10.3389/fncel.2018.00528).

  8. M. Radom, M. Machnicka, J. Krwawicz, J. Bujnicki, P. Formanowicz (2019) Petri net–based model of the human DNA base excision repair pathway, PLOS ONE 14(9): e0217913 (doi:10.1371/journal.pone.0217913).

  9. D. Kogut, K., A. Poterala-Hejmo, J. Smieja, D. Formanowicz, P.Formanowicz (2019) Petri nets and ODE as complementary tools in analysis of signaling pathways, Proceedings of 11th International Conference on Bioinformatics and Computational Biology, vol. 60, 150-160 (doi:10.29007/542h).

  10. J. Carrascoza Mayén, J. Rydzewski, N. Szostak, J. Blazewicz, W. Nowak (2019) Prebiotic Soup Components Trapped in Montmorillonite Nanoclay Form New Molecules: Car-Parrinnello Ab Initio Simulations, Life 9(2), 46 (doi:10.3390/life9020046).

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

  12. S. Wasik, N. Szostak, M. Kudla, M. Wachowiak, K. Krawiec, J. Blazewicz (2019) Detecting Life Signatures with RNA Sequence Similarity Measures, Journal of Theoretical Biology, vol. 463, 110-120 (doi:10.1016/j.jtbi.2018.12.018).

  13. K. Gutowska, D. Formanowicz, P. Formanowicz (2019) Selected Aspects of Tobacco-Induced Prothrombotic State, Inflammation and Oxidative Stress: Modeled and Analyzed Using Petri Nets, Interdisciplinary Sciences Computational Life Sciences 11(6), 373-386 (doi:10.1007/s12539-018-0310-7).

  14. P. Jackowiak, A. Lis, M. Luczak, I. Stolarek, M. Figlerowicz (2019) Functional characterization of RNA fragments using high-throughput interactome screening, Journal of Proteomics 193, 173-183 (doi:10.1016/j.jprot.2018.10.007).

  15. M. Pokornowska, M. Milewski, K. Ciechanowska, A. Szczepańska, M. Wojnicka, Z. Radogostowicz, M. Figlerowicz, A. Kurzynska-Kokorniak (2019) The RNA-RNA base pairing potential of human Dicer and Ago2 proteins, Cellular and Molecular Life Sciences (doi:10.1007/s00018-019-03344-6).

  16. T. Machałowski, M. Wysokowski, M. Tsurkan, R. Galli, C. Schimpf, D. Rafaja, E. Brendler, C. Viehweger, S. Zoltowska-Aksamitowska, I. Petrenko, K. Czaczyk, M. Kraft, M. Bertau, N. Bechmann, K. Guan, S. Bornstein, A. Voronkina, A. Fursov, M. Bejger, K. Biniek-Antosiak, W. Rypniewski, M. Figlerowicz, O. Pokrovsky, T. Jesionowski, H. Ehrlich (2019) Spider Chitin: An Ultrafast Microwave-Assisted Method for Chitin Isolation from Caribena versicolor Spider Molt Cuticle, Molecules 24(20): 3736 (doi:10.3390/molecules24203736).

  17. T. Machalowski, M. Wysokowski, S. Zoltowska-Aksamitowska, N. Bechmann, B. Binnewerg, M. Schubert, K. Guan, S. Bornstein, K. Czaczyk, O. Pokrovsky, M. Kraft, M. Bertau, C. Schimpf, D. Rafaja, M. Tsurkan, R. Galli, H. Meissner, I. Petrenko, A. Fursov, A. Voronkina, M. Figlerowicz, Y. Joseph, T. Jesionowski, H. Ehrlich (2019) Spider Chitin. The biomimetic potential and applications of Caribena versicolor tubular chitin, Carbohydrate Polymers, vol. 226, 115301 (doi:10.1016/j.carbpol.2019.115301).

  18. L. Gutowski, K. Gutowska, M. Piorunska-Stolzmann, P. Formanowicz, D. Formanowicz (2019) Systems Approach to Study Associations between OxLDL and Abdominal Aortic Aneurysms, International Journal of Molecular Sciences 20(16): 3909 (doi:10.3390/ijms20163909).

  19. S. Wasik, M. Jaroszewski, M. Nowaczyk, J. Blazewicz (2019) VirDB: Crowdsourced Database for Evaluation of Dynamical Viral Infection Models, Current Bioinformatics 14(8) (doi:10.2174/1574893614666190308155904).

2018


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

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

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

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

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

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

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

2017


  1. P. Jackowiak, A. Hojka-Osińska, A. Philips, A. Zmienko, L. Budzko, P. Maillard, A. Budkowska, M. Figlerowicz (2017). Small RNA fragments derived from multiple RNA classes - the missing element of multi-omics characteristics of the hepatitis C virus cell culture model. BMC Genomics, vol. 18 (502), (doi: 10.1186/s12864-017-3891-3).

  2. A. Rybarczyk, P. Jackowiak, M. Figlerowicz, J. Blazewicz (2017). Computational prediction of nonenzymatic RNA degradation patterns, Acta Biochimica Polonica 63 (4), 745-751 (doi:10.18388/abp.2016_1331).

  3. K. Chmielewska, D. Formanowicz, P. Formanowicz (2017). The effect of cigarette smoking on endothelial damage and atherosclerosis development - modeled and analyzed using Petri nets. Archives of Control Sciences, 27(2), 211-228 (doi:10.1515/acsc-2017-0013).

  4. J. Wiedemann, T. Zok, M. Milostan, M. Szachniuk (2017). LCS-TA to identify similar fragments in RNA 3D structures, BMC Bioinformatics 18, 456 (doi:10.1186/s12859-017-1867-6).

  5. J. Miskiewicz, K. Tomczyk, A. Mickiewicz, J. Sarzynska, M. Szachniuk (2017). Bioinformatics study of structural patterns in plant microRNA precursors. BioMed Research International vol. 2017, article ID 6783010, 8 pages (doi:10.1155/2017/6783010).

  6. Z. Miao, R.W. Adamiak, M. Antczak, R.T. Batey, A.J. Becka, M. Biesiada, M.J. Boniecki, J.M. Bujnicki, S-J. Chen, C.Y. Cheng, F-C. Chou, A.R. Ferre-D'Amare, R. Das, W.K. Dawson, F. Ding, N.V. Dokholyan, S. Dunin-Horkawicz, C. Geniesse, K. Kappel, W. Kladwang, A. Krokhotin, G.E. Lach, F. Major, T.H. Mann, M. Magnus, K. Pachulska-Wieczorek, D.J. Patel, J.A. Piccirilli, M. Popenda, K.J. Purzycka, A. Ren, G.M. Rice, J. Jr. Santalucia, J. Sarzynska, M. Szachniuk, A. Tandon, J.J. Trausch, S. Tian, J. Wang, K.M. Weeks, B. Williams II, Y. Xiao, X. Xu, D. Zhang, T. Zok, E. Westhof (2017). RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme, RNA, (doi:10.1261/rna.060368.116).

  7. N. Szostak, J. Synak, M. Borowski, S. Wasik, J. Blazewicz (2017). Simulating the origins of life: The dual role of RNA replicases as an obstacle to evolution. PloS One 12 (7), (doi:10.1371/journal.pone.0180827).

  8. N. Szostak, S. Wasik, J. Blazewicz (2017). Understanding Life: A Bioinformatics Perspective. European Review 25 (2), 231-245 (doi:10.1017/S1062798716000570).

  9. A. Mickiewicz, J. Sarzyńska, M. Miłostan, A. Kurzyńska-Kokorniak, A. Rybarczyk, P. Łukasiak, T. Kuliński, M. Figlerowicz, J. Błażewicz (2017). Modeling of the catalytic core of Arabidopsis thaliana Dicer-like 4 protein and its complex with double-stranded RNA. Comput Biol Chem 66, 44–56 (doi:10.1016/j.compbiolchem.2016.11.003).

  10. A. Rybarczyk, A. Hertz, M. Kasprzak, J. Blazewicz (2017). Tabu Search for the RNA Partial Degradation Problem. International Journal of Applied Mathematics and Computer Science 27, 401–415 (doi:10.1515/amcs-2017-0028).