M. Antczak, M. Szachniuk, Towards increasing the credibility of RNA design, in Alexander Churkin, Danny Barash (ed.) RNA Design. Methods in Molecular Biology 2847, Springer, Humana New York, NY, 137-151 (doi:10.1007/978-1-0716-4079-1_9).
» 2015
K.J. Purzycka, M. Popenda, M. Szachniuk, M. Antczak, P. Lukasiak, J. Blazewicz, R.W. Adamiak, Automated 3D RNA structure prediction using the RNAComposer method for riboswitches, in Shi-Jie Chen, Donald H. Burke-Aguero (eds.) Methods in Enzymology: Computational Methods for Understanding Riboswitches 553, Elsevier, 2015, 3-34 (doi:10.1016/bs.mie.2014.10.050).
O. Ludwiczak, M. Antczak, M. Szachniuk, Assessing interface accuracy in macromolecular complexes, PLoS ONE, 2025, 20(4):e0319917 (doi:10.1371/journal.pone.0319917).
» 2024
F. Bu, Y. Adam, R.W. Adamiak, M. Antczak, B.R.H. de Aquino, N.G. Badepally, R.T. Batey, E.F. Baulin, P. Boinski, M.J. Boniecki, J.M. Bujnicki, K.A. Carpenter, J. Chacon, S.-J. Chen, W. Chiu, P. Cordero, N.K. Das, R. Das, W.K. Dawson, F. DiMaio, F. Ding, A.-C. Dock-Bregeon, N.V. Dokholyan, R.O. Dror, S. Dunin-Horkawicz, S. Eismann, E. Ennifar, R. Esmaeeli, M.A. Farsani, A.R. Ferré-D’Amaré, C. Geniesse, G.E. Ghanim, H.V. Guzman, I.V. Hood, L. Huang, D.S. Jain, F. Jaryani, L. Jin, A. Joshi, M. Karelina, J.S. Kieft, W. Kladwang, S. Kmiecik, D. Koirala, M. Kollmann, R.C. Kretsch, M. Kurcinski, J. Li, S. Li, M. Magnus, B. Masquida, S.N. Moafinejad, A. Mondal, S. Mukherjee, T.H.D. Nguyen, G. Nikolaev, C. Nithin, G. Nye, I.P.N. Pandaranadar Jeyeram, A. Perez, P. Pham, J.A. Piccirilli, S.P. Pilla, R. Pluta, S. Poblete, A. Ponce-Salvatierra, M. Popenda, L. Popenda, F. Pucci, R. Rangan, A. Ray, A. Ren, J. Sarzynska, C.M. Sha, F. Stefaniak, Z. Su, K.C. Suddala, M. Szachniuk, R. Townshend, R.J. Trachman III, J. Wang, W. Wang, A. Watkins, T.K. Wirecki, Y. Xiao, P. Xiong, Y. Xiong, J. Yang, J.D. Yesselman, J. Zhang, Y. Zhang, Z. Zhang, Y. Zhou, T. Zok, D. Zhang, S. Zhang, A. Zyla, E. Westhof, Z. Miao, RNA-Puzzles Round V: Blind predictions of 23 RNA structures, Nature Methods, 2024, (doi:s41592-024-02543-9).
B.A. Gren*, M. Antczak*, T. Zok, J.I. Sulkowska, M. Szachniuk, Knotted artifacts in predicted 3D RNA structures, PLOS Computational Biology, 2024, 20(6), pp. e1011959 (doi:10.1371/journal.pcbi.1011959).
M. Zurkowski, M. Swiercz, F. Wozny, M. Antczak, M. Szachniuk, RNAhugs web server for customized 3D RNA structure alignment, Nucleic Acids Research, 2024, 52(W1), pp. W348-W353 (doi:10.1093/nar/gkae259).
» 2023
J. Sarzynska, M. Popenda, M. Antczak, M. Szachniuk, RNA tertiary structure prediction using RNAComposer in CASP15, PROTEINS: Structure, Function, and Bioinformatics, 2023, 91(12), pp. 1790-1799 (doi:10.1002/prot.26578).
A. Kryshtafovych, M. Antczak, M. Szachniuk, T. Zok, R.C. Kretsch, R. Rangan, P. Pham, R. Das, X. Robin, G. Studer, J. Durairaj, J. Eberhardt, A. Sweeney, M. Topf, T. Schwede, K. Fidelis, J. Moult, New prediction categories in CASP15, PROTEINS: Structure, Function, and Bioinformatics, 2023, 91(12), pp. 1550-1557 (doi:10.1002/prot.26515).
M. Justyna, M. Antczak, M. Szachniuk, Machine learning for RNA 2D structure prediction benchmarked on experimental data, Briefings in Bioinformatics, 2023, 24(3), (doi:10.1093/bib/bbad153).
» 2022
J. Wiedemann, J. Kaczor, M. Milostan, T. Zok, J. Blazewicz, M. Szachniuk, M. Antczak, RNAloops: a database of RNA multiloops, Bioinformatics, 2022, 38(17), pp. 4200-4205 (doi:10.1093/bioinformatics/btac484).
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, Computational pipeline for reference-free comparative analysis of RNA 3D structures applied to SARS-CoV-2 UTR models, International Journal of Molecular Sciences, 2022, 23(17), pp. 9630 (doi:10.3390/ijms23179630).
B. Adamczyk, M. Antczak, M. Szachniuk, RNAsolo: a repository of clean, experimentally determined RNA 3D structures, Bioinformatics, 2022, 38(14), pp. 3668-3670 (doi:10.1093/bioinformatics/btac386). The best students' publication in years 2022-2023 awarded by the RNA Salon Poznan supported by RNA Society & Lexogen company.
K. Luwanski, V. Hlushchenko, M. Popenda, T. Zok, J. Sarzynska, D. Martsich, M. Szachniuk, M. Antczak, RNAspider: a webserver to analyze entanglements in RNA 3D structures, Nucleic Acids Research, 2022, 50(W1), pp. W663–W669 (doi:10.1093/nar/gkac218).
F. Carrascoza*, M. Antczak*, Z. Miao, E. Westhof, M. Szachniuk, Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions, RNA, 2022, 28(2), pp. 250–262 (doi:10.1261/rna.078685.121).
» 2021
M. Popenda, T. Zok, J. Sarzynska, A. Korpeta, R.W. Adamiak, M. Antczak, M. Szachniuk, Entanglements of structure elements revealed in RNA 3D models, Nucleic Acids Research, 2021, 49(17), pp. 9625–9632 (doi:10.1093/nar/gkab716).
» 2020
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, pp. 982-995 (doi:10.1261/rna.075341.120) [PDF].
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), pp. 315-324 (doi:10.34768/amcs-2020-0024) [PDF].
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(2), pp. 576-588 (doi:10.1093/nar/gkz1108) [PDF].
» 2019
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(1), pp. 152-155 (doi:10.1093/bioinformatics/bty609) [PDF].
» 2018
M. Antczak, T. Zok, M. Osowiecki, M. Popenda, R.W. Adamiak, M. Szachniuk, RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures, BMC Bioinformatics, 2018, 19, pp. 304 (doi:10.1186/s12859-018-2317-9) [PDF].
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), pp. W30-W35 (doi:10.1093/nar/gky314) [PDF].
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), pp. 3:1-3:34 (doi:10.1145/3143560) [PDF].
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), pp. 1304-1312 (doi:10.1093/bioinformatics/btx783) [PDF].
» 2017
S. Wasik, M. Antczak, J. Badura, A. Laskowski, T. Sternal, A Survey on Online Judge Systems and Their Applications, ACM Computing Surveys pre-print on arXiv.org, 2017 [PDF].
Z. Miao, R.W. Adamiak, M. Antczak, R.T. Batey, A. 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, RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme, RNA, 2017, 23(5), pp. 655-672 (doi:10.1261/rna.060368.116) [PDF].
» 2016
M. Antczak, M. Kasprzak, P. Lukasiak, J. Blazewicz, Structural alignment of protein descriptors - a combinatorial model, BMC Bioinformatics, 2016, 17, pp. 383 (doi:10.1186/s12859-016-1237-9) [PDF].
M. Antczak, M. Popenda, T. Zok, J. Sarzynska, T. Ratajczak, K. Tomczyk, R.W. Adamiak, M. Szachniuk, New functionality of RNAComposer: application to shape the axis of miR160 precursor structure, Acta Biochimica Polonica, 2016, 63(4), pp. 737–744 (doi:10.18388/abp.2016_1329) [PDF].
M. Chlopkowski, M. Antczak, M. Slusarczyk, A. Wdowinski, M. Zajaczkowski, M. Kasprzak, High-order statistical compressor for long-term storage of DNA sequencing data, RAIRO - Operations Research, 2016, 50(2), pp. 351-361
(doi:10.1051/ro/2015039) [PDF].
» 2015
A. Rybarczyk, N. Szostak, M. Antczak, T. Zok, M. Popenda, R.W. Adamiak, J. Blazewicz, M. Szachniuk, New in silico approach to assessing RNA secondary structures with non-canonical base pairs, BMC Bioinformatics, 2015, 16(1), pp. 276 (doi:10.1186/s12859-015-0718-6) [PDF].
P. Lukasiak, M. Antczak, T. Ratajczak, M. Szachniuk, M. Popenda, R.W. Adamiak, J. Blazewicz, RNAssess - a web server for quality assessment of RNA 3D structures, Nucleic Acids Research, 2015, 43(W1), pp. W502-506 (doi:10.1093/nar/gkv557) [PDF].
T. Zok, M. Antczak, M. Riedel, D. Nebel, T. Villmann, P. Lukasiak, J. Blazewicz, M. Szachniuk, Building the library of RNA 3D nucleotide conformations using clustering approach, International Journal of Applied Mathematics and Computer Science, 2015, 25(3), pp. 689-700 (doi:10.1515/amcs-2015-0050) [PDF].
» 2014
M. Antczak*, T. Zok*, M. Popenda, P. Lukasiak, R.W. Adamiak, J. Blazewicz, M. Szachniuk, RNApdbee – a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs, Nucleic Acids Research, 2014, 42(W1), pp. W368-72 (doi:10.1093/nar/gku330) [PDF].
» 2013
P. Lukasiak, M. Antczak, T. Ratajczak, J. M. Bujnicki, M. Szachniuk, M. Popenda, R. W. Adamiak, J. Blazewicz, RNAlyzer - novel approach for quality analysis of RNA structural models, Nucleic Acids Research, 2013, 41(12), pp. 5978-5990 (doi:10.1093/nar/gkt318) [PDF].
» 2012
M. Popenda, M. Szachniuk, M. Antczak, K.J. Purzycka, P. Lukasiak, N. Bartol, J. Blazewicz, R. W. Adamiak, Automated 3D structure composition for large RNAs, Nucleic Acids Research, 2012, 40(14):e112 (doi:10.1093/nar/gks339) [PDF].
» 2011
M. Antczak, J. Blazewicz, P. Lukasiak, M. Milostan, N. Krasnogor, G. Palik, DomAns—Pattern based method for protein domain boundaries prediction and analysis, Foundations of Computing and Decision Sciences, 2011, 36(2), pp. 99-119 [PDF].
S. Wasik, M. Antczak, J. Badura, A. Laskowski, Evaluation as a Service architecture and crowdsourced problems solving implemented in Optil.io platform, (Proceedings of the Data Science meets Optimization Workshop at Federated Artificial Intelligence meeting (DSO@FAIM), Stockholm, Sweden, 14.07.2018), 2018 [PDF].
» 2017
S. Wasik, M. Antczak, J. Badura, A. Laskowski, M. Olszowy, T. Sternal, K. Wedrowicz, Optil.io Platform: Evaluation as a Service for Metaheuristics, (Proceedings of the 12th Metaheuristics International Conference (MIC), Barcelona, Spain, 04-07.07.2017), 2017, pp. 225-227 [PDF].
» 2016
T. Zok, M. Antczak, M. Popenda, J. Sarzynska, T. Ratajczak, R.W. Adamiak, M. Szachniuk, RNAComposer: new developments to increase accuracy of 3D RNA structure prediction, Acta Biochimica Polonica, 2016, 63(2) Supplement, pp. 174 [PDF].
N. Szostak, A. Rybarczyk, M. Antczak, T. Zok, M. Popenda, R.W. Adamiak, J. Blazewicz, M. Szachniuk, New in silico approach to assess RNA secondary structures with non-canonical base pairs, Acta Biochimica Polonica, 2016, 63(2) Supplement, pp. 172 [PDF].
S. Wasik, M. Antczak, J. Badura, A. Laskowski, T. Sternal, Optil.io: Cloud Based Platform For Solving Optimization Problems Using Crowdsourcing Approach, (Proceedings of the 19th ACM Conference on Computer Supported Cooperative Work and Social Computing Companion (CSCW), San Francisco, USA, 27.02-02.03.2016), 2016, pp. 433-436 (doi:10.1145/2818052.2869098) [PDF].
» 2015
P. Lukasiak, M. Antczak, T. Ratajczak, J. Blazewicz, SphereGrinder - reference structure-based tool for quality assessment of protein structural models, (Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Washington D.C., USA, 9.11-12.11.2015), 2015, pp. 665-668 (doi:10.1109/BIBM.2015.7359765) [PDF].
N. Szostak, A. Rybarczyk, M. Antczak, T. Zok, M. Popenda, R.W. Adamiak, J. Blazewicz, M. Szachniuk, New in silico approach to assess RNA secondary structures with non-canonical base pairs, Machine Learning Reports (Proceedings of the ICOLE2015 – German - Polish Workshop on Computational Biology, Perspectives of Bioinformatics, Operations Research and Machine Learning, Lessach, Austria, 28.9-3.10.2015), 2015, pp. 13, [PDF].
P. Ceranek, T. Zok, M. Antczak, M. Szachniuk, RNAsprite - a concept of tool to calculate RNA structural data, Machine Learning Reports (Proceedings of the ICOLE2015 – German - Polish Workshop on Computational Biology, Perspectives of Bioinformatics, Operations Research and Machine Learning, Lessach, Austria, 28.9-3.10.2015), 2015, pp. 14, [PDF].
P. Lukasiak, T. Ratajczak, M. Antczak, Computational approaches for quality analysis of RNA structures, Machine Learning Reports (Proceedings of the ICOLE2015 – German - Polish Workshop on Computational Biology, Perspectives of Bioinformatics, Operations Research and Machine Learning, Lessach, Austria, 28.9-3.10.2015), 2015, pp. 15, [PDF].
T. Zok, M. Antczak, M. Riedel, D. Nebel, T. Villmann, P. Lukasiak, J. Blazewicz, M. Szachniuk, Clustering approach to create libraries of representative RNA conformers, Machine Learning Reports (Proceedings of the ICOLE2015 – German - Polish Workshop on Computational Biology, Perspectives of Bioinformatics, Operations Research and Machine Learning, Lessach, Austria, 28.9-3.10.2015), 2015, pp. 18, [PDF].
» 2011
M. Antczak, P. Lukasiak, K. Fidelis, A. Kryshtafovych, J. Blazewicz, Protein structure quality assessment and modeling support techniques, Machine Learning Reports (Proceedings of the ICOLE2011 – German - Polish Workshop on Computational Biology, Perspectives of Bioinformatics, Operations Research and Machine Learning, Lessach, Austria, 18.09-24.09.2011), 2011, pp. 21, [PDF].
» 2010
T. Zok, M. Szachniuk, M. Antczak, Comparison of RNA structures in torsional angle space, Machine Learning Reports (Proceedings of the ICOLE2010 – German - Polish Workshop on Computational Biology, Perspectives of Bioinformatics, Operations Research and Machine Learning, Lessach, Austria, 26.09-02.10.2010), 2010, pp. 14, [PDF].
P. Lukasiak, K. Fidelis, M. Antczak, A. Kryshtafovych, J. Blazewicz, Automated prediction of 3D structure of proteins based on descriptors approach, Machine Learning Reports (Proceedings of the ICOLE2010 – German - Polish Workshop on Computational Biology, Perspectives of Bioinformatics, Operations Research and Machine Learning, Lessach, Austria, 26.09-02.10.2010), 2010, pp. 19, [PDF].
M. Szachniuk, M. Popenda, M. Antczak, K.J. Purzycka, P. Lukasiak, N. Bartol, J. Blazewicz, R. W. Adamiak, RNAComposer and the art of composing RNA structures, Machine Learning Reports (Proceedings of the ICOLE2010 – German - Polish Workshop on Computational Biology, Perspectives of Bioinformatics, Operations Research and Machine Learning, Lessach, Austria, 26.09-02.10.2010), 2010, pp. 26, [PDF].
» 2009
M. Milostan, J. Sarzynska, A. Mickiewicz, M. Antczak, P. Lukasiak, J. Blazewicz, Protein structure modelling–case study, TU Clausthal Technical Report Series (Proceedings of the ICOLE2009 – German - Polish Workshop on Computational Biology, Perspectives of Bioinformatics, Operations Research and Machine Learning, Lessach, Austria, 25.05-29.05.2009), 2009, pp. 47, [PDF].
P. Lukasiak, M. Antczak, A. Hoffa, W. Biniecki, M. Wojciechowski, ProDomAn-Protein Domains Analysis platform, TU Clausthal Technical Report Series (Proceedings of the ICOLE2009 – German - Polish Workshop on Computational Biology, Perspectives of Bioinformatics, Operations Research and Machine Learning, Lessach, Austria, 25.05-29.05.2009), 2009, pp. 60, [PDF].
» 2008
M. Antczak, R. W. Adamiak, P. Lukasiak, M. Popenda, M. Szachniuk, G. Palik, J. Blazewicz, 3D–RNA–Pred: An Automatic Construction of Three–Dimensional RNA Structures, TU Clausthal Technical Report Series (Proceedings of the ICOLE2008 – German - Polish Workshop on Computational Biology, Perspectives of Bioinformatics, Operations Research and Machine Learning, Lessach, Austria, 09.06-13.06.2008), 2008, pp.46, [PDF].
» 2007
J. Blazewicz, P. Lukasiak, M. Antczak, M. Milostan, G. Palik, Domain Analysis Server (DomAnS)–Protein domains prediction algorithm (DomAn), TU Clausthal Technical Report Series (Proceedings of the ICOLE2007 – German - Polish Workshop on Computational Biology, Perspectives of Bioinformatics, Operations Research and Machine Learning, Lessach, Austria, 27.05-02.06.2007), 2007, pp. 18, [PDF].
M. Milostan, J. Blazewicz, P. Lukasiak, M. Antczak, Graph clustering approach for protein domain decomposition, TU Clausthal Technical Report Series (Proceedings of the ICOLE2007 – German - Polish Workshop on Computational Biology, Perspectives of Bioinformatics, Operations Research and Machine Learning, Lessach, Austria, 27.05-02.06.2007), 2007, pp. 22, [PDF].
T. Zok, M. Antczak, Przewidywanie konformacji przestrzennych zasad azotowych na podstawie łańcucha głównego cząsteczki RNA, Technical Report RB-1/2014, Faculty of Computing, Poznan University of Technology.
» 2013
M. Antczak, Algorytmiczne aspekty modelowania i ewaluacji biomolekuł (Algorithmic aspects of modeling and evaluation of biomolecules), Ph.D. thesis, Faculty of Computing, Poznan University of Technology.
» 2005
M. Antczak, Modelowanie i wyznaczanie niepewnych pozycji min morskich, M.Sc. thesis, Computer Science and Management Faculty, Poznan University of Technology.
» 2003
M. Antczak, W. Jankun, D. Kowalczyk, J. Solawa, Portal internetowy opisujący nowoczesne sieci optyczne, B.Sc. thesis, Electrical Engineering Faculty, Poznan University of Technology.