When Will RNA Get Its AlphaFold Moment? B. Schneider, B.A. Sweeney, A. Bateman, J. Cerny, T. Zok, M. Szachniuk. Nucleic Acids Research. 2023. gkad726. doi:10.1093/nar/gkad726
New Prediction Categories in CASP15. 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. Proteins: Structure, Function, and Bioinformatics. 2023. prot.26515. doi:10.1002/prot.26515
WebTetrado: A Webserver to Explore Quadruplexes in Nucleic Acid 3D Structures. B. Adamczyk, M. Zurkowski, M. Szachniuk, T. Zok. Nucleic Acids Research. 2023. gkad346. doi:10.1093/nar/gkad346
RNAloops: A Database of RNA Multiloops. J. Wiedemann, J. Kaczor, M. Milostan, T. Zok, J. Blazewicz, M. Szachniuk, M. Antczak. Bioinformatics. 2022. 38(17):4200–4205. doi:10.1093/bioinformatics/btac484
Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models. 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. International Journal of Molecular Sciences. 2022. 23(17):9630. doi:10.3390/ijms23179630
DrawTetrado to Create Layer Diagrams of G4 Structures. M. Zurkowski, T. Zok, M. Szachniuk. Bioinformatics. 2022. 38(15):3835–3836. doi:10.1093/bioinformatics/btac394
RNAspider: A Webserver to Analyze Entanglements in RNA 3D Structures. K. Luwanski, V. Hlushchenko, M. Popenda, T. Zok, J. Sarzynska, D. Martsich, M. Szachniuk, M. Antczak. Nucleic Acids Research. 2022. 50(W1):W663–W669. doi:10.1093/nar/gkac218
Characterizing Domain-Specific Open Educational Resources by Linking ISCB Communities of Special Interest to Wikipedia. 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. Bioinformatics. 2022. 38(Supplement_1):i19–i27. doi:10.1093/bioinformatics/btac236
ONQUADRO: A Database of Experimentally Determined Quadruplex Structures. T. Zok, N. Kraszewska, J. Miskiewicz, P. Pielacinska, M. Zurkowski, M. Szachniuk. Nucleic Acids Research. 2022. 50(D1):D253–D258. doi:10.1093/nar/gkab1118
Entanglements of Structure Elements Revealed in RNA 3D Models. M. Popenda, T. Zok, J. Sarzynska, A. Korpeta, R. Adamiak, M. Antczak, M. Szachniuk. Nucleic Acids Research. 2021. 49(17):9625–9632. doi:10.1093/nar/gkab716
BioCommons: A Robust Java Library for RNA Structural Bioinformatics. T. Zok. Bioinformatics. 2021. 37(17):2766–2767. doi:10.1093/bioinformatics/btab069
Progress in the Transferability of Fusion Workflows Across HPC Systems. A. Gutierrez-Milla, T. Zok, M. Owsiak, M. Plociennik, M. Mantsinen. Plasma Physics and Controlled Fusion. 2021. 63(8):084004. doi:10.1088/1361-6587/ac08f8
ElTetrado: A Tool for Identification and Classification of Tetrads and Quadruplexes. T. Zok, M. Popenda, M. Szachniuk. BMC Bioinformatics. 2020. 21(1):40. doi:10.1186/s12859-020-3385-1
RNAthor – Fast, Accurate Normalization, Visualization and Statistical Analysis of RNA Probing Data Resolved by Capillary Electrophoresis. J. Gumna, T. Zok, K. Figurski, K. Pachulska-Wieczorek, M. Szachniuk. PLoS One. 2020. 15(10):e0239287. doi:10.1371/journal.pone.0239287
RNA-Puzzles Round IV: 3D Structure Predictions of Four Ribozymes and Two Aptamers. 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.H. Mann, P. Piatkowski, R. Pluta, M. Popenda, J. Sarzynska, L. Sun, M. Szachniuk, S. Tian, J. Wang, J. Wang, A.M. Watkins, J. Wiedemann, Y. Xiao, X. Xu, J.D. Yesselman, D. Zhang, Y. 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. RNA. 2020. 26:982–995. doi:10.1261/rna.075341.120
New Models and Algorithms for RNA Pseudoknot Order Assignment. T. Zok, J. Badura, S. Swat, K. Figurski, M. Popenda, M. Antczak. International Journal of Applied Mathematics and Computer Science. 2020. 30(2):315–324. doi:10.34768/amcs-2020-0024
Morality, Protection, Security and Gain: Lessons from a Minimalistic, Economically Inspired Multi-Agent Model. M. Komosinski, T. Zok. Foundations of Computing and Decision Sciences. 2020. 45(1):17–33. doi:10.2478/fcds-2020-0002
Topology-Based Classification of Tetrads and Quadruplex Structures. M. Popenda, J. Miskiewicz, J. Sarzynska, T. Zok, M. Szachniuk. Bioinformatics. 2020. 36(4):1129–1134. doi:10.1093/bioinformatics/btz738
RNA-Puzzles Toolkit: A Computational Resource of RNA 3D Structure Benchmark Datasets, Structure Manipulation and Evaluation Tools. M. Magnus, M. Antczak, T. Zok, J. Wiedemann, P. Lukasiak, Y. Cao, J.M. Bujnicki, E. Westhof, M. Szachniuk, Z. Miao. Nucleic Acids Research. 2020. 48(2):576–588. doi:10.1093/nar/gkz1108
RNAvista: A Webserver to Assess RNA Secondary Structures with Non-Canonical Base Pairs. M. Antczak, M. Zablocki, T. Zok, A. Rybarczyk, J. Blazewicz, M. Szachniuk. Bioinformatics. 2019. 35(1):152–155. doi:10.1093/bioinformatics/bty609
INDIGO-DataCloud: A Platform to Facilitate Seamless Access to e-Infrastructures. D. Salomoni, I. Campos, L. Gaido, J.M. de Lucas, P. Solagna, J. Gomes, L. Matyska, P. Fuhrman, M. Hardt, G. Donvito, L. Dutka, M. Plociennik, R. Barbera, I. Blanquer, A. Ceccanti, E. Cetinic, M. David, C. Duma, A. López-García, G. Moltó, P. Orviz, Z. Sustr, M. Viljoen, F. Aguilar, L. Alves, M. Antonacci, L.A. Antonelli, S. Bagnasco, A.M.J.J. Bonvin, R. Bruno, Y. Chen, A. Costa, D. Davidovic, B. Ertl, M. Fargetta, S. Fiore, S. Gallozzi, Z. Kurkcuoglu, L. Lloret, J. Martins, A. Nuzzo, P. Nassisi, C. Palazzo, J. Pina, E. Sciacca, D. Spiga, M. Tangaro, M. Urbaniak, S. Vallero, B. Wegh, V. Zaccolo, F. Zambelli, T. Zok. Journal of Grid Computing. 2018. 16(3):381–408. doi:10.1007/s10723-018-9453-3
RNAfitme: A Webserver for Modeling Nucleobase and Nucleoside Residue Conformation in Fixed-Backbone RNA Structures. M. Antczak, T. Zok, M. Osowiecki, M. Popenda, R.W. Adamiak, M. Szachniuk. BMC Bioinformatics. 2018. 19(1):304. doi:10.1186/s12859-018-2317-9
RNApdbee 2.0: Multifunctional Tool for RNA Structure Annotation. T. Zok, M. Antczak, M. Zurkowski, M. Popenda, J. Blazewicz, R.W. Adamiak, M. Szachniuk. Nucleic Acids Research. 2018. 46(W1):W30–W35. doi:10.1093/nar/gky314
New Algorithms to Represent Complex Pseudoknotted RNA Structures in Dot-Bracket Notation. M. Antczak, M. Popenda, T. Zok, M. Zurkowski, R.W. Adamiak, M. Szachniuk. Bioinformatics. 2018. 34(8):1304–1312. doi:10.1093/bioinformatics/btx783
LCS-TA to Identify Similar Fragments in RNA 3D Structures. J. Wiedemann, T. Zok, M. Milostan, M. Szachniuk. BMC Bioinformatics. 2017. 18(1):456. doi:10.1186/s12859-017-1867-6
RNA-Puzzles Round III: 3D RNA Structure Prediction of Five Riboswitches and One Ribozyme. 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. Ferré-D’Amaré, 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.J. Santalucia, J. Sarzynska, M. Szachniuk, A. Tandon, J.J. Trausch, S. Tian, J. Wang, K.M. Weeks, B.W. II, Y. Xiao, X. Xu, D. Zhang, T. Zok, E. Westhof. RNA. 2017. 23(5):655–672. doi:10.1261/rna.060368.116
Running Simultaneous Kepler Sessions for the Parallelization of Parametric Scans and Optimization Studies Applied to Complex Workflows. M. Owsiak, M. Plociennik, B. Palak, T. Zok, C. Reux, L.D. Gallo, D. Kalupin, T. Johnson, M. Schneider. Journal of Computational Science. 2017. 20:103–111. doi:10.1016/j.jocs.2016.12.005
New Functionality of RNAComposer: Application to Shape the Axis of miR160 Precursor Structure. M. Antczak, M. Popenda, T. Zok, J. Sarzynska, T. Ratajczak, K. Tomczyk, R.W. Adamiak, M. Szachniuk. Acta Biochimica Polonica. 2017. 63(4): doi:10.18388/abp.2016_1329
Building the Library of RNA 3D Nucleotide Conformations Using Clustering Approach. T. Zok, M. Antczak, M. Riedel, D. Nebel, T. Villmann, P. Lukasiak, J. Blazewicz, M. Szachniuk. International Journal of Applied Mathematics and Computer Science. 2015. 25(3):689–700. doi:10.1515/amcs-2015-0050
New in Silico Approach to Assess RNA Secondary Structures with Non-Canonical Base Pairs. A. Rybarczyk, N. Szostak, M. Antczak, T. Zok, M. Popenda, R.W. Adamiak, J. Blazewicz, M. Szachniuk. BMC Bioinformatics. 2015. 16(1):276. doi:10.1186/s12859-015-0718-6
RNA-Puzzles Round II: Assessment of RNA Structure Prediction Programs Applied to Three Large RNA Structures. Z. Miao, R.W. Adamiak, M.-F. Blanchet, M. Boniecki, J.M. Bujnicki, S.-J. Chen, C. Cheng, G. Chojnowski, F.-C. Chou, P. Cordero, J.A. Cruz, A.R. Ferré-D’Amaré, R. Das, F. Ding, N.V. Dokholyan, S. Dunin-Horkawicz, W. Kladwang, A. Krokhotin, G. Lach, M. Magnus, F. Major, T.H. Mann, B. Masquida, D. Matelska, M. Meyer, A. Peselis, M. Popenda, K.J. Purzycka, A. Serganov, J. Stasiewicz, M. Szachniuk, A. Tandon, S. Tian, J. Wang, Y. Xiao, X. Xu, J. Zhang, P. Zhao, T. Zok, E. Westhof. RNA. 2015. 21(6):1066–1084. doi:10.1261/rna.049502.114
MCQ4Structures to Compute Similarity of Molecule Structures. T. Zok, M. Popenda, M. Szachniuk. Central European Journal of Operations Research. 2014. 22(3):457–473. doi:10.1007/s10100-013-0296-5
RNApdbee – a Webserver to Derive Secondary Structures from Pdb Files of Knotted and Unknotted RNAs. M. Antczak, T. Zok, M. Popenda, P. Lukasiak, R.W. Adamiak, J. Blazewicz, M. Szachniuk. Nucleic Acids Research. 2014. 42(W1):W368–W372. doi:10.1093/nar/gku330
The European Integrated Tokamak Modelling (ITM) Effort: Achievements and First Physics Results. G.L. Falchetto, D. Coster, R. Coelho, B.D. Scott, L. Figini, D. Kalupin, E. Nardon, S. Nowak, L.L. Alves, J.F. Artaud, V. Basiuk, J.P.S. Bizarro, C. Boulbe, A. Dinklage, D. Farina, B. Faugeras, J. Ferreira, A. Figueiredo, P. Huynh, F. Imbeaux, I. Ivanova-Stanik, T. Jonsson, H.-J. Klingshirn, C. Konz, A. Kus, N.B. Marushchenko, G. Pereverzev, M. Owsiak, E. Poli, Y. Peysson, R. Reimer, J. Signoret, O. Sauter, R. Stankiewicz, P. Strand, I. Voitsekhovitch, E. Westerhof, T. Zok, W. Zwingmann, I.-T. Contributors, the A.U. Team, J.-E. Contributors. Nuclear Fusion. 2014. 54(4):043018. doi:10.1088/0029-5515/54/4/043018
Approaches to Distributed Execution of Scientific Workflows in Kepler. M. Plociennik, T. Zok, I. Altintas, J. Wang, D. Crawl, D. Abramson, F. Imbeaux, B. Guillerminet, M. Lopez-Caniego, I.C. Plasencia, W. Pych, P. Ciecielag, B. Palak, M. Owsiak, Y. Frauel. Fundamenta Informaticae. 2013. 128(3):281–302. doi:10.3233/fi-2013-947
Kepler-Based Workflow Environment for Astronomy. P. Ciecielag, M. Plociennik, P. Spyra, M. Urbaniak, T. Zok, W. Pych, A. Hypki. eScience on Distributed Computing Infrastructure. 2014. 8500:278–292. doi:10.1007/978-3-319-10894-0_20
User-Friendly Frameworks for Accessing Computational Resources. B. Palak, P. Wolniewicz, M. Plociennik, M. Owsiak, T. Zok. Building a National Distributed e-Infrastructure – PL-Grid. 2012. 7136:191–204. doi:10.1007/978-3-642-28267-6_15
Distributed and Cloud-Based Multi-Model Analytics Experiments on Large Volumes of Climate Change Data in the Earth System Grid Federation Eco-System. S. Fiore, M. Plociennik, C. Doutriaux, C. Palazzo, J. Boutte, T. Zok, D. Elia, M. Owsiak, A. D’Anca, Z. Shaheen, R. Bruno, M. Fargetta, M. Caballer, G. Molto, I. Blanquer, R. Barbera, M. David, G. Donvito, D.N. Williams, V. Anantharaj, D. Salomoni, G. Aloisio. 2016 IEEE International Conference on Big Data. 2016. 2911–2918. doi:10.1109/bigdata.2016.7840941
Best Practices in Debugging Kepler Workflows. M. Owsiak, M. Plociennik, B. Palak, T. Zok, O. Hoenen. Procedia Computer Science. 2016. 80:2332–2337. doi:10.1016/j.procs.2016.05.433
Running Simultaneous Kepler Sessions for the Parallelization of Parametric Scans and Optimization Studies Applied to Complex Workflows. M. Owsiak, M. Plociennik, B. Palak, T. Zok, C. Reux, L. Di Gallo, M. Schneider, T. Johnson, D. Kalupin. Procedia Computer Science. 2016. 80:690–699. doi:10.1016/j.procs.2016.05.362
Clustering Approach to Create Libraries of Representative RNA Conformers. T. Zok, M. Antczak, M. Riedel, D. Nebel, T. Villmann, P. Lukasiak, J. Blazewicz, M. Szachniuk. Machine Learning Reports. 2015. 04/2015:18.
Tools, Methods and Services Enhancing the Usage of the Kepler-Based Scientific Workflow Framework. M. Plociennik, S. Winczewski, P. Ciecielag, F. Imbeaux, B. Guillerminet, P. Huynh, M. Owsiak, P. Spyra, T. Aniel, B. Palak, T. Zok, W. Pych, J. Rybicki. Procedia Computer Science. 2014. 29:1733–1744. doi:10.1016/j.procs.2014.05.158
Flexible Approach to Astronomical Data Reduction Workflows in Kepler. P. Ciecielag, M. Plociennik, P. Spyra, M. Urbaniak, T. Zok, W. Pych. Procedia Computer Science. 2014. 29:1756–1761. doi:10.1016/j.procs.2014.05.160
Application Scenarios Using Serpens Suite for Kepler Scientific Workflow System. M. Plociennik, M. Owsiak, T. Zok, B. Palak, A. Gomez-Iglesias, F. Castejon, M. Lopez-Caniego, I.C. Plasencia, A. Costantini, D. Yadykin, P. Strand. Procedia Computer Science. 2012. 9:1604–1613. doi:10.1016/j.procs.2012.04.176
Serpens Suite for Kepler Workflow Orchestration System. T. Zok, M. Plociennik, M. Owsiak. UNICORE Summit Proceedings. 2011. 9:11–23.
Comparison of RNA Structures in Torsional Angle Space. T. Zok, M. Szachniuk, M. Antczak. Machine Learning Reports. 2011. 01/2011:14–18.
Comparison of RNA Structures - Concepts and Measures. T. Zok, M. Popenda, M. Szachniuk. TU Clausthal Technical Reports. 2008. Ifi-08-06:42–44.
Pseudotorsion-based probabilistic sampling of RNA 3D conformational space. T. Zok. Technical Report. January 2019. Institute of Computing Science, Poznan University of Technology
Biblioteka funkcji do łącznej analizy struktur 3D RNA w przestrzeni kartezjańskiej i geometrycznej. T. Zok. Technical Report. February 2018. Institute of Computing Science, Poznan University of Technology
Przewidywanie konformacji przestrzennych zasad azotowych na podstawie łańcucha głównego cząsteczki RNA. T. Zok, M. Antczak. Technical Report. December 2015. Institute of Computing Science, Poznan University of Technology