1.

RNAtango: analysing and comparing RNA 3D structures via torsional angles / Marta Mackowiak (WIiT), Bartosz Adamczyk (WIiT), Marta Szachniuk (WIiT), Tomasz Żok (WIiT) // PLoS Computational Biology - 2024, vol. 20, iss. 10, p. e1012500-1-e1012500-15

Scientific article 140 3,8

2.

Knotted artifacts in predicted 3D RNA structures / Bartosz Ambroży Greń, Maciej Antczak (WIiT), Tomasz Żok (WIiT), Joanna Ida Sułkowska, Marta Szachniuk (WIiT) // PLoS Computational Biology - 2024, vol. 20, iss. 6, p. e1011959-1-e1011959-16

Scientific article 140 3,8

3.

WebTetrado: a webserver to explore quadruplexes in nucleic acid 3D structures / Bartosz Adamczyk (WIiT), Michał Żurkowski (WIiT), Marta Szachniuk (WIiT), Tomasz Żok (WIiT) // Nucleic Acids Research - 2023, vol. 51, iss. W1, p. W607-W612

Scientific article 200 16,6

4.

New prediction categories in CASP15 / Andriy Kryshtafovych, Maciej Antczak (WIiT), Marta Szachniuk (WIiT), Tomasz Żok (WIiT), Rachael C. Kretsch, Ramya Rangan, Phillip Pham, Rhiju Das, Xavier Robin, Gabriel Studer, Janani Durairaj, Jerome Eberhardt, Aaron Sweeney, Maya Topf, Torsten Schwede, Krzysztof Fidelis, John Moult // Proteins: Structure, Function and Bioinformatics - 2023, vol. 91, iss. 12, p. 1550-1557

Scientific article 100 3,2

5.

When will RNA get its AlphaFold moment? / Bohdan Schneider, Blake Alexander Sweeney, Alex Bateman, Jiri Cerny, Tomasz Żok (WIiT), Marta Szachniuk (WIiT) // Nucleic Acids Research - 2023, vol. 51, iss. 18, p. 9522-9532

Scientific article 200 16,6

6.

Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models / Julita Gumna, Maciej Antczak (WIiT), Ryszard W. Adamiak (WIiT), Janusz M. Bujnicki, Shi-Jie Chen, Feng Ding, Pritha Ghosh, Jun Li, Sunandan Mukherjee, Chandran Nithin, Katarzyna Pachulska-Wieczorek, Almudena Ponce-Salvatierra, Mariusz Popenda, Joanna Sarzyńska, Tomasz Wirecki, Dong Zhang, Sicheng Zhang, Tomasz Żok (WIiT), Eric Westhof, Zhichao Miao, Marta Szachniuk (WIiT), Agnieszka Rybarczyk (WIiT) // International Journal of Molecular Sciences - 2022, vol. 23, iss. 17, p. 9630-1-9630-20

Scientific article 140 5,6

7.

RNAloops: a database of RNA multiloops / Jakub Wiedemann (WIiT), Jacek Kaczor (WIiT), Maciej Miłostan (WIiT), Tomasz Żok (WIiT), Jacek Błażewicz (WIiT), Marta Szachniuk (WIiT), Maciej Antczak (WIiT) // Bioinformatics - 2022, vol. 38, iss. 17, p. 4200-4205

Scientific article 200 5,8

8.

DrawTetrado to create layer diagrams of G4 structures / Michał Żurkowski (WIiT), Tomasz Żok (WIiT), Marta Szachniuk (WIiT) // Bioinformatics - 2022, vol. 38, iss. 15, p. 3835-3836

Scientific article 200 5,8

9.

Characterizing domain-specific open educational resources by linking ISCB Communities of Special Interest to Wikipedia / Alastair M. Kilpatrick, Farzana Rahman, Audra Anjum, Sayane Shome, K. M. Salim Andalib, Shrabonti Banik, Sanjana F. Chowdhury, Peter Coombe, Yesid Cuesta Astroz, J. Maxwell Douglas, Pradeep Eranti, Aleyna D. Kiran, Sachendra Kumar, Hyeri Lim, Valentina Lorenzi, Tiago Lubiana, Sakib Mahmud, Rafael Puche, Agnieszka Rybarczyk (WIiT), Syed Muktadir Al Sium, David Twesigomwe, Tomasz Żok (WIiT), Christine A. Orengo, Iddo Friedberg, Janet F. Kelso, Lonnie Welch // Bioinformatics - 2022, vol. 38, iss. Supplement_1, p. i19-i27

Scientific article 200 5,8

10.

RNAspider: a webserver to analyze entanglements in RNA 3D structures / Kamil Luwański (WIiT), Vladyslav Hlushchenko (WIiT), Mariusz Popenda, Tomasz Żok (WIiT), Joanna Sarzyńska, Daniil Martsich (WIiT), Marta Szachniuk (WIiT), Maciej Antczak (WIiT) // Nucleic Acids Research - 2022, vol. 50, iss. W1, p. W663-W669

Scientific article 200 14,9

11.

ONQUADRO: a database of experimentally determined quadruplex structures / Tomasz Żok (WIiT), Natalia Kraszewska, Joanna Miśkiewicz (WIiT), Paulina Pielacińska, Michał Żurkowski (WIiT), Marta Szachniuk (WIiT) // Nucleic Acids Research - 2022, vol. 50, iss. D1, p. D253-D258

Scientific article 200 14,9

12.

BioCommons: a robust Java library for RNA structural bioinformatics / Tomasz Żok (WIiT) // Bioinformatics - 2021, vol. 37, iss. 17, p. 2766-2767

Scientific article 200 6,931

13.

Entanglements of structure elements revealed in RNA 3D models / Mariusz Popenda, Tomasz Żok (WIiT), Joanna Sarzyńska, Agnieszka Korpeta, Ryszard W. Adamiak, Maciej Antczak, Marta Szachniuk (WIiT) // Nucleic Acids Research - 2021, vol. 49, iss. 17, p. 9625-9632

Scientific article 200 19,16

14.

Progress in the transferability of fusion workflows across HPC systems / Albert Gutierrez-Milla, Tomasz Żok (WIiT), Michał Owsiak, Marcin Plociennik, Mervi Mantsinen // Plasma Physics and Controlled Fusion - 2021, vol. 63, no. 8

Scientific article 100 2,532

15.

ElTetrado: a tool for identification and classification of tetrads and quadruplexes / Tomasz Żok (WIiT), Mariusz Popenda, Marta Szachniuk (WIiT) // BMC Bioinformatics - 2020, vol. 21, p. 40-1-40-7

Scientific article 100 3,169

16.

Morality, protection, security and gain: lessons from a minimalistic, economically inspired multi-agent model / Maciej Komosiński (WIiT), Tomasz Żok (WIiT) // Foundations of Computing and Decision Sciences - 2020, vol. 45, no. 1, p. 17-33

Scientific article 20

17.

New models and algorithms for RNA pseudoknot order assignment / Tomasz Żok (WIiT), Jan Badura (WIiT), Sylwester Swat (WIiT), Kacper Figurski, Mariusz Popenda, Maciej Antczak // International Journal of Applied Mathematics and Computer Science - 2020, vol. 30, no. 2, p. 315-324

Scientific article 100 1,417

18.

RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers / Zhichao Miao, Ryszard Adamiak, Maciej Antczak (WIiT), Michał Boniecki, Janusz M. Bujnicki, Shi-Jie Chen, Clarence Y. Cheng, Yi Cheng, Fang-Chieh Chou, Rhiju Das, Nikolay V. Dokholyan, Feng Ding, Caleb Geniesse, Yangwei Jiang, Astha Joshi, Andrey Krokhotin, Marcin Magnus, Olivier Mailhot, Francois Major, Thomas H. Mann, Paweł Piątkowski, Radosław Pluta, Mariusz Popenda, Joanna Sarzyńska, Lizhen Sun, Marta Szachniuk (WIiT), Sigi Tian, Jian Wang, Andrew M. Watkins, Jakub Wiedemann (WIiT), Xiaojun Xu, Joseph D. Yesselman, Dong Zhang, Zhenzhen Zhang, Chenhan Zhao, Peinan Zhao, Yuanzhe Zhou, Tomasz Żok (WIiT), Adriana Żyła, Aiming Ren, Robert T. Batey, Barbara L. Golden, Lin Huang, David M. Lilley, Yijin Liu, Dinshaw J. Patel, Eric Westhof // RNA - 2020, vol. 26, no. 12, p. 982-995

Scientific article 140 4,942

19.

RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools / Marcin Magnus, Maciej Antczak, Tomasz Żok (WIiT), Jakub Wiedemann (WIiT), Piotr Łukasiak (WIiT), Cao Yang, Janusz M. Bujnicki, Eric Westhof, Marta Szachniuk (WIiT), Zhichao Miao // Nucleic Acids Research - 2020, vol. 48, iss. 2, p. 576-588

Scientific article 200 16,971

20.

RNAthor - fast, accurate normalization, visualization and statistical analysis of RNA probing data resolved by capillary electrophoresis / Julita Gumna, Tomasz Żok (WIiT), Kacper Figurski, Katarzyna Pachulska-Wieczorek, Marta Szachniuk (WIiT) // PLoS ONE - 2020, vol. 15, iss. 10, p. e0239287-1-e0239287-12

Scientific article 100 3,24

21.

Topology-based classification of tetrads and quadruplex structures / Mariusz Popenda, Joanna Miśkiewicz (WIiT), Joanna Sarzyńska, Tomasz Żok (WIiT), Marta Szachniuk (WIiT) // Bioinformatics - 2020, vol. 36, iss. 4, p. 1129-1134

Scientific article 200 6,937

22.

RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs / Maciej Antczak (WI), Marcin Zabłocki (WI), Tomasz Żok (WI), Agnieszka Rybarczyk (WI), Jacek Błażewicz (WI), Marta Szachniuk (WI) // Bioinformatics - 2019, vol. 35, iss. 1, p. 152-155

Scientific article 200 5,61

23.

New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation / Maciej Antczak (WI), Mariusz Popenda, Tomasz Żok (WI), Michał Żurkowski (WI), Ryszard W. Adamiak, Marta Szachniuk // Bioinformatics - 2018, vol. 34, iss. 8, p. 1304-1312

Scientific article 45 4,531

24.

RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures / Maciej Antczak (WI), Tomasz Żok (WI), Maciej Osowiecki, Mariusz Popenda, Ryszard Adamiak (WI), Marta Szachniuk // BMC Bioinformatics - 2018, vol. 19, p. 1-11

Scientific article 35 2,511

25.

RNApdbee 2.0: multifunctional tool for RNA structure annotation / Tomasz Żok (WI), Maciej Antczak (WI), Michał Żurkowski (WI), Mariusz Popenda, Jacek Błażewicz (WI), Ryszard Adamiak, Marta Szachniuk // Nucleic Acids Research - 2018, vol. 46, iss. Web Server, p. W30-W35

Scientific article 40 11,147

26.

LCS-TA to identify similar fragments in RNA 3D structures / Jakub Wiedemann (WI), Tomasz Żok (WI), Maciej Miłostan (WI), Marta Szachniuk (WI) // BMC Bioinformatics - 2017, vol. 18, p. 456-469

Scientific article 35 2,213

27.

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme / Z. Miao, Ryszard Adamiak (WI), Maciej Antczak (WI), Robert Batey, Alexander Becka, Marcin Biesiada, M. Boniecki, Janusz M. Bujnicki, S. J. Chen, C. Cheng, F. C. Chou, A. R. Ferre-D'Amare, R. Das, Wayne Dawson, F. Ding, N. V. Dokholyan, S. Dunin-Horkawicz, C. Geniesse, Kalli Kappel, W. Kladwang, A. Krokhotin, G. Lach, F. Major, T. H. Mann, M. Magnus, Katarzyna Pachulska-Wieczorek, Dinshaw Patel, Joseph Piccirilli, Mariusz Popenda, Katarzyna J. Purzycka, Aiming Ren, Gregorry Rice, John Santalucia, Joanna Sarzyńska, Marta Szachniuk (WI), A. Tandon, Jeremiah Trausch, S. Tian, J. Wang, Kevin Weeks, Benfeard Williams, Y. Xiao, X. Xu, Dong Zhang, Tomasz Żok (WI), E. Westhof // RNA - 2017, vol. 23, no. 5, p. 655-672

Scientific article 35 4,49

28.

Running simultaneous Kepler sessions for the parallelization of parametric scans and optimization studies applied to complex workflows / Michał Owsiak, Marcin Płóciennik, Bartek Palak, Tomasz Żok, Cedric Reux, Luc Di Gallo, Denis Kalupin, Thomas Johnson, Mireille Schneider // Journal of Computational Science - 2017, vol. 20, p. 103-111

Scientific article 30 1,925

29.

New functionality of RNAComposer: an application to shape the axis of miR160 precursor structure / Maciej Antczak (WI), Mariusz Popenda, Tomasz Żok (WI), Joanna Sarzyńska, Tomasz Ratajczak (WI), Katarzyna Tomczyk (WI), Ryszard W. Adamiak, Marta Szachniuk (WI) // Acta Biochimica Polonica - 2016, vol. 63, no. 4, p. 737-744

Scientific article 15 1,159

30.

Building the Library of RNA 3D Nucleotide Conformations Using the Clustering Approach / Tomasz Żok (WI), Maciej Antczak (WI), Martin Riedel, David Nebel, Thomas Villmann, Piotr Łukasiak (WI), Jacek Błażewicz (WI), Marta Szachniuk (WI) // International Journal of Applied Mathematics and Computer Science - 2015, vol. 25, no. 3, p. 689-700

Scientific article 25 1,037

31.

New in silico approach to assessing RNA secondary structures with non-canonical base pairs / Agnieszka Rybarczyk, Natalia Szóstak, Maciej Antczak (WI), Tomasz Żok (WI), Mariusz Popenda, Ryszard Adamiak, Jacek Błażewicz (WI), Marta Szachniuk // BMC Bioinformatics - 2015, vol. 16, p. 276-1-276-12

Scientific article 35 2,435

32.

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. Ferre-D'Amare, F. Ding, R. Das, 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, Marta Szachniuk (WI), A. Tandon, S. Tian, J. Wang, Y. Xiao, X. Xu, J. Zhang, P. Zhao, Tomasz Żok (WI), E. Westhof // RNA - 2015, vol. 21, no. 6, p. 1066-1084

Scientific article 35

33.

MCQ4Structures to compute similarity of molecule structures / Tomasz Żok (WI), Mariusz Popenda, Marta Szachniuk (WI) // Central European Journal of Operations Research - 2014, vol. 22, iss. 3, p. 457-473

Scientific article 20 0,832

34.

RNApdbee - a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs / Maciej Antczak (WI), Tomasz Żok (WI), Mariusz Popenda, Piotr Łukasiak (WI), Ryszard W. Adamiak (WI), Jacek Błażewicz (WI), Marta Szachniuk // Nucleic Acids Research - 2014, vol. 42, iss. W1, p. W368-W372

Scientific article 40 9,112