1.

RNAhugs web server for customized 3D RNA structure alignment / Michał Żurkowski (WIiT), Mateusz Świercz (WIiT), Filip Woźny (WIiT), Maciej Antczak (WIiT), Marta Szachniuk (WIiT) // Nucleic Acids Research - 2024, vol. 52, iss. W1, p. W348-W353

Scientific article 200 16,6

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.

Toward Increasing the Credibility of RNA Design / Maciej Antczak (WIiT), Marta Szachniuk (WIiT) // Methods in molecular biology (Clifton, N.J.) - 2024, vol. 2847, p. 137-151

Scientific article 70

4.

High-quality, customizable heuristics for RNA 3D structure alignment / Michał Żurkowski (WIiT), Maciej Antczak (WIiT), Marta Szachniuk (WIiT) // Bioinformatics - 2023, vol. 39, iss. 5, p. btad315-1-btad315-9

Scientific article 200 4,4

5.

Machine learning for RNA 2D structure prediction benchmarked on experimental data / Marek Justyna (WIiT), Maciej Antczak (WIiT), Marta Szachniuk (WIiT) // Briefings in Bioinformatics - 2023, vol. 24, no. 3, p. bbad153-1-bbad153-9

Scientific article 140 6,8

6.

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

7.

RNA tertiary structure prediction using RNAComposer in CASP15 / Joanna Sarzynska, Mariusz Popenda, Maciej Antczak, Marta Szachniuk (WIiT) // Proteins: Structure, Function and Bioinformatics - 2023, vol. 91, iss. 12, p. 1790-1799

Scientific article 100 3,2

8.

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

9.

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

10.

RNAsolo: a repository of cleaned PDB-derived RNA 3D structures / Bartosz Adamczyk (WIiT), Maciej Antczak (WIiT), Marta Szachniuk (WIiT) // Bioinformatics - 2022, vol. 38, iss. 14, p. 3668-3670

Scientific article 200 5,8

11.

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

12.

Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions / Francisco Carrascoza (WIiT), Maciej Antczak (WIiT), Zhichao Miao, Eric Westhof, Marta Szachniuk (WIiT) // RNA - 2022, vol. 28, no. 2, p. 250-262

Scientific article 140 4,5

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.

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

15.

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

16.

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

17.

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

18.

A Survey on Online Judge Systems and Their Applications / Szymon Wąsik (WI), Maciej Antczak (WI), Jan Badura (WI), Artur Laskowski (WI), Tomasz Sternal (WI) // ACM Computing Surveys - 2018, vol. 51, no. 1, p. 3-1-3-34

Scientific article 50 6,131

19.

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

20.

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

21.

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

22.

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

23.

High-order statistical compressor for long-term storage of DNA sequencing data / Marek Chłopkowski (WI), Maciej Antczak (WI), Michał Ślusarczyk (WI), Aleksander Wdowiński (WI), Michał Zajączkowski (WI), Marta Kasprzak // RAIRO - Operations Research - 2016, vol. 50, no. 2, p. 351-361

Scientific article 15 0,55

24.

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

25.

Structural alignment of protein descriptors – a combinatorial model / Maciej Antczak (WI), Marta Kasprzak (WI), Piotr Łukasiak (WI), Jacek Błażewicz (WI) // BMC Bioinformatics - 2016, vol. 17, p. 383-1-383-14

Scientific article 35 2,448

26.

Automated 3D RNA structure prediction using the RNAComposer method for riboswitches / K. J. Purzycka, M. Popenda, Marta Szachniuk, Maciej Antczak (WI), Piotr Łukasiak, Jacek Błażewicz, R. W. Adamiak // Methods in Enzymology - 2015, vol. 553, p. 3-34

Scientific article 25

27.

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

28.

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

29.

RNAssess - a web server for quality assessment of RNA 3D structures / Piotr Łukasiak, Maciej Antczak (WI), Tomasz Ratajczak (WI), Marta Szachniuk, Mariusz Popenda, Ryszard Adamiak (WI), Jacek Błażewicz (WI) // Nucleic Acids Research - 2015, vol. 43, no. W1, p. W502-W-506

Scientific article 40 9,202

30.

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

31.

RNAlyzer-novel approach for quality analysis of RNA structural models / Piotr Łukasiak, Maciej Antczak (WI), Tomasz Ratajczak (WI), Janusz M. Bujnicki, Marta Szachniuk, Ryszard W. Adamiak, Mariusz Popenda, Jacek Błażewicz // Nucleic Acids Research - 2013, vol. 41, iss. 12, p. 5978-5990

Scientific article 40 8,808

32.

DomAns - pattern based method for protein domain boundaries prediction and analysis / Maciej Antczak (WI), Jacek Błażewicz (WI), Piotr Łukasiak (WI), Maciej Miłostan (WI), Natalio Krasnogor, Grzegorz Palik // Foundations of Computing and Decision Sciences - 2011, vol. 36, no. 2, p. 99-119

Scientific article

33.

Wpływ wykrawania blach obwodu magnetycznego maszyny prądu stałego na rozkład pola / Maciej Antczak (WI), Paweł Idziak (WE) // Maszyny Elektryczne : zeszyty problemowe - 2011, nr 96, p. 228-234

Scientific article