1.

A new molecular mechanism of RNA circularization and the microRNA sponge formation / Agnieszka Belter, Mariusz Popenda, Marcin Sajek, Tomasz Woźniak, Mirosława Z. Naskręt-Barciszewska, Marta Szachniuk (WIiT), Stefan Jurga, Jan Barciszewski // Journal of Biomolecular Structure and Dynamics - 2022, vol. 40, no. 7, p. 3038-3045

Scientific article 70.0

2.

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, in press

Scientific article 200.0 16.971

3.

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 200.0 16.971

4.

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 100.0 3.169

5.

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 100.0 1.417

6.

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 140.0 4.942

7.

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 200.0 6.937

8.

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 45.0 4.531

9.

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 35.0 2.511

10.

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 40.0 11.147

11.

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 35.0 4.490

12.

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 15.0 1.159

13.

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 25.0

14.

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 35.0 2.435

15.

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 35.0

16.

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 40.0 9.202

17.

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 0.832

18.

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 40.0 9.112

19.

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 40.0 8.808