1.

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

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, vol. 50, iss. W1, p. W663-W669

Scientific article 200 14,9

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 19,16

4.

How bioinformatics resources work with G4 RNAs / Joanna Miśkiewicz (WIiT), Joanna Sarzyńska, Marta Szachniuk (WIiT) // Briefings in Bioinformatics - 2021, vol. 22, no. 3, p. bbaa201-1-bbaa201-14

Scientific article 140 13,994

5.

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

6.

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

7.

Bioinformatics Study of Structural Patterns in Plant MicroRNA Precursors / Joanna Miśkiewicz (WI), Katarzyna Tomczyk (WI), Agnieszka Mickiewicz, Joanna Sarzyńska, Marta Szachniuk (WI) // BioMed Research International - 2017, vol. 2017, p. 6783010-1-6783010-8

Scientific article 25 2,583

8.

Modeling of the catalytic core of Arabidopsis thaliana Dicer-like 4 protein and its complex with double-stranded RNA / Agnieszka Mickiewicz, Joanna Sarzyńska, Maciej Miłostan (WI), Anna Kurzyńska-Kokorniak, Agnieszka Rybarczyk, Piotr Łukasiak (WI), Tadeusz Kuliński, Marek Figlerowicz, Jacek Błażewicz (WI) // Computational Biology and Chemistry - 2017, vol. 66, p. 44-56

Scientific article 25 1,412

9.

Mutations in human AID differentially affect its ability to deaminate cytidine and 5-methylcytidine in ssDNA substrates in vitro / Lucyna Budźko, Paulina Jackowiak, Karol Kamel, Joanna Sarzyńska, Janusz M. Bujnicki, Marek Figlerowicz // Scientific Reports - 2017, vol. 7, p. 3873-1-3873-16

Scientific article 40 4,122

10.

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

11.

AmiRNA Designer - new method of artificial miRNA design / Agnieszka Mickiewicz, Agnieszka Rybarczyk, Joanna Sarzyńska, Marek Figlerowicz, Jacek Błażewicz (WI) // Acta Biochimica Polonica - 2016, vol. 63, no. 1, p. 71-77

Scientific article 15 1,159

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 1,159

13.

Flexibility of dicer studied by implicity solvent molecular dynamics simulations / Joanna Sarzyńska, Agnieszka Mickiewicz, Maciej Miłostan, Piotr Łukasiak, Jacek Błażewicz, Marek Figlerowicz, Tadeusz Kuliński // Computational Methods in Science and Technology - 2010, vol. 16, no. 1, p. 97-104

Scientific article