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2020 – today
- 2024
[j24]Bartosz Ambrozy Gren
, Maciej Antczak, Tomasz Zok, Joanna I. Sulkowska, Marta Szachniuk:
Knotted artifacts in predicted 3D RNA structures. PLoS Comput. Biol. 20(6): 1011959 (2024)- [j23]Marta Mackowiak, Bartosz Adamczyk, Marta Szachniuk, Tomasz Zok:
RNAtango: Analysing and comparing RNA 3D structures via torsional angles. PLoS Comput. Biol. 20(10): 1012500 (2024) - 2023
- [j22]Bartosz Adamczyk, Michal Zurkowski, Marta Szachniuk, Tomasz Zok:
WebTetrado: a webserver to explore quadruplexes in nucleic acid 3D structures. Nucleic Acids Res. 51(W1): 607-612 (2023) - 2022
- [j21]Michal Zurkowski, Tomasz Zok, Marta Szachniuk:
DrawTetrado to create layer diagrams of G4 structures. Bioinform. 38(15): 3835-3836 (2022) - [j20]Jakub Wiedemann, Jacek Kaczor, Maciej Milostan, Tomasz Zok, Jacek Blazewicz, Marta Szachniuk, Maciej Antczak:
RNAloops: a database of RNA multiloops. Bioinform. 38(17): 4200-4205 (2022) - [j19]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, Syed Muktadir Al Sium, David Twesigomwe, Tomasz Zok, Christine A. Orengo, Iddo Friedberg, Janet Kelso, Lonnie R. Welch:
Characterizing domain-specific open educational resources by linking ISCB Communities of Special Interest to Wikipedia. Bioinform. 38(Supplement_1): i19-i27 (2022) - [j18]Tomasz Zok, Natalia Kraszewska, Joanna Miskiewicz, Paulina Pielacinska, Michal Zurkowski, Marta Szachniuk:
ONQUADRO: a database of experimentally determined quadruplex structures. Nucleic Acids Res. 50(D1): 253-258 (2022) - [j17]Kamil Luwanski, Vladyslav Hlushchenko, Mariusz Popenda, Tomasz Zok, Joanna Sarzynska, Daniil Martsich, Marta Szachniuk, Maciej Antczak:
RNAspider: a webserver to analyze entanglements in RNA 3D structures. Nucleic Acids Res. 50(W1): 663-669 (2022) - 2021
- [j16]Tomasz Zok:
BioCommons: a robust java library for RNA structural bioinformatics. Bioinform. 37(17): 2766-2767 (2021) - 2020
- [j15]Tomasz Zok, Jan Badura, Sylwester Swat, Kacper Figurski, Mariusz Popenda, Maciej Antczak:
New models and algorithms for RNA pseudoknot order assignment. Int. J. Appl. Math. Comput. Sci. 30(2): 315-324 (2020) - [j14]Mariusz Popenda, Joanna Miskiewicz, Joanna Sarzynska, Tomasz Zok, Marta Szachniuk:
Topology-based classification of tetrads and quadruplex structures. Bioinform. 36(4): 1129-1134 (2020) - [j13]Tomasz Zok, Mariusz Popenda, Marta Szachniuk:
ElTetrado: a tool for identification and classification of tetrads and quadruplexes. BMC Bioinform. 21(1): 40 (2020)
2010 – 2019
- 2019
- [j12]Maciej Antczak, Marcin Zablocki, Tomasz Zok, Agnieszka Rybarczyk, Jacek Blazewicz, Marta Szachniuk:
RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs. Bioinform. 35(1): 152-155 (2019) - 2018
- [j11]Maciej Antczak, Mariusz Popenda, Tomasz Zok, Michal Zurkowski, Ryszard W. Adamiak, Marta Szachniuk:
New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation. Bioinform. 34(8): 1304-1312 (2018) - [j10]Maciej Antczak, Tomasz Zok, Maciej Osowiecki, Mariusz Popenda, Ryszard W. Adamiak, Marta Szachniuk:
RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures. BMC Bioinform. 19(1): 304:1-304:11 (2018) - [j9]Davide Salomoni, Isabel Campos Plasencia, Luciano Gaido, Jesús E. Marco de Lucas, P. Solagna, Jorge Gomes, Ludek Matyska, P. Fuhrman, Marcus Hardt, Giacinto Donvito, Lukasz Dutka, Marcin Plóciennik, Roberto Barbera, Ignacio Blanquer, Andrea Ceccanti, Eva Cetinic, Mário David, Doina Cristina Duma, Álvaro López García, Germán Moltó, Pablo Orviz Fernández, Zdenek Sustr, Matthew Viljoen, Fernando Aguilar, Luís Alves, Marica Antonacci, Lucio Angelo Antonelli, Stefano Bagnasco, A. Bonving, Riccardo Bruno, Y. Chen, Alessandro Costa, Davor Davidovic, Benjamin Ertl, Marco Fargetta, Sandro Fiore, S. Gallozzi, Z. Kurkcuoglu, Lara Lloret Iglesias, J. Martins, Alessandra Nuzzo, Paola Nassisi, Cosimo Palazzo, João Murta Pina, Eva Sciacca, Daniele Spiga, Marco Antonio Tangaro, Michal Urbaniak, Sara Vallero, Bas Wegh, Valentina Zaccolo, Federico Zambelli, Tomasz Zok:
INDIGO-DataCloud: a Platform to Facilitate Seamless Access to E-Infrastructures. J. Grid Comput. 16(3): 381-408 (2018) - [j8]Tomasz Zok, Maciej Antczak, Michal Zurkowski, Mariusz Popenda, Jacek Blazewicz, Ryszard W. Adamiak, Marta Szachniuk:
RNApdbee 2.0: multifunctional tool for RNA structure annotation. Nucleic Acids Res. 46(Webserver-Issue): W30-W35 (2018) - 2017
- [j7]Jakub Wiedemann, Tomasz Zok, Maciej Milostan, Marta Szachniuk:
LCS-TA to identify similar fragments in RNA 3D structures. BMC Bioinform. 18(1): 456 (2017) - [j6]Michal Owsiak, Marcin Plóciennik, Bartek Palak, Tomasz Zok, Cedric Reux, Luc Di Gallo, Denis Kalupin, Thomas Johnson, Mireille Schneider:
Running simultaneous Kepler sessions for the parallelization of parametric scans and optimization studies applied to complex workflows. J. Comput. Sci. 20: 103-111 (2017) - [i1]Davide Salomoni, Luciano Gaido, Isabel Campos Plasencia, Jesús E. Marco de Lucas, P. Solagna, Jorge Gomes, Ludek Matyska, P. Fuhrman, Marcus Hardt, Giacinto Donvito, Lukasz Dutka, Marcin Plóciennik, Roberto Barbera, Cristina Aiftimiei, Ignacio Blanquer, Andrea Ceccanti, Mário David, Álvaro López García, Germán Moltó, Pablo Orviz Fernández, Zdenek Sustr, Matthew Viljoen, Fernando Aguilar, Luís Alves, A. Bonving, Riccardo Bruno, Davor Davidovic, Marco Fargetta, Y. Chen, Sandro Fiore, Z. Kurkcuoglu, Lara Lloret Iglesias, J. Martins, Alessandra Nuzzo, Paola Nassisi, João Murta Pina, Eva Sciacca, Daniele Spiga, Marco Antonio Tangaro, Michal Urbaniak, Bas Wegh, Tomasz Zok:
INDIGO-DataCloud: A data and computing platform to facilitate seamless access to e-infrastructures. CoRR abs/1711.01981 (2017) - 2016
- [c8]Sandro Fiore, Marcin Plóciennik, Charles M. Doutriaux, Cosimo Palazzo, J. Boutte, Tomasz Zok, Donatello Elia, Michal Owsiak, Alessandro D'Anca, Z. Shaheen, Riccardo Bruno, Marco Fargetta, Miguel Caballer, Germán Moltó, Ignacio Blanquer, Roberto Barbera, Mário David, Giacinto Donvito, Dean N. Williams, V. Anantharaj, Davide Salomoni, Giovanni Aloisio:
Distributed and cloud-based multi-model analytics experiments on large volumes of climate change data in the earth system grid federation eco-system. IEEE BigData 2016: 2911-2918 - [c7]Michal Owsiak, Marcin Plóciennik, Bartek Palak, Tomasz Zok, Cedric Reux, Luc Di Gallo, Mireille Schneider, Thomas Johnson, Denis Kalupin:
Running Simultaneous Kepler Sessions for the Parallelization of Parametric Scans and Optimization Studies Applied to Complex Workflows. ICCS 2016: 690-699 - [c6]Michal Owsiak, Marcin Plóciennik, Bartek Palak, Tomasz Zok, Olivier Hoenen:
Best Practices in Debugging Kepler Workflows. ICCS 2016: 2332-2337 - 2015
- [j5]Tomasz Zok, Maciej Antczak, Martin Riedel, David Nebel, Thomas Villmann, Piotr Lukasiak, Jacek Blazewicz, Marta Szachniuk:
Building the Library of Rna 3D Nucleotide Conformations Using the Clustering Approach. Int. J. Appl. Math. Comput. Sci. 25(3): 689-700 (2015) - [j4]Agnieszka Rybarczyk, Natalia Szostak, Maciej Antczak, Tomasz Zok, Mariusz Popenda, Ryszard W. Adamiak, Jacek Blazewicz, Marta Szachniuk:
New in silico approach to assessing RNA secondary structures with non-canonical base pairs. BMC Bioinform. 16: 276:1-276:12 (2015) - 2014
- [j3]Tomasz Zok, Mariusz Popenda, Marta Szachniuk:
MCQ4Structures to compute similarity of molecule structures. Central Eur. J. Oper. Res. 22(3): 457-473 (2014) - [j2]Maciej Antczak, Tomasz Zok, Mariusz Popenda, Piotr Lukasiak, Ryszard W. Adamiak, Jacek Blazewicz, Marta Szachniuk:
RNApdbee - a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs. Nucleic Acids Res. 42(Webserver-Issue): 368-372 (2014) - [c5]Marcin Plóciennik, Szymon Winczewski, Pawel Ciecielag, Frederic Imbeaux, Bernard Guillerminet, Philippe Huynh, Michal Owsiak, Piotr Spyra, Thierry Aniel, Bartek Palak, Tomasz Zok, Wojciech Pych, Jaroslaw Rybicki:
Tools, Methods and Services Enhancing the Usage of the Kepler-based Scientific Workflow Framework. ICCS 2014: 1733-1744 - [c4]Pawel Ciecielag, Marcin Plóciennik, Piotr Spyra, Michal Urbaniak, Tomasz Zok, Wojciech Pych:
Flexible Approach to Astronomical Data Reduction Workflows in Kepler. ICCS 2014: 1756-1761 - [p2]Pawel Ciecielag, Marcin Plóciennik, Piotr Spyra, Michal Urbaniak, Tomasz Zok, Wojciech Pych, Arkadiusz Hypki:
Kepler-Based Workflow Environment for Astronomy. PL-Grid 2014: 278-292 - 2013
- [j1]Marcin Plóciennik, Tomasz Zok, Ilkay Altintas, Jianwu Wang, Daniel Crawl, David Abramson, Frederic Imbeaux, Bernard Guillerminet, Marcos López-Caniego, Isabel Campos Plasencia, Wojciech Pych, Pawel Ciecielag, Bartek Palak, Michal Owsiak, Yann Frauel:
Approaches to Distributed Execution of Scientific Workflows in Kepler. Fundam. Informaticae 128(3): 281-302 (2013) - 2012
- [c3]Marcin Plóciennik, Tomasz Zok, Michal Owsiak, Bartek Palak, Bernard Guillerminet, Yann Frauel, Frederic Imbeaux, Bruce D. Scott:
High level tools for fusion simulations workflows in distributed computing environment. HPCS 2012: 602-608 - [c2]Marcin Plóciennik, Tomasz Zok, Antonio Gómez-Iglesias, Francisco Castejón, Andrés Bustos, Manuel Aurelio Rodriguez Pascual, Jose Luis Velasco:
Workflows orchestration in distributed computing infrastructures. HPCS 2012: 616-622 - [c1]Marcin Plóciennik, Michal Owsiak, Tomasz Zok, Bartek Palak, Antonio Gómez-Iglesias, Francisco Castejón, Marcos López-Caniego, Isabel Campos Plasencia, Alessandro Costantini, Dimitriy Yadykin, Per Strand:
Application Scenarios Using Serpens Suite for Kepler Scientific Workflow System. ICCS 2012: 1604-1613 - [p1]Bartek Palak, Pawel Wolniewicz, Marcin Plóciennik, Michal Owsiak, Tomasz Zok:
User-Friendly Frameworks for Accessing Computational Resources. PL-Grid 2012: 191-204
Coauthor Index
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