Tomasz Zok

According to our database, Tomasz Zok authored at least 33 papers between 2012 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

RNAtango: Analysing and comparing RNA 3D structures via torsional angles.

Marta Mackowiak, Bartosz Adamczyk, Marta Szachniuk, Tomasz Zok

PLoS Comput. Biol., 2024

Knotted artifacts in predicted 3D RNA structures.

Bartosz Ambrozy Gren, Maciej Antczak, Tomasz Zok, Joanna I. Sulkowska, Marta Szachniuk

PLoS Comput. Biol., 2024

2023

WebTetrado: a webserver to explore quadruplexes in nucleic acid 3D structures.

Bartosz Adamczyk, Michal Zurkowski, Marta Szachniuk, Tomasz Zok

Nucleic Acids Res., July, 2023

2022

ONQUADRO: a database of experimentally determined quadruplex structures.

Tomasz Zok, Natalia Kraszewska, Joanna Miskiewicz, Paulina Pielacinska, Michal Zurkowski, Marta Szachniuk

Nucleic Acids Res., 2022

RNAspider: a webserver to analyze entanglements in RNA 3D structures.

Kamil Luwanski, Vladyslav Hlushchenko, Mariusz Popenda, Tomasz Zok, Joanna Sarzynska, Daniil Martsich, Marta Szachniuk, Maciej Antczak

Nucleic Acids Res., 2022

DrawTetrado to create layer diagrams of G4 structures.

Michal Zurkowski, Tomasz Zok, Marta Szachniuk

Bioinform., 2022

RNAloops: a database of RNA multiloops.

Jakub Wiedemann, Jacek Kaczor, Maciej Milostan, Tomasz Zok, Jacek Blazewicz, Marta Szachniuk, Maciej Antczak

Bioinform., 2022

2021

BioCommons: a robust java library for RNA structural bioinformatics.

Tomasz Zok

Bioinform., 2021

2020

ElTetrado: a tool for identification and classification of tetrads and quadruplexes.

Tomasz Zok, Mariusz Popenda, Marta Szachniuk

BMC Bioinform., 2020

Topology-based classification of tetrads and quadruplex structures.

Mariusz Popenda, Joanna Miskiewicz, Joanna Sarzynska, Tomasz Zok, Marta Szachniuk

Bioinform., 2020

New models and algorithms for RNA pseudoknot order assignment.

Tomasz Zok, Jan Badura, Sylwester Swat, Kacper Figurski, Mariusz Popenda, Maciej Antczak

Int. J. Appl. Math. Comput. Sci., 2020

2019

RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs.

Maciej Antczak, Marcin Zablocki, Tomasz Zok, Agnieszka Rybarczyk, Jacek Blazewicz, Marta Szachniuk

Bioinform., 2019

2018

RNApdbee 2.0: multifunctional tool for RNA structure annotation.

Tomasz Zok, Maciej Antczak, Michal Zurkowski, Mariusz Popenda, Jacek Blazewicz, Ryszard W. Adamiak, Marta Szachniuk

Nucleic Acids Res., 2018

INDIGO-DataCloud: a Platform to Facilitate Seamless Access to E-Infrastructures.

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

J. Grid Comput., 2018

RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures.

Maciej Antczak, Tomasz Zok, Maciej Osowiecki, Mariusz Popenda, Ryszard W. Adamiak, Marta Szachniuk

BMC Bioinform., 2018

New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation.

Maciej Antczak, Mariusz Popenda, Tomasz Zok, Michal Zurkowski, Ryszard W. Adamiak, Marta Szachniuk

Bioinform., 2018

2017

Running simultaneous Kepler sessions for the parallelization of parametric scans and optimization studies applied to complex workflows.

Michal Owsiak, Marcin Plóciennik, Bartek Palak, Tomasz Zok, Cedric Reux, Luc Di Gallo, Denis Kalupin, Thomas Johnson, Mireille Schneider

J. Comput. Sci., 2017

INDIGO-DataCloud: A data and computing platform to facilitate seamless access to e-infrastructures.

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

CoRR, 2017

LCS-TA to identify similar fragments in RNA 3D structures.

Jakub Wiedemann, Tomasz Zok, Maciej Milostan, Marta Szachniuk

BMC Bioinform., 2017

2016

Best Practices in Debugging Kepler Workflows.

Michal Owsiak, Marcin Plóciennik, Bartek Palak, Tomasz Zok, Olivier Hoenen

Proceedings of the International Conference on Computational Science 2016, 2016

Distributed and cloud-based multi-model analytics experiments on large volumes of climate change data in the earth system grid federation eco-system.

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

Proceedings of the 2016 IEEE International Conference on Big Data (IEEE BigData 2016), 2016

2015

New in silico approach to assessing RNA secondary structures with non-canonical base pairs.

Agnieszka Rybarczyk, Natalia Szostak, Maciej Antczak, Tomasz Zok, Mariusz Popenda, Ryszard W. Adamiak, Jacek Blazewicz, Marta Szachniuk

BMC Bioinform., 2015

Building the Library of Rna 3D Nucleotide Conformations Using the Clustering Approach.

Tomasz Zok, Maciej Antczak, Martin Riedel, David Nebel, Thomas Villmann, Piotr Lukasiak, Jacek Blazewicz, Marta Szachniuk

Int. J. Appl. Math. Comput. Sci., 2015

2014

RNApdbee - a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs.

Maciej Antczak, Tomasz Zok, Mariusz Popenda, Piotr Lukasiak, Ryszard W. Adamiak, Jacek Blazewicz, Marta Szachniuk

Nucleic Acids Res., 2014

MCQ4Structures to compute similarity of molecule structures.

Tomasz Zok, Mariusz Popenda, Marta Szachniuk

Central Eur. J. Oper. Res., 2014

Tools, Methods and Services Enhancing the Usage of the Kepler-based Scientific Workflow Framework.

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

Proceedings of the International Conference on Computational Science, 2014

Flexible Approach to Astronomical Data Reduction Workflows in Kepler.

Pawel Ciecielag, Marcin Plóciennik, Piotr Spyra, Michal Urbaniak, Tomasz Zok, Wojciech Pych

Proceedings of the International Conference on Computational Science, 2014

Kepler-Based Workflow Environment for Astronomy.

Pawel Ciecielag, Marcin Plóciennik, Piotr Spyra, Michal Urbaniak, Tomasz Zok, Wojciech Pych, Arkadiusz Hypki

Proceedings of the eScience on Distributed Computing Infrastructure, 2014

2013

Approaches to Distributed Execution of Scientific Workflows in Kepler.

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

Fundam. Informaticae, 2013

2012

Application Scenarios Using Serpens Suite for Kepler Scientific Workflow System.

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

Proceedings of the International Conference on Computational Science, 2012

High level tools for fusion simulations workflows in distributed computing environment.

Marcin Plóciennik, Tomasz Zok, Michal Owsiak, Bartek Palak, Bernard Guillerminet, Yann Frauel, Frederic Imbeaux, Bruce D. Scott

Proceedings of the 2012 International Conference on High Performance Computing & Simulation, 2012

Workflows orchestration in distributed computing infrastructures.

Marcin Plóciennik, Tomasz Zok, Antonio Gómez-Iglesias, Francisco Castejón, Andrés Bustos, Manuel Aurelio Rodriguez Pascual, Jose Luis Velasco

Proceedings of the 2012 International Conference on High Performance Computing & Simulation, 2012

User-Friendly Frameworks for Accessing Computational Resources.

Bartek Palak, Pawel Wolniewicz, Marcin Plóciennik, Michal Owsiak, Tomasz Zok

Proceedings of the Building a National Distributed e-Infrastructure - PL-Grid, 2012