Tomasz Zok

Publication Activity (10 Years)

Years Active: 2012-2023
Publications (10 Years): 20

Top Topics

Secondary Structure

Representative Subset

Free Parameters

Scientific Workflows

Top Venues

Nucleic Acids Res.

Publications

Bartosz Adamczyk, Michal Zurkowski, Marta Szachniuk, Tomasz Zok
WebTetrado: a webserver to explore quadruplexes in nucleic acid 3D structures. Nucleic Acids Res. 51 (W1) (2023)
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) (2022)
Jakub Wiedemann, Jacek Kaczor, Maciej Milostan, Tomasz Zok, Jacek Blazewicz, Marta Szachniuk, Maciej Antczak
RNAloops: a database of RNA multiloops. Bioinform. 38 (17) (2022)
Michal Zurkowski, Tomasz Zok, Marta Szachniuk
DrawTetrado to create layer diagrams of G4 structures. Bioinform. 38 (15) (2022)
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) (2022)
Tomasz Zok
BioCommons: a robust java library for RNA structural bioinformatics. Bioinform. 37 (17) (2021)
Mariusz Popenda, Joanna Miskiewicz, Joanna Sarzynska, Tomasz Zok, Marta Szachniuk
Topology-based classification of tetrads and quadruplex structures. Bioinform. 36 (4) (2020)
Tomasz Zok, Mariusz Popenda, Marta Szachniuk
ElTetrado: a tool for identification and classification of tetrads and quadruplexes. BMC Bioinform. 21 (1) (2020)
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) (2020)
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) (2019)
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) (2018)
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) (2018)
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) (2018)
Davide Salomoni, Isabel Campos Plasencia, Luciano Gaido, Jesús E. Marco de Lucas, P. Solagna, Jorge Gomes, Ludek Matyska, P. Fuhrman, Marcus Hardt, Giacinto Donvito, L. 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, M. Tangaro, Michal Urbaniak, Sara Vallero, Bas Wegh, Valentina Zaccolo, F. Zambelli, Tomasz Zok
INDIGO-DataCloud: a Platform to Facilitate Seamless Access to E-Infrastructures. J. Grid Comput. 16 (3) (2018)
Jakub Wiedemann, Tomasz Zok, Maciej Milostan, Marta Szachniuk
LCS-TA to identify similar fragments in RNA 3D structures. BMC Bioinform. 18 (1) (2017)
Davide Salomoni, Luciano Gaido, Isabel Campos Plasencia, Jesús E. Marco de Lucas, P. Solagna, Jorge Gomes, Ludek Matyska, P. Fuhrman, Marcus Hardt, Giacinto Donvito, L. 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, M. Tangaro, Michal Urbaniak, Bas Wegh, Tomasz Zok
INDIGO-DataCloud: A data and computing platform to facilitate seamless access to e-infrastructures. CoRR (2017)
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 (2017)
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)
Michal Owsiak, Marcin Plóciennik, Bartek Palak, Tomasz Zok, Olivier Hoenen
Best Practices in Debugging Kepler Workflows. ICCS (2016)
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)
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 (2015)
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) (2015)
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)
Pawel Ciecielag, Marcin Plóciennik, Piotr Spyra, Michal Urbaniak, Tomasz Zok, Wojciech Pych
Flexible Approach to Astronomical Data Reduction Workflows in Kepler. ICCS (2014)
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) (2014)
Tomasz Zok, Mariusz Popenda, Marta Szachniuk
MCQ4Structures to compute similarity of molecule structures. Central Eur. J. Oper. Res. 22 (3) (2014)
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) (2013)
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)
Marcin Plóciennik, Tomasz Zok, Michal Owsiak, Bartek Palak, Bernard Guillerminet, Yann Frauel, Frederic Imbeaux, Bruce Scott
High level tools for fusion simulations workflows in distributed computing environment. HPCS (2012)
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)