User-Friendly Frameworks for Accessing Computational Resources. - Bartek Palak; Pawel Wolniewicz; Marcin Plóciennik; Michal Owsiak; Tomasz Zok (PL-Grid, 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 (HPCS, 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 (HPCS, 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 (ICCS, 2012)

Approaches to Distributed Execution of Scientific Workflows in Kepler. - Marcin Plóciennik; Tomasz Zok; Ilkay Altintas; Jianwu Wang 001; Daniel Crawl; David Abramson 001; Frederic Imbeaux; Bernard Guillerminet; Marcos López-Caniego; Isabel Campos Plasencia; Wojciech Pych; Pawel Ciecielag; et al. (Fundam. Informaticae, 2013)

Kepler-Based Workflow Environment for Astronomy. - Pawel Ciecielag; Marcin Plóciennik; Piotr Spyra; Michal Urbaniak; Tomasz Zok; Wojciech Pych; Arkadiusz Hypki (PL-Grid, 2014)

Flexible Approach to Astronomical Data Reduction Workflows in Kepler. - Pawel Ciecielag; Marcin Plóciennik; Piotr Spyra; Michal Urbaniak; Tomasz Zok; Wojciech Pych (ICCS, 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; et al. (ICCS, 2014)

MCQ4Structures to compute similarity of molecule structures. - Tomasz Zok; Mariusz Popenda; Marta Szachniuk (Central Eur. J. Oper. Res., 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)

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)

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)

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; et al. (IEEE BigData, 2016)

Best Practices in Debugging Kepler Workflows. - Michal Owsiak; Marcin Plóciennik; Bartek Palak; Tomasz Zok; Olivier Hoenen (ICCS, 2016)

LCS-TA to identify similar fragments in RNA 3D structures. - Jakub Wiedemann; Tomasz Zok; Maciej Milostan; Marta Szachniuk (BMC Bioinform., 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 001; Ludek Matyska; P. Fuhrman; Marcus Hardt; Giacinto Donvito; Lukasz Dutka; Marcin Plóciennik; et al. (CoRR, 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)

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)

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)

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 001; Ludek Matyska; P. Fuhrman; Marcus Hardt; Giacinto Donvito; Lukasz Dutka; Marcin Plóciennik; et al. (J. Grid Comput., 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)

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)

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)

Topology-based classification of tetrads and quadruplex structures. - Mariusz Popenda; Joanna Miskiewicz; Joanna Sarzynska; Tomasz Zok; Marta Szachniuk (Bioinform., 2020)

ElTetrado: a tool for identification and classification of tetrads and quadruplexes. - Tomasz Zok; Mariusz Popenda; Marta Szachniuk (BMC Bioinform., 2020)

BioCommons: a robust java library for RNA structural bioinformatics. - Tomasz Zok (Bioinform., 2021)

Characterizing domain-specific open educational resources by linking ISCB Communities of Special Interest to Wikipedia. - 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; et al. (Bioinform., 2022)

RNAloops: a database of RNA multiloops. - Jakub Wiedemann; Jacek Kaczor; Maciej Milostan; Tomasz Zok; Jacek Blazewicz; Marta Szachniuk; Maciej Antczak (Bioinform., 2022)

DrawTetrado to create layer diagrams of G4 structures. - Michal Zurkowski; Tomasz Zok; Marta Szachniuk (Bioinform., 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)

ONQUADRO: a database of experimentally determined quadruplex structures. - Tomasz Zok; Natalia Kraszewska; Joanna Miskiewicz; Paulina Pielacinska; Michal Zurkowski; Marta Szachniuk (Nucleic Acids Res., 2022)

WebTetrado: a webserver to explore quadruplexes in nucleic acid 3D structures. - Bartosz Adamczyk; Michal Zurkowski; Marta Szachniuk; Tomasz Zok (Nucleic Acids Res., 2023)

Knotted artifacts in predicted 3D RNA structures. - Bartosz Ambrozy Gren; Maciej Antczak; Tomasz Zok; Joanna I. Sulkowska; Marta Szachniuk (PLoS Comput. Biol., 2024)

RNAtango: Analysing and comparing RNA 3D structures via torsional angles. - Marta Mackowiak; Bartosz Adamczyk; Marta Szachniuk; Tomasz Zok (PLoS Comput. Biol., 2024)