RNA Partial Degradation Problem: Motivation, Complexity, Algorithm. - Jacek Blazewicz; Marek Figlerowicz; Marta Kasprzak; Martyna Nowacka; Agnieszka Rybarczyk (J. Comput. Biol., 2011)

Poseidon: An information retrieval and extraction system for metagenomic marine science. - Marcin Radom; Agnieszka Rybarczyk; Renzo Kottmann; Piotr Formanowicz; Marta Szachniuk; Frank Oliver Glöckner; Dietrich Rebholz-Schuhmann; Jacek Blazewicz (Ecol. Informatics, 2012)

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)

Tabu Search for the RNA Partial Degradation Problem. - Agnieszka Rybarczyk; Alain Hertz; Marta Kasprzak; Jacek Blazewicz (Int. J. Appl. Math. Comput. Sci., 2017)

Holmes: a graphical tool for development, simulation and analysis of Petri net based models of complex biological systems. - Marcin Radom; Agnieszka Rybarczyk; Bartlomiej Szawulak; Hubert Andrzejewski; Piotr Chabelski; Adam Kozak; Piotr Formanowicz (Bioinform., 2017)

Modeling of the catalytic core of Arabidopsis thaliana Dicer-like 4 protein and its complex with double-stranded RNA. - Agnieszka Mickiewicz; Joanna Sarzynska; Maciej Milostan; Anna Kurzynska-Kokorniak; Agnieszka Rybarczyk; Piotr Lukasiak; Tadeusz Kulinski; Marek Figlerowicz; Jacek Blazewicz (Comput. Biol. Chem., 2017)

The role of Fenton reaction in ROS-induced toxicity underlying atherosclerosis - modeled and analyzed using a Petri net-based approach. - Dorota Formanowicz; Marcin Radom; Agnieszka Rybarczyk; Piotr Formanowicz (Biosyst., 2018)

Factors Influencing Essential Hypertension and Cardiovascular Disease Modeled and Analyzed using Stochastic Petri Nets. - Dorota Formanowicz; Agnieszka Rybarczyk; Piotr Formanowicz (Fundam. Informaticae, 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)

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)

RNA World Modeling: A Comparison of Two Complementary Approaches. - Jaroslaw Synak; Agnieszka Rybarczyk; Jacek Blazewicz (Entropy, 2022)

Algorithms for evaluation of minimal cut sets. - Marcin Radom; Agnieszka Rybarczyk; Igor Piekarz; Piotr Formanowicz (J. Biomed. Informatics, 2024)