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)

Hemojuvelin-hepcidin axis modeled and analyzed using Petri nets. - Dorota Formanowicz; Adam Kozak; Tomasz Glowacki; Marcin Radom; Piotr Formanowicz (J. Biomed. Informatics, 2013)

A multilevel ant colony optimization algorithm for classical and isothermic DNA sequencing by hybridization with multiplicity information available. - Kamil Kwarciak; Marcin Radom; Piotr Formanowicz (Comput. Biol. Chem., 2016)

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)

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)

Comparing Petri net-based models of biological systems using Holmes. - Bartlomiej Szawulak; Marcin Radom; Piotr Formanowicz (Bioinform., 2022)

Extended time Petri nets. - Marcin Radom; Piotr Formanowicz (CoRR, 2024)

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

Comparison by partition - Finding Petri nets similarity on the basis of subnets. - Bartlomiej Szawulak; Marcin Radom; Piotr Formanowicz (Comput. Biol. Medicine, 2025)