MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. - Tomás Pluskal; Sandra Castillo; Alejandro Villar-Briones; Matej Oresic (BMC Bioinform., 2010)

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. - Egon L. Willighagen; John W. Mayfield; Jonathan Alvarsson; Arvid Berg; Lars Carlsson; Nina Jeliazkova; Stefan Kuhn 001; Tomás Pluskal; Miquel Rojas-Chertó; Ola Spjuth; Gilleain M. Torrance; Chris T. A. Evelo; et al. (J. Cheminformatics, 2017)

Erratum to: The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. - Egon L. Willighagen; John W. Mayfield; Jonathan Alvarsson; Arvid Berg; Lars Carlsson; Nina Jeliazkova; Stefan Kuhn 001; Tomás Pluskal; Miquel Rojas-Chertó; Ola Spjuth; Gilleain M. Torrance; Chris T. A. Evelo; et al. (J. Cheminformatics, 2017)

transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation. - Timothy R. Fallon; Tereza Calounová; Martin Mokrejs; Jing-Ke Weng; Tomás Pluskal (BMC Bioinform., 2023)

Learning to design protein-protein interactions with enhanced generalization. - Anton Bushuiev; Roman Bushuiev; Petr Kouba; Anatolii Filkin; Marketa Gabrielova; Michal Gabriel; Jirí Sedlár; Tomás Pluskal; Jirí Damborský; Stanislav Mazurenko; Josef Sivic (ICLR, 2024)

MassSpecGym: A benchmark for the discovery and identification of molecules. - Roman Bushuiev; Anton Bushuiev; Niek F. de Jonge; Adamo Young; Fleming Kretschmer; Raman Samusevich; Janne Heirman; Fei Wang 062; Luke Zhang; Kai Dührkop; Marcus Ludwig; Nils A. Haupt; et al. (NeurIPS, 2024)

Revealing data leakage in protein interaction benchmarks. - Anton Bushuiev; Roman Bushuiev; Jirí Sedlár; Tomás Pluskal; Jirí Damborský; Stanislav Mazurenko; Josef Sivic (CoRR, 2024)

Training on test proteins improves fitness, structure, and function prediction. - Anton Bushuiev; Roman Bushuiev; Nikola Zadorozhny; Raman Samusevich; Hannes Stärk; Jirí Sedlár; Tomás Pluskal; Josef Sivic (CoRR, 2024)

Machine Learning for Protein-Protein and Protein-Ligand Interactions (Dagstuhl Seminar 24451). - Anne-Florence Bitbol; Jennifer Listgarten; Tomás Pluskal; Anton Bushuiev; Roman Bushuiev (Dagstuhl Reports, 2024)

An evaluation methodology for machine learning-based tandem mass spectra similarity prediction. - Michael Strobel 002; Alberto Gil-de-la-Fuente; Mohammad Reza Shahneh; Yasin El Abiead; Roman Bushuiev; Anton Bushuiev; Tomás Pluskal; Mingxun Wang 001 (BMC Bioinform., 2025)