Tomás Pluskal

14 papers A* 2Journal 12
YearRankTypeTitle / Venue / Authors
2026 J jnl
MARTS-DB: a database of mechanisms and reactions of terpene synthases.
BMC Bioinform.
Martin Engst, Martin Brokes, Tereza Calounová, Raman Samusevich, Roman Bushuiev, Anton Bushuiev, Ratthachat Chatpatanasiri, Adéla Tajovská, Safa Mert Akmese, Milana Perkovic, Matous Soldát, Josef Sivic, Tomás Pluskal
2025 J jnl
An evaluation methodology for machine learning-based tandem mass spectra similarity prediction.
BMC Bioinform.
Michael Strobel, Alberto Gil-de-la-Fuente, Mohammad Reza Shahneh, Yasin El Abiead, Roman Bushuiev, Anton Bushuiev, Tomás Pluskal, Mingxun Wang
2025 J jnl
De novo generation of functional terpene synthases using TpsGPT.
CoRR
Hamsini Ramanathan, Roman Bushuiev, Matous Soldát, Jirí Kohout, Téo Hebra, Joshua David Smith, Josef Sivic, Tomás Pluskal
2024 A* conf
Learning to design protein-protein interactions with enhanced generalization.
ICLR
Anton Bushuiev, Roman Bushuiev, Petr Kouba, Anatolii Filkin, Marketa Gabrielova, Michal Gabriel, Jirí Sedlár, Tomás Pluskal, Jirí Damborský, Stanislav Mazurenko, Josef Sivic
2024 J jnl
Machine Learning for Protein-Protein and Protein-Ligand Interactions (Dagstuhl Seminar 24451).
Dagstuhl Reports
Anne-Florence Bitbol, Jennifer Listgarten, Tomás Pluskal, Anton Bushuiev, Roman Bushuiev
2024 A* conf
MassSpecGym: A benchmark for the discovery and identification of molecules.
NeurIPS
Roman Bushuiev, Anton Bushuiev, Niek F. de Jonge, Adamo Young, Fleming Kretschmer, Raman Samusevich, Janne Heirman, Fei Wang, Luke Zhang, Kai Dührkop, Marcus Ludwig, Nils A. Haupt, Apurva Kalia, Corinna Brungs, Robin Schmid, Russell Greiner, Bo Wang, David S. Wishart, Liping Liu, Juho Rousu, Wout Bittremieux, Hannes Rost, Tytus D. Mak, Soha Hassoun, Florian Huber, Justin J. J. van der Hooft, Michael A. Stravs, Sebastian Böcker, Josef Sivic, Tomás Pluskal
2024 J jnl
MassSpecGym: A benchmark for the discovery and identification of molecules.
CoRR
Roman Bushuiev, Anton Bushuiev, Niek F. de Jonge, Adamo Young, Fleming Kretschmer, Raman Samusevich, Janne Heirman, Fei Wang, Luke Zhang, Kai Dührkop, Marcus Ludwig, Nils A. Haupt, Apurva Kalia, Corinna Brungs, Robin Schmid, Russell Greiner, Bo Wang, David S. Wishart, Li-Ping Liu, Juho Rousu, Wout Bittremieux, Hannes Rost, Tytus D. Mak, Soha Hassoun, Florian Huber, Justin J. J. van der Hooft, Michael A. Stravs, Sebastian Böcker, Josef Sivic, Tomás Pluskal
2024 J jnl
Revealing data leakage in protein interaction benchmarks.
CoRR
Anton Bushuiev, Roman Bushuiev, Jirí Sedlár, Tomás Pluskal, Jirí Damborský, Stanislav Mazurenko, Josef Sivic
2024 J jnl
Training on test proteins improves fitness, structure, and function prediction.
CoRR
Anton Bushuiev, Roman Bushuiev, Nikola Zadorozhny, Raman Samusevich, Hannes Stärk, Jirí Sedlár, Tomás Pluskal, Josef Sivic
2023 J jnl
Learning to design protein-protein interactions with enhanced generalization.
CoRR
Anton Bushuiev, Roman Bushuiev, Anatolii Filkin, Petr Kouba, Marketa Gabrielova, Michal Gabriel, Jirí Sedlár, Tomás Pluskal, Jirí Damborský, Stanislav Mazurenko, Josef Sivic
2023 J jnl
transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation.
BMC Bioinform.
Timothy R. Fallon, Tereza Calounová, Martin Mokrejs, Jing-Ke Weng, Tomás Pluskal
2017 J jnl
Erratum to: The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching.
J. Cheminformatics
Egon L. Willighagen, John W. Mayfield, Jonathan Alvarsson, Arvid Berg, Lars Carlsson, Nina Jeliazkova, Stefan Kuhn, Tomás Pluskal, Miquel Rojas-Chertó, Ola Spjuth, Gilleain M. Torrance, Chris T. A. Evelo, Rajarshi Guha, Christoph Steinbeck
2017 J jnl
The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching.
J. Cheminformatics
Egon L. Willighagen, John W. Mayfield, Jonathan Alvarsson, Arvid Berg, Lars Carlsson, Nina Jeliazkova, Stefan Kuhn, Tomás Pluskal, Miquel Rojas-Chertó, Ola Spjuth, Gilleain M. Torrance, Chris T. A. Evelo, Rajarshi Guha, Christoph Steinbeck
2010 J jnl
MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data.
BMC Bioinform.
Tomás Pluskal, Sandra Castillo, Alejandro Villar-Briones, Matej Oresic