Tomás Pluskal

According to our database, Tomás Pluskal authored at least 14 papers between 2010 and 2026.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2026

MARTS-DB: a database of mechanisms and reactions of terpene synthases.

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

BMC Bioinform., December, 2026

2025

De novo generation of functional terpene synthases using TpsGPT.

Hamsini Ramanathan, Roman Bushuiev, Matous Soldát, Jirí Kohout, Téo Hebra, Joshua David Smith, Josef Sivic, Tomás Pluskal

CoRR, December, 2025

An evaluation methodology for machine learning-based tandem mass spectra similarity prediction.

Michael Strobel, Alberto Gil-de-la-Fuente, Mohammad Reza Shahneh, Yasin El Abiead, Roman Bushuiev, Anton Bushuiev, Tomás Pluskal, Mingxun Wang

BMC Bioinform., December, 2025

MARTS-DB: A Database of Mechanisms And Reactions of Terpene Synthases V1.5.

Martin Engst, Tereza Calounová, Raman Samusevich, Roman Bushuiev, Anton Bushuiev, Ratthachat Chatpatanasiri, Safa Mert Akmese, Milana Perkovic, Matous Soldát, Adéla Tajovská, Tomás Pluskal, Josef Sivic

Dataset, November, 2025

MARTS-DB: A Database of Mechanisms And Reactions of Terpene Synthases V1.0.

Martin Engst, Tereza Calounová, Raman Samusevich, Roman Bushuiev, Anton Bushuiev, Ratthachat Chatpatanasiri, Safa Mert Akmese, Milana Perkovic, Matous Soldát, Adéla Tajovská, Tomás Pluskal, Josef Sivic

Dataset, October, 2025

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

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

Revealing data leakage in protein interaction benchmarks.

Anton Bushuiev, Roman Bushuiev, Jirí Sedlár, Tomás Pluskal, Jirí Damborský, Stanislav Mazurenko, Josef Sivic

CoRR, 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, 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

Proceedings of the Advances in Neural Information Processing Systems 38: Annual Conference on Neural Information Processing Systems 2024, 2024

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

Proceedings of the Twelfth International Conference on Learning Representations, 2024

2023

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., December, 2023

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, Tomás Pluskal, Miquel Rojas-Chertó, Ola Spjuth, Gilleain M. Torrance, Chris T. A. Evelo, Rajarshi Guha, Christoph Steinbeck

J. Cheminformatics, 2017

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, Tomás Pluskal, Miquel Rojas-Chertó, Ola Spjuth, Gilleain M. Torrance, Chris T. A. Evelo, Rajarshi Guha, Christoph Steinbeck

J. Cheminformatics, 2017

2010

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