Publications
Exploring Biosynthesis & Chemodiversity of Natural Products
Remarkable diversity of alkaloid scaffolds in Piper fimbriulatum.
Damiani, T., Smith, J., Hebra, T., Perkovic, M., Cicak, M., Kadlecova, A., ... & Pluskal, T.
bioRxiv, 2024 • biorxiv.org
The biosynthetic origin of psychoactive kavalactones in kava.
Pluskal, T., Torrens-Spence, M. P., Fallon, T. R., De Abreu, A., Shi, C. H., & Weng, J. K.
Nature plants, 2019 • nature.com
Computational metabolomics
Statistical analysis of feature-based molecular networking results from non-targeted metabolomics data.
Pakkir Shah, A. K., Walter, A., Ottosson, F., Russo, F., Navarro-Diaz, M., Boldt, J., ... & Petras, D.
Nature protocols, 2025 • nature.com
MassSpecGym: A benchmark for the discovery and identification of molecules.
Bushuiev, R., Bushuiev, A., de Jonge, N., Young, A., Kretschmer, F., Samusevich, R., ... & Pluskal, T.
Advances in Neural Information Processing Systems, 2025 • proceedings.neurips.cc
Reproducible mass spectrometry data processing and compound annotation in MZmine 3.
Heuckeroth, S., Damiani, T., Smirnov, A., Mokshyna, O., Brungs, C., Korf, A., ... & Pluskal, T.
Nature protocols, 2024 • nature.com
Machine Learning Powered Enzyme Development
Highly accurate discovery of terpene synthases powered by machine learning reveals functional terpene cyclization in Archaea.
Samusevich, R., Hebra, T., Bushuiev, R., Bushuiev, A., Čalounová, T., Smrčková, H., ... & Pluskal, T.
BioRxiv, 2024 • biorxiv.org
Revealing data leakage in protein interaction benchmarks.
Bushuiev, A., Bushuiev, R., Sedlar, J., Pluskal, T., Damborsky, J., Mazurenko, S., & Sivic, J.
International Conference on Learning Representations, 2024
Learning to design protein-protein interactions with enhanced generalization.
Bushuiev, A., Bushuiev, R., Kouba, P., Filkin, A., Gabrielova, M., Gabriel, M., ... & Sivic, J.
International Conference on Learning Representations, 2024
Synthetic Biology
POMBOX: A Fission Yeast Cloning Toolkit for Molecular and Synthetic Biology
T Hebra, H Smrčková, B Elkatmis, M Prevorovsky, T Pluskal.
ACS Synthetic Biology, 2023 • ACS Publications