Publications

2025

  1. dreams.png
    Self-supervised learning of molecular representations from millions of tandem mass spectra using DreaMS
    Roman Bushuiev*, Anton Bushuiev*, Raman Samusevich, and 3 more authors
    Nature Biotechnology, 2025
    DOI Code Dataset Tutorials Poster NEWS
  2. proteinttt.gif
    One protein is all you need
    Anton Bushuiev*, Roman Bushuiev*, Olga Pimenova, and 9 more authors
    arXiv, 2025
    DOI Code
  3. enzymeexplorer.png
    Structure-enabled enzyme function prediction unveils elusive terpenoid biosynthesis in archaea
    Raman Samusevich, Téo Hebra, Roman Bushuiev, and 15 more authors
    bioRxiv, 2025
    DOI Code
  4. boltzgen.jpeg
    BoltzGen: Toward Universal Binder Design
    Hannes Stark, Felix Faltings*, MinGyu Choi*, and 35 more authors
    bioRxiv, 2025
    DOI Blog Code
  5. tpsgpt.png
    De novo generation of functional terpene synthases using TpsGPT
    Hamsini Ramanathan, Roman Bushuiev, Matouš Soldát, and 5 more authors
    NeurIPS 2025 AI for Science Workshop and MLSB 2025, 2025
    DOI
  6. marts-db.png
    MARTS-DB: A Database of Mechanisms And Reactions of Terpene Synthases
    Martin Engst, Martin Brokeš, Tereza Čalounová, and 10 more authors
    BMC bioinformatics, 2025
    DOI Dataset
  7. strobel2025evaluation.png
    An evaluation methodology for machine learning-based tandem mass spectra similarity prediction
    Michael Strobel, Alberto Gil-de-la-Fuente, Mohammad Reza Zare Shahneh, and 5 more authors
    BMC bioinformatics, 2025
    DOI

2024

  1. massspecgym.png
    MassSpecGym: A benchmark for the discovery and identification of molecules
    Roman Bushuiev, Anton Bushuiev, Niek F. Jonge, and 27 more authors
    NeurIPS Datasets & Benchmarks (Spotlight paper), 2024
    DOI Video Code Dataset Poster NEWS
  2. ppiformer.png
    Learning to design protein-protein interactions with enhanced generalization
    Anton Bushuiev*, Roman Bushuiev*, Petr Kouba, and 8 more authors
    ICLR, 2024
    DOI Video Code Dataset NEWS
  3. ppileakage.png
    Revealing data leakage in protein interaction benchmarks
    Anton Bushuiev*, Roman Bushuiev*, Jiřı́ Sedlář, and 4 more authors
    ICLR GEM workshop, 2024
    DOI Poster

2023

  1. mzmine3.png
    Integrative analysis of multimodal mass spectrometry data in MZmine 3
    Robin Schmid, Steffen Heuckeroth, Ansgar Korf, and 39 more authors
    Nature Biotechnology, 2023
    DOI