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.png
    Training on test proteins improves fitness, structure, and function prediction
    Anton Bushuiev*, Roman Bushuiev*, Nikola Zadorozhny, and 5 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

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

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