Roman Bushuiev

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I’m a third-year PhD student at IOCB Prague and the Czech Technical University, co-supervised by Dr. Tomáš Pluskal and Dr. Josef Sivic. I am a part of the ELLIS PhD program and supported by a Google PhD Fellowship.

My primary research interest lies in developing machine learning methods for discovering new molecules from nature (e.g., new medicines from plants). I am also interested in protein language models, enzyme function prediction, and protein design. I work closely with my twin brother Anton Bushuiev.

While I work on method development, I’m particularly passionate about the biological discoveries and real-world impact that machine learning can unlock. I deeply value collaboration—please feel free to reach out! 😉

Outside of research, I enjoy exploring art and doing sports, espcecially Uechi-Ryū karate at the dojo of my research supervisor, Dr. Tomáš Pluskal.

News

Oct 27, 2025 Check out our new paper “One protein is all you need” (X thread summary).
May 09, 2025 I will be doing a research internship in Martin Steinegger’s lab from July to September.
Apr 22, 2025 Check out an interview with me and my brother on CzechCrunch (in Czech).
Dec 15, 2024 MassSpecGym has been integrated to Polaris. Check out my interview with Valence Labs.

Selected publications

  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
  2. 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
  3. ppiformer.png
    Learning to design protein-protein interactions with enhanced generalization
    Anton Bushuiev*, Roman Bushuiev*, Petr Kouba, and 8 more authors
    ICLR, 2024
  4. proteinttt.gif
    One protein is all you need
    Anton Bushuiev*, Roman Bushuiev*, Olga Pimenova, and 9 more authors
    arXiv, 2025
  5. ppileakage.png
    Revealing data leakage in protein interaction benchmarks
    Anton Bushuiev*, Roman Bushuiev*, Jiřı́ Sedlář, and 4 more authors
    ICLR GEM workshop, 2024