Erik Hartman

I am currently at the University of Pennsylvania as a visiting research scholar under César de la Fuente in the Machine Biology Group. I am doing my PhD in computational biology at the infection medicine proteomics lab, Lund University, Sweden. During my PhD I’ve also spent time as a research student at A*STAR, Singapore, under Dr. Peter J Bond.

My work has been scattered in various fields of computational biology, but mainly focusing on infection medicine in terms of both diagnostic and designing treatments. The research question I’m most passionate about is the role of protein degradation and the encrypted peptide hypothesis.

I’ve been passionate about science and research for as long as I can remember and am alumni of Anders Wall Schlolars, The Sweden-America Foundation, the Swedish Society for Young Scientist (Unga Forskare), Society for Science, International Science and Engineering Fair, and international Genetically Engineered Machine (iGEM).

GitHub: https://github.com/ErikHartman

selected publications

Learning proteomic disease trajectories with flow matching

Erik Hartman, Christofer Karlsson, and Johan Malmström

bioRxiv, Jul 2026

Bib

@article{Hartman2026FlowMatching,
  title = {Learning proteomic disease trajectories with flow matching},
  url = {https://doi.org/10.64898/2026.07.08.737311},
  doi = {10.64898/2026.07.08.737311},
  journal = {bioRxiv},
  author = {Hartman, Erik and Karlsson, Christofer and Malmstr\"{o}m, Johan},
  year = {2026},
  month = jul,
}

Degradation graphs reveal hidden proteolytic activity in peptidomes

Erik Hartman, Johan Malmström, and Jonas Wallin

PLoS Computational Biology, Feb 2026

Bib

@article{Hartman2026DegradationGraphs,
  title = {Degradation graphs reveal hidden proteolytic activity in peptidomes},
  volume = {22},
  number = {2},
  pages = {e1013972},
  url = {https://doi.org/10.1371/journal.pcbi.1013972},
  doi = {10.1371/journal.pcbi.1013972},
  journal = {PLoS Computational Biology},
  author = {Hartman, Erik and Malmstr\"{o}m, Johan and Wallin, Jonas},
  year = {2026},
  month = feb,
}

Deep learning-guided evolutionary optimization for protein design

Erik Hartman, Di Tang, and Johan Malmström

Feb 2026

Controllable protein design through Feynman-Kac steering

Erik Hartman, Jonas Wallin, Johan Malmström, and 1 more author

Nov 2025

Bib

@misc{FK,
  doi = {10.48550/ARXIV.2511.09216},
  url = {https://arxiv.org/abs/2511.09216},
  author = {Hartman, Erik and Wallin, Jonas and Malmstr\"{o}m, Johan and Olsson, Jimmy},
  keywords = {Machine Learning (cs.LG),  Quantitative Methods (q-bio.QM),  Machine Learning (stat.ML),  FOS: Computer and information sciences,  FOS: Computer and information sciences,  FOS: Biological sciences,  FOS: Biological sciences},
  title = {Controllable protein design through Feynman-Kac steering},
  publisher = {arXiv},
  year = {2025},
  copyright = {arXiv.org perpetual,  non-exclusive license},
  month = nov,
}

Navigating the peptide sequence space in search for peptide binders with BoPep

Erik Hartman, Firdaus Samsudin, Malcolm Siljehag Alencar, and 4 more authors

Jan 2025

Peptide clustering enhances large-scale analyses and reveals proteolytic signatures in mass spectrometry data

Erik Hartman, Fredrik Forsberg, Sven Kjellström, and 6 more authors

Nature Communications, Aug 2024

Bib

@article{Hartman2024,
  title = {Peptide clustering enhances large-scale analyses and reveals proteolytic signatures in mass spectrometry data},
  url = {https://doi.org/10.1038/s41467-024-51589-y},
  doi = {https://doi.org/10.1038/s41467-024-51589-y},
  publisher = {Springer Science and Business Media LLC},
  journal = {Nature Communications},
  author = {Hartman, Erik and Forsberg, Fredrik and Kjellstr\"{o}m, Sven and Petrlova, Jitka and Luo, Congyu and Scott, Aaron and Puthia, Manoj and Malmstr\"{o}m, Johan and Schmidtchen, Artur},
  year = {2024},
  month = aug,
}

Interpreting biologically informed neural networks for enhanced proteomic biomarker discovery and pathway analysis

Erik Hartman, Aaron M. Scott, Christofer Karlsson, and 5 more authors

Nature Communications, Sep 2023

Bib

@article{Hartman2023,
  title = {Interpreting biologically informed neural networks for enhanced proteomic biomarker discovery and pathway analysis},
  volume = {14},
  issn = {2041-1723},
  url = {http://dx.doi.org/10.1038/s41467-023-41146-4},
  doi = {10.1038/s41467-023-41146-4},
  number = {1},
  journal = {Nature Communications},
  publisher = {Springer Science and Business Media LLC},
  author = {Hartman, Erik and Scott, Aaron M. and Karlsson, Christofer and Mohanty, Tirthankar and Vaara, Suvi T. and Linder, Adam and Malmstr\"{o}m, Lars and Malmstr\"{o}m, Johan},
  year = {2023},
  month = sep,
  dimensions = {true},
}