Publications

@misc{learning-proteomic-disease-trajectories-with-flow-matching,
  title = {Learning proteomic disease trajectories with flow matching},
  author = {Erik Hartman and Christofer Karlsson and Johan Malmström},
  year = {2026},
  howpublished = {bioRxiv},
  doi = {10.64898/2026.07.08.737311}
}

@misc{deep-learning-guided-evolutionary-optimization-for-protein-design,
  title = {Deep learning-guided evolutionary optimization for protein design},
  author = {Erik Hartman and Di Tang and Johan Malmström},
  year = {2026},
  howpublished = {arXiv},
  doi = {10.48550/ARXIV.2603.02753}
}

@article{degradation-graphs-reveal-hidden-proteolytic-activity-in-peptidomes,
  title = {Degradation graphs reveal hidden proteolytic activity in peptidomes},
  author = {Erik Hartman and Johan Malmström and Jonas Wallin},
  year = {2026},
  journal = {PLoS Computational Biology},
  doi = {10.1371/journal.pcbi.1013972}
}

@misc{controllable-protein-design-through-feynman-kac-steering,
  title = {Controllable protein design with particle-based Feynman-Kac steering},
  author = {Erik Hartman and Jonas Wallin and Johan Malmström and Jimmy Olsson},
  year = {2025},
  howpublished = {arXiv},
  doi = {10.48550/ARXIV.2511.09216}
}

@article{mass-spectrometry-peptidomics-data-from-infected-and-uninfected-porcine-wounds,
  title = {Mass spectrometry peptidomics data from infected and uninfected porcine wounds},
  author = {Fredrik Forsberg and Sven Kjellström and Jitka Petrlova and Manoj Puthia and Artur Schmidtchen and Johan Malmström and Erik Hartman},
  year = {2025},
  journal = {Scientific Data},
  doi = {10.1038/s41597-025-05842-8}
}

@article{temporal-dynamics-and-interrelations-of-cytokines-neutrophil-proteins-exudation-and-bacterial-colonization-in-epidermal-wound-healing,
  title = {Temporal dynamics and interrelations of cytokines, neutrophil proteins, exudation, and bacterial colonization in epidermal wound healing},
  author = {Sigrid Lundgren and Ganna Petruk and Karl Wallblom and José F. P. Cardoso and Ann-Charlotte Strömdahl and Fredrik Forsberg and Congyu Luo and Bo Nilson and Erik Hartman and Jane Fisher and Manoj Puthia and Karim Saleh and Artur Schmidtchen},
  year = {2025},
  journal = {Frontiers in Medicine},
  doi = {10.3389/fmed.2025.1609347}
}

@article{authors-must-follow-the-editorial-guidelines-on-the-use-of-large-language-models-in-review-papers,
  title = {Authors must follow the editorial guidelines on the use of large language models in review papers},
  author = {Roland Seifert and Erik Hartman and KeWei Wang and Daniela Yildiz},
  year = {2025},
  journal = {Naunyn-Schmiedeberg’s Archives of Pharmacology},
  doi = {10.1007/s00210-025-04102-1}
}

@article{epitope-mapping-with-sidewinder-an-xl-ms-and-structural-modeling-approach,
  title = {Epitope Mapping with Sidewinder: An XL-MS and Structural Modeling Approach},
  author = {Joel Ströbaek and Di Tang and Carlos Gueto-Tettay and Alejandro Gomez Toledo and Berit Olofsson and Erik Hartman and Moritz Heusel and Johan Malmström and Lars Malmström},
  year = {2025},
  journal = {International Journal of Molecular Sciences},
  doi = {10.3390/ijms26041488}
}

@misc{navigating-the-peptide-sequence-space-in-search-for-peptide-binders-with-bopep,
  title = {Navigating the peptide sequence space in search for peptide binders with BoPep},
  author = {Erik Hartman and Firdaus Samsudin and Malcolm Siljehag Alencar and Di Tang and Peter J Bond and Artur Schmidtchen and Johan Malmstrom},
  year = {2025},
  howpublished = {bioRxiv},
  doi = {10.1101/2025.01.20.633551}
}

@article{peptide-clustering-enhances-large-scale-analyses-and-reveals-proteolytic-signatures-in-mass-spectrometry-data,
  title = {Peptide clustering enhances large-scale analyses and reveals proteolytic signatures in mass spectrometry data},
  author = {Erik Hartman and Fredrik Forsberg and Sven Kjellström and Jitka Petrlova and Congyu Luo and Aaron Scott and Manoj Puthia and Johan Malmström and Artur Schmidtchen},
  year = {2024},
  journal = {Nature Communications},
  doi = {10.1038/s41467-024-51589-y}
}

@article{selective-protein-aggregation-confines-and-inhibits-endotoxins-in-wounds-linking-host-defense-to-amyloid-formation,
  title = {Selective protein aggregation confines and inhibits endotoxins in wounds: Linking host defense to amyloid formation},
  author = {Jitka Petrlova and Erik Hartman and Ganna Petruk and Jeremy Chun Hwee Lim and Sunil Shankar Adav and Sven Kjellström and Manoj Puthia and Artur Schmidtchen},
  year = {2023},
  journal = {iScience},
  doi = {10.1016/j.isci.2023.107951}
}

@article{interpreting-biologically-informed-neural-networks-for-enhanced-proteomic-biomarker-discovery-and-pathway-analysis,
  title = {Interpreting biologically informed neural networks for enhanced proteomic biomarker discovery and pathway analysis},
  author = {Erik Hartman and Aaron M. Scott and Christofer Karlsson and Tirthankar Mohanty and Suvi T. Vaara and Adam Linder and Lars Malmström and Johan Malmström},
  year = {2023},
  journal = {Nature Communications},
  doi = {10.1038/s41467-023-41146-4}
}

@article{bioactive-suture-with-added-innate-defense-functionality-for-the-reduction-of-bacterial-infection-and-inflammation,
  title = {Bioactive Suture with Added Innate Defense Functionality for the Reduction of Bacterial Infection and Inflammation},
  author = {Manoj Puthia and Jitka Petrlova and Ganna Petruk and Marta Butrym and Firdaus Samsudin and Madelene Å Andersson and Ann‐Charlotte Strömdahl and Sebastian Wasserstrom and Erik Hartman and Sven Kjellström and Lucrezia Caselli and Oxana Klementieva and Peter J. Bond and Martin Malmsten and Deepak Bushan Raina and Artur Schmidtchen},
  year = {2023},
  journal = {Advanced Healthcare Materials},
  doi = {10.1002/adhm.202300987}
}

@misc{explainable-machine-learning-for-the-identification-of-proteome-states-via-the-data-processing-kitchen-sink,
  title = {Explainable machine learning for the identification of proteome states via the data processing kitchen sink},
  author = {Aaron M. Scott and Erik Hartman and Johan Malmström and Lars Malmström},
  year = {2023},
  howpublished = {bioRxiv},
  doi = {10.1101/2023.08.30.555506}
}

@article{generalized-precursor-prediction-boosts-identification-rates-and-accuracy-in-mass-spectrometry-based-proteomics,
  title = {Generalized precursor prediction boosts identification rates and accuracy in mass spectrometry based proteomics},
  author = {Aaron M. Scott and Christofer Karlsson and Tirthankar Mohanty and Erik Hartman and Suvi T. Vaara and Adam Linder and Johan Malmström and Lars Malmström},
  year = {2023},
  journal = {Communications Biology},
  doi = {10.1038/s42003-023-04977-x}
}

@article{peptimetric-quantifying-and-visualizing-differences-in-peptidomic-data,
  title = {Peptimetric: Quantifying and Visualizing Differences in Peptidomic Data},
  author = {Erik Hartman and Simon Mahdavi and Sven Kjellström and Artur Schmidtchen},
  year = {2021},
  journal = {Frontiers in Bioinformatics},
  doi = {10.3389/fbinf.2021.722466}
}

@article{bioinformatic-analysis-of-the-wound-peptidome-reveals-potential-biomarkers-and-antimicrobial-peptides,
  title = {Bioinformatic Analysis of the Wound Peptidome Reveals Potential Biomarkers and Antimicrobial Peptides},
  author = {Erik Hartman and Karl Wallblom and Mariena J. A. van der Plas and Jitka Petrlova and Jun Cai and Karim Saleh and Sven Kjellström and Artur Schmidtchen},
  year = {2021},
  journal = {Frontiers in Immunology},
  doi = {10.3389/fimmu.2020.620707}
}

@article{the-role-of-full-length-apoe-in-clearance-of-gram-negative-bacteria-and-their-endotoxins,
  title = {The role of full-length apoE in clearance of Gram-negative bacteria and their endotoxins},
  author = {Ganna Petruk and Malin Elvén and Erik Hartman and Mina Davoudi and Artur Schmidtchen and Manoj Puthia and Jitka Petrlova},
  year = {2021},
  journal = {Journal of Lipid Research},
  doi = {10.1016/j.jlr.2021.100086}
}