publications | Erik Hartman

2025

Mining the endogenous peptidome for peptide binders with deep learning-driven optimization and molecular simulations

Erik Hartman, Firdaus Samsudin, Peter J Bond, and 2 more authors

Jan 2025

Epitope Mapping with Sidewinder: An XL-MS and Structural Modeling Approach

Joel Ströbaek, Di Tang, Carlos Gueto-Tettay, and 6 more authors

International Journal of Molecular Sciences, Feb 2025

Bib

@article{Strbaek2025,
  title = {Epitope Mapping with Sidewinder: An XL-MS and Structural Modeling Approach},
  volume = {26},
  issn = {1422-0067},
  url = {http://dx.doi.org/10.3390/ijms26041488},
  doi = {10.3390/ijms26041488},
  number = {4},
  journal = {International Journal of Molecular Sciences},
  publisher = {MDPI AG},
  author = {Str\"{o}baek, Joel and Tang, Di and Gueto-Tettay, Carlos and Gomez Toledo, Alejandro and Olofsson, Berit and Hartman, Erik and Heusel, Moritz and Malmstr\"{o}m, Johan and Malmstr\"{o}m, Lars},
  year = {2025},
  month = feb,
  show_bibtex = {true},
  pages = {1488}
}

Temporal dynamics and interrelations of cytokines, neutrophil proteins, exudation, and bacterial colonization in epidermal wound healing

Sigrid Lundgren, Ganna Petruk, Karl Wallblom, and 10 more authors

Frontiers in Medicine, Jul 2025

Bib

@article{Lundgren2025,
  title = {Temporal dynamics and interrelations of cytokines,  neutrophil proteins,  exudation,  and bacterial colonization in epidermal wound healing},
  volume = {12},
  issn = {2296-858X},
  url = {http://dx.doi.org/10.3389/fmed.2025.1609347},
  doi = {10.3389/fmed.2025.1609347},
  journal = {Frontiers in Medicine},
  publisher = {Frontiers Media SA},
  author = {Lundgren, Sigrid and Petruk, Ganna and Wallblom, Karl and Cardoso, José F. P. and Str\"{o}mdahl, Ann-Charlotte and Forsberg, Fredrik and Luo, Congyu and Nilson, Bo and Hartman, Erik and Fisher, Jane and Puthia, Manoj and Saleh, Karim and Schmidtchen, Artur},
  year = {2025},
  show_bibtex = {true},
  month = jul
}

2024

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,
}

2023

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},
}

Explainable machine learning for the identification of proteome states via the data processing kitchen sink

Aaron M. Scott, Erik Hartman, Johan Malmström, and 1 more author

Aug 2023

Bib

@article{Scott2023,
  title = {Explainable machine learning for the identification of proteome states via the data processing kitchen sink},
  url = {http://dx.doi.org/10.1101/2023.08.30.555506},
  doi = {10.1101/2023.08.30.555506},
  publisher = {Cold Spring Harbor Laboratory},
  author = {Scott, Aaron M. and Hartman, Erik and Malmstr\"{o}m, Johan and Malmstr\"{o}m, Lars},
  year = {2023},
  month = aug
}

Generalized precursor prediction boosts identification rates and accuracy in mass spectrometry based proteomics

Aaron M. Scott, Christofer Karlsson, Tirthankar Mohanty, and 5 more authors

Communications Biology, Jun 2023

Bib

@article{Scott2024,
  title = {Generalized precursor prediction boosts identification rates and accuracy in mass spectrometry based proteomics},
  volume = {6},
  issn = {2399-3642},
  url = {http://dx.doi.org/10.1038/s42003-023-04977-x},
  doi = {10.1038/s42003-023-04977-x},
  number = {1},
  journal = {Communications Biology},
  publisher = {Springer Science and Business Media LLC},
  author = {Scott, Aaron M. and Karlsson, Christofer and Mohanty, Tirthankar and Hartman, Erik and Vaara, Suvi T. and Linder, Adam and Malmstr\"{o}m, Johan and Malmstr\"{o}m, Lars},
  year = {2023},
  month = jun
}

Selective protein aggregation confines and inhibits endotoxins in wounds: Linking host defense to amyloid formation

Jitka Petrlova, Erik Hartman, Ganna Petruk, and 5 more authors

iScience, Oct 2023

Analysis of bacteria, inflammation, and exudation in epidermal suction blister wounds reveals dynamic changes during wound healing

Sigrid Lundgren, Ganna Petruk, Karl Wallblom, and 10 more authors

Dec 2023

Bib

@article{Lundgren2023,
  title = {Analysis of bacteria,  inflammation,  and exudation in epidermal suction blister wounds reveals dynamic changes during wound healing},
  url = {http://dx.doi.org/10.1101/2023.12.07.23299659},
  doi = {10.1101/2023.12.07.23299659},
  publisher = {Cold Spring Harbor Laboratory},
  author = {Lundgren, Sigrid and Petruk, Ganna and Wallblom, Karl and Cardoso, José FP and Str\"{o}mdahl, Ann-Charlotte and Forsberg, Fredrik and Luo, Congyu and Nilson, Bo and Hartman, Erik and Fisher, Jane and Puthia, Manoj and Saleh, Karim and Schmidtchen, Artur},
  year = {2023},
  show_bibtex = {true},
  month = dec
}

Bioactive Suture with Added Innate Defense Functionality for the Reduction of Bacterial Infection and Inflammation

Manoj Puthia, Jitka Petrlova, Ganna Petruk, and 13 more authors

Advanced Healthcare Materials, Sep 2023

2021

Peptimetric: Quantifying and Visualizing Differences in Peptidomic Data

Erik Hartman, Simon Mahdavi, Sven Kjellström, and 1 more author

Frontiers in Bioinformatics, Aug 2021

Bib

@article{Hartman2021,
  title = {Peptimetric: Quantifying and Visualizing Differences in Peptidomic Data},
  volume = {1},
  issn = {2673-7647},
  url = {http://dx.doi.org/10.3389/fbinf.2021.722466},
  doi = {10.3389/fbinf.2021.722466},
  journal = {Frontiers in Bioinformatics},
  publisher = {Frontiers Media SA},
  author = {Hartman, Erik and Mahdavi, Simon and Kjellstr\"{o}m, Sven and Schmidtchen, Artur},
  year = {2021},
  month = aug
}

Bioinformatic Analysis of the Wound Peptidome Reveals Potential Biomarkers and Antimicrobial Peptides

Erik Hartman, Karl Wallblom, Mariena J. A. Plas, and 5 more authors

Frontiers in Immunology, Feb 2021

Bib

@article{Hartman2022,
  title = {Bioinformatic Analysis of the Wound Peptidome Reveals Potential Biomarkers and Antimicrobial Peptides},
  volume = {11},
  issn = {1664-3224},
  url = {http://dx.doi.org/10.3389/fimmu.2020.620707},
  doi = {10.3389/fimmu.2020.620707},
  journal = {Frontiers in Immunology},
  publisher = {Frontiers Media SA},
  author = {Hartman, Erik and Wallblom, Karl and van der Plas, Mariena J. A. and Petrlova, Jitka and Cai, Jun and Saleh, Karim and Kjellstr\"{o}m, Sven and Schmidtchen, Artur},
  year = {2021},
  show_bibtex = {true},
  month = feb
}

The role of full-length apoE in clearance of Gram-negative bacteria and their endotoxins

Ganna Petruk, Malin Elvén, Erik Hartman, and 4 more authors

Journal of Lipid Research, Feb 2021