publications

2024

1. 

   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

1. 

   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},
   }

2. 

   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
   }

3. 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
   }

4. 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
5. 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
6. 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

1. 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
   }

2. 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},
     month = feb
   }

3. 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