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Whole-genome prediction of bacterial pathogenic capacity on novel bacteria using protein language models with PathogenFinder2.

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Title: Whole-genome prediction of bacterial pathogenic capacity on novel bacteria using protein language models with PathogenFinder2.
Authors: Ferrer Florensa A; Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, 2800, Denmark., Almagro Armenteros JJ; Informatics and Predictive Sciences Research, Bristol Myers Squibb Company, Sevilla, 41092, Spain., Kaas RS; Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, 2800, Denmark., Clausen PTLC; Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, 2800, Denmark., Nielsen H; Bioinformatics, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, 2800, Denmark., Rost B; Rostlab, Department of Bioinformatics and Computational Biology, Technical University of Munich, Munich, 85748, Germany., Aarestrup FM; Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, 2800, Denmark.
Source: Bioinformatics (Oxford, England) [Bioinformatics] 2026 May 03; Vol. 42 (5).
Publication Type: Journal Article
Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE
Database: MEDLINE Ultimate
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  Data: Whole-genome prediction of bacterial pathogenic capacity on novel bacteria using protein language models with PathogenFinder2.
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  Data: <searchLink fieldCode="AU" term="%22Ferrer+Florensa+A%22">Ferrer Florensa A</searchLink>; Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, 2800, Denmark.<br /><searchLink fieldCode="AU" term="%22Almagro+Armenteros+JJ%22">Almagro Armenteros JJ</searchLink>; Informatics and Predictive Sciences Research, Bristol Myers Squibb Company, Sevilla, 41092, Spain.<br /><searchLink fieldCode="AU" term="%22Kaas+RS%22">Kaas RS</searchLink>; Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, 2800, Denmark.<br /><searchLink fieldCode="AU" term="%22Clausen+PTLC%22">Clausen PTLC</searchLink>; Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, 2800, Denmark.<br /><searchLink fieldCode="AU" term="%22Nielsen+H%22">Nielsen H</searchLink>; Bioinformatics, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, 2800, Denmark.<br /><searchLink fieldCode="AU" term="%22Rost+B%22">Rost B</searchLink>; Rostlab, Department of Bioinformatics and Computational Biology, Technical University of Munich, Munich, 85748, Germany.<br /><searchLink fieldCode="AU" term="%22Aarestrup+FM%22">Aarestrup FM</searchLink>; Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, 2800, Denmark.
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  Data: <searchLink fieldCode="JN" term="%229808944%22">Bioinformatics (Oxford, England)</searchLink> [Bioinformatics] 2026 May 03; Vol. 42 (5).
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        Value: 10.1093/bioinformatics/btag129
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              Text: 2026 May 03
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