{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T02:57:05Z","timestamp":1782874625592,"version":"3.54.5"},"reference-count":66,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2026,3,21]],"date-time":"2026-03-21T00:00:00Z","timestamp":1774051200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Union\u2019s Horizon 2020","award":["874735"],"award-info":[{"award-number":["874735"]}]},{"name":"National Institute Of Allergy And Infectious Diseases of the National Institutes of Health","award":["U24AI183840"],"award-info":[{"award-number":["U24AI183840"]}]},{"DOI":"10.13039\/501100009708","name":"Novo Nordisk Foundation","doi-asserted-by":"publisher","award":["NNF26SA0109818"],"award-info":[{"award-number":["NNF26SA0109818"]}],"id":[{"id":"10.13039\/501100009708","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,5,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Infectious diseases continue to be a leading cause of mortality and pose a significant global health threat. Thus, the development of tools for surveillance and early detection of emerging pathogens is needed.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We introduce PathogenFinder2, a novel, alignment-free, taxonomy-agnostic model for predicting bacterial pathogenic capacity in humans using protein language models. It outperforms previous methods, particularly for novel taxa, and provides interpretable outputs by highlighting proteins most relevant to pathogenic potential. These insights aid the identification of virulence factors, vaccine targets, and infection-related metabolic pathways. Furthermore, we introduce the Bacterial Pathogenic Capacity Landscape, which reveals patterns linked to host condition, infection site, microbial antagonism, and environmental origin.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability<\/jats:title>\n                    <jats:p>The model is freely available online at https:\/\/genepi.dk\/pathogenfinder2, or as a standalone program (https:\/\/github.com\/genomicepidemiology\/PathogenFinder2).<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag129","type":"journal-article","created":{"date-parts":[[2026,3,21]],"date-time":"2026-03-21T10:15:07Z","timestamp":1774088107000},"source":"Crossref","is-referenced-by-count":4,"title":["Whole-genome prediction of bacterial pathogenic capacity on novel bacteria using protein language models with 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Technical University of Denmark , Kongens Lyngby, 2800,","place":["Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8197-7520","authenticated-orcid":false,"given":"Philip Thomas Lanken Conradsen","family":"Clausen","sequence":"additional","affiliation":[{"name":"Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark , Kongens Lyngby, 2800,","place":["Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9412-9643","authenticated-orcid":false,"given":"Henrik","family":"Nielsen","sequence":"additional","affiliation":[{"name":"Bioinformatics, Department of Health Technology, Technical University of Denmark , Kongens Lyngby, 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