{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T05:29:00Z","timestamp":1790659740180,"version":"4.1.0"},"reference-count":134,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T00:00:00Z","timestamp":1772064000000},"content-version":"vor","delay-in-days":56,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001186","name":"Australian Cystic Fibrosis Research Trust","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001186","id-type":"DOI","asserted-by":"publisher"}]},{"name":"CFWA Golf Classic Innovation"},{"name":"WA Cystic Fibrosis Collaborative Program 2025 Fellowship"},{"DOI":"10.13039\/100031095","name":"Cure4 Cystic Fibrosis Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100031095","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Western Australian Future Health Research & Innovation Fund","award":["IC2023-GAIA\/21"],"award-info":[{"award-number":["IC2023-GAIA\/21"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Strain-level prediction of phage\u2013host interactions (PHIs) is essential for developing targeted phage therapies. Traditional empirical and homology-based methods often lack the resolution and scalability needed for precision applications. Recently, a new generation of artificial intelligence-driven models has emerged leveraging genomic information to infer PHIs at strain-level resolution. Here, we review recent advances in strain-level PHI prediction, spanning biologically grounded feature-based models, hybrid representation-learning frameworks, phylogeny-agnostic machine learning approaches, and end-to-end deep learning architectures. We examine how these modelling strategies navigate shared structural constraints arising from sparse and imbalanced outcome data, assay-dependent labels, infection complexity, and limited generalization. We further analyse how evaluation design, negative definition, and train-test splitting strategies shape apparent strain-level performance, and why inappropriate benchmarking can inflate claims of biological resolution. Framing these issues in the context of clinical phage therapy, we examine how current strain-level PHI prediction frameworks perform under the biological, experimental, and data constraints characteristic of real-world therapeutic settings. Finally, we outline pragmatic pathways toward more robust, interpretable, and clinically translatable PHI prediction systems.<\/jats:p>","DOI":"10.1093\/bib\/bbag085","type":"journal-article","created":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T12:44:33Z","timestamp":1770986673000},"source":"Crossref","is-referenced-by-count":14,"title":["Towards accurate artificial intelligence models for strain-level phage\u2013host prediction"],"prefix":"10.1093","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8865-090X","authenticated-orcid":false,"given":"Chris J","family":"Malajczuk","sequence":"first","affiliation":[{"name":"Wal-yan Respiratory Research Centre, The Kids Research Institute \u00a0","place":["Australia, Western Australia, Perth, 6009, Australia"]},{"name":"UWA Centre for Child Health Research, University of Western Australia, Western Australia, Perth, 6009, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew","family":"Vaitekenas","sequence":"additional","affiliation":[{"name":"Wal-yan Respiratory Research Centre, The Kids Research Institute \u00a0","place":["Australia, Western Australia, Perth, 6009, Australia"]},{"name":"UWA Centre for Child Health Research, University of Western Australia, Western Australia, Perth, 6009, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6394-5058","authenticated-orcid":false,"given":"Joshua J","family":"Iszatt","sequence":"additional","affiliation":[{"name":"Wal-yan Respiratory Research Centre, The Kids Research Institute \u00a0","place":["Australia, Western Australia, Perth, 6009, Australia"]},{"name":"UWA Centre for Child Health Research, University of Western Australia, Western Australia, Perth, 6009, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen M","family":"Stick","sequence":"additional","affiliation":[{"name":"Department of Respiratory and Sleep Medicine, Perth Children\u2019s Hospital, Western Australia, Perth, 6009, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0008-9733","authenticated-orcid":false,"given":"Anthony","family":"Kicic","sequence":"additional","affiliation":[{"name":"Wal-yan Respiratory Research Centre, The Kids Research Institute \u00a0","place":["Australia, Western Australia, Perth, 6009, Australia"]},{"name":"UWA Centre for Child Health Research, University of Western Australia, Western Australia, Perth, 6009, Australia"},{"name":"School of Population Health, Curtin University, Western Australia, Perth, 6102, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuliya V","family":"Karpievitch","sequence":"additional","affiliation":[{"name":"Wal-yan Respiratory Research Centre, The Kids Research Institute \u00a0","place":["Australia, Western Australia, Perth, 6009, Australia"]},{"name":"School of Population Health, Curtin University, Western Australia, Perth, 6102, Australia"},{"name":"School of Biomedical Sciences, University of Western Australia, Western Australia, Perth, 6009, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,2,26]]},"reference":[{"key":"2026022605354941400_ref1","doi-asserted-by":"publisher","first-page":"1434","DOI":"10.1038\/s41564-024-01705-x","article-title":"Personalized bacteriophage therapy outcomes for 100 consecutive cases: a multicentre, multinational, retrospective observational study","volume":"9","author":"Pirnay","year":"2024","journal-title":"Nat Microbiol"},{"key":"2026022605354941400_ref2","doi-asserted-by":"publisher","first-page":"e70108","DOI":"10.1111\/1751-7915.70108","article-title":"Harnessing bacteriophages for sustainable crop protection in the face of climate 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