Lytras, Spyros and Lamb, Kieran D. and Ito, Jumpei and Grove, Joe and Yuan, Ke and Sato, Kei and Hughes, Joseph and Robertson, David L. (2025) Pathogen genomic surveillance and the AI revolution. Journal of Virology, 99 (2): e0160124. ISSN 0022-538X
AI Summary:
The unprecedented sequencing efforts during the COVID-19 pandemic have paved the way for genomic surveillance to become a powerful tool. Protein language models (pLMs) can be used to effectively analyze pathogen genomic data.AI Topics:
The unprecedented sequencing efforts during the COVID-19 pandemic paved the way for genomic surveillance to become a powerful tool for monitoring the evolution of circulating viruses. Herein, we discuss how a state-of-the-art artificial intelligence approach called protein language models (pLMs) can be used for effectively analyzing pathogen genomic data. We highlight examples of pLMs applied to predicting viral properties and evolution and lay out a framework for integrating pLMs into genomic surveillance pipelines.
Lytras, Spyros
Author
Lytras, Spyros and Lamb, Kieran D. and Ito, Jumpei and Grove, Joe and Yuan, Ke and Sato, Kei and Hughes, Joseph and Robertson, David L. (2025) Pathogen genomic surveillance and the AI revolution. Journal of Virology, 99 (2): e0160124. ISSN 0022-538X
Lamb, Kieran D. and Hughes, Joseph and Lytras, Spyros and Young, Francesca and Koci, Orges and Herzig, James and Lovell, Simon C, and Grove, Joe and Yuan, Ke and Robertson, David L. (2024) From a single sequence to evolutionary trajectories: protein language models capture the evolutionary potential of SARS-CoV-2 protein sequences. bioRxiv.
See full publications listLamb, Kieran D.
Author
Lytras, Spyros and Lamb, Kieran D. and Ito, Jumpei and Grove, Joe and Yuan, Ke and Sato, Kei and Hughes, Joseph and Robertson, David L. (2025) Pathogen genomic surveillance and the AI revolution. Journal of Virology, 99 (2): e0160124. ISSN 0022-538X
Liu, Dan and Young, Francesca and Lamb, Kieran D. and Claudio Quiros, Adalberto and Pancheva, Alexandrina and Miller, Crispin and Macdonald, Craig and Robertson, David L. and Yuan, Ke (2024) PLM-interact: extending protein language models to predict protein-protein interactions. bioRxiv.
Lamb, Kieran D. and Hughes, Joseph and Lytras, Spyros and Young, Francesca and Koci, Orges and Herzig, James and Lovell, Simon C, and Grove, Joe and Yuan, Ke and Robertson, David L. (2024) From a single sequence to evolutionary trajectories: protein language models capture the evolutionary potential of SARS-CoV-2 protein sequences. bioRxiv.
See full publications listIto, Jumpei
Author
Lytras, Spyros and Lamb, Kieran D. and Ito, Jumpei and Grove, Joe and Yuan, Ke and Sato, Kei and Hughes, Joseph and Robertson, David L. (2025) Pathogen genomic surveillance and the AI revolution. Journal of Virology, 99 (2): e0160124. ISSN 0022-538X
See full publications listGrove, Joe
Author
Lytras, Spyros and Lamb, Kieran D. and Ito, Jumpei and Grove, Joe and Yuan, Ke and Sato, Kei and Hughes, Joseph and Robertson, David L. (2025) Pathogen genomic surveillance and the AI revolution. Journal of Virology, 99 (2): e0160124. ISSN 0022-538X
Lamb, Kieran D. and Hughes, Joseph and Lytras, Spyros and Young, Francesca and Koci, Orges and Herzig, James and Lovell, Simon C, and Grove, Joe and Yuan, Ke and Robertson, David L. (2024) From a single sequence to evolutionary trajectories: protein language models capture the evolutionary potential of SARS-CoV-2 protein sequences. bioRxiv.
See full publications listYuan, Ke
Author
Farndale, Lucas and Insall, Robert and Yuan, Ke (2025) TriDeNT: Triple deep network training for privileged knowledge distillation in histopathology. Medical Image Analysis, 102: 103479. ISSN 1361-8415
Ji, Yanni and Cutiongco, Marie F.A. and Jensen, Bjørn Sand and Yuan, Ke (2025) Generating realistic single-cell images from CellProfiler representations. Medical Image Analysis. ISSN 1361-8415 (In Press)
Coudray, Nicolas and Juarez, Michelle C. and Criscito, Maressa C. and Claudio Quiros, Adalberto and Wilken, Reason and Jackson Cullison, Stephanie R. and Stevenson, Mary L. and Doudican, Nicole A. and Yuan, Ke and Aquino, Jamie D. and Klufas, Daniel M. and North, Jeffrey P. and Yu, Siegrid S. and Murad, Fadi and Ruiz, Emily and Schmults, Chrysalyne D. and Cardona Machado, Cristian D. and Cañueto, Javier and Choudhary, Anirudh and Hughes, Alysia N. and Stockard, Alyssa and Leibovit-Reiben, Zachary and Mangold, Aaron R. and Tsirigos, Aristotelis and Carucci, John A. (2025) Self supervised artificial intelligence predicts poor outcome from primary cutaneous squamous cell carcinoma at diagnosis. npj Digital Medicine, 8 (1): 105. ISSN 2398-6352
See full publications listSato, Kei
Author
Lytras, Spyros and Lamb, Kieran D. and Ito, Jumpei and Grove, Joe and Yuan, Ke and Sato, Kei and Hughes, Joseph and Robertson, David L. (2025) Pathogen genomic surveillance and the AI revolution. Journal of Virology, 99 (2): e0160124. ISSN 0022-538X
See full publications listHughes, Joseph
Author
Lytras, Spyros and Lamb, Kieran D. and Ito, Jumpei and Grove, Joe and Yuan, Ke and Sato, Kei and Hughes, Joseph and Robertson, David L. (2025) Pathogen genomic surveillance and the AI revolution. Journal of Virology, 99 (2): e0160124. ISSN 0022-538X
Lamb, Kieran D. and Hughes, Joseph and Lytras, Spyros and Young, Francesca and Koci, Orges and Herzig, James and Lovell, Simon C, and Grove, Joe and Yuan, Ke and Robertson, David L. (2024) From a single sequence to evolutionary trajectories: protein language models capture the evolutionary potential of SARS-CoV-2 protein sequences. bioRxiv.
See full publications listRobertson, David L.
Author
Lytras, Spyros and Lamb, Kieran D. and Ito, Jumpei and Grove, Joe and Yuan, Ke and Sato, Kei and Hughes, Joseph and Robertson, David L. (2025) Pathogen genomic surveillance and the AI revolution. Journal of Virology, 99 (2): e0160124. ISSN 0022-538X
Liu, Dan and Young, Francesca and Lamb, Kieran D. and Claudio Quiros, Adalberto and Pancheva, Alexandrina and Miller, Crispin and Macdonald, Craig and Robertson, David L. and Yuan, Ke (2024) PLM-interact: extending protein language models to predict protein-protein interactions. bioRxiv.
Lamb, Kieran D. and Hughes, Joseph and Lytras, Spyros and Young, Francesca and Koci, Orges and Herzig, James and Lovell, Simon C, and Grove, Joe and Yuan, Ke and Robertson, David L. (2024) From a single sequence to evolutionary trajectories: protein language models capture the evolutionary potential of SARS-CoV-2 protein sequences. bioRxiv.
See full publications listAvailable under License Creative Commons Attribution.
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