2025

Lytras, Spyros, Lamb, Kieran D., Ito, Jumpei, Grove, Joe ORCID: https://orcid.org/0000-0001-5390-7579, Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460, Sato, Kei, Hughes, Joseph ORCID: https://orcid.org/0000-0003-2556-2563 and Robertson, David L. ORCID: https://orcid.org/0000-0001-6338-0221 (2025) Pathogen genomic surveillance and the AI revolution. Journal of Virology, 99(2), e0160124. (doi: 10.1128/jvi.01601-24) (PMID:39878472) (PMCID:39878472)

2024

Liu, Dan, Young, Francesca, Lamb, Kieran D., Claudio Quiros, Adalberto, Pancheva, Alexandrina, Miller, Crispin ORCID: https://orcid.org/0000-0003-4341-1283, Macdonald, Craig ORCID: https://orcid.org/0000-0003-3143-279X, Robertson, David L. ORCID: https://orcid.org/0000-0001-6338-0221 and Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460 (2024) PLM-interact: extending protein language models to predict protein-protein interactions. bioRxiv, (doi: 10.1101/2024.11.05.622169)

Liu, Dan, Young, Francesca, Lamb, Kieran D., Robertson, David L. ORCID: https://orcid.org/0000-0001-6338-0221 and Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460 (2024) Prediction of virus-host associations using protein language models and multiple instance learning. PLoS Computational Biology, 20(11), e1012597. (doi: 10.1371/journal.pcbi.1012597) (PMID:39561204) (PMCID:PMC11614202)

Lamb, Kieran D., Hughes, Joseph ORCID: https://orcid.org/0000-0003-2556-2563, Lytras, Spyros, Young, Francesca, Koci, Orges, Herzig, James, Lovell, Simon C,, Grove, Joe ORCID: https://orcid.org/0000-0001-5390-7579, Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460 and Robertson, David L. ORCID: https://orcid.org/0000-0001-6338-0221 (2024) From a single sequence to evolutionary trajectories: protein language models capture the evolutionary potential of SARS-CoV-2 protein sequences. bioRxiv, (doi: 10.1101/2024.07.05.602129)

Lamb, Kieran D., Luka, Martha M., Saathoff, Megan, Orton, Richard J. ORCID: https://orcid.org/0000-0002-3389-4325, Phan, My V.T., Cotten, Matthew ORCID: https://orcid.org/0000-0002-3361-3351, Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460 and Robertson, David L. ORCID: https://orcid.org/0000-0001-6338-0221 (2024) Mutational signature dynamics indicate SARS-CoV-2's evolutionary capacity is driven by host antiviral molecules. PLoS Computational Biology, 20(1), e1011795. (doi: 10.1371/journal.pcbi.1011795) (PMID:38271457) (PMCID:PMC10868779)

Articles

Lytras, Spyros, Lamb, Kieran D., Ito, Jumpei, Grove, Joe ORCID: https://orcid.org/0000-0001-5390-7579, Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460, Sato, Kei, Hughes, Joseph ORCID: https://orcid.org/0000-0003-2556-2563 and Robertson, David L. ORCID: https://orcid.org/0000-0001-6338-0221 (2025) Pathogen genomic surveillance and the AI revolution. Journal of Virology, 99(2), e0160124. (doi: 10.1128/jvi.01601-24) (PMID:39878472) (PMCID:39878472)

Liu, Dan, Young, Francesca, Lamb, Kieran D., Claudio Quiros, Adalberto, Pancheva, Alexandrina, Miller, Crispin ORCID: https://orcid.org/0000-0003-4341-1283, Macdonald, Craig ORCID: https://orcid.org/0000-0003-3143-279X, Robertson, David L. ORCID: https://orcid.org/0000-0001-6338-0221 and Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460 (2024) PLM-interact: extending protein language models to predict protein-protein interactions. bioRxiv, (doi: 10.1101/2024.11.05.622169)

Liu, Dan, Young, Francesca, Lamb, Kieran D., Robertson, David L. ORCID: https://orcid.org/0000-0001-6338-0221 and Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460 (2024) Prediction of virus-host associations using protein language models and multiple instance learning. PLoS Computational Biology, 20(11), e1012597. (doi: 10.1371/journal.pcbi.1012597) (PMID:39561204) (PMCID:PMC11614202)

Lamb, Kieran D., Hughes, Joseph ORCID: https://orcid.org/0000-0003-2556-2563, Lytras, Spyros, Young, Francesca, Koci, Orges, Herzig, James, Lovell, Simon C,, Grove, Joe ORCID: https://orcid.org/0000-0001-5390-7579, Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460 and Robertson, David L. ORCID: https://orcid.org/0000-0001-6338-0221 (2024) From a single sequence to evolutionary trajectories: protein language models capture the evolutionary potential of SARS-CoV-2 protein sequences. bioRxiv, (doi: 10.1101/2024.07.05.602129)

Lamb, Kieran D., Luka, Martha M., Saathoff, Megan, Orton, Richard J. ORCID: https://orcid.org/0000-0002-3389-4325, Phan, My V.T., Cotten, Matthew ORCID: https://orcid.org/0000-0002-3361-3351, Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460 and Robertson, David L. ORCID: https://orcid.org/0000-0001-6338-0221 (2024) Mutational signature dynamics indicate SARS-CoV-2's evolutionary capacity is driven by host antiviral molecules. PLoS Computational Biology, 20(1), e1011795. (doi: 10.1371/journal.pcbi.1011795) (PMID:38271457) (PMCID:PMC10868779)