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Publications

Unsupervised identification of significant lineages of SARS-CoV-2 through scalable machine learning methods

Cahuantzi R. et al, (2024), Proceedings of the National Academy of Sciences, 121

Prevalence of persistent SARS-CoV-2 in a large community surveillance study

Ghafari M. et al, (2024), Nature, 626, 1094 - 1101

Risk of SARS-CoV-2 reinfection during multiple Omicron variant waves in the UK general population

Wei J. et al, (2024), Nature Communications, 15

Lineage replacement and evolution captured by 3 years of the United Kingdom Coronavirus (COVID-19) Infection Survey

Lythgoe KA. et al, (2023), Proceedings of the Royal Society B: Biological Sciences, 290

Viral burden is associated with age, vaccination, and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection-related sampling bias

Fryer HR. et al, (2023), PLOS Pathogens, 19, e1011461 - e1011461

The evolution of SARS-CoV-2.

Markov PV. et al, (2023), Nature reviews. Microbiology, 21, 361 - 379

Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning

Nickbakhsh S. et al, (2022), Scientific Reports, 12

The mutational spectrum of SARS-CoV-2 genomic and antigenomic RNA

Zhao L. et al, (2022), Proceedings of the Royal Society B: Biological Sciences, 289

Using phylogenetics to infer HIV-1 transmission direction between known transmission pairs

Villabona-Arenas CJ. et al, (2022), Proceedings of the National Academy of Sciences, 119

EpiBeds: Data informed modelling of the COVID-19 hospital burden in England

Overton CE. et al, (2022), PLOS Computational Biology, 18, e1010406 - e1010406

SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway

Willett BJ. et al, (2022), Nature Microbiology, 7, 1161 - 1179

Viral infection and transmission in a large, well-traced outbreak caused by the SARS-CoV-2 Delta variant.

Li B. et al, (2022), Nature communications, 13

Possible future waves of SARS-CoV-2 infection generated by variants of concern with a range of characteristics

Dyson L. et al, (2021), Nature Communications, 12

Antibody responses to SARS-CoV-2 vaccines in 45,965 adults from the general population of the United Kingdom

Wei J. et al, (2021), Nature Microbiology, 6, 1140 - 1149

Challenges in control of COVID-19: short doubling time and long delay to effect of interventions

Pellis L. et al, (2021), Philosophical Transactions of the Royal Society B: Biological Sciences, 376, 20200264 - 20200264

OpenABM-Covid19-An agent-based model for non-pharmaceutical interventions against COVID-19 including contact tracing.

Hinch R. et al, (2021), PLoS computational biology, 17

USING PHYLOGENETICS TO ACCURATELY INFER HIV-1 TRANSMISSION DIRECTION

Villabona-Arenas CJ. et al, (2021)

SARS-CoV-2 within-host diversity and transmission

Lythgoe KA. et al, (2021), Science, 372

Time to evaluate COVID-19 contact-tracing apps

Colizza V. et al, (2021), Nature Medicine, 27, 361 - 362

Bimodal distribution and set point HBV DNA viral loads in chronic infection: retrospective analysis of cohorts from the UK and South Africa

Downs LO. et al, (2020), Wellcome Open Research, 5, 113 - 113

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