Publications

Learning patterns of HIV-1 resistance to broadly neutralizing antibodies with reduced subtype bias using multi-task learning

Igiraneza AB. et al, (2024), PLOS Computational Biology, 20, e1012618 - e1012618

Drivers of epidemic dynamics in real time from daily digital COVID-19 measurements.

Kendall M. et al, (2024), Science (New York, N.Y.)

Estimating the contribution of setting-specific contacts to SARS-CoV-2 transmission using digital contact tracing data.

Wang Z. et al, (2024), Nature communications, 15

Increasing intra- and inter-subtype HIV diversity despite declining HIV incidence in Uganda

Kim S. et al, (2024)

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

Ghafari M. et al, (2024), Nature

Digital measurement of SARS-CoV-2 transmission risk from 7 million contacts

Ferretti L. et al, (2024), Nature, 626, 145 - 150

Biased estimates of phylogenetic branch lengths resulting from the discretised Gamma model of site rate heterogeneity

Ferretti L. et al, (2024)

Demographics of sources of HIV-1 transmission in Zambia: a molecular epidemiology analysis in the HPTN 071 PopART study.

Hall M. et al, (2023), The Lancet. Microbe

Longitudinal population-level HIV epidemiologic and genomic surveillance highlights growing gender disparity of HIV transmission in Uganda.

Monod M. et al, (2023), Nature microbiology

Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1

Tsui JL-H. et al, (2023), Science, 381, 336 - 343

Uptake of medical male circumcision with household-based testing, and the association of traditional male circumcision and HIV infection

Zewdie K. et al, (2023), AIDS, 37, 795 - 802

Growing gender disparity in HIV infection in Africa: sources and policy implications

Ratmann O. et al, (2023)

Frequency matters: comparison of drug resistance mutation detection by Sanger and next-generation sequencing in HIV-1

Balakrishna S. et al, (2023), Journal of Antimicrobial Chemotherapy, 78, 656 - 664

How to avoid a local epidemic becoming a global pandemic.

Stenseth NC. et al, (2023), Proceedings of the National Academy of Sciences of the United States of America, 120

Large-scale calibration and simulation of COVID-19 epidemiologic scenarios to support healthcare planning

Groves-Kirkby N. et al, (2023), Epidemics, 42, 100662 - 100662

Epidemiological impacts of the NHS COVID-19 app in England and Wales throughout its first year

Kendall M. et al, (2023), Nature Communications, 14

Learning patterns of HIV-1 co-resistance to broadly neutralizing antibodies with reduced subtype bias using multi-task learning

Igiraneza AB. et al, (2023)

Quantification of the time-varying epidemic growth rate and of the delays between symptom onset and presenting to healthcare for the mpox epidemic in the UK in 2022

Panovska-Griffiths J. et al, (2023)

Viral burdens are associated with age 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, (2022)

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

Slowly declining growth rates and dynamic reporting delays characterise the Monkeypox epidemic in the UK over May-August 2022

Panovska-Griffiths J. et al, (2022)

Projected outcomes of universal testing and treatment in a generalised HIV epidemic in Zambia and South Africa (the HPTN 071 [PopART] trial): a modelling study.

Probert WJM. et al, (2022), The lancet. HIV, 9, e771 - e780

Epidemiological dynamics of bacteriocin competition and antibiotic resistance

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

Estimating SARS-CoV-2 variant fitness and the impact of interventions in England using statistical and geo-spatial agent-based models

Hinch R. et al, (2022), Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 380

Statistical and agent-based modelling of the transmissibility of different SARS-CoV-2 variants in England and impact of different interventions

Panovska-Griffiths J. et al, (2022), Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 380

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

Willett BJ. et al, (2022), Nature Microbiology, 7, 1709 - 1709

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

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

Estimating the potential to prevent locally acquired HIV infections in a UNAIDS Fast-Track City, Amsterdam

Blenkinsop A. et al, (2022), eLife, 11

HIV drug resistance in a community‐randomized trial of universal testing and treatment: HPTN 071 (PopART)

Fogel JM. et al, (2022), Journal of the International AIDS Society, 25

Improving Post-Release Care Engagement for People Living with HIV Involved in the Criminal Justice System: A Systematic Review

Moher M. et al, (2022), AIDS and Behavior, 26, 1607 - 1617

Human Immunodeficiency Virus (HIV) Genetic Diversity Informs Stage of HIV-1 Infection Among Patients Receiving Antiretroviral Therapy in Botswana

Ragonnet-Cronin M. et al, (2022), The Journal of Infectious Diseases, 225, 1330 - 1338

Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load

Zhao L. et al, (2022), Virus Evolution, 8

Deep-sequence phylogenetics to quantify patterns of HIV transmission in the context of a universal testing and treatment trial – BCPP/Ya Tsie trial

Magosi LE. et al, (2022), eLife, 11

A highly virulent variant of HIV-1 circulating in the Netherlands

Wymant C. et al, (2022), Science, 375, 540 - 545

Lineage replacement and evolution captured by three years of the United Kingdom Covid Infection Survey

Lythgoe K. et al, (2022)

Statistical and agent-based modelling of the transmissibility of different SARS-CoV-2 variants in England and impact of different interventions

Panovska-Griffiths J. et al, (2022)

The hyper-transmissible SARS-CoV-2 Omicron variant exhibits significant antigenic change, vaccine escape and a switch in cell entry mechanism

Willett BJ. et al, (2022)

A rapid, integrated method to monitor HIV viral load, drug resistance, and transmission patterns from finger-prick blood samples

Chaudron SE. et al, (2022), JOURNAL OF THE INTERNATIONAL AIDS SOCIETY, 25, 19 - 20

Depressive symptoms and HIV risk behaviours among adolescents enrolled in the HPTN071 (PopART) trial in Zambia and South Africa.

Shanaube K. et al, (2022), PloS one, 17

Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study

Twohig KA. et al, (2022), The Lancet Infectious Diseases, 22, 35 - 42

Many but small HIV-1 non-B transmission chains in the Netherlands

Bezemer D. et al, (2022), AIDS, 36, 83 - 94

Publisher Correction: Monitoring key epidemiological parameters of SARS-CoV-2 transmission

Kraemer MUG. et al, (2022), Nature Medicine, 28, 213 - 213

Rates of viral suppression in a cohort of people with stable HIV from two community models of ART delivery versus facility-based HIV care in Lusaka, Zambia: a cluster-randomised, non-inferiority trial nested in the HPTN 071 (PopART) trial

Limbada M. et al, (2022), The Lancet HIV, 9, e13 - e23

Context-specific emergence and growth of the SARS-CoV-2 Delta variant

McCrone JT. et al, (2021)

Genomics-informed outbreak investigations of SARS-CoV-2 using civet

O’Toole Á. et al, (2021)

Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant.

Elliott P. et al, (2021), Science (New York, N.Y.), 374

Monitoring key epidemiological parameters of SARS-CoV-2 transmission

Kraemer MUG. et al, (2021), Nature Medicine, 27, 1854 - 1855

The impact of viral mutations on recognition by SARS-CoV-2 specific T cells

de Silva TI. et al, (2021), iScience, 24, 103353 - 103353

Demographics of people who transmit HIV-1 in Zambia: a molecular epidemiology analysis in the HPTN-071 PopART study

Hall M. et al, (2021)

Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 lineages circulating in Brazil

Clemens SAC. et al, (2021), Nature Communications, 12

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Publications