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Supervisor for Hosts, Pathogens and Global Health DTP and Precision Medicine DTP

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Personal profile


I am an infectious disease modeller with a particular interest in HIV, antimicrobial resistance and vaccines. 


I am course director for Infectious Disease Epidemiology (run through the MSc Epidemiology programme). 

I teach on the Hosts Pathogens and Global Health DTP curriculum.

Current Research Interests

My work focuses on understanding the dynamics of infectious disease through modelling and phylogenetics. 

My ERC Starting Grant uses quantitative tools to understand HIV infection immediately after exposure. Our recent work published in Science found that more genetic variants are transmitted during the early stages of infection. Ongoing work is trying to understand why some routes of transmission are incredibly permissive to HIV infection despite showing similar genetic bottlenecks as those less permissive, and whether this can be explained by events happening in the first week after exposure. We integrate mathematical modelling with phylogenetics to understand processes that cannot be monitored directly.

My work funded by the Wellcome Trust is understanding how drug resistant bacteria are transmitted between people, and how this is affected by vaccines. Specifically, we are modelling a cluster randomised trial for pneumococcal conjugate vaccine in Vietnam. For this, we are using mathematical modelling tools in addition to phylogenetic analysis


Research students


James Baxter

Emma Pujol-Hodge

Yicong Liu (to start 2022)

Administrative Roles

Usher Institute EDI Committee

Edinburgh Infectious Diseases Executive Committee

Research Groups

Group members

Julian Villabona-Arenas (LSHTM)
James Baxter
Emma Pujol-Hodge
Yicong Liu


BSc, MRes, PhD

External positions

(Honorary) Scientist, Public Health England

1 Jan 20151 Nov 2024

Associate Professor, London School of Hygiene & Tropical Medicine

1 Nov 20141 Nov 2024


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