Senior Group Leader in Pathogen Dynamics, Nuffield Department of Medicine
I am a Senior Group Leader in Pathogen Dynamics at the Big Data Institute, and Professor in the Nuffield Department of Medicine. I am interested in studying the population dynamics and epidemiology of pathogens, and translating this knowledge to public health. The primary tools used in my group are mathematical modelling and pathogen genomics.
I trained in theoretical particle physics, and converted to mathematical biology after his PhD, in 1998. I was Royal Society URF and then Professor in the Department of Infectious Disease Epidemiology at Imperial College before joining the BDI at Oxford in 2016.
Current topics of interest are: HIV virulence; HIV treatment as prevention; HIV genomics; pneumococcal genomics; antibiotic resistance; outbreak response.
Current projects: BEEHIVE is cross-European study of HIV genomics and virulence amongst seroconverters. HPTN071 (PopART) is a cluster-randomized trial of HIV prevention including universal test and treat, in a population of 1.2 million people at high risk in Zambia and South Africa. PANGEA is a consortium mapping HIV-1 genomic diversity and linking to prevention modelling across sub-Saharan Africa. For MIDAS, we study the spread and dynamics of antibiotic resistance in Streptococcus pneumoniae in the USA. We have been involved in responses to outbreaks, such as SARS in 2003, H1N1pdm in 2009, and more recently MERS and Ebola.
I lead a friendly group of currently eight postdocs at various stages of their careers, a project officer and a scientific manager. We are recruiting postdocs at regular intervals and can supervise PhD students from several PhD programmes at Oxford University. Please don't hesitate to get in touch if you are interested in joining the group or collaborating with us.
Link between the numbers of particles and variants founding new HIV-1 infections depends on the timing of transmission.
Thompson RN. et al, (2019), Virus evolution, 5
Phylogenetic methods inconsistently predict direction of HIV transmission among heterosexual pairs in the HPTN052 cohort.
Rose R. et al, (2018), The Journal of infectious diseases
Prediction of post-vaccine population structure of Streptococcus pneumoniae using accessory gene frequencies
Azarian T. et al, (2018)
Evolution of HIV-1 within untreated individuals and at the population scale in Uganda.
Raghwani J. et al, (2018), PLoS pathogens, 14
HIV genotyping and phylogenetics in the HPTN 071 (PopART) study: validation of a high-throughput sequencing assay for viral load quantification, genotyping, resistance testing and high-resolution transmission networking
Bonsall D. et al, (2018), JOURNAL OF THE INTERNATIONAL AIDS SOCIETY, 21, 58 - 59