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Dr Stephane Hue

MSc PhD

Associate Professor
in Epidemiology, Biostatistics & Bioinformatics

Room
113

LSHTM
Keppel Street
London
WC1E 7HT
United Kingdom

Tel.
00 44 (0) 20 792 675

I am a computational biologist specialised in viral evolution and molecular epidemiology. My research activity focuses on the reconstruction of pathogen transmission dynamics.

After graduating at the University Paul Sabatier in Toulouse, France, I moved to the United Kingdom to complete a Masters in Medical Molecular Microbiology at the University of Nottingham. This was followed by a PhD in the molecular epidemiology of HIV-1 at University College London. After completing postdoctoral positions at the University of Oxford and University College London, I have joined LSHTM in 2014, where I am currently holding an associate professor position.

Affiliations

Faculty of Epidemiology and Population Health
Department of Infectious Disease Epidemiology

Centres

Centre for the Mathematical Modelling of Infectious Diseases (CMMID)

Teaching

I have been teaching viral evolution, molecular epidemiology and phylogenetics to undergraduate and postgraduate students since 2008.

I am the co-organiser of the MSc modules 'Epidemiology and Omics' and 'Genomic Health Data'.

Research

I primarily study pathogen transmission through the joint analysis of epidemiological and gene sequence data. My work involves the implementation of statistical models in phylogenetic studies, particularly in the context of reconstructing time and spatial trends of viral transmissions. 

While my research activity was primarily oriented towards the study of HIV-1, I am applying my skills to a broad range of viruses and bacteria, including Dengue virus, Ebola virus and Streptococcus pneumonia

Research Area
Bacteria
Drug resistance
Viruses
Discipline
Genomics
Molecular epidemiology
Virology
Bioinformatics
Disease and Health Conditions
HIV/AIDS
Dengue
Emerging Infectious Disease
Country
Fiji
United Kingdom
Singapore
Vietnam
Region
East Asia & Pacific (all income levels)
European Union

Selected Publications

Demographic characteristics of the reporting study population at enrolment
Biggs J; Sy AK; Ashall J; Santoso MS; Brady OJ; Reyes MAJ; Quinones MA; Jones-Warner W; Tandoc AO; Sucaldito NL
2022
Sensitivity (95%CI) of NS1 RDTs in capturing DENV1-4 infections stratified by immune status among patients from Vietnam (N:1,217)
Biggs J; Sy AK; Ashall J; Santoso MS; Brady OJ; Reyes MAJ; Quinones MA; Jones-Warner W; Tandoc AO; Sucaldito NL
2022
A summary of data collected from suspected dengue patients included in the study population from Indonesia, Vietnam and the Philippines
Biggs JR; Sy AK; Ashall J; Santoso MS; Brady OJ; Reyes MAJ; Quinones MA; Jones-Warner W; Tandoc AO; Sucaldito NL
2022
Combining rapid diagnostic tests to estimate primary and post-primary dengue immune status at the point of care.
Biggs JR; Sy AK; Ashall J; Santoso MS; Brady OJ; Reyes MAJ; Quinones MA; Jones-Warner W; Tandoc AO; Sucaldito NL
2022
PLoS Neglected Tropical Diseases
Characterising within-hospitalSARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves.
Lindsey BB; Villabona-Arenas CJ; Campbell F; Keeley AJ; Parker MD; Shah DR; Parsons H; Zhang P; Kakkar N; Gallis M
2022
Nature communications
Using phylogenetics to infer HIV-1 transmission direction between known transmission pairs.
Villabona-Arenas CJ; Hué S; Baxter JAC; Hall M; Lythgoe KA; Bradley J; Atkins KE
2022
Proceedings of the National Academy of Sciences of the United States of America
Drug resistance mutations in HIV: new bioinformatics approaches and challenges.
Blassel L; Zhukova A; Villabona-Arenas CJ; Atkins KE; Hué S; Gascuel O
2021
Current opinion in virology
Effectiveness of BNT162b2 and ChAdOx1 against SARS-CoV-2 household transmission: a prospective cohort study in England
Clifford S; Waight P; Hackman J; Hué S; Gower CM; Kirsebom FCM; Skarnes C; Letley L; Bernal JL; Andrews N
2021
See more Publications