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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

Department of Infectious Disease Epidemiology
Faculty of Epidemiology and Population Health

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

Interactions between timing and transmissibility explain diverse flavivirus dynamics in Fiji.
Henderson AD; Kama M; Aubry M; Hue S; Teissier A; Naivalu T; Bechu VD; Kailawadoko J; Rabukawaqa I; Sahukhan A
2021
Nature communications
USING PHYLOGENETICS TO INFER HIV-1 TRANSMISSION DIRECTION BETWEEN KNOWN TRANSMISSION PAIRS
Villabona-Arenas CJ; Hué S; Baxter J; Hall M; Lythgoe K; Bradley J; Atkins K
2021
Number of HIV-1 founder variants is determined by the recency of the source partner infection.
Villabona-Arenas CJ; Hall M; Lythgoe KA; Gaffney SG; Regoes RR; Hué S; Atkins KE
2020
SCIENCE
Phylogenetic investigation of HCV-4d epidemic in Paris MSM HIV population reveals a still active outbreak and a strong link to the Netherlands.
Visseaux B; Hué S; Le Hingrat Q; Salmona M; Lebourgeois S; Delaugerre C; Descamps D; Chaix M-L; Ghosn J
2020
Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases
Nosocomial transmission of influenza: A retrospective cross-sectional study using next generation sequencing at a hospital in England (2012-2014).
Blackburn RM; Frampton D; Smith CM; Fragaszy EB; Watson SJ; Ferns RB; Binter Š; Coen PG; Grant P; Shallcross LJ
2019
Influenza and Other Respiratory Viruses
A39 Reconstruction of Ebola chains of transmission using sequence and epidemiological data
Robert A; Edmunds J; Eggo R; Henao-Restrepo A-M; Gsell P-S; Watson CH; Longini IM; Rambaut A; Camacho A; Hué S
2019
Virus Evolution
HIV-1 founder variant multiplicity is determined by the infection stage of the source partner
Villabona-Arenas CJ; Hall M; Lythgoe K; Gaffney S; Regoes R; Hué S; Atkins K
2019
See more Publications