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Dr Stephane Hue

Assoc. Prof. in Epi. & Co-Prog. Dir. MSc

London School of Hygiene & Tropical Medicine
Keppel Street
London
SE11 4BY
United Kingdom

Jump to: Affiliations Teaching Research Publications
I am a computational biologist specialised in pathgen genomics and the molecular epidemiology of infectious diseases. My research activity focuses on the reconstruction of pathogen transmission for surveillance or in outbreak situations.

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 and Dynamics
Faculty of Epidemiology and Population Health

Centres

Centre for Mathematical Modelling of Infectious Diseases

Teaching

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

At LSHTM, I am teaching a range of lectures and practical sessions for the MSc Epidemiology (Introduction to Molecular Epidemiology, Introduction of Omics in Epidemiology, Omics Applications to Communicable Diseases, Genomics in the age of COVID-19, Molecular Epidemiology of Infectious Diseases, Introduction to Phylogenetics), for the MSc Health Data Science (Genetic Variation, Pathogen Genomics, Disease Outbreak Studies), for the MSc Medical Microbiology (HIV Drug Resistance, Molecular Epidemiology of Viruses) and for the short course 'Introduction to the Modelling of Infectious diseases' (Introduction to Phylodynamics).

I am Programme Director of the MSc Health Data Science and co-organiser of the modules 'Epidemiology and Omics' (2484) and 'Genomic Health Data' (2492).

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 range of other viruses and bacteria, including Dengue virus, Hepatitis Delta Virus, SARS-CoV-2 and Streptococcus pneumonia.
Research Area
Bioinformatics
Genomics
Molecular epidemiology
Virology
Disease and Health Conditions
HIV/AIDS
Dengue
Hepatitis
Emerging infectious diseases
Respiratory diseases
Country
United Kingdom
Vietnam
Gambia
Region
European Union
East Asia & Pacific (developing only)
Sub-Saharan Africa (all income levels)

Selected Publications
Evaluating methods for identifying and quantifying <i>Streptococcus pneumoniae</i> co-colonization using next-generation sequencing data.
Hackman, J; Hibberd, ML; Swarthout, TD; Hinds, J; Ashall, J; Sheppard, C; Tonkin-Hill, G; Gould, K; Brown, C; Msefula, J; Mataya, AA; Toizumi, M; Yoshida, L-M; French, N; Heyderman, RS; FLASCHE, S; Kwambana, B; Hué, S;
2024
Microbiology spectrum
Reconciling founder variant multiplicity of HIV-1 infection with the rate of CD4+ decline.
Baxter, J; Villabona-Arenas, CJ; Thompson, RN; Hué, S; Regoes, RR; Kouyos, RD; Günthard, HF; Albert, J; Leigh Brown, A; ATKINS, KE;
2024
Journal of the Royal Society, Interface / the Royal Society
Could prophylactic antivirals reduce dengue incidence in a high-prevalence endemic area?
Jafari, Y; BRADY, OJ; BIGGS, JR; Lien, LT; Mai, HK; Nguyen, HA T; Van Loock, M; Herrera-Taracena, G; Menten, J; Iwasaki, C; Takegata, M; Kitamura, N; Do Thai, H; Minh, BX; Morita, K; Anh, DD; Clifford, S; PREM, K; Hafalla, J; EDMUNDS, WJ; Yoshida, LM; HIBBERD, ML; Hué, S;
2024
PLoS neglected tropical diseases
Emergence of Novel Norovirus GII.4 Variant.
Chhabra, P; TULLY, DC; Mans, J; Niendorf, S; Barclay, L; Cannon, JL; Montmayeur, AM; Pan, C-Y; Page, N; Williams, R; Tutill, H; Roy, S; Celma, C; Beard, S; Mallory, ML; Manouana, GP; Velavan, TP; Adegnika, AA; Kremsner, PG; Lindesmith, LC; Hué, S; Baric, RS; Breuer, J; Vinjé, J;
2023
Emerging infectious diseases
Reconstructing the phylodynamic history and geographic spread of the CRF01_AE-predominant HIV-1 epidemic in the Philippines from PR/RT sequences sampled from 2008 to 2018.
Polotan, FG M; Salazar, CR P; Morito, HL E; Abulencia, MF B; Pantoni, RA R; Mercado, ES; Hué, S; Ditangco, RA;
2023
Virus evolution
Phylogenetic inference of pneumococcal transmission from cross-sectional data, a pilot study
Hackman, J; Sheppard, C; PHELAN, J; JONES-WARNER, W; Sobkowiak, B; SHAH, S; Litt, D; Fry, N; Toizumi, M; Yoshida, L-M; Hibberd, M; MILLER, E; FLASCHE, S; Hué, S;
2023
Wellcome Open Res
Phylogenetic inference of pneumococcal transmission from cross-sectional data, a pilot study.
Hackman, J; Sheppard, C; PHELAN, J; JONES-WARNER, W; Sobkowiak, B; SHAH, S; Litt, D; Fry, NK; Toizumi, M; Yoshida, L-M; HIBBERD, M; MILLER, E; FLASCHE, S; Hué, S;
2023
Wellcome open research
Quantifying the value of viral genomics when inferring who infected whom in the 2014-16 Ebola virus outbreak in Guinea.
ROBERT, A; Tsui Lok Hei, J; Watson, CH; Gsell, P-S; Hall, Y; Rambaut, A; Longini, IM; Sakoba, K; KUCHARSKI, AJ; Touré, A; Danmadji Nadlaou, S; Saidou Barry, M; Fofana, TO; Lansana Kaba, I; Sylla, L; Diaby, ML; Soumah, O; Diallo, A; Niare, A; Diallo, A; EGGO, RM; Caroll, MW; Henao-Restrepo, AM; EDMUNDS, WJ; Hué, S;
2023
Virus evolution
Genomic epidemiology of SARS-CoV-2 infections in The Gambia: an analysis of routinely collected surveillance data between March, 2020, and January, 2022.
KANTEH, A; Jallow, HS; Manneh, J; SANYANG, B; Kujabi, MA; Ndure, SL; JARJU, S; Sey, AP; Damilare K, D; Bah, Y; Sambou, S; Jarju, G; Manjang, B; Jagne, A; Bittaye, SO; Bittaye, M; FORREST, K; Tiruneh, DA; Samateh, AL; Jagne, S; Hué, S; MOHAMMED, N; AMAMBUA-NGWA, A; KAMPMANN, B; D'ALESSANDRO, U; ... SESAY, AK.
2023
The Lancet Global health
Dengue virus type 4 isolate DET-P-0428-1 polyprotein (POLY) gene, complete cds; and sfRNA2 lncRNA gene, partial sequence
Ashall, J; SHAH, S; Biggs, JR; Chang, J-NR; Jafari, Y; Brady, OJ; Mai, HK; Lien, LT; Do Thai, H; Nguyen, HA T; Anh, DD; Iwasaki, C; Kitamura, N; Van Loock, M; Herrera-Taracena, G; Rasschaert, F; Van Wesenbeeck, L; Yoshida, L-M; HAFALLA, JC R; HUE, S; HIBBERD, ML;
2023
National Center for Biotechnology Information
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Stephane Hue

Contact

London School of Hygiene & Tropical Medicine
Keppel Street
London
SE11 4BY
United Kingdom

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Related links

https://www.lshtm.ac.uk/aboutus/people/hue.stephane