Imperial College London


Faculty of MedicineSchool of Public Health

Lecturer in Genetic Analysis



+44 (0)20 7594 3658t.jombart Website




UG11Norfolk PlaceSt Mary's Campus





I am a biometrician working on statistical genetics of pathogen populations. I am currently working as a research associate with Neil Ferguson, Christophe Fraser and Simon Cauchemez. My work aims to develop novel statistical approaches for extracting information from pathogen genomes and gain insights into the spatio-temporal dynamics of infectious diseases. The methodological approaches I use include multivariate analysis, Bayesian statisticsspatial statisticsgraph theory, and phylogenetics. I am also interested in using simulations to understand which and how biological processes shape the genetic diversity observed in biological populations.


I am also extensively involved with the development of free software for the analysis of genetic and epidemiological data. I have recently organized a R hackathon on disease outbreak modelling using molecular data, hosted by the MRC Center for Outbreak Analysis and Modelling in January 2013

I am author or contributor for the following R packages:

- adegenet (author): multivariate analysis for genetic/genomic data

- adephylo (author): tools for testing and describing the  phylogenetic signal

- geoGraph (author): large-scale modelling of spatial data

- ade4 (contributor): multivariate analysis, graphics, spatial statistics

phylobase (contributor): handling and analyses of phylogenetic comparative data

- sedaR (contributor): spatial statistics for ecological data

- outbreaker (author): Bayesian reconstruction of disease outbreaks using genomic data

- epibase (author): basic tools for the disease outbreak analysis



More information is available from my  webpage.



Beugin M-P, Gayet T, Pontier D, et al., 2018, A fast likelihood solution to the genetic clustering problem, Methods in Ecology and Evolution, ISSN:2041-210X

Cori A, Donnelly CA, Dorigatti I, et al., 2017, Key data for outbreak evaluation: building on the Ebola experience, Philosophical Transactions of the Royal Society B-biological Sciences, Vol:372, ISSN:0962-8436

Garske T, Cori A, Ariyarajah A, et al., 2017, Heterogeneities in the case fatality ratio in the West African Ebola outbreak 2013-2016, Philosophical Transactions of the Royal Society B-biological Sciences, Vol:372, ISSN:0962-8436

Bertranpetit E, Jombart T, Paradis E, et al., 2017, Phylogeography of Toxoplasma gondii points to a South American origin, Infection Genetics and Evolution, Vol:48, ISSN:1567-1348, Pages:150-155

Nouvellet P, Cori A, Garske T, et al., 2017, A simple approach to measure transmissibility and forecast incidence., Epidemics

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