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 statistics, spatial statistics, graph 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.
et al., 2018, A graph-based evidence synthesis approach to detecting outbreak clusters: An application to dog rabies, Plos Computational Biology, Vol:14, ISSN:1553-7358
et al., 2018, outbreaker2: a modular platform for outbreak reconstruction, Bmc Bioinformatics, Vol:19, ISSN:1471-2105
et al., 2019, reconhub/incidence 1.5, v.1.5
et al., 2018, reconhub/incidence: Incidence version 1.5.3, v.1.5.3