Summary
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.
Publications
Journals
Dighe A, Jombart T, Van Kerkhove MD, et al., 2019, A systematic review of MERS-CoV seroprevalence and RNA prevalence in dromedary camels: implications for animal vaccination, Epidemics, Vol:29, ISSN:1755-4365
Thompson R, Stockwin J, van Gaalen R, et al., 2019, Improved inference of time-varying reproduction numbers during infectious disease outbreaks, Epidemics, Vol:29, ISSN:1755-4365, Pages:1-11
Moraga P, Dorigatti I, Kamvar ZN, et al., epiflows: an R package for risk assessment of travel-related spread of disease, F1000research, Vol:7, Pages:1374-1374
Moraga P, Dorigatti I, Kamvar ZN, et al., 2019, epiflows: an R package for risk assessment of travel-related spread of disease, F1000research, Vol:7, Pages:1374-1374
Software
Cori A, Kamvar ZN, Stockwin J, et al., 2019, annecori/EpiEstim: EpiEstim Cran 2.2-1, v.2.2-0