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
Evans B, Keiser O, Kaiser L, et al., 2023, Analysis of global routine immunisation coverage shows disruption and stagnation during the first two-years of the COVID-19 pandemic with tentative recovery in 2022, Vaccine: X, Vol:15, ISSN:2590-1362
Qian GY, Edmunds WJ, Bausch DG, et al., 2023, A mathematical model of Marburg virus disease outbreaks and the potential role of vaccination in control., Bmc Med, Vol:21
Zeng W, Samaha H, Yao M, et al., 2023, The cost of public health interventions to respond to the 10th Ebola outbreak in the Democratic Republic of the Congo., Bmj Glob Health, Vol:8, ISSN:2059-7908
Geismar C, Nguyen V, Fragaszy E, et al., 2023, Bayesian reconstruction of SARS-CoV-2 transmissions highlights substantial proportion of negative serial intervals, Epidemics: the Journal of Infectious Disease Dynamics, Vol:44, ISSN:1755-4365
Qian GY, Jombart T, Edmunds WJ, 2023, Assessing the feasibility of Phase 3 vaccine trials against Marburg Virus Disease: A modelling study, Vaccine: X, Vol:14, ISSN:2590-1362