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