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
Kamvar Z, Cai J, Pulliam JRC, et al., 2019, Epidemic curves made easy using the R package incidence
Cori A, Nouvellet P, Garske T, 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
Campbell F, Didelot X, Fitzjohn R, et al., 2018, outbreaker2: a modular platform for outbreak reconstruction, Bmc Bioinformatics, Vol:19, ISSN:1471-2105
Software
Jombart T, Kamvar ZN, Cai J, et al., 2019, reconhub/incidence 1.5, v.1.5
Jombart T, Kamvar Z, Cai J, et al., 2018, reconhub/incidence: Incidence version 1.5.3, v.1.5.3