I am a lecturer working in statistical & population genetics and genetic epidemiology. I did my PhD on detecting recent positive selection in the human genome, supervised by David Balding and co-supervised by Ewan Birney.
In terms of methodology development I am currently working on several projects relating to inversion polymorpishms with Lachlan Coin, and a method, MultiPhen, for jointly modelling multiple phenotypes in genome-wide association studies (GWAS). I also perform population genetics and GWAS related work on the Northern Finland Birth Cohort (NFBC1966) with Marjo-Riitta Jarvelin.
For my personal homepage click here.
Methods & Software
MultiPhen method - for modelling and testing multiple phenotypes jointly in GWAS. This method is fast and can be applied to imputed data, and is available as a CRAN package (see here)that can also perform standard univariate GWAS. Paper describing the method, with results on the NFBC data, under review.
- Ped/Pop method(click link for paper) - for detecting recent positive selection. Compares population-based recombination rate estimates (underestimated due to recent common ancestor at selected locus) with pedigree-based recombination rate estimates (unaffected by selection).
invertFREGENE (click link for paper) - software for simulating inversion polymorphisms in population genetic data. Documentation and code:
- BAYESFST - software/method for detecting selection. Method described in Beaumont and Balding (2004) takes a Bayesian approach to identifying loci with divergent allele frequencies between sub-populations (based on Fst). Contributed to the software code by extending to deal with genome-wide linked markers, primarily by incorporation of a prior term between hyper-parameters to model the correlation between adjacent markers. The program, implemented via MCMC, and coded in C, can be downloaded here.
et al., 2013, Common genetic variants regulating ADD3 gene expression alter biliary atresia risk, Journal of Hepatology, Vol:59, ISSN:0168-8278, Pages:1285-1291
et al., 2013, Lumbar disc degeneration is linked to a carbohydrate sulfotransferase 3 variant, Journal of Clinical Investigation, Vol:123, ISSN:0021-9738, Pages:4909-4917
et al., 2013, Identification of heart rate-associated loci and their effects on cardiac conduction and rhythm disorders, Nature Genetics, Vol:45, ISSN:1061-4036, Pages:621-+
et al., 2013, Long-term Leisure-time Physical Activity and Serum Metabolome, Circulation, Vol:127, ISSN:0009-7322, Pages:340-+
et al., 2013, The Effect of Genomic Inversions on Estimation of Population Genetic Parameters from SNP Data, Genetics, Vol:193, ISSN:0016-6731, Pages:243-253