Imperial College London


Faculty of MedicineSchool of Public Health

Honorary Senior Lecturer



+44 (0)20 7594 3349paul.oreilly04




Norfolk PlaceSt Mary's Campus





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.



Cheng G, Tang CS-M, Wong EH-M, 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

Song Y-Q, Karasugi T, Cheung KMC, 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

den Hoed M, Eijgelsheim M, Esko T, 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-+

Kujala UM, Makinen V-P, Heinonen I, et al., 2013, Long-term Leisure-time Physical Activity and Serum Metabolome, Circulation, Vol:127, ISSN:0009-7322, Pages:340-+

al Basatena N-KS, Hoggart CJ, Coin LJ, 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

More Publications