Fregene: Simulation of realistic sequence-level data in populations and ascertained samples. - Marc Chadeau-Hyam; Clive J. Hoggart; Paul F. O'Reilly; John C. Whittaker; Maria De Iorio; David J. Balding (BMC Bioinform., 2008)

invertFREGENE: software for simulating inversions in population genetic data. - Paul F. O'Reilly; Lachlan J. M. Coin; Clive J. Hoggart (Bioinform., 2010)

Assessing multivariate gene-metabolome associations with rare variants using Bayesian reduced rank regression. - Pekka Marttinen; Matti Pirinen; Antti-Pekka Sarin; Jussi Gillberg; Johannes Kettunen; Ida Surakka; Antti J. Kangas; Pasi Soininen; Paul F. O'Reilly; Marika Kaakinen; Mika Kähönen; Terho Lehtimäki; et al. (Bioinform., 2014)

PRSice: Polygenic Risk Score software. - Jack Euesden; Cathryn M. Lewis; Paul F. O'Reilly (Bioinform., 2015)