Functional genomics and systems biology of host-pathogen interactions in domestic animals with a specific focus on diseases caused by mycobacterial infections; particularly, bovine tuberculosis caused by infection with Mycobacterium bovis and Johne's disease in cattle caused by infection with M. avium subspecies paratuberculosis. Epigenomics of economically important traits in livestock. Evolutionary origins and population genomics of domestic cattle. Palaeogenomics of domestic livestock and their wild ancestors. Genome mapping in domestic animal species. Equine physiological genomics for performance and health traits. Application of genomics to commercial animal breeding and food production. As an independent Principal Investigator, I have managed, coordinated and delivered many large research programmes in these areas since 2000 (18 years). This research work has contributed to the generation and exploitation of significant intellectual property and Prof. MacHugh is a co-founder and shareholder in IdentiGEN Ltd. (www.identigen.com), Equinome Ltd. (www.equinome.com) and Plusvital Ltd. (www.plusvital.com).