I am interested in what large datasets tell us about biological function, and how we can correlate patterns in big data with phenotypes of interest in farm animal health, disease and productivity.
- We have been studying ruminant microbiomes using whole-genome shotgun sequencing data since 2011 and are currently running possibly one of the biggest cattle gut microbiome projects ever carried out - whole-genome-shotgun metagenomics of over 300 cattle, richly phenotyped for feed-conversion-ratio and methane emissions (segregated by diet and breed). This is in collaboration with SRUC and Aberdeen
- Funded by BBSRC and TSB, we are mining rumen gut metagenome data for novel enzymes in relation to biocatalysis
- We are also interested in the chicken gut microbiome and are associating changes in the gut flora with diet and response to vaccines
- Genomics and the consequences of genome variation are also of interest. We work with animal breeders to help them understand the possible consequences of variation in their herds, and what that variation can tell us about gene function. We have worked on improving the pig genome and assembled Sscrofa 11.1, a PacBio+nanopore+Illumina pig genome assembly to be released in 2017
- We have an active interest in sequencing technologies, and have released poRe, one of the first tools to work with data from Oxford Nanopore's MinION
- We also have an interest in bioinformatics methods and pipelines, and have produced improved pipelines for both metagenomic analysis and RNA-Seq analysis. In particular, we focus on precision in RNA-Seq, and attempts to identify uncertainty in terms of genes that we cannot measure accurately.
- I am the programme leader of programme 5 of the centre for tropical livestock genetics and health (CTLGH: www.ctlgh.org
), a Gates-funded centre focused on genomic-improvement of African livestock
- We work with Prof Venu Nair at The Pirbright Institute on avian oncogenic viruese, using mRNA-Seq, microRNA-Seq and ChIP-Seq to understand how these viruses subvert the host cell machinery
- We work with Alain Kohl, Esther Schnettler and Isabelle Dietrich on analysis of viRNA and piRNA responses in insect vectors of viral diseases, using our software viRome (10.1093/bioinformatics/btt297)
- We work with David Griffiths on ovine pulmonary adenocarcinoma, again using next-generation-sequencing to understand the virus and how it interacts with the host