We use computational approaches to study research questions in genomics, with a focus on human epigenomics. Our primary research focuses on understanding the causes and consequences of epigenetic variation in humans. Most projects in the lab are multidisciplinary and combine the analysis of large-scale genomic datasets (e.g. DNA methylation, DNA sequence, 16S microbiome) with statistical genetic and epigenetic tools. Some of the key research areas are listed below.
One key aim is to identify genetic variants that influence DNA methylation levels and variability within and across tissues. Research questions include exploring shared impacts on multiple epigenetic processes and on gene expression variation, cell specific effects, and understanding mechanisms of cis and trans QTL impacts.
A major research focus is on epigenome-wide association scans (EWAS) methodology and applications in humans. Our work focuses on study design and statistical analysis, EWAS power, meta-analyses, and application to a wide range of human disease, including age-related, metabolic, cardiovascular, and immune traits.
Our main interest in this area is to identify tissue-specific and tissue-shared DNA methylation markers of specific environmental exposures including smoking, alcohol consumption, physical activity, and components of diet.
We are exploring different approaches to quantification and prediction of DNA methylation profiles in humans, including comparison of DNA methylation profiling methods from different assays, and methods of imputation.
We are interested in identifying host genetic and environmental impacts on the human gut microbiome; and characterising gut microbiome variation linked to obesity. Targetted projects also include comparison of human gut microbiome variation with human genetic, epigenetic, transcriptomic, and metabolomic signatures in disease or with specific environmental exposures.
Our overall aim is to study the genetic basis of complex traits in human populations. The primary focus is on characterising the genetic architecture of epigenetic variation, but we also study the genetic basis of metabolomic, microbiome, and complex trait profiles. Specific projects here explore epistasis, gene-environment interactions, parent-of-origin, and maternal effects.