I carry out research in genetic epidemiology and precision medicine with focus on autoimmune and infectious diseases.
Genetic susceptibility to a disease is typically determined by tiny effects from thousands of sites on the genome at which people differ from each other. I am developing new methods of genetic analysis, based on adding up the effects of all these variant sites on each gene to identify the core genes that cause disease.
My research projects/code repositories.
The method is based on the Omnigenic model (Boyle et al., 2017) and can be applied to detect effector (core) genes mediating the disease. The pipeline makes use of the GENOSCORES platform to compute eQTL and pQTL scores and aggregate the trans QTL effects into genomewide scores which are then tested for association with the disease.
Work is supported by UK/Canada Collaboration on the genetics of long-term diabetes complications.
I am a lead developer and maintainer of the GENOSCORES code base, server and database.
GENOSCORES consists of:
GENOSCORES is used with any individual-level dataset consisting of genome-wide SNP genotypes to calculate genotypic scores for the intermediate phenotypes stored in the database.
Work is supported by The Academy of Medical Sciences Springboard award
I train predictive models with hierarchical shrinkage priors using hsstan package to predict treatment response using panels of biomarkers predictive of synovial pathotypes in RA.
This is a collaborative project within TRACT-RA collaboration.
I use GENOSCORES and GATE method to detect effector (core) genes mediating systemic lupus.
This is a collaboration with Centro Pfizer – Universidad de Granada – Junta de Andalucía de Genómica e Investigación Oncológica GENYO.
I co-initiated, managed and developed the web platform for the 3D printing service at the University of Southampton.
The access is restricted only to the registered users since UoS moved the application behind the firewall.
Some languages/frameworks I use.
Technologies I work with at work or as a hobby.