The major research focus of my group is applying bioinformatics and computational methods to health applications. This includes research in personalized medicine, understanding disease mutations, and working with next-generation sequencing technologies.
Understanding Disease and Phenotypic Mutations
A large proportion of Mendelian disease can be attributed to mutations in coding genes. I created the SIFT algorithm to predict the effect an amino acid substitution has on protein function. The SIFT algorithm is often applied to nonsynonymous variants. We have extended SIFT to work on other organisms besides human, and offer precomputed databases for mouse, worm, and over 200 other organisms.
Specific mutations in cancers can guide personalized therapies for stratified medicine. A patient's DNA is sequenced for mutations, and a drug regiment is recommended based on the patient's mutations. My group has provided bioinformatics, LIMS, and IT support for a CAP-accredited lab to execute NGS clinical tests. We have released a test for gastrointestinal and colorectal cancer via POLARIS
Social Media for Understanding Health
We are mining social media to better understand human health. We looked at public consumer reviews on drugs. We found that consumer reviews matched published clinical trials, and also offered additional insights (ref