Genomic Analysis Laboratory
Genomic Analysis Laboratory and Center of Excellence for Stem Cell Genomics
Gene expression is an intricately coordinated event. The spatio-temporal regulation of gene expression is controlled at several levels. I focus on three facets - the epigenetic, transcriptional and post-transcriptional layers of gene regulation. As a computational biologist, I analyze genomics data generated by high-throughput technologies in an effort to uncover these molecular connections, with special focus on human health and disease.
The selective chemical modification (addition of a methyl group) at the fifth carbon atom of cytosine in the DNA (commonly referred to as DNA methylation) is a key epigenetic aspect that has direct effects on gene regulation. At the Ecker lab I work towards unraveling the mechanics of how DNA methylation affects gene regulation in a variety of systems. We are part of the ENCODE Consortium Project (phase 3) where we look into the differential methylation patterns across various organs (spatial) in selected stages (temporal) of mouse embryonic development and study its effect on gene expression. These stages correspond to those at which several human developmental disorders are manifested. We have recently discovered several novel patterns of DNA methylation that assert their effects on gene expression profiles of various organs across four individuals.
I play a lead role in the activities of the recently established Center of Excellence for Stem Cell Genomics (CESCG). This center, funded by the California Institute of Regenerative Medicine (CIRM), aims to foster collaborations with stem-cell biologists in the state of California and the two nodal CESCGs (at Salk Institute and Stanford University). We have initiated several interesting projects, which "apply genomics and bioinformatics approaches to stem cell research to accelerate fundamental understanding of human biology and disease mechanisms, enhance cell and tissue production and advance personalized cellular therapeutics." We are collaborating with four of the seven applicants selected for this program: (1) Prof. Gay Crooks at UCLA to identify and overcome transcriptome barriers to generating hematopoietic stem cells from pluripotent stem cells, (2) Prof. Guoping Fan at UCLA for genomic analysis of stem cell differentiation in human overgrowth syndrome, (3) Prof. Kelly Frazer at UCSD for population wide study of functional genomics of drug induced electrophysical phenotypes in human cardiomyocites and (4) Prof. Benoit Bruneau at UCSF to study the epigenomics of human cardiac differentiation and congenital heart disease.
For more information on my research activities (including past research) and background, please visit my website by clicking here»