My research is focused on genomic and epigenomic analyses of human embryonic stem cell differentiation and mammalian development. My lab has contributed to the annotation of transcriptional regulatory sequences in the human and mouse genomes, characterization of epigenomes of the human cell types, and understanding of the chromatin architecture in mammalian cells. I have been a participant of the ENCODE consortium since 2003, and a member of the NIH Roadmap Epigenomic Project since 2008.
I am a member of the Ludwig Institute in San Diego where I lead the effort to generate epigenomic profiles for several neuronal cell types during different development stages.
I received my PhD training in gene regulation from Dr. Tom Maniatis at Harvard University, then extended my research in genomics and global analysis of gene expression by working as a postdoctoral fellow in Dr. Richard Young’s lab at Whitehead Institute. During this time I developed the ChIP-chip technology, one of the main genomic approaches for studying in vivo transcription factor binding and chromatin modification states.
From 2003 to 2007 I led one of the ENCODE pilot production projects to demonstrate the feasibility of ChIP-chip as a general approach for identification of transcriptional regulatory elements in the human genome. My lab produced the first high-resolution map of human promoters, enhancers and potential insulators, and discovered unique chromatin modification signatures at enhancers. Since 2008 I have been directing the San Diego Epigenome Center, one of four Reference Epigenome Mapping Centers supported by the NIH Epigenome Roadmap program.
Our center has produced detailed maps, histone modifications, DNA methylation and transcriptome for a number of pluripotent and lineage-committed human cell types, and has made several original discoveries related to epigenetic signatures of stem cells. Our current research is a natural extension of epigenomic analysis and will likely lead not only to new experimental paradigms for neural development research, but also to new insights into the role of epigenomes in glutamateric and GATAergic neurons.