2016 - presentpresent
Gene regulatory networks are central to many developmental and disease biological processes. Currently, our understanding of regulatory networks in mammalian systems is limited to a few cell types. Advances in genomics and efforts from the ENCODE and the NIH Roadmap Epigenomics Mapping have collected high quality regulatory genomics datasets, providing new opportunities to study regulatory networks in diverse cell types and primary tissues. This project proposes to develop novel computational methods to construct regulatory networks in new and rare cell types and infer connections among multiple levels of gene regulation. We will apply our computational methods to examine regulatory network dynamics in two mammalian systems: cellular reprogramming from differentiated cells to pluripotent states, and a forward differentiation process of pluripotent cells to differentiated cell types.