I am using ultra-high-throughput sequencing, comparative genomics and modelling to study the evolution of gene regulatory networks (GRNs) in flies and yeast. The systems offer complementary motivations: yeast are an ideal system for studying regulatory change after gene duplication and flies are the best model for the evolution of development.
I am currently obtaining medium depth sequence coverage from diverged clades of yeast (and flies) and am developing techniques to assemble and align sequence derived from short reads. I will use comparative genomics to analyze these data and infer conserved GRNs for each clade (each of which consists of multiple closely related species). By comparing multiple yeast (or fly) GRNs I will test hypotheses regarding the evolution of transcriptional regulation.
Eisen Lab Publications:
Liu Z,Scannell DR, Eisen MB, Tjian R. (2011) Control of Embryonic Stem Cell Lineage Commitment by Core Promoter Factor, TAF3. Cell. 2011 Sep 2;146(5):720-31