In general, we are interested in understanding the molecular interaction networks in cells that confer basically all functions and phenomena that the cells display. These interactions are encoded the genome of the cells by two types of DNA sequences: the coding sequences and regulatory sequences. The former specifies the part list of the cell: proteins, RNAs and metabolites, while the later determines what, when, where, how much and fast these proteins, RNAs and metabolites should be produced in a cells through their interactions with transcriptional regulators. The unique combination of these proteins and RNAs in a cell determines the functional state and type of the cell.
Although we have gained a quite good understanding of coding sequences in numerous sequenced genomes thanks to the development of powerful computational and experimental tools for their characterization, we have still had only a very limited understanding of regulatory sequences in virtually all sequenced genomes due to the difficulty of their elucidation. Therefore, our current research focuses on genome-wide characterization of regulatory sequences in both prokaryotes and eukaryotes using a combination of computational and experiments studies. We are particularly interested in how the genetic programs are encoded in an animal’s genome, which guide the differentiation and development of cells during the embryogenesis.