Research summary:

We use systems biology approaches to study cellular differentiation and evolution. We aim to address two scientific questions: 1) how gene expression evolves as a consequence of genome sequence evolution; and 2) how genetic networks regulate early cell fate decision. Our focus biological processes include: 1) differentiation of human and mouse embryonic stem cells, and 2) preimplantation embryonic development in mouse, cattle, pig and opossum. We generate genomic, transcriptomic, epigenomic, TF-DNA binding and genetic perturbation data, develop probabilistic models and computational algorithms, use statistical inference and experimental validation to understand how gene expression is regulated and how such regulatory mechanisms evolve. 

Individual projects:
 

Comparative analysis of transcription networks. The control of gene transcription is a crucial component in regulating many important biological processes. For example, in the early stages of development, cell fate decisions and differentiation programs are often controlled by the expression of key transcription factor and receptor molecules whose presence or absence help to specify the cell fate, or to activate or suppress a particular differentiation pathway. We study the structure, dynamics and evolution of transcription networks.

Identification and comparison of signaling and regulatory pathways that regulate cells' response to environmental stimuli. We integrate gene expression, genome sequence and epigenomic data from multiple species to discover essential regulatory pathways underlying fundamental biological processes such as aging and fat loss.  

Stem cell differentiation. We aim to discover novel regulatory genes and proteins that regulate the self-renewal or differentiation of embryonic stem cells, and then promote the efficiency of cellular reprogramming and guided differentiation. 

Partial list of collaboration projects and collaborators

• Signaling networks in embryonic stem cells, collaborating with Huck Hui Ng, Fei Wang, Tetsuya Tanaka.

• Preimplantation development, collaborating with Harris Lewin, Chad Cowan.

• Regulation of Hox genes, collaborating with Robb Krumlauf.

• Social-genomics and behavioral maturation, collaborating with Gene Robinson.

• Fat loss, collaborating with Gene Robinson.

• Evolution of cis-regulatory elements, collaborating with H. Rex Gaskins.

• Gene copy number change and colon cancer, collaborating with Hanlee Ji and Ronald Davis

• Genomics of life history evolution in Drosophila, collaborating with Kimberly Hughes

Research support from

NSF

NIH

National Center for Supercomputing Applications (NSCA)

Illinois Regenerative Medicine Institute (IRMI)

Carle Foundation

University of Illinois Research Board