(This award is funded through the American Recovery and Reinvestment Act of 2009: Public Law 111-5).
This is a CAREER award to support the research of Dr. Sheng Zhong, in the Department of bioengineering at University of Illinois at Urbana-Champaign. Dr. Zhong is a fourth-year, tenure-track Assistant Professor. Understanding cellular processes, such as development and differentiation, requires understanding how cells control the rate of protein production, especially gene transcription. A gene regulatory network (GRN) is a collection of DNA segments in a genome, which interact with each other and with other substances in the cell, thereby governing the rates at which genes in a network are transcribed into messenger RNA. Most computational tools for identification of eukaryote GRNs were developed for the single cell eukaryote, Saccharomyces cerevisiae (baker's yeast). The complexity of GRNs in multicellular organisms and especially in vertebrates is several magnitudes greater than that of the yeast GRNs. The greater complexity arises from how genes are controlled by complex patterns of DNA regulatory elements, called cis-regulatory modules; how larger genome size provides a greater template for cis-regulatory modules to evolve; and the stochastic process of transcription, which is activated by the interaction of regulatory proteins and cis-regulatory modules. A new framework for the identification of GRNs in multicellular organisms is being developed by Dr. Zhong. Quantitative evolution models and joint models of gene expression and protein-DNA interaction data are being developed in this project. The project is advancing the state of the art of systems biology through developing a theoretical framework of eukaryote GRN evolution, a variety of GRN identification and analysis methods, prototype systems for analysis of genomic data, and through discovery of engineering principles in cell biology. Databases and tools produced under this project will be accessible via the PI?s website at http://bioinformatics.bioen.uiuc.edu/
As a part of his CAREER plan, Dr. Zhong is training a new generation of interdisciplinary researchers by engaging undergraduate students in research; developing new courses and participating in outreach activities with Illinois middle school and high school students, including a bioinformatics camp for middle school girls, as one of the Girls Adventures in Mathematics, Engineering, and Science (G.A.M.E.S) camp program.
