Abstract:
Gene expression regulation is a complex process that involves a large number of genetic elements - mainly transcription factors and cis-regulatory DNA sequence elements (cis-elements) - and their interactions.  Understanding mechanisms of transcriptional regulation is an important albeit difficult task.  In order to elucidate transcriptional regulation and understand abiotic stress tolerance and adaptation in plants, we have been developing computational methods, algorithms and software tools for  (1). identification of cis-elements from the promoter sequences of a large number of differentially expressed genes  and  (2). construction of networks of genes co-expressed under particular physiological conditions.  In particular, in this talk, I will discuss a steganalysis-based motif finding algorithm, called WordSpy, for genome-wide cis-element identification and a novel and efficient method for finding weak community structures in a large
(biological) network.  In addition to discussing computational aspects of these methods, I will also present some of their biological applications, including finding cell-cycle related cis-elements in S. cerevisiae and A. thaliana, and constructing co-expression networks of genes in A. thaliana in response to abiotic stresses such as drought, low temperature and salinity.

Biography :
Professor Weixiong Zhang is associate professor in Computer Science and Genetics at Washington University in St. Louis, USA.  He received his B.S. and M.S. in computer engineering from Tsinghua University, Beijing, China, and his Ph.D. in computer science from University of California at Los Angeles (UCLA).  Professor Zhang's research areas include computational molecular biology and genomics, artificial intelligence and combinatorial optimization.  Detailed information of his research and activities in these areas can be found at http://www.cse.wustl.edu/~zhang.