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CS Colloquium 10/5/2011 "Computational Modeling Towards Two-Dimensional Annotation of Genomes"

Posted Oct. 3, 2011

Computational Modeling Towards Two-Dimensional Annotation of Genomes
Dr. Xuewen Chen
Electrical Engineering and Computer Science
University of Kansas

3:45 pm, 5 October 2011, 228 MSB


While much of molecular biology research has led to a wealth of knowledge about individual cellular components and their functions, it has become increasingly clear that most cellular functions are carried out by complex networks of interconnected components, and that the characterization of isolated cellular components is not sufficient to understand the cell's complexity. In recent years, the development of high-throughput technologies has provided the scientific community with exciting new opportunities for systematically studying cellular components on a genome scale. Consequently, one of the great challenges currently confronting scientists in systems biology research is how to computationally elucidate the function of gene products (one-dimensional genome annotation) and model the complex biological networks (two-dimensional genome annotation) from these high-throughput biological data. In this talk, I will discuss our recent research efforts towards two-dimensional annotation of genomes. Particularly, I will talk about a data mining method for automatic protein function annotation using information extracted from cross-species protein-protein interaction networks. For two-dimensional genome annotation, I will discuss an integrative model for genetic regulatory network reconstruction: this model first applies a hidden Markov model-based method for dimensionality reduction and then a structure learning approach for gene network reconstruction.

Short Bio

Xue-wen Chen is currently an Associate Professor in the Department of Electrical Engineering and Computer Science and the Director of the Bioinformatics and Computational Life Sciences Laboratory in the Information and Telecommunication Technology Center at the University of Kansas. He is a senior IEEE member. He is the co-editor-in-Chief of the International Journal of Data Mining and Bioinformatics and also serves in the editorial board in three other international journals including IEEE Trans. on Information Technology on Biomedicine.

Dr. Chen received his PhD degree from Carnegie Mellon University, Pittsburgh, USA in 2001. He was a recipient of the prestigious NSF CAREER Award in 2007. He received the Miller Professional Development Award for Distinguished Research in 2007 and for Distinguished Service in 2008 from The School of Engineering at the University of Kansas. He served as conference chair (and co-chairs) for the IEEE Conference on Healthcare Informatics, Imaging and Systems Biology in 2011, he IEEE International Conference on Bioinformatics and Biomedicine in 2009 and the International Conference in Machine Learning and Applications in 2008 and 2011. He also served as a program committee member in numerous conferences such as KDD, CIKM, ICDM, and CEC. He will be the conference chair for CIKM 2012. His research interest includes machine learning, data mining, bioinformatics, systems biology, and statistical modeling.