Fordham University            The Jesuit University of New York

CIS Department Talk- November 8, 2004

The Department of Computer and Information Science & The Society of Computer Science Present

Distinguished Lecture Series in Computational Sciences

Speaker:Dr. Ying Xu, Institute of Bioinformatics and Department of Biochemistry and Molecular Biology, University of Georgia
Topic:Computational Inference of Biological Networds in Microbes
Date:Monday, November 8, 2004; 2:30pm - 3:30pm
Place:John Mulcahy Hall, Room 404
Refreshments:John Mulcahy Hall, Room 312 at 1:00pm


In this talk, I will present our recent work on a computational framework for inference and prediction of biological networks in microbes. Our network-inference methods includes four key components: (a) construction of template networks in genomes with great amount of experimental data, (b) mapping template networks to a target genome, (c) network refinement using information derived through mining genome sequences and microarray data, and (d) experimental validation of predicted network models. We have developed a suite of computational tools in support of our network predictions. These tools include (1) operon and regulon structure predictions, (2) prediction of transcription regulatory elements, (3) prediction of protein-protein interactions and protein-DNA interactions, etc. I will touch on some of the basic computational issues involved in the development of these tools.

Bio: Ying Xu is a chair professor of bioinformatics and computational biology in the Biochemistry and Molecular Biology Department, and the director of the Institute of Bioinformatics, University of Georgia (UGA). Before joining UGA in September, 2003, he was a senior staff scientist and group leader at Oak Ridge National Laboratory (ORNL), where he still holds a joint position. He received his Ph.D. degree in theoretical computer science from the University of Colorado at Boulder in 1991. Between 1991 and 1993, he was a visiting assistant professor at the Colorado School of Mines. He started his bioinformatics career in 1993 when he joined Ed Uberbacher's group at ORNL to work on the GRAIL project. Since then, he has been working in the field of bioinformatics and computation biology. His current research interests include (a) protein structure prediction and modeling, (b) computational inference of biological pathways, (c) large-scale biological data mining, and (d) cancer bioinformatics. He is interested in both development of bioinformatics tools and study of biological problems using in silico approaches. He has over 100 publications in the open literature, including two books in bioinformatics ("Current Topics in Computational Molecular Biology", MIT Press, 2002) and genomics ("Microbial Functional Genomics", John Wiley and Sons, March 2004). He has also given over 90 invited/contributed talks at conferences, workshops, research organizations and universities. In 2003-2004, he is the Program Committee (co)Chair of the IEEE Computational Systems Bioinformatics Conference (CSB'04), and a Subject-area Chair in the Program Committee of the joint ISMB/ECCB conference in 2004. He currently serves on the editorial boards of three international journals. He has also served on review panels/study sessions for major funding agencies such as NSF, NIH and DOE.

For more information, contact:
Ms. Diane Roche (718) 817-4480 (
Ms. Michelle Ciraco (
Mr. Michael Rogalewski; (

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