ISCB-Asia/SCCG 2012, BGI Special Session


Francis Chin
The University of Hong Kong

Meta-genomics Assembly and Binning

Abstract

Meta-genomics is the study of the collective genomes of all microorganisms from an environmental sample (also known as environmental genomics, or community genomics), for example, the diversity of microbes in humans is found to be associated with some common diseases such as gastrointestinal disturbance and inflammatory bowel disease. High-throughput next-generation sequencing (NGS) techniques enable researchers to directly sequence the genomes of multiple species obtained from such an environmental sample for analysis.

In this talk, we address two important problems in meta-genomic analysis based on NGS data: (1) assembly – to reconstruct the genomes of each species; (2) binning – to group DNA fragments (or reads) from similar species together. Both of these problem are very difficult especially when up to 99% of the species found in environmental samples are unknown. The bioinformatics team at HKU has developed a series of IDBA assembly and MetaCluster binning tools for meta-genomics study. The main ideas of these software tools will be presented in this talk.

Biography

Professor Chin is the Associate Dean of Engineering, Taikoo Professor of Engineering and Chair of Computer Science at the University of Hong Kong. Professor Chin received the B.A.Sc. degree from the University of Toronto, Canada, in 1972, and the M.S., M.A. and Ph.D. degrees from Princeton University, in 1974, 1975, and 1976, respectively. Since 1975, he has taught at the University of Maryland, Baltimore County, University of California, San Diego, University of Alberta, Chinese University of Hong Kong, and University of Texas at Dallas.

He joined the University of Hong Kong (HKU) in 1985, where he is the Chair of the Department of Computer Science and was the founding Head of the department from its establishment until December 31, 1999. Between 1992-1996, he served as the Associated Dean of Graduate School. In 1996, Prof. Chin was elected to the grade of IEEE Fellow. Professor Chin is currently serving as Manager Editor of the International Journal of Foundations of Computer Science and is also on the editorial boards of several journals. He has served on the program committees, including RECOMB 2013, and as conference chairman, including APBC 2007 and TAMC 2013, of numerous international workshops and conferences. Professor Chin's research interests are bioinformatics, design and analysis of algorithms and on-line algorithms.