Basser Seminar Series

Global Alignment of Multiple Biological Networks with Applications

Speaker: Dr Chung-Shou Liao

Time: Wednesday 13 February 2013, 3:00pm to 4:00pm

Location: The University of Sydney, School of IT Building, Lecture Theatre (Room 123), Level 1

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Abstract

With the increasing availability of large protein interaction networks, the question of biological network alignment is becoming central to systems biology. Global alignment of protein interaction networks attempts to find an optimal mapping between the nodes of the networks that best represents conserved biological function. We introduce IsoRankN a global multiple network alignment tool based on spectral clustering on the induced graph of pairwise alignment scores. IsoRankN integrates sequence data with protein interaction information to help in more accurately identifying functionally related proteins across species. That is, proteins within each of these clusters derived by IsoRankN are more likely to share similar Gene Ontology (GO) annotation. In particular, we construct IsoBase, the first publicly available ortholog database that focuses on functionally related proteins based on the IsoRankN algorithm.

In addition, the flexible nature of this algorithm makes it suitable for different applications of network alignment. This algorithm can yield interesting insights into the evolutionary dynamics of related species. In recent years, when investigating the phylogenetic properties of organisms from a systems-level perspective, most studies have focused on the classification of organisms based on local structural comparison of metabolic pathways. We use IsoRankN to more comprehensively incorporate topological information of metabolic networks to explore the phylogenetic relationships between microorganisms. The classification result reveals differences in metabolic features between phylogenetically closely related organisms. With the ongoing increase in the number of metabolic annotations, the approach will help identify phenotypic variations that may not be apparent based solely on sequence-based classification.

This is joint work with Prof Bonnie Berger's Lab, CSAIL, MIT.

Speaker's biography

Dr Chung-Shou Liao joined the Institute of Information Science (IIS), Academia Sinica since January 2002, after he obtained his MS degree in the Combinatorial Mathematics group of Applied Mathematics from National Chiao Tung University. He has worked in the Algorithms and Computation Laboratory at IIS, Sinica and pursued the PhD program at the Department of Computer Science and Information Engineering (CSIE), National Taiwan University since 2004. He obtained his PhD degree in July 2009 and has served as an assistant professor in the Dept. Industrial Engineering and Engineering Management, National Tsing Hua University since February, 2010. Dr Liao’s research mainly focuses on designing efficient combinatorial and graph algorithms that can be used to solve optimization problems from real applications. He has been interested in problems related primarily to network design and systems biology. Other areas of interest include computational geometry, graph theory, and on-line decision learning.