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Open Access Highly Accessed Commentary

Biomolecular network querying: a promising approach in systems biology

Shihua Zhang12, Xiang-Sun Zhang1 and Luonan Chen3456*

Author Affiliations

1 Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100080, China

2 Graduate University of Chinese Academy of Sciences, Beijing 100049, China

3 Institute of Systems Biology, Shanghai University, Shanghai 200444, China

4 Department of Electrical Engineering, Osaka Sangyo University, Osaka 574-8530, Japan

5 ERATO Aihara Complexity Modelling Project, JST, Tokyo 153-8505, Japan

6 Institute of Industrial Science, University of Tokyo, Tokyo 153-8505, Japan

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BMC Systems Biology 2008, 2:5  doi:10.1186/1752-0509-2-5

Published: 18 January 2008


The rapid accumulation of various network-related data from multiple species and conditions (e.g. disease versus normal) provides unprecedented opportunities to study the function and evolution of biological systems. Comparison of biomolecular networks between species or conditions is a promising approach to understanding the essential mechanisms used by living organisms. Computationally, the basic goal of this network comparison or 'querying' is to uncover identical or similar subnetworks by mapping the queried network (e.g. a pathway or functional module) to another network or network database. Such comparative analysis may reveal biologically or clinically important pathways or regulatory networks. In particular, we argue that user-friendly tools for network querying will greatly enhance our ability to study the fundamental properties of biomolecular networks at a system-wide level.