248 Modules in Biological Networks: Identification and Application Bing Zhang Vanderbilt University School of Medicine, USA Zhiao Shi Vanderbilt University, USA Chapter 11 ABSTRACT One of the most prominent properties of networks representing complex systems is modularity. Network- based module identification has captured the attention of a diverse group of scientists from various domains and a variety of methods have been developed. The ability to decompose complex biological systems into modules allows the use of modules rather than individual genes as units in biological studies. A modular view is shaping research methods in biology. Module-based approaches have found broad applications in protein complex identification, protein function prediction, protein expression prediction, as well as disease studies. Compared to single gene-level analyses, module-level analyses offer higher robustness and sensitivity. More importantly, module-level analyses can lead to a better understanding of the design and organization of complex biological systems. INTRODUCTION The twentieth-century biology has been focused on individual cellular components and their func- tions. Despite the huge success of this approach, a discrete biological function can rarely be attributed to an individual molecule (Hartwell et al., 1999). It is increasingly clear that the cell can be understood DOI: 10.4018/978-1-60960-491-2.ch011 as a complex network of interacting components (Barabasi & Oltvai, 2004). Unraveling the interac- tions between the components of a cell constitutes a major goal of the post-genomic era. With recent advances in high-throughput ex- perimental technologies, genomic data are now available for the reconstruction of large-scale biological networks, in which nodes are biologi- cal molecules (e.g. proteins, genes, metabolites, microRNAs, etc.) and edges are functional re- Copyright © 2011, IGI Global. Copying or distributing in print or electronic forms without written permission of IGI Global is prohibited.