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Computational Intelligence and Pattern Analysis in Biological Informatics by Jason T. Wang, Sanghamitra Bandyopadhyay, Ujjwal Maulik

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CHAPTER 16

ANALYZING TOPOLOGICAL PROPERTIES OF PROTEIN–PROTEIN INTERACTION NETWORKS: A PERSPECTIVE TOWARD SYSTEMS BIOLOGY

MALAY BHATTACHARYYA AND SANGHAMITRA BANDYOPADHYAY

16.1 INTRODUCTION

Biological systems are too complex to be represented with a stand-alone computational model [1,2]. The intricacies involved in the genomic or proteomic level of an organism, even in one of the simplest (e.g., amoeba), is hard to replicate. In spite of the complexities involved in the biological systems, they abide by a set of protocols [3]. The systematic study of such complex protocols in biological systems is the main concern in systems biology. In an analytical view, systems biology cares about the emergence of phenotypic characteristics from the genotypes and figures out the protocols behind the response to alterations of these characteristics in the environment or in the system components.

Many high-throughput technologies evolved in recent decades have enabled the analysis of various properties of the transcriptome and proteome of several organisms. These properties are occasionally mapped to an interaction network structure [4]. The identification of significant modules of genes and proteins, which have a high degree of association with each other in these networks, can add potentials to this direction of research. Individual or combined mining of gene and protein cointeraction networks is a nascent area of research that has seen promise through such module-specific studies [5–7]. A ...

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