Bioinformatics Algorithms: Techniques and Applications

3
GRAPH THEORETICAL APPROACHES
TO DELINEATE DYNAMICS OF
BIOLOGICAL PROCESSES
Teresa M. Przytycka
National Center for Biotechnology Information, National Library of Medicine, National
Institutes of Health, Bethesda, MD, USA
Elena Zotenko
National Center for Biotechnology Information, National Library of Medicine, National
Institutes of Health, Bethesda, MD, USA, and Department of Computer Science, University of
Maryland, College Park, MD, USA
3.1 INTRODUCTION
Graphs are used in Computational Biology to model the relationships between
biological entities. For example, experimentally determined protein interactions
are commonly represented by a graph, the so-called protein interaction network,
where proteins are nodes and every pair of interacting proteins is connected by
an edge. Even though such a representation may not capture all the complexity of
protein interactions in underlying biological processes, the study of the topological
properties of these networks has become an important tool in searching for general
principles that govern the organization of molecular networks. For example, it was
observed that in protein interaction networks some types of small-size subnetworks
are much more abundant than would be expected by chance [54]. The discovery of
these overrepresented subnetworks or network motifs has led to investigation of their
Bioinformatics Algorithms: Techniques and Applications, Edited by Ion I. Mǎndoiu
and Alexander Zelikovsky
Copyright © 2008 John Wiley & Sons, Inc.
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