Recent developments in molecular biology have resulted in experimental data that entails the relationships and interactions between biomolecules. Biomolecular interaction data, generally referred to as biological or cellular networks, are frequently abstracted using graph models. In systems biology, comparative analysis of these networks provides understanding of functional modularity in the cell by integrating cellular organization, functional hierarchy, and evolutionary conservation. In this study, we address a number of algorithmic issues associated with comparative analysis of molecular interaction networks. We first discuss the problem of identifying common sub-networks in a collection of molecular interaction networks belonging to diverse species. With a view to understanding the conservation and divergence of functional modules, we also develop network alignment techniques, grounded in theoretical models of network evolution. Finally, we probabilistically analyze the existence of highly connected and conserved subgraphs in random graphs, in order to assess the statistical significance of the patterns identified by our algorithms.
Molecular networks provide descriptions of the organization of various biological processes, including cellular signaling, metabolism, and genetic regulation. Knowledge on molecular networks is commonly used for systems level analysis of biological function; research and method development in this area has grown tremendously in the past few years. This book will provide a detailed review of existing knowledge on the functional characterization of biological networks. In 15 chapters authored by an international group of prolific systems biology and bioinformatics researchers, it will organize, conceptualize, and summarize the existing core of research results and computational methods on understanding biological function from a network perspective.