Abstract
The functionality of the living cell is enabled by an intricate network of biochemical, metabolic and information transporting processes. These processes are carried out by the different network systems that comprise the cell’s activity, among which are the transcriptional regulatory network, the protein–protein interaction network and the metabolic network. To understand the functional design of these complex systems, it is worth referring to their abstract representation as graphs, where the interacting components, be them proteins, metabolites or genes, are designated as nodes, and the interactions between them as edges. Once the graphical description has been established, the tools of graph theory can be utilized to analyze the networks and obtain a better understanding of their overall construction. This approach has led to several groundbreaking discoveries on the nature of networks, crossing fields of research from biology to social science and technology. In this chapter we present the basic tools and concepts brought forth by the graph theoretic approach, and show their application to biological networks. We especially focus on the universal appearance of various features, such as small-world topologies, scale-free degree distributions and hierarchical and modular structures. These recurring patterns in the structure of the cellular networks are key to understanding their evolution, their design principles, and, most importantly, the way they function.
Published Version
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