24. Molecular Networks – Representation and Analysis

Molecular networks, their representation and analysis have attracted increasing interest in recent years. Although the importance of molecular networks has been recognized for a long time, only the advent of new technologies during the last two decades has delivered the necessary data for a systematic study of molecular networks and their complex behavior. Especially the surge of genome-wide data as well as the increase in computational power have contributed to establishing network and systems biology as new paradigms. The conceptual framework is generally based on an integrated approach of computational and experimental methods. In this chapter, we introduce basic concepts and outline mathematical formalisms for representing and analyzing molecular networks. In particular, we review the study of transcriptional regulatory networks in prokaryotes and of protein interaction networks in humans as prime examples of network-orientated approaches to complex systems. The chapter is concluded with a discussion of current challenges and future directions of network biology.