6. Biological Networks and Graph Theory

  1. Matthew He1 and
  2. Sergey Petoukhov2

Published Online: 12 OCT 2010

DOI: 10.1002/9780470904640.ch6

Mathematics of Bioinformatics: Theory, Practice, and Applications

Mathematics of Bioinformatics: Theory, Practice, and Applications

How to Cite

He, M. and Petoukhov, S. (2010) Biological Networks and Graph Theory, in Mathematics of Bioinformatics: Theory, Practice, and Applications, John Wiley & Sons, Inc., Hoboken, NJ, USA. doi: 10.1002/9780470904640.ch6

Author Information

  1. 1

    Nova Southeastern University, Fort Lauderdale, Florida, USA

  2. 2

    Russian Academy of Sciences, Moscow, Russia

Publication History

  1. Published Online: 12 OCT 2010
  2. Published Print: 17 DEC 2010

Book Series:

  1. Bioinformatics: Computational Techniques and Engineering

Book Series Editors:

  1. Yi Pan and
  2. Albert Y. Zomaya

ISBN Information

Print ISBN: 9780470404430

Online ISBN: 9780470904640



  • biological networks;
  • biomolecular networks;
  • Boolean networks;
  • graph theory;
  • mathematical framework structures


This chapter discusses biological applications of the theory of graphs and networks. It focus on the three biomolecular networks: 1. Transcriptional regulatory networks (or genetic regulatory networks), which describe the regulatory interactions between different genes 2. Protein interaction networks of the physical interactions between an organism's proteins 3. Metabolic networks of biochemical reactions between metabolic substrates. The chapter introduces the principal notations of graph theory and recall some basic definitions and facts from graph theory. It discusses four of the most fundamental quantities: 1. Degree distribution 2. Clustering coefficient 3. Subgraphs and motifs 4. Centrality (degree, closeness, betweenness, and eigenvector) and essentiality. Several mathematical framework structures, such as a system of differential equations and Boolean networks for biological networks are discussed.

Controlled Vocabulary Terms

biological techniques; Boolean functions