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Briefings in Bioinformatics Advance Access originally published online on April 24, 2008
Briefings in Bioinformatics 2008 9(5):422-436; doi:10.1093/bib/bbn018
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© The Author 2008. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

A critical examination of stoichiometric and path-finding approaches to metabolic pathways

Francisco J. Planes and John E. Beasley

Corresponding author. John E. Beasley, Mathematical Sciences, Brunel University, Uxbridge, UB8 3PH, UK. Tel: +44 1895 266219; Fax: +44 1895 269732; E-mail: john.beasley{at}brunel.ac.uk

Advances in the field of genomics have enabled computational analysis of metabolic pathways at the genome scale. Singular attention has been devoted in the literature to stoichiometric approaches, and path-finding approaches, to metabolic pathways. Stoichiometric approaches make use of reaction stoichiometry when trying to determine metabolic pathways. Stoichiometric approaches involve elementary flux modes and extreme pathways. In contrast, path-finding approaches propose an alternative view based on graph theory in which reaction stoichiometry is not considered. Path-finding approaches use shortest path and k-shortest path concepts. In this article we give a critical overview of the theory, applications and key research challenges of stoichiometric and path-finding approaches to metabolic pathways.

Keywords: metabolic pathways, extreme pathways, elementary flux modes, path finding, shortest path, systems biology

Submitted: January 16, 2008. Received (in revised form): March 19, 2008.


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