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Brief Bioinform. 2008 Sep;9(5):422-36. doi: 10.1093/bib/bbn018. Epub 2008 Apr 24.

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

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  • 1Mathematical Sciences, Brunel University, Uxbridge, UB8 3PH, UK.

Abstract

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.

PMID:
18436574
[PubMed - indexed for MEDLINE]
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