title: A critical examination of stoichiometric and path-finding approaches to metabolic pathways.
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.
authors.affiliation: Mathematical Sciences, Brunel University, Uxbridge, UB8 3PH, UK.
authors.forename: Francisco J
authors.initials: FJ
authors.lastname: Planes
authors.forename: John E
authors.initials: JE
authors.lastname: Beasley
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D008954:Models, Biological; D011381:Programming Languages; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D012984:Software
chemical_list: D020543:Proteome