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Path finding methods accounting for stoichiometry in metabolic networks

Jon Pey1, Joaquín Prada1, John E Beasley2* and Francisco J Planes1*

Author Affiliations

1 CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain

2 Mathematical Sciences Department, Brunel University, Kingston Lane, UB8 3PH, Uxbridge, UK

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Genome Biology 2011, 12:R49  doi:10.1186/gb-2011-12-5-r49

Published: 27 May 2011


Graph-based methods have been widely used for the analysis of biological networks. Their application to metabolic networks has been much discussed, in particular noting that an important weakness in such methods is that reaction stoichiometry is neglected. In this study, we show that reaction stoichiometry can be incorporated into path-finding approaches via mixed-integer linear programming. This major advance at the modeling level results in improved prediction of topological and functional properties in metabolic networks.