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.
Pey, J., Prada, J., Beasley, J. E., & Planes, F. J. (2011). Path finding methods accounting for stoichiometry in metabolic networks. Genome Biology, 12(5). https://doi.org/10.1186/gb-2011-12-5-r49