title: Genome-scale metabolic networks.
abstract: During the last decade, models have been developed to characterize cellular metabolism at the level of an entire metabolic network. The main concept that underlies whole-network metabolic modeling is the identification and mathematical definition of constraints. Here, we review large-scale metabolic network modeling, in particular, stoichiometric- and constraint-based approaches. Although many such models have been reconstructed, few networks have been extensively validated and tested experimentally, and we focus on these. We describe how metabolic networks can be represented using stoichiometric matrices and well-defined constraints on metabolic fluxes. We then discuss relatively successful approaches, including flux balance analysis (FBA), pathway analysis, and common extensions or modifications to these approaches. Finally, we describe techniques for integrating these approaches with models of other biological processes.
authors.affiliation: Department of Biosystems Science and Engineering, ETH Zurich, Switzerland.
authors.forename: Marco
authors.initials: M
authors.lastname: Terzer
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, CA, USA.
authors.forename: Nathaniel D
authors.initials: ND
authors.lastname: Maynard
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, CA, USA.
authors.forename: Markus W
authors.initials: MW
authors.lastname: Covert
authors.affiliation: Department of Biosystems Science and Engineering, ETH Zurich, Switzerland.
authors.forename: Jörg
authors.initials: J
authors.lastname: Stelling
mesh_terms: D016678:Genome; D016680:Genome, Bacterial; D016681:Genome, Fungal; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D015203:Reproducibility of Results; D049490:Systems Biology / Q000379:methods*