title: Mathematical optimization applications in metabolic networks.
abstract: Genome-scale metabolic models are increasingly becoming available for a variety of microorganisms. This has spurred the development of a wide array of computational tools, and in particular, mathematical optimization approaches, to assist in fundamental metabolic network analyses and redesign efforts. This review highlights a number of optimization-based frameworks developed towards addressing challenges in the analysis and engineering of metabolic networks. In particular, three major types of studies are covered here including exploring model predictions, correction and improvement of models of metabolism, and redesign of metabolic networks for the targeted overproduction of a desired compound. Overall, the methods reviewed in this paper highlight the diversity of queries, breadth of questions and complexity of redesigns that are amenable to mathematical optimization strategies.
authors.affiliation: Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA.
authors.forename: Ali R
authors.initials: AR
authors.lastname: Zomorrodi
authors.forename: Patrick F
authors.initials: PF
authors.lastname: Suthers
authors.forename: Sridhar
authors.initials: S
authors.lastname: Ranganathan
authors.forename: Costas D
authors.initials: CD
authors.lastname: Maranas
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D005786:Gene Expression Regulation / Q000235:genetics*; D024861:Genetic Enhancement / Q000379:methods*; D055442:Metabolome / Q000502:physiology*; D008957:Models, Genetic; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*
chemical_list: D020543:Proteome