Mathematical optimization applications in metabolic networks

• Published in: Metabolic engineering 2012-11, Vol.14 (6), p.672-686
• Main Authors: Zomorrodi, Ali R., Suthers, Patrick F., Ranganathan, Sridhar, Maranas, Costas D.
• Format: Article
• Language: English
• Subjects: Algorithms; Computer applications; Computer Simulation; Gene Expression Regulation - genetics; Genetic Enhancement - methods; Genomes; Mathematical models; Mathematical optimization; metabolic engineering; Metabolic model; Metabolic network analysis; Metabolic network redesign; metabolic networks; Metabolome - physiology; Microorganisms; Models, Genetic; Proteome - metabolism; Reviews; Signal Transduction - physiology
• ISSN: 1096-7176; 1096-7184
• DOI: 10.1016/j.ymben.2012.09.005

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. ► Review of mathematical optimization applications in metabolic network analysis. ► Optimization techniques to explore model predictions. ► Optimization techniques to correct and improve models of metabolism. ► Optimization techniques to redesign metabolic networks for overproduction.