Mathematical optimization applications in metabolic networks

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 effort...

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Bibliographic Details
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
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Summary: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.
ISSN:1096-7176
1096-7184
DOI:10.1016/j.ymben.2012.09.005