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TitleDesign and application of genome-scale reconstructed metabolic models
Author(s)Rocha, I.
Förster, Jochen
Nielsen, Jens
KeywordsComputer simulation
Fluxome analysis
Genome annotation
Genome-scale reconstruction
Metabolic engineering
Metabolic flux analysis
Metabolic models
Metabolic networks
Issue date2008
PublisherHumana Press
CitationRocha, I.; Förster, J.; Nielsen, J., Design and application of genome-scale reconstructed metabolic models. In Andrei L. Osterman, Svetlana Y. Gerdes, Methods in Molecular Biology, Vol. 416: Microbial Gene Essentiality, Totowa, New Jersey: Humana Press, 2008. ISBN: 978-1-58829-378-7, 409-431
Abstract(s)In this chapter, the process for the reconstruction of genome-scale metabolic networks is described, and some of the main applications of such models are illustrated. The reconstruction process can be viewed as an iterative process where information obtained from several sources is combined to construct a preliminary set of reactions and constraints. This involves steps such as genome annotation; identification of the reactions from the annotated genome sequence and available literature; determination of the reaction stoichiometry; definition of compartmentation and assignment of localization; determination of the biomass composition; measurement, calculation, or fitting of energy requirements; and definition of additional constraints. The reaction and constraint sets, after debugging, may be integrated into a stoichiometric model that can be used for simulation using tools such as Flux Balance Analysis (Section 3.8). From the flux distributions obtained, physiologic parameters such as growth yields or minimal medium components can be calculated, and their distance from similar experimental data provides a basis from where the model may need to be improved.
TypeBook part
DescriptionSeries : Methods in molecular biology, vol. 416
Publisher version
AccessRestricted access (UMinho)
Appears in Collections:CEB - Livros e Capítulos de Livros / Books and Book Chapters

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