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Genome-scale metabolic models: reconstruction and analysis

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Abstract
Metabolism can be defined as the complete set of chemical reactions that occur in living organisms in order to maintain life. Enzymes are the main players in this process as they are responsible for catalyzing the chemical reactions. The enzyme–reaction relationships can be used for the reconstruction of a network of reactions, which leads to a metabolic model of metabolism. A genome-scale metabolic network of chemical reactions that take place inside a living organism is primarily reconstructed from the information that is present in its genome and the literature and involves steps such as functional annotation of the genome, identification of the associated reactions and determination of their stoichiometry, assignment of localization, determination of the biomass composition, estimation of energy requirements, and definition of model constraints. This information can be integrated into a stoichiometric model of metabolism that can be used for detailed analysis of the metabolic potential of the organism using constraint-based modeling approaches and hence is valuable in understanding its metabolic capabilities.
Keywords
Flux balance analysis, Constraint-based modeling, Metabolic flux analysis, Genome-scale metabolic network reconstruction, Metabolic networks

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Chicago
Baart, Gino, and Dirk E Martens. 2012. “Genome-scale Metabolic Models: Reconstruction and Analysis.” In Neisseria Meningitidis : Advanced Methods and Protocols, ed. Myron Christodoulides , 799:107–126. Clifton, NJ, USA: Humana Press.
APA
Baart, G., & Martens, D. E. (2012). Genome-scale metabolic models: reconstruction and analysis. In M. Christodoulides (Ed.), Neisseria meningitidis : advanced methods and protocols (Vol. 799, pp. 107–126). Clifton, NJ, USA: Humana Press.
Vancouver
1.
Baart G, Martens DE. Genome-scale metabolic models: reconstruction and analysis. In: Christodoulides M, editor. Neisseria meningitidis : advanced methods and protocols. Clifton, NJ, USA: Humana Press; 2012. p. 107–26.
MLA
Baart, Gino, and Dirk E Martens. “Genome-scale Metabolic Models: Reconstruction and Analysis.” Neisseria Meningitidis : Advanced Methods and Protocols. Ed. Myron Christodoulides . Vol. 799. Clifton, NJ, USA: Humana Press, 2012. 107–126. Print.
@incollection{2087361,
  abstract     = {Metabolism can be defined as the complete set of chemical reactions that occur in living organisms in order to maintain life. Enzymes are the main players in this process as they are responsible for catalyzing the chemical reactions. The enzyme--reaction relationships can be used for the reconstruction of a network of reactions, which leads to a metabolic model of metabolism. A genome-scale metabolic network of chemical reactions that take place inside a living organism is primarily reconstructed from the information that is present in its genome and the literature and involves steps such as functional annotation of the genome, identification of the associated reactions and determination of their stoichiometry, assignment of localization, determination of the biomass composition, estimation of energy requirements, and definition of model constraints. This information can be integrated into a stoichiometric model of metabolism that can be used for detailed analysis of the metabolic potential of the organism using constraint-based modeling approaches and hence is valuable in understanding its metabolic capabilities.},
  author       = {Baart, Gino and Martens, Dirk E},
  booktitle    = {Neisseria meningitidis : advanced methods and protocols},
  editor       = {Christodoulides , Myron},
  isbn         = {9781617793455},
  keyword      = {Flux balance analysis,Constraint-based modeling,Metabolic flux analysis,Genome-scale metabolic network reconstruction,Metabolic networks},
  language     = {eng},
  pages        = {107--126},
  publisher    = {Humana Press},
  series       = {Methods in Molecular Biology},
  title        = {Genome-scale metabolic models: reconstruction and analysis},
  url          = {http://dx.doi.org/10.1007/978-1-61779-346-2\_7},
  volume       = {799},
  year         = {2012},
}

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