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Genome-scale metabolic models: reconstruction and analysis

Gino Baart UGent and Dirk E Martens (2012) Neisseria meningitidis : advanced methods and protocols. In Methods in Molecular Biology 799. p.107-126
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.
Please use this url to cite or link to this publication:
author
organization
year
type
bookChapter
publication status
published
subject
keyword
Flux balance analysis, Constraint-based modeling, Metabolic flux analysis, Genome-scale metabolic network reconstruction, Metabolic networks
book title
Neisseria meningitidis : advanced methods and protocols
editor
Myron Christodoulides
series title
Methods in Molecular Biology
volume
799
pages
107 - 126
publisher
Humana Press
place of publication
Clifton, NJ, USA
ISBN
9781617793455
DOI
10.1007/978-1-61779-346-2_7
language
English
UGent publication?
yes
classification
B2
copyright statement
I have transferred the copyright for this publication to the publisher
id
2087361
handle
http://hdl.handle.net/1854/LU-2087361
date created
2012-04-16 15:16:47
date last changed
2017-01-02 09:54:50
@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},
}

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.