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Metabolic Models: From DNA to Physiology (and Back)

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Theoretical and Applied Aspects of Systems Biology

Part of the book series: Computational Biology ((COBO,volume 27))

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Abstract

Metabolic reconstructions constitute translations from genomic data to biochemical processes and serve as valuable tools to assess, along with mathematical models, the viability of organisms on different environments or the overproduction of industrially valuable metabolites following controlled manipulation of specific reaction rates. In the following, we review FBA, a constraint-based mathematical method which successfully predicts genome-wide metabolic fluxes, most notably the rate of accumulation of biomass precursors with stoichiometry determined by the cellular biomass composition. The practical implementation of the method on a synthetic metabolic model is offered as computer codes written for GNU-Octave, an open-source language with powerful numerical tools.

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Notes

  1. 1.

    Check http://systemsbiology.ucsd.edu/InSilicoOrganisms/OtherOrganisms or https://www.ebi.ac.uk/biomodels-main/ for an updated list.

  2. 2.

    Many organisms can, for instance, generate ATP either by respiration, fermentation, or both processes simultaneously [37].

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Authors and Affiliations

  1. Instituto de Física, Universidade Federal Fluminense (UFF), Niterói, Brazil

    Marcio Argollo de Menezes

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  1. Marcio Argollo de Menezes
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Correspondence to Marcio Argollo de Menezes .

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Editors and Affiliations

  1. Graduate Program in Computational Biology, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil

    Fabricio Alves Barbosa da Silva

  2. Graduate Program in Computational Biology, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil

    Nicolas Carels

  3. Graduate Program in Computational Biology, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil

    Floriano Paes Silva Junior

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Menezes, M.A.d. (2018). Metabolic Models: From DNA to Physiology (and Back). In: Alves Barbosa da Silva, F., Carels, N., Paes Silva Junior, F. (eds) Theoretical and Applied Aspects of Systems Biology. Computational Biology, vol 27. Springer, Cham. https://doi.org/10.1007/978-3-319-74974-7_4

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  • DOI: https://doi.org/10.1007/978-3-319-74974-7_4

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