2008
DOI: 10.1002/btpr.73
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A hybrid model of anaerobic E. coli GJT001: Combination of elementary flux modes and cybernetic variables

Abstract: Flux balance analysis (FBA) in combination with the decomposition of metabolic networks into elementary modes has provided a route to modeling cellular metabolism. It is dependent, however, on the availability of external fluxes such as substrate uptake or growth rate before estimates can become available of intracellular fluxes. The framework classically does not allow modeling of metabolic regulation or the formulation of dynamic models except through dynamic measurement of external fluxes. The cybernetic mo… Show more

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Cited by 89 publications
(54 citation statements)
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“…Modeling microbial consortia using indirect coupling can also be done by integrating EM analysis with a dynamic framework such as cybernetic models. The framework called hybrid cybernetic model (HCM) [127,128] identifies a relevant subset of EMs as metabolic options for accommodating the metabolic shift in individual species. Geng et al [129] applied HCM to model a situation where the culture medium contains four sugars (i.e., glucose, xylose, mannose, and galactose) which are competitively consumed by three yeast strains (i.e., S. cerevisiae, P. stipitis, and Kluyveromyces marxianus).…”
Section: Indirect Couplingmentioning
confidence: 99%
“…Modeling microbial consortia using indirect coupling can also be done by integrating EM analysis with a dynamic framework such as cybernetic models. The framework called hybrid cybernetic model (HCM) [127,128] identifies a relevant subset of EMs as metabolic options for accommodating the metabolic shift in individual species. Geng et al [129] applied HCM to model a situation where the culture medium contains four sugars (i.e., glucose, xylose, mannose, and galactose) which are competitively consumed by three yeast strains (i.e., S. cerevisiae, P. stipitis, and Kluyveromyces marxianus).…”
Section: Indirect Couplingmentioning
confidence: 99%
“…We considered a common case in which the same extracellular measurements of A e , B e , C e and cellmass were made on four hypothetical cell types, each having the same biological connectivity but different performance. Network dynamics were modeled using the hybrid cybernetic model with elementary modes (HCM) approach of Ramkrishna and coworkers [34]. In the HCM approach, metabolic networks are first decomposed into a set of elementary modes (EMs) (chemically balanced steady-state pathways, see [35]).…”
Section: Resultsmentioning
confidence: 99%
“…In a first step single cell kinetics are described by a state of the art hybrid cybernetic model (HCM) (see Kim et al (2008); ). The HCM allows a systematic derivation of the model equations from elementary mode analysis (see Stelling et al (2002)) and has a moderate complexity, which is useful for nonlinear analysis.…”
Section: Single Cell Modelmentioning
confidence: 99%