Network analysis of intermediary metabolism using linear optimization. I. Development of mathematical formalism.
TLDR
Analysis of metabolic networks using linear optimization theory allows one to quantify and understand the limitations imposed on the cell by its metabolic stoichiometry, and to understand how the flux through each pathway influences the overall behavior of metabolism.About:
This article is published in Journal of Theoretical Biology.The article was published on 1992-02-21 and is currently open access. It has received 255 citations till now.read more
Citations
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Robust flux balance analysis of multiscale biochemical reaction networks.
Yuekai Sun,Ronan M. T. Fleming,Ronan M. T. Fleming,Ines Thiele,Ines Thiele,Michael A. Saunders +5 more
TL;DR: Lifting techniques for flux balance analysis are implemented within the openCOBRA toolbox and demonstrated using the first integrated reconstruction of metabolism and macromolecular synthesis for E. coli.
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On-line optimization of glutamate production based on balanced metabolic control by RQ
TL;DR: The respiratory quotient (RQ) adaptive control based “balanced metabolic control” (BMC) strategy was proposed and used to regulate the TCA metabolic flux rate at an appropriate level to achieve the metabolic balance among glycolysis, glutamate synthesis, and T CA metabolic flux.
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Microbial transglutaminase production by Streptoverticillium mobaraense: analysis of amino acid metabolism using mass balances.
TL;DR: The distribution of metabolic flows of amino acids implies that growth and transglutaminase production are active as long as there are free amino acids available in the medium and suggests that a nitrogen source other than peptone and/or amino acids might improve growth and production.
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A genome-scale metabolic network model and machine learning predict amino acid concentrations in Chinese Hamster Ovary cell cultures.
TL;DR: In this paper, a machine learning-based approach is proposed to predict amino acid concentration in a culture medium throughout the production process, which can be used to control nutrient feeding to avoid premature nutrient depletion or provide early predictions of failed bioreactor runs.
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Dynamic Optimal Control of Homeostasis: An Integrative System Approach for Modeling of the Central Nitrogen Metabolism in Saccharomyces cerevisiae
TL;DR: The DOMC model is used successfully to predict the responses of pulses of ammonia and glutamine to nitrogen-limited continuous cultures of a wild-type strain and a glutamine synthetase-negative mutant.
References
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Book
Linear and nonlinear programming
David G. Luenberger,Yinyu Ye +1 more
TL;DR: Strodiot and Zentralblatt as discussed by the authors introduced the concept of unconstrained optimization, which is a generalization of linear programming, and showed that it is possible to obtain convergence properties for both standard and accelerated steepest descent methods.
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The pathways of glutamate and glutamine oxidation by tumor cell mitochondria. Role of mitochondrial NAD(P)+-dependent malic enzyme.
R W Moreadith,A L Lehninger +1 more
TL;DR: Analysis of oxidative pathways of glutamine and glutamate showed that extramitochondrial malate is oxidized almost quantitatively to pyruvate + CO2 by NAD(P)+-linked malic enzyme, present in the mitochondria of all tumors tested, but absent in heart, liver, and kidney mitochondria.