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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A protocol for generating a high-quality genome-scale metabolic reconstruction.
TL;DR: This protocol provides a helpful manual for all stages of the reconstruction process and presents a comprehensive protocol describing each step necessary to build a high-quality genome-scale metabolic reconstruction.
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Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110.
TL;DR: A predictive algorithm is formulated in order to apply the flux balance model to describe unsteady-state growth and by-product secretion in aerobic batch, fed-batch, and anaerobic batch cultures.
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Metabolic Flux Balancing: Basic Concepts, Scientific and Practical Use
TL;DR: The flux balance methodology allows the quantitative interpretation of metabolic physiology, gives an interpretation of experimental data, provides a guide to metabolic engineering, enables optimal medium formulation, and provides a method for bioprocess optimization.
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Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation.
Pedro Mendes,Douglas B. Kell +1 more
TL;DR: A generic approach to combine numerical optimization methods with biochemical kinetic simulations is described, suitable for use in the rational design of improved metabolic pathways with industrial significance and for solving the inverse problem of metabolic pathways.
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The biomass objective function
TL;DR: Fundamental issues associated with its formulation and use are reviewed and use to compute optimal growth states are reviewed.
References
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Evidence for the oxidation of glycolytic NADH by the malate-aspartate shuttle in ehrlich ascites tumor cells
TL;DR: It may be established that in Ehrlich ascites cells reducing equivalents generated in the cytosol during aerobic glycolysis strongly influence the NAD redox state when their intramitochondrial translocation is prevented by the inactivation of the malate-aspartate shuttle.
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Application of Gibbs' rule and a simple pathway method to microbial stoichiometry
S. P. Tsai,Y. H. Lee +1 more
TL;DR: The power of metabolic pathway stoichiometric for applications in bioreactor monitoring and control, in terms of the degrees of freedom, the calculation of reaction rates, and the validity of pathway models, is analyzed by using Gibbs' rule of stoichiometry.
Journal Article
Glutamate dehydrogenase activity related to histopathological grade of hepatocellular carcinoma in man.
TL;DR: Other serum enzymes, such as protocollagen proline hydroxylase, serum glutamic-oxalacetic transaminase, and alkaline phosphatase were elevated in most patients with primary hepatocellular carcinoma, irrespective of the grade of the tumor.
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Analysis of a framework using material balances in metabolic pathways to elucidate cellular metabolism.
S. C. Niranjan,Ka-Yiu San +1 more
TL;DR: A framework using material balances in metabolic pathways to study cellular metabolism is examined and the number of half reactions comprising the reaction network is found to be an important parameter.