Network analysis of intermediary metabolism using linear optimization. I. Development of mathematical formalism.
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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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Journal ArticleDOI
The future of whole-cell modeling
TL;DR: From the group's experience building a whole-cell model of Mycoplasma genitalium, several significant challenges to building models of more complex cells are identified.
Journal ArticleDOI
Genome scale models of yeast: towards standardized evaluation and consistent omic integration
TL;DR: The history of Saccharomyces cerevisiae's GEMs is reviewed, focusing on recent developments, and how these models are typically evaluated is studied, using both descriptive and predictive metrics.
Journal ArticleDOI
Integrated Energy and Flux Balance Based Multiobjective Framework for Large-Scale Metabolic Networks
Deepak Nagrath,Marco Avila-Elchiver,Francois Berthiaume,Arno W. Tilles,Achille Messac,Martin L. Yarmush +5 more
TL;DR: A multi-objective optimality analysis may help explain certain features of the metabolic control of hepatocytes, which is relevant to the response to hepatocytes and liver to various physiological stimuli and disease states.
Journal ArticleDOI
Systems interface biology
Francis J. Doyle,Jörg Stelling +1 more
TL;DR: The interface between systems and biology is of mutual benefit to both disciplines and in the same manner, these new classes of biological problems are motivating novel developments in theoretical systems approaches.
Book ChapterDOI
Metabolic Flux Analysis in Systems Biology of Mammalian Cells
Jens Niklas,Elmar Heinzle +1 more
TL;DR: MFA using the metabolite balancing methodology and the advantages and disadvantages of (13)C MFA in mammalian cell systems are reviewed and application examples of M FA in the optimisation of cell culture processes for the production of biopharmaceuticals are presented.
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.
Journal ArticleDOI
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.