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
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Patent
Systems and methods for constructing genomic-based phenotypic models
TL;DR: In this paper, the authors present a computer implemented process for constructing a scalable output network model of a bioparticle, which includes computer implemented steps of accessing a database of network gene components including an annotated network set of open reading frames (ORFs), forming a data structure associating the network gene component with network reaction components, and transforming the data set into a mathematical description of reactant fluxes defining the network model.
Book ChapterDOI
Metabolic Flux Analysis
TL;DR: Metabolic engineering emerged then as the scientific field aiming at the directed modification of the enzymatic, regulatory, or transport activities of the cell to improve cellular properties, with the use of recombinant DNA technology.
Journal ArticleDOI
Serine biosynthesis with one carbon catabolism and the glycine cleavage system represents a novel pathway for ATP generation.
TL;DR: A novel pathway for ATP generation that involves reactions from serine biosynthesis, one-carbon metabolism and the glycine cleavage system is uncovered and it is shown that the pathway is transcriptionally upregulated in an inducible murine model of Myc-driven liver tumorigenesis.
Journal ArticleDOI
Parametric sensitivity of stoichiometric flux balance models applied to wild‐type Escherichia coli metabolism
TL;DR: Model predictions are shown to be sensitive to the two parameters describing metabolic capacity, while they are relatively insensitive to the three parameters that describe the metabolic requirements for growth.
Journal ArticleDOI
Determination of metabolic flux changes during fed-batch cultivation from measurements of intracellular amino acids by LC-MS/MS.
Shintaro Iwatani,Stephen J. Van Dien,Kazutaka Shimbo,Kazuyuki Kubota,Naoko Kageyama,Daigo Iwahata,Hiroshi Miyano,Kazuo Hirayama,Yoshihiro Usuda,Kazuyuki Shimizu,Kazuhiko Matsui +10 more
TL;DR: An isotopomer balancing model was developed to elucidate flux distributions in the central metabolism and all amino acids synthetic pathways and a culture phase-dependent metabolic shift was detected in the fed-batch culture.
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.