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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Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows
TL;DR: An elaborate framework for formally modelling pathways in chemical reaction networks on a mechanistic level is presented, modelled mathematically as directed multi-hypergraphs, with vertices corresponding to molecules and hyperedges to reactions.
Elucidation and Synthetic Design of Biochemical Pathways using novoStoic
TL;DR: This dissertation discusses and demonstrates solutions to two key challenges in the development of computational designs for the biosynthesis of xenobiotics, including the capacity of various algorithms and computer-aided design (CAD) tools to conceive novel biosynthetic pathway designs while syncretizing various engineering challenges.
Patent
Articles of manufacture and methods for modeling Saccharomyces cerevisiae metabolism
TL;DR: In this article, an in-silico model for determining a S. cerevisiae physiological function was proposed, which includes a data structure that relates a plurality of S cerevisia reactants to a plurality or set of S. reactions, a constraint set for the plurality of reactions, and commands for determining the distribution of flux through the reactions.
Reference EntryDOI
Flux analysis of mammalian cell cultures : methods and applications
TL;DR: The Flux-Balance Models helped clarify the role of “cell reprograming” in the design of Mammalian Cell Culture and allowed us to assess the importance of cell reprogramming in both the design and application of the models.
Journal ArticleDOI
In Silico analysis of perturbed steroidogenesis and gonad growth in fathead minnows (P. promelas) exposed to 17α-ethynylestradiol
TL;DR: The analyses presented are the first-ever to successfully associate underlying flux properties of the steroidogenic network with gonad growth in fish, an approach which can incorporate in silico predictions with toxicological risk assessments.
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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.