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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Journal ArticleDOI
Genome-Scale NAD(H/+) Availability Patterns as a Differentiating Feature between Saccharomyces cerevisiae and Scheffersomyces stipitis in Relation to Fermentative Metabolism
TL;DR: Each yeast can be characterized by a significantly different metabolic response and flux span when growth is limited by oxygen uptake, both features suggesting a higher metabolic flexibility in S. cerevisiae.
Journal ArticleDOI
Design of process-compatible biological agents
J.P. Dean,G.A. Dervakos +1 more
TL;DR: In this work the problem of optimizing cellular metabolic networks has been formulated as a Mixed Integer Non-Linear Programming (MINLP) model, which can assist genetic engineers to identify which cellular enzymes should be modified and the new levels of activity required to produce an optimal network.
Journal ArticleDOI
Mathematical modeling of living cell metabolism using the method of steady-state stoichiometric flux balance.
TL;DR: This approach uses a set of algebraic linear equations for reaction rates (the method of steady- state stoichiometric flux balance) to model the purposeful metabolism of the living self-reproducing biochemical system (i.e. cell), which persists in steady-state growth.
Journal ArticleDOI
Model-guided development of an evolutionarily stable yeast chassis
Filipa Pereira,H. Lopes,Paulo Maia,Britta Meyer,Justyna Nocon,Paula Jouhten,Dimitrios Konstantinidis,Eleni Kafkia,Miguel Rocha,Peter Kötter,Isabel Rocha,Isabel Rocha,Kiran Raosaheb Patil +12 more
TL;DR: In this article, the authors report the development of Saccharomyces cerevisiae chassis strains for dicarboxylic acid production using genome-scale metabolic modelling, which is used for designing microbial chassis that are resilient against phenotype reversal due to adaptive mutations.
Book ChapterDOI
Automatic Control in Systems Biology
Henry Mirsky,Jörg Stelling,Rudiyanto Gunawan,Neda Bagheri,Stephanie R. Taylor,Eric C. Kwei,Jason E. Shoemaker,Francis J. Doyle +7 more
TL;DR: This chapter summarizes state-of-the-art developments of automatic control in systems biology with substantial theoretical background and illustrative examples.
References
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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.