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
Quantifying the metabolic capabilities of engineered Zymomonas mobilis using linear programming analysis
Ivi C. Tsantili,Ivi C. Tsantili,M. Nazmul Karim,Maria I. Klapa,Maria I. Klapa,Maria I. Klapa +5 more
TL;DR: The study indicated that ethanol and biomass production depend directly on anaerobic respiration stoichiometry and activity, and revealed the essential for bacterial growth reactions and elucidated the association between the metabolic pathways.
Journal ArticleDOI
An unconventional uptake rate objective function approach enhances applicability of genome-scale models for mammalian cells.
Yiqun Chen,Brian O. McConnell,Venkata Gayatri Dhara,Harnish Mukesh Naik,Chien-Ting Li,Maciek R. Antoniewicz,Michael J. Betenbaugh +6 more
TL;DR: The unconventional uptake-rate objective functions (UOFs) approach is able to distinguish metabolic differences between three distinct CHO cell lines not directly observed using the conventional biomass growth maximization solutions and managed to identify the correct cell line from metabolic flux data.
Book ChapterDOI
Computational Modeling of Human Metabolism and Its Application to Systems Biomedicine.
Maike K. Aurich,Ines Thiele +1 more
TL;DR: This chapter introduces constraint-based modeling and describes some of its contributions to systems biomedicine.
Journal ArticleDOI
Data reconciliation and parameter estimation in flux-balance analysis.
TL;DR: A formal methodology for data reconciliation and parameter estimation with underdetermined stoichiometric models is developed and assessed and it is verified that the f measurements required to get unbiased and reliable estimations is reduced if the LP approach is included as additional conatraints in the optimization.
Journal ArticleDOI
Mathematical models of cancer metabolism
Elke Markert,Alexei Vazquez +1 more
TL;DR: It is shown how the molecular hallmarks of cancer can be related to cell proliferation and tissue remodelling, the two major physiological requirements for the development of a multicellular structure.
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.