Metabolic capabilities of Escherichia coli: I. synthesis of biosynthetic precursors and cofactors.
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TLDR
This work uses specific objective functions and linear optimization to investigate the capability of E. coli catabolism to maximally produce the 12 biosynthetic precursors and three key cofactors within this solution space.About:
This article is published in Journal of Theoretical Biology.The article was published on 1993-12-21 and is currently open access. It has received 257 citations till now. The article focuses on the topics: Metabolic pathway.read more
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What is flux balance analysis
TL;DR: This primer covers the theoretical basis of the approach, several practical examples and a software toolbox for performing the calculations.
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Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
Jan Schellenberger,Richard Que,Ronan M. T. Fleming,Ines Thiele,Jeffrey D. Orth,Adam M. Feist,Daniel C. Zielinski,Aarash Bordbar,Nathan E. Lewis,Sorena Rahmanian,Joseph Kang,Daniel R. Hyduke,Bernhard O. Palsson +12 more
TL;DR: The constraint-based reconstruction and analysis toolbox as discussed by the authors is a software package running in the Matlab environment, which allows for quantitative prediction of cellular behavior using a constraintbased approach and allows predictive computations of both steady-state and dynamic optimal growth behavior, the effects of gene deletions, comprehensive robustness analyses, sampling the range of possible cellular metabolic states and the determination of network modules.
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A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information.
Adam M. Feist,Christopher S. Henry,Jennifer L. Reed,Markus Krummenacker,Andrew R. Joyce,Peter D. Karp,Linda J. Broadbelt,Vassily Hatzimanikatis,Bernhard O. Palsson +8 more
TL;DR: An updated genome‐scale reconstruction of the metabolic network in Escherichia coli K‐12 MG1655 with increased scope and computational capability is presented, expected to broaden the spectrum of both basic biology and applied systems biology studies of E. coli metabolism.
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Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110.
TL;DR: A predictive algorithm is formulated in order to apply the flux balance model to describe unsteady-state growth and by-product secretion in aerobic batch, fed-batch, and anaerobic batch cultures.
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Genome-Scale Reconstruction of the Saccharomyces cerevisiae Metabolic Network
TL;DR: The reconstructed metabolic network in the yeast Saccharomyces cerevisiae was reconstructed using currently available genomic, biochemical, and physiological information and may be used as the basis for in silico analysis of phenotypic functions.