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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OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities.
TL;DR: This study demonstrates the importance of trade-offs between species- and community-level fitness driving forces and lays the foundation for metabolic-driven analysis of various types of interactions in multi-species microbial systems using genome-scale metabolic models.
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Computationally efficient flux variability analysis
Steinn Gudmundsson,Ines Thiele +1 more
TL;DR: An open source implementation of flux variability analysis called fastFVA is presented, which makes large-scale flux variabilityAnalysis feasible and tractable allowing more complex biological questions regarding network flexibility and robustness to be addressed.
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Metabolic flux analysis of hybridoma cells in different culture media using mass balances.
H.P.J. Bonarius,Vassily Hatzimanikatis,K. P. H. Meesters,C.D. de Gooijer,Georg Schmid,Johannes Tramper +5 more
TL;DR: The flux distribution that is found using the Euclidean minimum norm as the additional theoretical constraint and taking either the CO2 or the NAD(P)H mass balance into account is shown to be in agreement with the measured O2 and CO2 metabolic rates.
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Synthetic biology of cyanobacteria: unique challenges and opportunities
Bertram M. Berla,Rajib Saha,Cheryl M. Immethun,Costas D. Maranas,Tae Seok Moon,Himadri B. Pakrasi +5 more
TL;DR: Some of the unique challenges of a diurnal, autotrophic lifestyle along with how the development of synthetic biology and biotechnology in cyanobacteria must fit within those constraints are discussed.
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Contribution of serine, folate and glycine metabolism to the ATP, NADPH and purine requirements of cancer cells
Philip M. Tedeschi,Elke Markert,Murugesan Gounder,Hongxia Lin,Dmitri Dvorzhinski,Sonia C. Dolfi,L. L.Y. Chan,J. Qiu,Robert S. DiPaola,Kim M. Hirshfield,Laszlo G. Boros,Joseph R. Bertino,Zoltán N. Oltvai,Alexei Vazquez +13 more
TL;DR: It is shown that the SOG pathway is upregulated at the level of gene expression in a subset of human tumors and that its level of expression correlates with gene signatures of cell proliferation and Myc target activation.
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.
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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.