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Items: 1 to 20 of 136

1.

Quantitative assessment of thermodynamic constraints on the solution space of genome-scale metabolic models.

Hamilton JJ, Dwivedi V, Reed JL.

Biophys J. 2013 Jul 16;105(2):512-22. doi: 10.1016/j.bpj.2013.06.011.

2.

Thermodynamics-based metabolic flux analysis.

Henry CS, Broadbelt LJ, Hatzimanikatis V.

Biophys J. 2007 Mar 1;92(5):1792-805. Epub 2006 Dec 15.

4.

A scalable algorithm to explore the Gibbs energy landscape of genome-scale metabolic networks.

De Martino D, Figliuzzi M, De Martino A, Marinari E.

PLoS Comput Biol. 2012;8(6):e1002562. doi: 10.1371/journal.pcbi.1002562. Epub 2012 Jun 21.

5.

A metabolite-centric view on flux distributions in genome-scale metabolic models.

Riemer SA, Rex R, Schomburg D.

BMC Syst Biol. 2013 Apr 12;7:33. doi: 10.1186/1752-0509-7-33.

6.

Systematic assignment of thermodynamic constraints in metabolic network models.

Kümmel A, Panke S, Heinemann M.

BMC Bioinformatics. 2006 Nov 23;7:512.

7.

NExT: integration of thermodynamic constraints and metabolomics data into a metabolic network.

Martínez VS, Nielsen LK.

Methods Mol Biol. 2014;1191:65-78. doi: 10.1007/978-1-4939-1170-7_4.

PMID:
25178784
8.

A model-driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K-12 MG1655 that is biochemically and thermodynamically consistent.

McCloskey D, Gangoiti JA, King ZA, Naviaux RK, Barshop BA, Palsson BO, Feist AM.

Biotechnol Bioeng. 2014 Apr;111(4):803-15. doi: 10.1002/bit.25133. Epub 2013 Nov 19.

PMID:
24249002
9.

anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data.

Zamboni N, Kümmel A, Heinemann M.

BMC Bioinformatics. 2008 Apr 16;9:199. doi: 10.1186/1471-2105-9-199.

10.

Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models.

Cotten C, Reed JL.

BMC Bioinformatics. 2013 Jan 30;14:32. doi: 10.1186/1471-2105-14-32.

11.

Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data.

Kümmel A, Panke S, Heinemann M.

Mol Syst Biol. 2006;2:2006.0034. Epub 2006 Jun 20.

12.

Connecting extracellular metabolomic measurements to intracellular flux states in yeast.

Mo ML, Palsson BO, Herrgård MJ.

BMC Syst Biol. 2009 Mar 25;3:37. doi: 10.1186/1752-0509-3-37.

13.
14.

Fast thermodynamically constrained flux variability analysis.

Müller AC, Bockmayr A.

Bioinformatics. 2013 Apr 1;29(7):903-9. doi: 10.1093/bioinformatics/btt059. Epub 2013 Feb 6.

15.

Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli.

Bennett BD, Kimball EH, Gao M, Osterhout R, Van Dien SJ, Rabinowitz JD.

Nat Chem Biol. 2009 Aug;5(8):593-9. doi: 10.1038/nchembio.186. Epub 2009 Jun 28.

16.

Systematic analysis of conservation relations in Escherichia coli genome-scale metabolic network reveals novel growth media.

Imielinski M, Belta C, Rubin H, Halász A.

Biophys J. 2006 Apr 15;90(8):2659-72. Epub 2006 Feb 3. Erratum in: Biophys J. 2007 Jul 15;93(2):704.

17.

Elimination of thermodynamically infeasible loops in steady-state metabolic models.

Schellenberger J, Lewis NE, Palsson BØ.

Biophys J. 2011 Feb 2;100(3):544-53. doi: 10.1016/j.bpj.2010.12.3707. Erratum in: Biophys J. 2011 Mar 2;100(5):1381.

18.

Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli.

Fleming RM, Thiele I, Nasheuer HP.

Biophys Chem. 2009 Dec;145(2-3):47-56. doi: 10.1016/j.bpc.2009.08.007. Epub 2009 Sep 1.

19.

Estimating Metabolic Fluxes Using a Maximum Network Flexibility Paradigm.

Megchelenbrink W, Rossell S, Huynen MA, Notebaart RA, Marchiori E.

PLoS One. 2015 Oct 12;10(10):e0139665. doi: 10.1371/journal.pone.0139665. eCollection 2015.

20.

Steady-state metabolite concentrations reflect a balance between maximizing enzyme efficiency and minimizing total metabolite load.

Tepper N, Noor E, Amador-Noguez D, Haraldsdóttir HS, Milo R, Rabinowitz J, Liebermeister W, Shlomi T.

PLoS One. 2013 Sep 26;8(9):e75370. doi: 10.1371/journal.pone.0075370. eCollection 2013.

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