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Items: 1 to 20 of 122

1.

Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods.

Lewis NE, Nagarajan H, Palsson BO.

Nat Rev Microbiol. 2012 Feb 27;10(4):291-305. doi: 10.1038/nrmicro2737. Review.

2.

Metabolic modeling of endosymbiont genome reduction on a temporal scale.

Yizhak K, Tuller T, Papp B, Ruppin E.

Mol Syst Biol. 2011 Mar 29;7:479. doi: 10.1038/msb.2011.11.

3.

Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli.

McCloskey D, Palsson BØ, Feist AM.

Mol Syst Biol. 2013;9:661. doi: 10.1038/msb.2013.18. Review.

4.
5.

In silico identification of gene amplification targets based on analysis of production and growth coupling.

Jian X, Zhou S, Zhang C, Hua Q.

Biosystems. 2016 Jul;145:1-8. doi: 10.1016/j.biosystems.2016.05.002. Epub 2016 May 6.

PMID:
27157785
6.

Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns.

Kaleta C, de Figueiredo LF, Schuster S.

Genome Res. 2009 Oct;19(10):1872-83. doi: 10.1101/gr.090639.108. Epub 2009 Jun 18.

7.

A practical guide to genome-scale metabolic models and their analysis.

Santos F, Boele J, Teusink B.

Methods Enzymol. 2011;500:509-32. doi: 10.1016/B978-0-12-385118-5.00024-4.

PMID:
21943912
8.

Constraint-based models predict metabolic and associated cellular functions.

Bordbar A, Monk JM, King ZA, Palsson BO.

Nat Rev Genet. 2014 Feb;15(2):107-20. doi: 10.1038/nrg3643. Epub 2014 Jan 16. Review.

PMID:
24430943
9.

Toward metabolic phenomics: analysis of genomic data using flux balances.

Schilling CH, Edwards JS, Palsson BO.

Biotechnol Prog. 1999 May-Jun;15(3):288-95.

PMID:
10356245
10.

Exploring metabolic pathways in genome-scale networks via generating flux modes.

Rezola A, de Figueiredo LF, Brock M, Pey J, Podhorski A, Wittmann C, Schuster S, Bockmayr A, Planes FJ.

Bioinformatics. 2011 Feb 15;27(4):534-40. doi: 10.1093/bioinformatics/btq681. Epub 2010 Dec 10.

PMID:
21149278
11.

Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction.

O'Brien EJ, Lerman JA, Chang RL, Hyduke DR, Palsson BØ.

Mol Syst Biol. 2013 Oct 1;9:693. doi: 10.1038/msb.2013.52.

12.

In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data.

Edwards JS, Ibarra RU, Palsson BO.

Nat Biotechnol. 2001 Feb;19(2):125-30.

PMID:
11175725
13.

Flux analysis and metabolomics for systematic metabolic engineering of microorganisms.

Toya Y, Shimizu H.

Biotechnol Adv. 2013 Nov;31(6):818-26. doi: 10.1016/j.biotechadv.2013.05.002. Epub 2013 May 13. Review.

PMID:
23680193
14.

Acorn: a grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface.

Sroka J, Bieniasz-Krzywiec L, Gwóźdź S, Leniowski D, Lącki J, Markowski M, Avignone-Rossa C, Bushell ME, McFadden J, Kierzek AM.

BMC Bioinformatics. 2011 May 24;12:196. doi: 10.1186/1471-2105-12-196.

15.

Identification of genome-scale metabolic network models using experimentally measured flux profiles.

Herrgård MJ, Fong SS, Palsson BØ.

PLoS Comput Biol. 2006 Jul 7;2(7):e72. Epub 2006 May 10.

16.

Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico.

McAnulty MJ, Yen JY, Freedman BG, Senger RS.

BMC Syst Biol. 2012 May 14;6:42. doi: 10.1186/1752-0509-6-42.

17.

Characterizing Escherichia coli DH5alpha growth and metabolism in a complex medium using genome-scale flux analysis.

Selvarasu S, Ow DS, Lee SY, Lee MM, Oh SK, Karimi IA, Lee DY.

Biotechnol Bioeng. 2009 Feb 15;102(3):923-34. doi: 10.1002/bit.22119.

PMID:
18853410
18.

OptFlux: an open-source software platform for in silico metabolic engineering.

Rocha I, Maia P, Evangelista P, Vilaça P, Soares S, Pinto JP, Nielsen J, Patil KR, Ferreira EC, Rocha M.

BMC Syst Biol. 2010 Apr 19;4:45. doi: 10.1186/1752-0509-4-45.

19.

Biosynthetic potentials from species-specific metabolic networks.

Basler G, Nikoloski Z, Ebenhöh O, Handorf T.

Genome Inform. 2008;20:135-48.

20.

Hands-on metabolism analysis of complex biochemical networks using elementary flux modes.

Schäuble S, Schuster S, Kaleta C.

Methods Enzymol. 2011;500:437-56. doi: 10.1016/B978-0-12-385118-5.00022-0.

PMID:
21943910

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