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Results: 1 to 20 of 111

1.

RELATCH: relative optimality in metabolic networks explains robust metabolic and regulatory responses to perturbations.

Kim J, Reed JL.

Genome Biol. 2012 Jul 5;13(9):R78. doi: 10.1186/gb-2012-13-9-r78.

PMID:
23013597
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

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.

PMID:
19321003
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Unveiling cellular biochemical reactions via metabolomics-driven approaches.

Saito N, Ohashi Y, Soga T, Tomita M.

Curr Opin Microbiol. 2010 Jun;13(3):358-62. doi: 10.1016/j.mib.2010.04.006. Epub 2010 Apr 27. Review.

PMID:
20430690
[PubMed - indexed for MEDLINE]
4.

Prediction of metabolic fluxes by incorporating genomic context and flux-converging pattern analyses.

Park JM, Kim TY, Lee SY.

Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14931-6. doi: 10.1073/pnas.1003740107. Epub 2010 Aug 2.

PMID:
20679215
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Flux imbalance analysis and the sensitivity of cellular growth to changes in metabolite pools.

Reznik E, Mehta P, Segrè D.

PLoS Comput Biol. 2013;9(8):e1003195. doi: 10.1371/journal.pcbi.1003195. Epub 2013 Aug 29.

PMID:
24009492
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Genome-level transcription data of Yersinia pestis analyzed with a new metabolic constraint-based approach.

Navid A, Almaas E.

BMC Syst Biol. 2012 Dec 6;6:150. doi: 10.1186/1752-0509-6-150.

PMID:
23216785
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism.

Buescher JM, Liebermeister W, Jules M, Uhr M, Muntel J, Botella E, Hessling B, Kleijn RJ, Le Chat L, Lecointe F, Mäder U, Nicolas P, Piersma S, Rügheimer F, Becher D, Bessieres P, Bidnenko E, Denham EL, Dervyn E, Devine KM, Doherty G, Drulhe S, Felicori L, Fogg MJ, Goelzer A, Hansen A, Harwood CR, Hecker M, Hubner S, Hultschig C, Jarmer H, Klipp E, Leduc A, Lewis P, Molina F, Noirot P, Peres S, Pigeonneau N, Pohl S, Rasmussen S, Rinn B, Schaffer M, Schnidder J, Schwikowski B, Van Dijl JM, Veiga P, Walsh S, Wilkinson AJ, Stelling J, Aymerich S, Sauer U.

Science. 2012 Mar 2;335(6072):1099-103. doi: 10.1126/science.1206871.

PMID:
22383848
[PubMed - indexed for MEDLINE]
Free Article
8.

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
[PubMed - indexed for MEDLINE]
9.

Computational analysis of phenotypic space in heterologous polyketide biosynthesis--applications to Escherichia coli, Bacillus subtilis, and Saccharomyces cerevisiae.

Boghigian BA, Lee K, Pfeifer BA.

J Theor Biol. 2010 Jan 21;262(2):197-207. doi: 10.1016/j.jtbi.2009.10.006. Epub 2009 Oct 13.

PMID:
19833139
[PubMed - indexed for MEDLINE]
10.

Prevalent positive epistasis in Escherichia coli and Saccharomyces cerevisiae metabolic networks.

He X, Qian W, Wang Z, Li Y, Zhang J.

Nat Genet. 2010 Mar;42(3):272-6. doi: 10.1038/ng.524. Epub 2010 Jan 24.

PMID:
20101242
[PubMed - indexed for MEDLINE]
Free PMC Article
11.
12.

Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p.

Moxley JF, Jewett MC, Antoniewicz MR, Villas-Boas SG, Alper H, Wheeler RT, Tong L, Hinnebusch AG, Ideker T, Nielsen J, Stephanopoulos G.

Proc Natl Acad Sci U S A. 2009 Apr 21;106(16):6477-82. doi: 10.1073/pnas.0811091106. Epub 2009 Apr 3.

PMID:
19346491
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis.

Goelzer A, Bekkal Brikci F, Martin-Verstraete I, Noirot P, Bessières P, Aymerich S, Fromion V.

BMC Syst Biol. 2008 Feb 26;2:20. doi: 10.1186/1752-0509-2-20.

PMID:
18302748
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model.

Yizhak K, Benyamini T, Liebermeister W, Ruppin E, Shlomi T.

Bioinformatics. 2010 Jun 15;26(12):i255-60. doi: 10.1093/bioinformatics/btq183.

PMID:
20529914
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Regulatory on/off minimization of metabolic flux changes after genetic perturbations.

Shlomi T, Berkman O, Ruppin E.

Proc Natl Acad Sci U S A. 2005 May 24;102(21):7695-700. Epub 2005 May 16.

PMID:
15897462
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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.

PMID:
19541909
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Comparative analysis of the transcription-factor gene regulatory networks of E. coli and S. cerevisiae.

Guzmán-Vargas L, Santillán M.

BMC Syst Biol. 2008 Jan 31;2:13. doi: 10.1186/1752-0509-2-13.

PMID:
18237429
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Integration of gene expression data into genome-scale metabolic models.

Akesson M, Förster J, Nielsen J.

Metab Eng. 2004 Oct;6(4):285-93.

PMID:
15491858
[PubMed - indexed for MEDLINE]
19.

Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae.

Herrgård MJ, Lee BS, Portnoy V, Palsson BØ.

Genome Res. 2006 May;16(5):627-35. Epub 2006 Apr 10.

PMID:
16606697
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Origin of co-expression patterns in E. coli and S. cerevisiae emerging from reverse engineering algorithms.

Zampieri M, Soranzo N, Bianchini D, Altafini C.

PLoS One. 2008 Aug 20;3(8):e2981. doi: 10.1371/journal.pone.0002981.

PMID:
18714358
[PubMed - indexed for MEDLINE]
Free PMC Article

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