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Results: 1 to 20 of 93

1.

The strength of chemical linkage as a criterion for pruning metabolic graphs.

Zhou W, Nakhleh L.

Bioinformatics. 2011 Jul 15;27(14):1957-63. doi: 10.1093/bioinformatics/btr271. Epub 2011 May 5.

PMID:
21551141
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Pathway identification by network pruning in the metabolic network of Escherichia coli.

Gerlee P, Lizana L, Sneppen K.

Bioinformatics. 2009 Dec 15;25(24):3282-8. doi: 10.1093/bioinformatics/btp575. Epub 2009 Oct 6.

PMID:
19808881
[PubMed - indexed for MEDLINE]
Free Article
3.

Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph.

Ma HW, Zhao XM, Yuan YJ, Zeng AP.

Bioinformatics. 2004 Aug 12;20(12):1870-6. Epub 2004 Mar 22.

PMID:
15037506
[PubMed - indexed for MEDLINE]
Free Article
4.

Properties of metabolic graphs: biological organization or representation artifacts?

Zhou W, Nakhleh L.

BMC Bioinformatics. 2011 May 4;12:132. doi: 10.1186/1471-2105-12-132.

PMID:
21542923
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Chemical basis of metabolic network organization.

Zhu Q, Qin T, Jiang YY, Ji C, Kong DX, Ma BG, Zhang HY.

PLoS Comput Biol. 2011 Oct;7(10):e1002214. doi: 10.1371/journal.pcbi.1002214. Epub 2011 Oct 13.

PMID:
22022254
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Metabolic pathfinding using RPAIR annotation.

Faust K, Croes D, van Helden J.

J Mol Biol. 2009 May 1;388(2):390-414. doi: 10.1016/j.jmb.2009.03.006. Epub 2009 Mar 10.

PMID:
19281817
[PubMed - indexed for MEDLINE]
7.

Discovering functional gene expression patterns in the metabolic network of Escherichia coli with wavelets transforms.

König R, Schramm G, Oswald M, Seitz H, Sager S, Zapatka M, Reinelt G, Eils R.

BMC Bioinformatics. 2006 Mar 8;7:119.

PMID:
16524469
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Phenotype prediction in regulated metabolic networks.

Kaleta C, Centler F, di Fenizio PS, Dittrich P.

BMC Syst Biol. 2008 Apr 25;2:37. doi: 10.1186/1752-0509-2-37.

PMID:
18439260
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Inferring meaningful pathways in weighted metabolic networks.

Croes D, Couche F, Wodak SJ, van Helden J.

J Mol Biol. 2006 Feb 10;356(1):222-36. Epub 2005 Oct 17.

PMID:
16337962
[PubMed - indexed for MEDLINE]
10.

Metabolome based reaction graphs of M. tuberculosis and M. leprae: a comparative network analysis.

Verkhedkar KD, Raman K, Chandra NR, Vishveshwara S.

PLoS One. 2007 Sep 12;2(9):e881.

PMID:
17849010
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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
12.

Supervised de novo reconstruction of metabolic pathways from metabolome-scale compound sets.

Kotera M, Tabei Y, Yamanishi Y, Tokimatsu T, Goto S.

Bioinformatics. 2013 Jul 1;29(13):i135-44. doi: 10.1093/bioinformatics/btt244.

PMID:
23812977
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Flux networks in metabolic graphs.

Warren PB, Queiros SM, Jones JL.

Phys Biol. 2009 Sep 22;6(4):046006. doi: 10.1088/1478-3975/6/4/046006.

PMID:
19773605
[PubMed - indexed for MEDLINE]
14.

Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism.

Nakahigashi K, Toya Y, Ishii N, Soga T, Hasegawa M, Watanabe H, Takai Y, Honma M, Mori H, Tomita M.

Mol Syst Biol. 2009;5:306. doi: 10.1038/msb.2009.65. Epub 2009 Sep 15.

PMID:
19756045
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Patterns of indirect protein interactions suggest a spatial organization to metabolism.

Pérez-Bercoff Å, McLysaght A, Conant GC.

Mol Biosyst. 2011 Nov;7(11):3056-64. doi: 10.1039/c1mb05168g. Epub 2011 Aug 31.

PMID:
21881679
[PubMed - indexed for MEDLINE]
16.

Environmental versatility promotes modularity in genome-scale metabolic networks.

Samal A, Wagner A, Martin OC.

BMC Syst Biol. 2011 Aug 24;5:135. doi: 10.1186/1752-0509-5-135.

PMID:
21864340
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC).

Rahman SA, Advani P, Schunk R, Schrader R, Schomburg D.

Bioinformatics. 2005 Apr 1;21(7):1189-93. Epub 2004 Nov 30.

PMID:
15572476
[PubMed - indexed for MEDLINE]
Free Article
18.

Qualitative modelling of regulated metabolic pathways: application to the tryptophan biosynthesis in E.coli.

Simão E, Remy E, Thieffry D, Chaouiya C.

Bioinformatics. 2005 Sep 1;21 Suppl 2:ii190-6.

PMID:
16204102
[PubMed - indexed for MEDLINE]
Free Article
19.

Integrated analysis of the gene neighbouring impact on bacterial metabolic networks.

Bordron P, Eveillard D, Rusu I.

IET Syst Biol. 2011 Jul;5(4):261-8. doi: 10.1049/iet-syb.2010.0070.

PMID:
21823757
[PubMed - indexed for MEDLINE]
20.

Quantifying and assessing the effect of chemical symmetry in metabolic pathways.

Zhou W, Nakhleh L.

J Chem Inf Model. 2012 Oct 22;52(10):2684-96. doi: 10.1021/ci300259u. Epub 2012 Sep 28.

PMID:
22985501
[PubMed - indexed for MEDLINE]

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