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Results: 1 to 20 of 514

1.

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
2.

Computing the shortest elementary flux modes in genome-scale metabolic networks.

de Figueiredo LF, Podhorski A, Rubio A, Kaleta C, Beasley JE, Schuster S, Planes FJ.

Bioinformatics. 2009 Dec 1;25(23):3158-65. doi: 10.1093/bioinformatics/btp564. Epub 2009 Sep 30.

PMID:
19793869
[PubMed - indexed for MEDLINE]
Free Article
3.

Predicting novel pathways in genome-scale metabolic networks.

Schuster S, de Figueiredo LF, Kaleta C.

Biochem Soc Trans. 2010 Oct;38(5):1202-5. doi: 10.1042/BST0381202.

PMID:
20863284
[PubMed - indexed for MEDLINE]
4.

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
[PubMed - indexed for MEDLINE]
Free Article
5.

A hybrid model of anaerobic E. coli GJT001: combination of elementary flux modes and cybernetic variables.

Kim JI, Varner JD, Ramkrishna D.

Biotechnol Prog. 2008 Sep-Oct;24(5):993-1006. doi: 10.1002/btpr.73.

PMID:
19194908
[PubMed - indexed for MEDLINE]
6.

Flux coupling analysis of metabolic networks is sensitive to missing reactions.

Marashi SA, Bockmayr A.

Biosystems. 2011 Jan;103(1):57-66. doi: 10.1016/j.biosystems.2010.09.011. Epub 2010 Oct 1.

PMID:
20888889
[PubMed - indexed for MEDLINE]
7.

Detecting structural invariants in biological reaction networks.

Behre J, de Figueiredo LF, Schuster S, Kaleta C.

Methods Mol Biol. 2012;804:377-407. doi: 10.1007/978-1-61779-361-5_20. Review.

PMID:
22144164
[PubMed - indexed for MEDLINE]
8.

Large-scale computation of elementary flux modes with bit pattern trees.

Terzer M, Stelling J.

Bioinformatics. 2008 Oct 1;24(19):2229-35. doi: 10.1093/bioinformatics/btn401. Epub 2008 Aug 1.

PMID:
18676417
[PubMed - indexed for MEDLINE]
Free Article
9.

Improved computational performance of MFA using elementary metabolite units and flux coupling.

Suthers PF, Chang YJ, Maranas CD.

Metab Eng. 2010 Mar;12(2):123-8. doi: 10.1016/j.ymben.2009.10.002. Epub 2009 Oct 27.

PMID:
19837183
[PubMed - indexed for MEDLINE]
10.

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
[PubMed - indexed for MEDLINE]
11.

Decomposing flux distributions into elementary flux modes in genome-scale metabolic networks.

Chan SH, Ji P.

Bioinformatics. 2011 Aug 15;27(16):2256-62. doi: 10.1093/bioinformatics/btr367. Epub 2011 Jun 17.

PMID:
21685054
[PubMed - indexed for MEDLINE]
Free Article
12.

Structural analysis of metabolic networks based on flux centrality.

Koschützki D, Junker BH, Schwender J, Schreiber F.

J Theor Biol. 2010 Aug 7;265(3):261-9. doi: 10.1016/j.jtbi.2010.05.009. Epub 2010 May 18.

PMID:
20471988
[PubMed - indexed for MEDLINE]
13.

Analysis on relationship between extreme pathways and correlated reaction sets.

Xi Y, Chen YP, Cao M, Wang W, Wang F.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S58. doi: 10.1186/1471-2105-10-S1-S58.

PMID:
19208161
[PubMed - indexed for MEDLINE]
Free PMC Article
14.
15.

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
16.

Genome-scale in silico aided metabolic analysis and flux comparisons of Escherichia coli to improve succinate production.

Wang Q, Chen X, Yang Y, Zhao X.

Appl Microbiol Biotechnol. 2006 Dec;73(4):887-94. Epub 2006 Aug 23.

PMID:
16927085
[PubMed - indexed for MEDLINE]
17.

Exploiting the pathway structure of metabolism to reveal high-order epistasis.

Imielinski M, Belta C.

BMC Syst Biol. 2008 Apr 30;2:40. doi: 10.1186/1752-0509-2-40.

PMID:
18447928
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Utilizing elementary mode analysis, pathway thermodynamics, and a genetic algorithm for metabolic flux determination and optimal metabolic network design.

Boghigian BA, Shi H, Lee K, Pfeifer BA.

BMC Syst Biol. 2010 Apr 23;4:49. doi: 10.1186/1752-0509-4-49.

PMID:
20416071
[PubMed - indexed for MEDLINE]
Free PMC Article
19.
20.

Analysis of complex metabolic behavior through pathway decomposition.

Ip K, Colijn C, Lun DS.

BMC Syst Biol. 2011 Jun 3;5:91. doi: 10.1186/1752-0509-5-91.

PMID:
21639889
[PubMed - indexed for MEDLINE]
Free PMC Article

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