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Results: 1 to 20 of 64

1.

A network-based method for predicting gene-nutrient interactions and its application to yeast amino-acid metabolism.

Diamant I, Eldar YC, Rokhlenko O, Ruppin E, Shlomi T.

Mol Biosyst. 2009 Dec;5(12):1732-9. doi: 10.1039/B823287N.

PMID:
19593469
[PubMed - indexed for MEDLINE]
2.

A copula method for modeling directional dependence of genes.

Kim JM, Jung YS, Sungur EA, Han KH, Park C, Sohn I.

BMC Bioinformatics. 2008 May 1;9:225. doi: 10.1186/1471-2105-9-225.

PMID:
18447957
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Correlation and prediction of gene expression level from amino acid and dipeptide composition of its protein.

Raghava GP, Han JH.

BMC Bioinformatics. 2005 Mar 17;6:59.

PMID:
15773999
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production.

Colijn C, Brandes A, Zucker J, Lun DS, Weiner B, Farhat MR, Cheng TY, Moody DB, Murray M, Galagan JE.

PLoS Comput Biol. 2009 Aug;5(8):e1000489. doi: 10.1371/journal.pcbi.1000489. Epub 2009 Aug 28.

PMID:
19714220
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Extrapolation of metabolic pathways as an aid to modelling completely sequenced nonSaccharomyces yeasts.

Iragne F, Nikolski M, Sherman D.

FEMS Yeast Res. 2008 Feb;8(1):132-9. Epub 2007 Aug 22.

PMID:
17714476
[PubMed - indexed for MEDLINE]
6.

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
[PubMed - indexed for MEDLINE]
7.

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox.

Becker SA, Feist AM, Mo ML, Hannum G, Palsson BØ, Herrgard MJ.

Nat Protoc. 2007;2(3):727-38.

PMID:
17406635
[PubMed - indexed for MEDLINE]
8.

Prediction of protein functions with gene ontology and interspecies protein homology data.

Mitrofanova A, Pavlovic V, Mishra B.

IEEE/ACM Trans Comput Biol Bioinform. 2011 May-Jun;8(3):775-84. doi: 10.1109/TCBB.2010.15.

PMID:
21393654
[PubMed - indexed for MEDLINE]
9.

Computational approaches to the topology, stability and dynamics of metabolic networks.

Steuer R.

Phytochemistry. 2007 Aug-Sep;68(16-18):2139-51. Epub 2007 Jun 14.

PMID:
17574639
[PubMed - indexed for MEDLINE]
10.

Predicting functional associations from metabolism using bi-partite network algorithms.

Veeramani B, Bader JS.

BMC Syst Biol. 2010 Jul 14;4:95. doi: 10.1186/1752-0509-4-95.

PMID:
20630077
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Computational identification of altered metabolism using gene expression and metabolic pathways.

Nam H, Lee J, Lee D.

Biotechnol Bioeng. 2009 Jul 1;103(4):835-43. doi: 10.1002/bit.22320.

PMID:
19378263
[PubMed - indexed for MEDLINE]
12.

Coordinations between gene modules control the operation of plant amino acid metabolic networks.

Less H, Galili G.

BMC Syst Biol. 2009 Jan 26;3:14. doi: 10.1186/1752-0509-3-14.

PMID:
19171064
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Genome-scale modeling and in silico analysis of mouse cell metabolic network.

Selvarasu S, Karimi IA, Ghim GH, Lee DY.

Mol Biosyst. 2010 Jan;6(1):152-61. doi: 10.1039/b912865d. Epub 2009 Sep 2.

PMID:
20024077
[PubMed - indexed for MEDLINE]
14.

Network-based prediction of human tissue-specific metabolism.

Shlomi T, Cabili MN, Herrgård MJ, Palsson BØ, Ruppin E.

Nat Biotechnol. 2008 Sep;26(9):1003-10. doi: 10.1038/nbt.1487.

PMID:
18711341
[PubMed - indexed for MEDLINE]
15.

Phenotype analysis using network motifs derived from changes in regulatory network dynamics.

Cavelier G, Anastassiou D.

Proteins. 2005 Aug 15;60(3):525-46.

PMID:
15971229
[PubMed - indexed for MEDLINE]
16.

Optimality criteria for the prediction of metabolic fluxes in yeast mutants.

Snitkin ES, Segrè D.

Genome Inform. 2008;20:123-34.

PMID:
19425128
[PubMed - indexed for MEDLINE]
17.

Mapping genetically compensatory pathways from synthetic lethal interactions in yeast.

Ma X, Tarone AM, Li W.

PLoS One. 2008 Apr 9;3(4):e1922. doi: 10.1371/journal.pone.0001922.

PMID:
18398455
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Towards the prediction of essential genes by integration of network topology, cellular localization and biological process information.

Acencio ML, Lemke N.

BMC Bioinformatics. 2009 Sep 16;10:290. doi: 10.1186/1471-2105-10-290.

PMID:
19758426
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Predicting biological system objectives de novo from internal state measurements.

Gianchandani EP, Oberhardt MA, Burgard AP, Maranas CD, Papin JA.

BMC Bioinformatics. 2008 Jan 24;9:43. doi: 10.1186/1471-2105-9-43.

PMID:
18218092
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Computational methods for the prediction of protein interactions.

Valencia A, Pazos F.

Curr Opin Struct Biol. 2002 Jun;12(3):368-73. Review.

PMID:
12127457
[PubMed - indexed for MEDLINE]

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