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Validation and refinement of gene-regulatory pathways on a network of physical interactions.

Yeang CH, Mak HC, McCuine S, Workman C, Jaakkola T, Ideker T.

Genome Biol. 2005;6(7):R62. Epub 2005 Jul 1.PMID: 15998451 [PubMed - indexed for MEDLINE]Related articlesFree article

Quantitative inference of dynamic regulatory pathways via microarray data.

Chang WC, Li CW, Chen BS.

BMC Bioinformatics. 2005 Mar 7;6:44.PMID: 15748298 [PubMed - indexed for MEDLINE]Related articlesFree article

Computational and experimental approaches for modeling gene regulatory networks.

Goutsias J, Lee NH.

Curr Pharm Des. 2007;13(14):1415-36. Review.PMID: 17504165 [PubMed - indexed for MEDLINE]Related articles

Sample scale-free gene regulatory network using gene ontology.

Chen G, Larsen P, Almasri E, Dai Y.

Conf Proc IEEE Eng Med Biol Soc. 2006;1:5523-6.PMID: 17946312 [PubMed - indexed for MEDLINE]Related articles

Reconciling gene expression data with known genome-scale regulatory network structures.

Herrgård MJ, Covert MW, Palsson BØ.

Genome Res. 2003 Nov;13(11):2423-34. Epub 2003 Oct 14.PMID: 14559784 [PubMed - indexed for MEDLINE]Related articlesFree article

Using large-scale perturbations in gene network reconstruction.

MacCarthy T, Pomiankowski A, Seymour R.

BMC Bioinformatics. 2005 Jan 19;6:11.PMID: 15659246 [PubMed - indexed for MEDLINE]Related articlesFree article

EXAMINE: a computational approach to reconstructing gene regulatory networks.

Deng X, Geng H, Ali H.

Biosystems. 2005 Aug;81(2):125-36.PMID: 15951103 [PubMed - indexed for MEDLINE]Related articles

Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102.

Su Z, Mao F, Dam P, Wu H, Olman V, Paulsen IT, Palenik B, Xu Y.

Nucleic Acids Res. 2006 Feb 10;34(3):1050-65. Print 2006.PMID: 16473855 [PubMed - indexed for MEDLINE]Related articlesFree article

A network biology approach to aging in yeast.

Lorenz DR, Cantor CR, Collins JJ.

Proc Natl Acad Sci U S A. 2009 Jan 27;106(4):1145-50. Epub 2009 Jan 21.PMID: 19164565 [PubMed - indexed for MEDLINE]Related articlesFree article

Gene networks: how to put the function in genomics.

Brazhnik P, de la Fuente A, Mendes P.

Trends Biotechnol. 2002 Nov;20(11):467-72. Review.PMID: 12413821 [PubMed - indexed for MEDLINE]Related articles

Genome-wide prediction of transcriptional regulatory elements of human promoters using gene expression and promoter analysis data.

Kim SY, Kim Y.

BMC Bioinformatics. 2006 Jul 4;7:330.PMID: 16817975 [PubMed - indexed for MEDLINE]Related articlesFree article

Genomic approaches for reconstructing gene networks.

Lee NH.

Pharmacogenomics. 2005 Apr;6(3):245-58. Review.PMID: 16013956 [PubMed - indexed for MEDLINE]Related articles

Alternative pathway approach for automating analysis and validation of cell perturbation networks and design of perturbation experiments.

Gong Y, Zhang Z.

Ann N Y Acad Sci. 2007 Dec;1115:267-85. Epub 2007 Oct 9.PMID: 17925355 [PubMed - indexed for MEDLINE]Related articles

Genetical genomics analysis of a yeast segregant population for transcription network inference.

Bing N, Hoeschele I.

Genetics. 2005 Jun;170(2):533-42. Epub 2005 Mar 21.PMID: 15781693 [PubMed - indexed for MEDLINE]Related articlesFree article

Detection of compound mode of action by computational integration of whole-genome measurements and genetic perturbations.

Hallén K, Björkegren J, Tegnér J.

BMC Bioinformatics. 2006 Feb 2;7:51.PMID: 16451737 [PubMed - indexed for MEDLINE]Related articlesFree article

A duplication growth model of gene expression networks.

Bhan A, Galas DJ, Dewey TG.

Bioinformatics. 2002 Nov;18(11):1486-93.PMID: 12424120 [PubMed - indexed for MEDLINE]Related articlesFree article

Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data.

Gao F, Foat BC, Bussemaker HJ.

BMC Bioinformatics. 2004 Mar 18;5:31.PMID: 15113405 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome-scale network analysis of imprinted human metabolic genes.

Sigurdsson MI, Jamshidi N, Jonsson JJ, Palsson BO.

Epigenetics. 2009 Jan;4(1):43-6. Epub 2009 Jan 31. Review.PMID: 19218833 [PubMed - indexed for MEDLINE]Related articles

A neural network based approach for inference and verification of transcriptional regulatory interactions.

Knott S, Mostafavi S, Mousavi P.

Conf Proc IEEE Eng Med Biol Soc. 2006;1:5838-41.PMID: 17946339 [PubMed - indexed for MEDLINE]Related articles

ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context.

Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Dalla Favera R, Califano A.

BMC Bioinformatics. 2006 Mar 20;7 Suppl 1:S7.PMID: 16723010 [PubMed - indexed for MEDLINE]Related articlesFree article