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Results: 1 to 20 of 73

1.

Revealing signaling pathway deregulation by using gene expression signatures and regulatory motif analysis.

Liu Y, Ringnér M.

Genome Biol. 2007;8(5):R77.

PMID:
17498287
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Transcriptional control of Shh/Ptc1 signaling in embryonic development.

Lin SL, Chang SJ, Ying SY.

Gene. 2006 Feb 15;367:56-65. Epub 2005 Dec 5.

PMID:
16330160
[PubMed - indexed for MEDLINE]
3.

Biological data warehousing system for identifying transcriptional regulatory sites from gene expressions of microarray data.

Tsou AP, Sun YM, Liu CL, Huang HD, Horng JT, Tsai MF, Liu BJ.

IEEE Trans Inf Technol Biomed. 2006 Jul;10(3):550-8.

PMID:
16871724
[PubMed - indexed for MEDLINE]
4.
5.

Identifying pattern-defined regulatory islands in mammalian genomes.

Cheung TH, Barthel KK, Kwan YL, Liu X.

Proc Natl Acad Sci U S A. 2007 Jun 12;104(24):10116-21. Epub 2007 May 29.

PMID:
17535887
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Graph-based identification of cancer signaling pathways from published gene expression signatures using PubLiME.

Finocchiaro G, Mancuso FM, Cittaro D, Muller H.

Nucleic Acids Res. 2007;35(7):2343-55. Epub 2007 Mar 27.

PMID:
17389643
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Transcriptome analyses of mouse and human mammary cell subpopulations reveal multiple conserved genes and pathways.

Lim E, Wu D, Pal B, Bouras T, Asselin-Labat ML, Vaillant F, Yagita H, Lindeman GJ, Smyth GK, Visvader JE.

Breast Cancer Res. 2010;12(2):R21. doi: 10.1186/bcr2560. Epub 2010 Mar 26.

PMID:
20346151
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Exploring potential target genes of signaling pathways by predicting conserved transcription factor binding sites.

Dieterich C, Herwig R, Vingron M.

Bioinformatics. 2003 Oct;19 Suppl 2:ii50-6.

PMID:
14534171
[PubMed - indexed for MEDLINE]
Free Article
9.

Inferring quantitative models of regulatory networks from expression data.

Nachman I, Regev A, Friedman N.

Bioinformatics. 2004 Aug 4;20 Suppl 1:i248-56.

PMID:
15262806
[PubMed - indexed for MEDLINE]
Free Article
10.

Knowledge-guided multi-scale independent component analysis for biomarker identification.

Chen L, Xuan J, Wang C, Shih IeM, Wang Y, Zhang Z, Hoffman E, Clarke R.

BMC Bioinformatics. 2008 Oct 6;9:416. doi: 10.1186/1471-2105-9-416.

PMID:
18837990
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Scleroderma gene expression and pathway signatures.

Sargent JL, Milano A, Connolly MK, Whitfield ML.

Curr Rheumatol Rep. 2008 Jul;10(3):205-11. Review.

PMID:
18638428
[PubMed - indexed for MEDLINE]
12.

Predicting genetic regulatory response using classification.

Middendorf M, Kundaje A, Wiggins C, Freund Y, Leslie C.

Bioinformatics. 2004 Aug 4;20 Suppl 1:i232-40.

PMID:
15262804
[PubMed - indexed for MEDLINE]
Free Article
13.

Comparative analysis of regulatory motif discovery tools for transcription factor binding sites.

Wei W, Yu XD.

Genomics Proteomics Bioinformatics. 2007 May;5(2):131-42.

PMID:
17893078
[PubMed - indexed for MEDLINE]
Free Article
14.

Oncogenic pathway signatures in human cancers as a guide to targeted therapies.

Bild AH, Yao G, Chang JT, Wang Q, Potti A, Chasse D, Joshi MB, Harpole D, Lancaster JM, Berchuck A, Olson JA Jr, Marks JR, Dressman HK, West M, Nevins JR.

Nature. 2006 Jan 19;439(7074):353-7. Epub 2005 Nov 6.

PMID:
16273092
[PubMed - indexed for MEDLINE]
15.

Deciphering transcriptional regulatory elements that encode specific cell cycle phasing by comparative genomics analysis.

Linhart C, Elkon R, Shiloh Y, Shamir R.

Cell Cycle. 2005 Dec;4(12):1788-97. Epub 2005 Dec 13.

PMID:
16294034
[PubMed - indexed for MEDLINE]
Free Article
16.

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]
Free PMC Article
17.

Biomarker discovery: identification of a growth factor gene signature.

Loboda A, Nebozhyn M, Cheng C, Vessey R, Huang P, Dai H, Watters JW.

Clin Pharmacol Ther. 2009 Jul;86(1):92-6. doi: 10.1038/clpt.2009.48. Epub 2009 Apr 22.

PMID:
19387436
[PubMed - indexed for MEDLINE]
18.

Identification of transcriptional regulators using binding site enrichment analysis.

Kim TM, Jung MH.

In Silico Biol. 2006;6(6):531-44.

PMID:
17518763
[PubMed - indexed for MEDLINE]
19.

Bioinformatic identification of novel putative photoreceptor specific cis-elements.

Danko CG, McIlvain VA, Qin M, Knox BE, Pertsov AM.

BMC Bioinformatics. 2007 Oct 22;8:407.

PMID:
17953763
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Master regulators used as breast cancer metastasis classifier.

Lim WK, Lyashenko E, Califano A.

Pac Symp Biocomput. 2009:504-15.

PMID:
19209726
[PubMed - indexed for MEDLINE]
Free PMC Article

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