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Results: 1 to 20 of 65

1.

Profiling gene expression using onto-express.

Khatri P, Draghici S, Ostermeier GC, Krawetz SA.

Genomics. 2002 Feb;79(2):266-70.

PMID:
11829497
[PubMed - indexed for MEDLINE]
2.

Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate.

Draghici S, Khatri P, Bhavsar P, Shah A, Krawetz SA, Tainsky MA.

Nucleic Acids Res. 2003 Jul 1;31(13):3775-81.

PMID:
12824416
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'.

Kuhn A, Luthi-Carter R, Delorenzi M.

BMC Bioinformatics. 2008 Jan 17;9:26. doi: 10.1186/1471-2105-9-26.

PMID:
18201381
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

GEM-TREND: a web tool for gene expression data mining toward relevant network discovery.

Feng C, Araki M, Kunimoto R, Tamon A, Makiguchi H, Niijima S, Tsujimoto G, Okuno Y.

BMC Genomics. 2009 Sep 3;10:411. doi: 10.1186/1471-2164-10-411.

PMID:
19728865
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Accurate detection of aneuploidies in array CGH and gene expression microarray data.

Myers CL, Dunham MJ, Kung SY, Troyanskaya OG.

Bioinformatics. 2004 Dec 12;20(18):3533-43. Epub 2004 Jul 29.

PMID:
15284100
[PubMed - indexed for MEDLINE]
Free Article
6.

Global functional profiling of gene expression.

Draghici S, Khatri P, Martins RP, Ostermeier GC, Krawetz SA.

Genomics. 2003 Feb;81(2):98-104.

PMID:
12620386
[PubMed - indexed for MEDLINE]
7.

Interactively optimizing signal-to-noise ratios in expression profiling: project-specific algorithm selection and detection p-value weighting in Affymetrix microarrays.

Seo J, Bakay M, Chen YW, Hilmer S, Shneiderman B, Hoffman EP.

Bioinformatics. 2004 Nov 1;20(16):2534-44. Epub 2004 Apr 29.

PMID:
15117752
[PubMed - indexed for MEDLINE]
Free Article
8.

Inferring biological functions and associated transcriptional regulators using gene set expression coherence analysis.

Kim TM, Chung YJ, Rhyu MG, Jung MH.

BMC Bioinformatics. 2007 Nov 17;8:453.

PMID:
18021416
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

ADGO: analysis of differentially expressed gene sets using composite GO annotation.

Nam D, Kim SB, Kim SK, Yang S, Kim SY, Chu IS.

Bioinformatics. 2006 Sep 15;22(18):2249-53. Epub 2006 Jul 12.

PMID:
16837524
[PubMed - indexed for MEDLINE]
Free Article
10.

A mixture model with random-effects components for clustering correlated gene-expression profiles.

Ng SK, McLachlan GJ, Wang K, Ben-Tovim Jones L, Ng SW.

Bioinformatics. 2006 Jul 15;22(14):1745-52. Epub 2006 May 3.

PMID:
16675467
[PubMed - indexed for MEDLINE]
Free Article
11.

Constructing gene co-expression networks and predicting functions of unknown genes by random matrix theory.

Luo F, Yang Y, Zhong J, Gao H, Khan L, Thompson DK, Zhou J.

BMC Bioinformatics. 2007 Aug 14;8:299.

PMID:
17697349
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Congruence of tissue expression profiles from Gene Expression Atlas, SAGEmap and TissueInfo databases.

Huminiecki L, Lloyd AT, Wolfe KH.

BMC Genomics. 2003 Jul 29;4(1):31.

PMID:
12885301
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

GEPS: the Gene Expression Pattern Scanner.

Wang YP, Liang L, Han BC, Quan Y, Wang X, Tao T, Ji ZL.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W492-7.

PMID:
16845057
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Construction, visualisation, and clustering of transcription networks from microarray expression data.

Freeman TC, Goldovsky L, Brosch M, van Dongen S, Mazière P, Grocock RJ, Freilich S, Thornton J, Enright AJ.

PLoS Comput Biol. 2007 Oct;3(10):2032-42.

PMID:
17967053
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

ChipInfo: Software for extracting gene annotation and gene ontology information for microarray analysis.

Zhong S, Li C, Wong WH.

Nucleic Acids Res. 2003 Jul 1;31(13):3483-6.

PMID:
12824349
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Network visualization and analysis of gene expression data using BioLayout Express(3D).

Theocharidis A, van Dongen S, Enright AJ, Freeman TC.

Nat Protoc. 2009;4(10):1535-50. doi: 10.1038/nprot.2009.177. Epub 2009 Oct 1.

PMID:
19798086
[PubMed - indexed for MEDLINE]
17.

DGEM--a microarray gene expression database for primary human disease tissues.

Xia Y, Campen A, Rigsby D, Guo Y, Feng X, Su EW, Palakal M, Li S.

Mol Diagn Ther. 2007;11(3):145-9.

PMID:
17570735
[PubMed - indexed for MEDLINE]
18.

GObar: a gene ontology based analysis and visualization tool for gene sets.

Lee JS, Katari G, Sachidanandam R.

BMC Bioinformatics. 2005 Jul 25;6:189.

PMID:
16042800
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Gene Aging Nexus: a web database and data mining platform for microarray data on aging.

Pan F, Chiu CH, Pulapura S, Mehan MR, Nunez-Iglesias J, Zhang K, Kamath K, Waterman MS, Finch CE, Zhou XJ.

Nucleic Acids Res. 2007 Jan;35(Database issue):D756-9. Epub 2006 Nov 7.

PMID:
17090592
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

EMMA: a platform for consistent storage and efficient analysis of microarray data.

Dondrup M, Goesmann A, Bartels D, Kalinowski J, Krause L, Linke B, Rupp O, Sczyrba A, Pühler A, Meyer F.

J Biotechnol. 2003 Dec 19;106(2-3):135-46.

PMID:
14651856
[PubMed - indexed for MEDLINE]

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