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Items: 1 to 20 of 62

1.

Uncovering hidden duplicated content in public transcriptomics data.

Rosikiewicz M, Comte A, Niknejad A, Robinson-Rechavi M, Bastian FB.

Database (Oxford). 2013 Mar 13;2013:bat010. doi: 10.1093/database/bat010. Print 2013.

2.

ArrayExpress--a public repository for microarray gene expression data at the EBI.

Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Rocca-Serra P, Sansone SA.

Nucleic Acids Res. 2003 Jan 1;31(1):68-71.

3.

ArrayExpress--a public database of microarray experiments and gene expression profiles.

Parkinson H, Kapushesky M, Shojatalab M, Abeygunawardena N, Coulson R, Farne A, Holloway E, Kolesnykov N, Lilja P, Lukk M, Mani R, Rayner T, Sharma A, William E, Sarkans U, Brazma A.

Nucleic Acids Res. 2007 Jan;35(Database issue):D747-50. Epub 2006 Nov 28.

4.

ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression.

Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, Abeygunawardena N, Berube H, Dylag M, Emam I, Farne A, Holloway E, Lukk M, Malone J, Mani R, Pilicheva E, Rayner TF, Rezwan F, Sharma A, Williams E, Bradley XZ, Adamusiak T, Brandizi M, Burdett T, Coulson R, Krestyaninova M, Kurnosov P, Maguire E, Neogi SG, Rocca-Serra P, Sansone SA, Sklyar N, Zhao M, Sarkans U, Brazma A.

Nucleic Acids Res. 2009 Jan;37(Database issue):D868-72. doi: 10.1093/nar/gkn889. Epub 2008 Nov 10.

5.

ArrayExpress--a public repository for microarray gene expression data at the EBI.

Parkinson H, Sarkans U, Shojatalab M, Abeygunawardena N, Contrino S, Coulson R, Farne A, Lara GG, Holloway E, Kapushesky M, Lilja P, Mukherjee G, Oezcimen A, Rayner T, Rocca-Serra P, Sharma A, Sansone S, Brazma A.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D553-5.

6.

Insights into global mechanisms and disease by gene expression profiling.

Sánchez-Cabo F, Rainer J, Dopazo A, Trajanoski Z, Hackl H.

Methods Mol Biol. 2011;719:269-98. doi: 10.1007/978-1-61779-027-0_13.

PMID:
21370089
7.

Microarray meta-analysis database (M(2)DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database.

Cheng WC, Tsai ML, Chang CW, Huang CL, Chen CR, Shu WY, Lee YS, Wang TH, Hong JH, Li CY, Hsu IC.

BMC Bioinformatics. 2010 Aug 10;11:421. doi: 10.1186/1471-2105-11-421.

8.

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments.

Parkinson H, Sarkans U, Kolesnikov N, Abeygunawardena N, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Holloway E, Kurbatova N, Lukk M, Malone J, Mani R, Pilicheva E, Rustici G, Sharma A, Williams E, Adamusiak T, Brandizi M, Sklyar N, Brazma A.

Nucleic Acids Res. 2011 Jan;39(Database issue):D1002-4. doi: 10.1093/nar/gkq1040. Epub 2010 Nov 10.

9.

Microarray retriever: a web-based tool for searching and large scale retrieval of public microarray data.

Ivliev AE, 't Hoen PA, Villerius MP, den Dunnen JT, Brandt BW.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W327-31. doi: 10.1093/nar/gkn213. Epub 2008 May 7.

10.

Generation and analysis of transcriptomics data.

Glaves PD, Tugwood JD.

Methods Mol Biol. 2011;691:167-85. doi: 10.1007/978-1-60761-849-2_10.

PMID:
20972753
11.

ArrayExpress service for reviewers/editors of DNA microarray papers.

Brazma A, Parkinson H; ArrayExpress team, EMBL-EBI.

Nat Biotechnol. 2006 Nov;24(11):1321-2. No abstract available.

PMID:
17093465
12.

DSSTox chemical-index files for exposure-related experiments in ArrayExpress and Gene Expression Omnibus: enabling toxico-chemogenomics data linkages.

Williams-DeVane CR, Wolf MA, Richard AM.

Bioinformatics. 2009 Mar 1;25(5):692-4. doi: 10.1093/bioinformatics/btp042. Epub 2009 Jan 21.

PMID:
19158160
13.

Mining microarray data at NCBI's Gene Expression Omnibus (GEO)*.

Barrett T, Edgar R.

Methods Mol Biol. 2006;338:175-90.

14.

NCBI GEO: mining millions of expression profiles--database and tools.

Barrett T, Suzek TO, Troup DB, Wilhite SE, Ngau WC, Ledoux P, Rudnev D, Lash AE, Fujibuchi W, Edgar R.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D562-6.

15.

inSilicoDb: an R/Bioconductor package for accessing human Affymetrix expert-curated datasets from GEO.

Taminau J, Steenhoff D, Coletta A, Meganck S, Lazar C, de Schaetzen V, Duque R, Molter C, Bersini H, Nowé A, Weiss Solís DY.

Bioinformatics. 2011 Nov 15;27(22):3204-5. doi: 10.1093/bioinformatics/btr529. Epub 2011 Sep 21.

PMID:
21937664
16.

HugeIndex: a database with visualization tools for high-density oligonucleotide array data from normal human tissues.

Haverty PM, Weng Z, Best NL, Auerbach KR, Hsiao LL, Jensen RV, Gullans SR.

Nucleic Acids Res. 2002 Jan 1;30(1):214-7.

17.

The ArrayExpress gene expression database: a software engineering and implementation perspective.

Sarkans U, Parkinson H, Lara GG, Oezcimen A, Sharma A, Abeygunawardena N, Contrino S, Holloway E, Rocca-Serra P, Mukherjee G, Shojatalab M, Kapushesky M, Sansone SA, Farne A, Rayner T, Brazma A.

Bioinformatics. 2005 Apr 15;21(8):1495-501. Epub 2004 Nov 25.

PMID:
15564302
18.

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository.

Edgar R, Domrachev M, Lash AE.

Nucleic Acids Res. 2002 Jan 1;30(1):207-10.

19.

SiPaGene: A new repository for instant online retrieval, sharing and meta-analyses of GeneChip expression data.

Menssen A, Edinger G, Grün JR, Haase U, Baumgrass R, Grützkau A, Radbruch A, Burmester GR, Häupl T.

BMC Genomics. 2009 Mar 5;10:98. doi: 10.1186/1471-2164-10-98.

20.

The genopolis microarray database.

Splendiani A, Brandizi M, Even G, Beretta O, Pavelka N, Pelizzola M, Mayhaus M, Foti M, Mauri G, Ricciardi-Castagnoli P.

BMC Bioinformatics. 2007 Mar 8;8 Suppl 1:S21.

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