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Plant-based microarray data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a submission tool for Arabidopsis gene expression data to ArrayExpress.
Mukherjee G, Abeygunawardena N, Parkinson H, Contrino S, Durinck S, Farne A, Holloway E, Lilja P, Moreau Y, Oezcimen A, Rayner T, Sharma A, Brazma A, Sarkans U, Shojatalab M. Mukherjee G, et al. Among authors: rayner t. Plant Physiol. 2005 Oct;139(2):632-6. doi: 10.1104/pp.105.063156. Plant Physiol. 2005. PMID: 16219923 Free PMC article.
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.
Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E, Irizarry RA, Liu J, Maier DS, Miller M, Petersen K, Quackenbush J, Sherlock G, Stoeckert CJ Jr, White J, Whetzel PL, Wymore F, Parkinson H, Sarkans U, Ball CA, Brazma A. Rayner TF, et al. BMC Bioinformatics. 2006 Nov 6;7:489. doi: 10.1186/1471-2105-7-489. BMC Bioinformatics. 2006. PMID: 17087822 Free PMC article.
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. Parkinson H, et al. Among authors: rayner tf. Nucleic Acids Res. 2009 Jan;37(Database issue):D868-72. doi: 10.1093/nar/gkn889. Epub 2008 Nov 10. Nucleic Acids Res. 2009. PMID: 19015125 Free PMC article.
Importing ArrayExpress datasets into R/Bioconductor.
Kauffmann A, Rayner TF, Parkinson H, Kapushesky M, Lukk M, Brazma A, Huber W. Kauffmann A, et al. Bioinformatics. 2009 Aug 15;25(16):2092-4. doi: 10.1093/bioinformatics/btp354. Epub 2009 Jun 8. Bioinformatics. 2009. PMID: 19505942 Free PMC article.
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. Parkinson H, et al. Among authors: rayner t. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D553-5. doi: 10.1093/nar/gki056. Nucleic Acids Res. 2005. PMID: 15608260 Free PMC article.
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. Parkinson H, et al. Among authors: rayner t. Nucleic Acids Res. 2007 Jan;35(Database issue):D747-50. doi: 10.1093/nar/gkl995. Epub 2006 Nov 28. Nucleic Acids Res. 2007. PMID: 17132828 Free PMC article.
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. Sarkans U, et al. Among authors: rayner t. Bioinformatics. 2005 Apr 15;21(8):1495-501. doi: 10.1093/bioinformatics/bti157. Epub 2004 Nov 25. Bioinformatics. 2005. PMID: 15564302
The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?".
Sansone SA, Rocca-Serra P, Brandizi M, Brazma A, Field D, Fostel J, Garrow AG, Gilbert J, Goodsaid F, Hardy N, Jones P, Lister A, Miller M, Morrison N, Rayner T, Sklyar N, Taylor C, Tong W, Warner G, Wiemann S; Members of the RSBI Working Group. Sansone SA, et al. Among authors: rayner t. OMICS. 2008 Jun;12(2):143-9. doi: 10.1089/omi.2008.0019. OMICS. 2008. PMID: 18447634
120 results