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Annotation of environmental OMICS data: application to the transcriptomics domain.
Morrison N, Wood AJ, Hancock D, Shah S, Hakes L, Gray T, Tiwari B, Kille P, Cossins A, Hegarty M, Allen MJ, Wilson WH, Olive P, Last K, Kramer C, Bailhache T, Reeves J, Pallett D, Warne J, Nashar K, Parkinson H, Sansone SA, Rocca-Serra P, Stevens R, Snape J, Brass A, Field D. Morrison N, et al. Among authors: parkinson h. OMICS. 2006 Summer;10(2):172-8. doi: 10.1089/omi.2006.10.172. OMICS. 2006. PMID: 16901223 Review.
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. Brazma A, et al. Among authors: parkinson h. Nucleic Acids Res. 2003 Jan 1;31(1):68-71. doi: 10.1093/nar/gkg091. Nucleic Acids Res. 2003. PMID: 12519949 Free PMC article.
ArrayExpress: a public database of gene expression data at EBI.
Rocca-Serra P, Brazma A, Parkinson H, Sarkans U, Shojatalab M, Contrino S, Vilo J, Abeygunawardena N, Mukherjee G, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Sansone SA. Rocca-Serra P, et al. Among authors: parkinson h. C R Biol. 2003 Oct-Nov;326(10-11):1075-8. doi: 10.1016/j.crvi.2003.09.026. C R Biol. 2003. PMID: 14744115 Free article.
Submission of microarray data to public repositories.
Ball CA, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, Taylor R, White J, Winegarden N. Ball CA, et al. Among authors: parkinson h. PLoS Biol. 2004 Sep;2(9):E317. doi: 10.1371/journal.pbio.0020317. Epub 2004 Aug 31. PLoS Biol. 2004. PMID: 15340489 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: parkinson h. Bioinformatics. 2005 Apr 15;21(8):1495-501. doi: 10.1093/bioinformatics/bti157. Epub 2004 Nov 25. Bioinformatics. 2005. PMID: 15564302
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. 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.
The MGED Ontology: a resource for semantics-based description of microarray experiments.
Whetzel PL, Parkinson H, Causton HC, Fan L, Fostel J, Fragoso G, Game L, Heiskanen M, Morrison N, Rocca-Serra P, Sansone SA, Taylor C, White J, Stoeckert CJ Jr. Whetzel PL, et al. Among authors: parkinson h. Bioinformatics. 2006 Apr 1;22(7):866-73. doi: 10.1093/bioinformatics/btl005. Epub 2006 Jan 21. Bioinformatics. 2006. PMID: 16428806
Development of FuGO: an ontology for functional genomics investigations.
Whetzel PL, Brinkman RR, Causton HC, Fan L, Field D, Fostel J, Fragoso G, Gray T, Heiskanen M, Hernandez-Boussard T, Morrison N, Parkinson H, Rocca-Serra P, Sansone SA, Schober D, Smith B, Stevens R, Stoeckert CJ Jr, Taylor C, White J, Wood A; FuGO Working Group. Whetzel PL, et al. Among authors: parkinson h. OMICS. 2006 Summer;10(2):199-204. doi: 10.1089/omi.2006.10.199. OMICS. 2006. PMID: 16901226 Free PMC article. Review.
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. Among authors: parkinson h. 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. 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.
189 results