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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. Plant Physiol. 2005 Oct;139(2):632-6. doi: 10.1104/pp.105.063156. Plant Physiol. 2005. PMID: 16219923 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: mukherjee g. 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.
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: mukherjee g. 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. Among authors: mukherjee g. 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.
MIAME/Plant - adding value to plant microarrray experiments.
Zimmermann P, Schildknecht B, Craigon D, Garcia-Hernandez M, Gruissem W, May S, Mukherjee G, Parkinson H, Rhee S, Wagner U, Hennig L. Zimmermann P, et al. Among authors: mukherjee g. Plant Methods. 2006 Jan 9;2:1. doi: 10.1186/1746-4811-2-1. Plant Methods. 2006. PMID: 16401339 Free PMC article.
Petabyte-scale innovations at the European Nucleotide Archive.
Cochrane G, Akhtar R, Bonfield J, Bower L, Demiralp F, Faruque N, Gibson R, Hoad G, Hubbard T, Hunter C, Jang M, Juhos S, Leinonen R, Leonard S, Lin Q, Lopez R, Lorenc D, McWilliam H, Mukherjee G, Plaister S, Radhakrishnan R, Robinson S, Sobhany S, Hoopen PT, Vaughan R, Zalunin V, Birney E. Cochrane G, et al. Among authors: mukherjee g. Nucleic Acids Res. 2009 Jan;37(Database issue):D19-25. doi: 10.1093/nar/gkn765. Epub 2008 Oct 31. Nucleic Acids Res. 2009. PMID: 18978013 Free PMC article.
EMBL Nucleotide Sequence Database: developments in 2005.
Cochrane G, Aldebert P, Althorpe N, Andersson M, Baker W, Baldwin A, Bates K, Bhattacharyya S, Browne P, van den Broek A, Castro M, Duggan K, Eberhardt R, Faruque N, Gamble J, Kanz C, Kulikova T, Lee C, Leinonen R, Lin Q, Lombard V, Lopez R, McHale M, McWilliam H, Mukherjee G, Nardone F, Pastor MP, Sobhany S, Stoehr P, Tzouvara K, Vaughan R, Wu D, Zhu W, Apweiler R. Cochrane G, et al. Among authors: mukherjee g. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D10-5. doi: 10.1093/nar/gkj130. Nucleic Acids Res. 2006. PMID: 16381823 Free PMC article.
Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database.
Cochrane G, Akhtar R, Aldebert P, Althorpe N, Baldwin A, Bates K, Bhattacharyya S, Bonfield J, Bower L, Browne P, Castro M, Cox T, Demiralp F, Eberhardt R, Faruque N, Hoad G, Jang M, Kulikova T, Labarga A, Leinonen R, Leonard S, Lin Q, Lopez R, Lorenc D, McWilliam H, Mukherjee G, Nardone F, Plaister S, Robinson S, Sobhany S, Vaughan R, Wu D, Zhu W, Apweiler R, Hubbard T, Birney E. Cochrane G, et al. Among authors: mukherjee g. Nucleic Acids Res. 2008 Jan;36(Database issue):D5-12. doi: 10.1093/nar/gkm1018. Epub 2007 Nov 26. Nucleic Acids Res. 2008. PMID: 18039715 Free PMC article.
EMBL Nucleotide Sequence Database in 2006.
Kulikova T, Akhtar R, Aldebert P, Althorpe N, Andersson M, Baldwin A, Bates K, Bhattacharyya S, Bower L, Browne P, Castro M, Cochrane G, Duggan K, Eberhardt R, Faruque N, Hoad G, Kanz C, Lee C, Leinonen R, Lin Q, Lombard V, Lopez R, Lorenc D, McWilliam H, Mukherjee G, Nardone F, Pastor MP, Plaister S, Sobhany S, Stoehr P, Vaughan R, Wu D, Zhu W, Apweiler R. Kulikova T, et al. Among authors: mukherjee g. Nucleic Acids Res. 2007 Jan;35(Database issue):D16-20. doi: 10.1093/nar/gkl913. Epub 2006 Dec 5. Nucleic Acids Res. 2007. PMID: 17148479 Free PMC article.
GENCODE: the reference human genome annotation for The ENCODE Project.
Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, Mukherjee G, Rajan J, Despacio-Reyes G, Saunders G, Steward C, Harte R, Lin M, Howald C, Tanzer A, Derrien T, Chrast J, Walters N, Balasubramanian S, Pei B, Tress M, Rodriguez JM, Ezkurdia I, van Baren J, Brent M, Haussler D, Kellis M, Valencia A, Reymond A, Gerstein M, Guigó R, Hubbard TJ. Harrow J, et al. Among authors: mukherjee g. Genome Res. 2012 Sep;22(9):1760-74. doi: 10.1101/gr.135350.111. Genome Res. 2012. PMID: 22955987 Free PMC article.
343 results