Methodology article  

Jetset: selecting the optimal microarray probe set to represent a gene

Qiyuan Li, Nicolai J Birkbak, Balazs Gyorffy, Zoltan Szallasi, Aron C Eklund BMC Bioinformatics 2011, 12:474 (15 December 2011)

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Methodology article  

Consistent annotation of gene expression arrays

Benoît Ballester, Nathan Johnson, Glenn Proctor, Paul Flicek BMC Genomics 2010, 11:294 (11 May 2010)

This article is part of a collection on Ensembl update 2010

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Database  

GATExplorer: Genomic and Transcriptomic Explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs

Alberto Risueño, Celia Fontanillo, Marcel E Dinger, Javier De Las Rivas BMC Bioinformatics 2010, 11:221 (29 April 2010)

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Research article  

Integrating multiple genome annotation databases improves the interpretation of microarray gene expression data

Jun Yin, Sarah McLoughlin, Ian B Jeffery, Antonino Glaviano, Breandan Kennedy, Desmond G Higgins BMC Genomics 2010, 11:50 (20 January 2010)

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Methodology article  

High resolution analysis of the human transcriptome: detection of extensive alternative splicing independent of transcriptional activity

Weiyin Zhou, Margaret A Calciano, Heather Jordan, Michael Brenner, Seth Johnson, Darong Wu, Lin Lei, Diego Pallares, Pascale Beurdeley, Fabien Rouet, Pritmohinder S Gill, Laurent Bracco, Cyril Soucaille, Richard Einstein BMC Genetics 2009, 10:63 (5 October 2009)

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Research  

Comparison of three microarray probe annotation pipelines: differences in strategies and their effect on downstream analysis

Pieter BT Neerincx, Pierrot Casel, Dennis Prickett, Haisheng Nie, Michael Watson, Jack AM Leunissen, Martien AM Groenen, Christophe Klopp BMC Proceedings 2009, 3(Suppl 4):S1 (16 July 2009)

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Methodology article  

Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees

Donna M Toleno, Gabriel Renaud, Tyra G Wolfsberg, Munirul Islam, Derek E Wildman, Kimberly D Siegmund, Joseph G Hacia BMC Bioinformatics 2009, 10:77 (5 March 2009)

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Method  

Quantitative methods for genome-scale analysis of in situ hybridization and correlation with microarray data

Chang-Kyu Lee, Susan M Sunkin, Chihchau Kuan, Carol L Thompson, Sayan Pathak, Lydia Ng, Chris Lau, Shanna Fischer, Marty Mortrud, Cliff Slaughterbeck, Allan Jones, Ed Lein, Michael Hawrylycz Genome Biology 2008, 9:R23 (30 January 2008)

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Software  

Novel definition files for human GeneChips based on GeneAnnot

Francesco Ferrari, Stefania Bortoluzzi, Alessandro Coppe, Alexandra Sirota, Marilyn Safran, Michael Shmoish, Sergio Ferrari, Doron Lancet, Gian Danieli, Silvio Bicciato BMC Bioinformatics 2007, 8:446 (15 November 2007)

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Research article  

A detailed transcript-level probe annotation reveals alternative splicing based microarray platform differences

Joseph C Lee, David Stiles, Jun Lu, Margaret C Cam BMC Genomics 2007, 8:284 (20 August 2007)

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