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This article is part of the supplement: EGASP '05: ENCODE Genome Annotation Assessment Project

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AceView: a comprehensive cDNA-supported gene and transcripts annotation

Danielle Thierry-Mieg* and Jean Thierry-Mieg

Genome Biology 2006, 7(Suppl 1):S12 doi:10.1186/gb-2006-7-s1-s12

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Transcriptome sequencing of the Microarray Quality Control (MAQC) RNA reference samples using next generation sequencing

Shrinivasrao P Mane, Clive Evans, Kristal L Cooper, Oswald R Crasta, Otto Folkerts, Stephen K Hutchison, Timothy T Harkins, Danielle Thierry-Mieg, Jean Thierry-Mieg, Roderick V Jensen BMC Genomics 2009, 10:264 (12 June 2009)

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Profile analysis and prediction of tissue-specific CpG island methylation classes

Christopher Previti, Oscar Harari, Igor Zwir, Coral del Val BMC Bioinformatics 2009, 10:116 (21 April 2009)

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Studying alternative splicing regulatory networks through partial correlation analysis

Liang Chen, Sika Zheng Genome Biology 2009, 10:R3 (9 January 2009)

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The identification of links between exons and their regulators or targets and between co-spliced exons in human, mouse and rat provides novel insights into the alternative splicing regulatory network.

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SpliceCenter: A suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies

Michael C Ryan, Barry R Zeeberg, Natasha J Caplen, James A Cleland, Ari B Kahn, Hongfang Liu, John N Weinstein BMC Bioinformatics 2008, 9:313 (18 July 2008)

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The metazoan history of the COE transcription factors. Selection of a variant HLH motif by mandatory inclusion of a duplicated exon in vertebrates

Virginie Daburon, Sébastien Mella, Jean-Louis Plouhinec, Sylvie Mazan, Michèle Crozatier, Alain Vincent BMC Evolutionary Biology 2008, 8:131 (2 May 2008)

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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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Decline of nucleotide excision repair capacity in aging Caenorhabditis elegans

Joel N Meyer, Windy A Boyd, Gregory A Azzam, Astrid C Haugen, Jonathan H Freedman, Bennett Van Houten Genome Biology 2007, 8:R70 (1 May 2007)

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Repair of UVC-induced DNA damage in Caenorhabditis elegans is similar kinetically and genetically to repair in humans, and it slows significantly in aging C. elegans.

Methodology article   Open Access

Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays

Jun Lu, Joseph C Lee, Marc L Salit, Margaret C Cam BMC Bioinformatics 2007, 8:108 (29 March 2007)

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