This article is part of the supplement: EGASP '05: ENCODE Genome Annotation Assessment Project
GENCODE: producing a reference annotation for ENCODE
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* Corresponding author: Jennifer Harrow jla1@sanger.ac.uk
- † Equal contributors
Genome Biology 2006, 7(Suppl 1):S4 doi:10.1186/gb-2006-7-s1-s4
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Research article
Philipp Kapranov, Georges St Laurent, Tal Raz, Fatih Ozsolak, C Patrick Reynolds, Poul HB Sorensen, Gregory Reaman, Patrice Milos, Robert J Arceci, John F Thompson, Timothy J Triche BMC Biology 2010, 8:149 (21 December 2010) There is considerable debate over the prevalence and importance of non-coding, or 'dark matter', RNAs. Kapranov and colleagues contribute with a single-molecule sequencing study, agreeing with previous suggestions that non-coding transcripts are more abundant in the cell than protein-coding RNAs.
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Research
Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing Anna Wetterbom, Adam Ameur, Lars Feuk, Ulf Gyllensten, Lucia Cavelier Genome Biology 2010, 11:R78 (23 July 2010) Sequencing of chimpanzee transcriptomes from different tissues and individuals using RNA-seq reveals novel transcribed regions.
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Commentary
Studying chromosome-wide transcriptional networks: new insights into disease? Philipp Kapranov Genome Medicine 2009, 1:50 (11 May 2009) Recent findings challenge the notion of a gene as a separate, discrete genomic unit, and transcriptional networks will be key to understanding sequence variation data as well as to identifying new biomarkers of disease.
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Minireview
From transcription start site to cell biology Philipp Kapranov Genome Biology 2009, 10:217 (20 April 2009) RNAs transcribed from previously unsuspected start sites add yet greater complexity to the mammalian transcriptome.
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Research
Proteomics studies confirm the presence of alternative protein isoforms on a large scale Michael L Tress, Bernd Bodenmiller, Ruedi Aebersold, Alfonso Valencia Genome Biology 2008, 9:R162 (18 November 2008) Stably expressed alternatively-spliced protein isoforms are produced on a genome-wide scale in Drosophila. |
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Research
Elizabeth A Hart, Mario Caccamo, Jennifer L Harrow, Sean J Humphray, James GR Gilbert, Steve Trevanion, Tim Hubbard, Jane Rogers, Max F Rothschild Genome Biology 2007, 8:R168 (17 August 2007) The sequencing, annotation and comparative analysis of an 8Mb region of pig chromosome 17 allows the coverage and quality of the pig genome sequencing project to be assessed |
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Research
Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA Sarah Djebali, Franck Delaplace, Hugues Crollius Genome Biology 2006, 7(Suppl 1):S7 (7 August 2006) |
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Review
EGASP: the human ENCODE Genome Annotation Assessment Project Roderic Guigó, Paul Flicek, Josep F Abril, Alexandre Reymond, Julien Lagarde, France Denoeud, Stylianos Antonarakis, Michael Ashburner, Vladimir B Bajic, Ewan Birney, Robert Castelo, Eduardo Eyras, Catherine Ucla, Thomas R Gingeras, Jennifer Harrow, Tim Hubbard, Suzanna E Lewis, Martin G Reese Genome Biology 2006, 7(Suppl 1):S2 (7 August 2006) |