Genome Biology

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

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 and Martin G Reese*

Genome Biology 2006, 7(Suppl 1):S2 doi:10.1186/gb-2006-7-s1-s2

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Research   Open Access

Synergistic use of plant-prokaryote comparative genomics for functional annotations

Svetlana Gerdes, Basma El Yacoubi, Marc Bailly, Ian K Blaby, Crysten E Blaby-Haas, Linda Jeanguenin, Aurora Lara-Núñez, Anne Pribat, Jeffrey C Waller, Andreas Wilke, Ross Overbeek, Andrew D Hanson, Valérie de Crécy-Lagard BMC Genomics 2011, 12(Suppl 1):S2 (15 June 2011)

Methodology article   Open Access Highly Accessed

A novel and well-defined benchmarking method for second generation read mapping

Manuel Holtgrewe, Anne-Katrin Emde, David Weese, Knut Reinert BMC Bioinformatics 2011, 12:210 (26 May 2011)

Method   Open Access Highly Accessed

A standard variation file format for human genome sequences

Martin G Reese, Barry Moore, Colin Batchelor, Fidel Salas, Fiona Cunningham, Gabor T Marth, Lincoln Stein, Paul Flicek, Mark Yandell, Karen Eilbeck Genome Biology 2010, 11:R88 (26 August 2010)

The genome variation format (GVF) and the 10Gen dataset provide a resource for the standardization of variant files and data analysis.

Methodology article   Open Access Highly Accessed

Quantitative measures for the management and comparison of annotated genomes

Karen Eilbeck, Barry Moore, Carson Holt, Mark Yandell BMC Bioinformatics 2009, 10:67 (23 February 2009)

Method   Open Access Highly Accessed

Annotating genomes with massive-scale RNA sequencing

France Denoeud, Jean-Marc Aury, Corinne Da Silva, Benjamin Noel, Odile Rogier, Massimo Delledonne, Michele Morgante, Giorgio Valle, Patrick Wincker, Claude Scarpelli, Olivier Jaillon, François Artiguenave Genome Biology 2008, 9:R175 (16 December 2008)

A method for de novo genome annotation using high-throughput cDNA sequencing data.

Research article   Open Access Highly Accessed

Identification and correction of abnormal, incomplete and mispredicted proteins in public databases

Alinda Nagy, Hédi Hegyi, Krisztina Farkas, Hedvig Tordai, Evelin Kozma, László Bányai, László Patthy BMC Bioinformatics 2008, 9:353 (27 August 2008)

The MisPred tool improves gene predictions within public databases by using five distinct approaches to detect incomplete or incorrect sequences, such as missing signal peptides or problems with domain integrity.

Method   Open Access Highly Accessed

CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction

Samuel S Gross, Chuong B Do, Marina Sirota, Serafim Batzoglou Genome Biology 2007, 8:R269 (20 December 2007)

CONTRAST is a gene predictor that directly incorporates information from multiple alignments and uses discriminative machine learning techniques to give large improvements in prediction over previous methods.

Minireview   Free

Gene prediction: compare and CONTRAST

Paul Flicek Genome Biology 2007, 8:233 (20 December 2007)

The new gene-prediction program CONTRAST offers significant advances in accuracy over previous methods.

Research   Open Access

Functional constraint and small insertions and deletions in the ENCODE regions of the human genome

Taane G Clark, Toby Andrew, Gregory M Cooper, Elliott H Margulies, James C Mullikin, David J Balding Genome Biology 2007, 8:R180 (4 September 2007)

Indel rates were observed to be reduced approximately twenty-fold in exonic ENCODE regions, five-fold in sequence that exhibits high evolutionary constraint in mammals and up to two-fold in some classes of regulatory elements.

Software   Open Access

An annotation infrastructure for the analysis and interpretation of Affymetrix exon array data

Michał J Okoniewski, Tim Yates, Siân Dibben, Crispin J Miller Genome Biology 2007, 8:R79 (11 May 2007)

An annotation database (X:MAP) and BioConductor/R package (exonmap) have been developed to support fine-grained analysis of exon array data.

Research   Open Access

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)