Ensembl 2011

The Ensembl project (http://www.ensembl.org) seeks to enable genomic science by providing high quality, integrated annotation on chordate and selected eukaryotic genomes within a consistent and accessible infrastructure. All supported species include comprehensive, evidence-based gene annotations and a selected set of genomes includes additional data focused on variation, comparative, evolutionary, functional and regulatory annotation. The most advanced resources are provided for key species including human, mouse, rat and zebrafish reflecting the popularity and importance of these species in biomedical research. As of Ensembl release 59 (August 2010), 56 species are supported of which 5 have been added in the past year. Since our previous report, we have substantially improved the presentation and integration of both data of disease relevance and the regulatory state of different cell types.

Daniel Rios | Yuan Chen | Paul Flicek | Fiona Cunningham | Maurice Hendrix | Xosé M. Fernández-Suárez | Albert J. Vilella | Leo Gordon | Simon White | Javier Herrero | Tim J. P. Hubbard | Ewan Birney | Nathan Johnson | Daniel Sobral | Peter Clapham | Y. Amy Tang | Daniel Barrell | Richard Durbin | Kathryn Beal | Stephen Keenan | William M. McLaren | Graham R. S. Ritchie | Magali Ruffier | Eugene Kulesha | Andreas Kähäri | Michael Schuster | Jan Vogel | Pontus Larsson | Ian Dunham | Anne Parker | Rhoda Kinsella | Jana Vandrovcova | Glenn Proctor | Bronwen L. Aken | Susan Fairley | Thibaut Hourlier | Felix Kokocinski | Amonida Zadissa | Stephen M. J. Searle | Stephen J. Trevanion | Guy Coates | Damian Keefe | Ian Longden | M. Ridwan Amode | Stephen Fitzgerald | Harpreet Singh Riat | Steven P. Wilder | Giulietta Spudich | Bert Overduin | Simon Brent | Bethan Pritchard | Jorge Zamora | R. Durbin | E. Birney | F. Kokocinski | D. Barrell | A. Zadissa | S. Searle | T. Hubbard | F. Cunningham | W. McLaren | G. Ritchie | P. Flicek | I. Dunham | Damian Keefe | Yuan Chen | Kathryn Beal | Guy Coates | Stephen Fitzgerald | Nathan Johnson | Andreas Kähäri | Eugene Kulesha | I. Longden | B. Overduin | Anne Parker | Bethan Pritchard | Daniel Rios | Michael Schuster | G. Spudich | S. Trevanion | J. Vogel | S. White | X. M. Fernández-Suárez | Javier Herrero | G. Proctor | S. Keenan | Magali Ruffier | H. Riat | S. Wilder | D. Sobral | R. Kinsella | Simon Brent | M. Amode | P. Clapham | Leo Gordon | Thibaut Hourlier | Pontus Larsson | S. Fairley | Y. A. Tang | J. Vandrovcova | S. Brent | Jorge Zamora | Fiona Cunningham | Maurice Hendrix | Kathryn M Beal | Ian Longden | Giulietta Spudich

[1]  Baris E. Suzek,et al.  The Universal Protein Resource (UniProt) in 2010 , 2009, Nucleic Acids Res..

[2]  James A. Smith,et al.  Using caching and optimization techniques to improve performance of the Ensembl website , 2010, BMC Bioinformatics.

[3]  Sean R. Eddy,et al.  The Distributed Annotation System , 2001, BMC Bioinformatics.

[4]  J. Harrow,et al.  GENCODE: producing a reference annotation for ENCODE , 2006, Genome Biology.

[5]  Sue Povey,et al.  The HGNC Database in 2008: a resource for the human genome , 2007, Nucleic Acids Res..

[6]  David J. Arenillas,et al.  JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles , 2009, Nucleic Acids Res..

[7]  William Stafford Noble,et al.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project , 2007, Nature.

[8]  E. Birney,et al.  The Ensembl core software libraries. , 2004, Genome research.

[9]  R. E. Tully,et al.  Locus Reference Genomic sequences: an improved basis for describing human DNA variants , 2010, Genome Medicine.

[10]  Daniel Rios,et al.  Bioinformatics Applications Note Databases and Ontologies Deriving the Consequences of Genomic Variants with the Ensembl Api and Snp Effect Predictor , 2022 .

[11]  P. Flicek,et al.  Consistent annotation of gene expression arrays , 2010, BMC Genomics.

[12]  Albert J. Vilella,et al.  EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. , 2009, Genome research.

[13]  Jonathan M. Mudge,et al.  The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. , 2009, Genome research.

[14]  P. Stenson,et al.  The Human Gene Mutation Database (HGMD) and Its Exploitation in the Study of Mutational Mechanisms , 2005, Current protocols in bioinformatics.

[15]  Laurent Gil,et al.  Ensembl variation resources , 2010, BMC Genomics.

[16]  E. Birney,et al.  Genome-wide nucleotide-level mammalian ancestor reconstruction. , 2008, Genome research.

[17]  E. Birney,et al.  Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. , 2008, Genome research.

[18]  Albert J. Vilella,et al.  The genome of a songbird , 2010, Nature.

[19]  Xosé M Fernández-Suárez,et al.  Touring Ensembl: A practical guide to genome browsing , 2010, BMC Genomics.

[20]  Daniel Rios,et al.  A database and API for variation, dense genotyping and resequencing data , 2010, BMC Bioinformatics.

[21]  Gautier Koscielny,et al.  Ensembl’s 10th year , 2009, Nucleic Acids Res..

[22]  S. Batzoglou,et al.  Distribution and intensity of constraint in mammalian genomic sequence. , 2005, Genome research.

[23]  Damian Smedley,et al.  BioMart – biological queries made easy , 2009, BMC Genomics.

[24]  Albert J. Vilella,et al.  Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis , 2010, PLoS biology.

[25]  Michael DiCuccio,et al.  Public data archives for genomic structural variation , 2010, Nature Genetics.

[26]  Benedict Paten,et al.  Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment , 2009, Bioinform..

[27]  Paul Flicek,et al.  eHive: An Artificial Intelligence workflow system for genomic analysis , 2010, BMC Bioinformatics.