Literature DB >> 15078858

An overview of Ensembl.

Ewan Birney1, T Daniel Andrews, Paul Bevan, Mario Caccamo, Yuan Chen, Laura Clarke, Guy Coates, James Cuff, Val Curwen, Tim Cutts, Thomas Down, Eduardo Eyras, Xose M Fernandez-Suarez, Paul Gane, Brian Gibbins, James Gilbert, Martin Hammond, Hans-Rudolf Hotz, Vivek Iyer, Kerstin Jekosch, Andreas Kahari, Arek Kasprzyk, Damian Keefe, Stephen Keenan, Heikki Lehvaslaiho, Graham McVicker, Craig Melsopp, Patrick Meidl, Emmanuel Mongin, Roger Pettett, Simon Potter, Glenn Proctor, Mark Rae, Steve Searle, Guy Slater, Damian Smedley, James Smith, Will Spooner, Arne Stabenau, James Stalker, Roy Storey, Abel Ureta-Vidal, K Cara Woodwark, Graham Cameron, Richard Durbin, Anthony Cox, Tim Hubbard, Michele Clamp.   

Abstract

Ensembl (http://www.ensembl.org/) is a bioinformatics project to organize biological information around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of individual genomes, and of the synteny and orthology relationships between them. It is also a framework for integration of any biological data that can be mapped onto features derived from the genomic sequence. Ensembl is available as an interactive Web site, a set of flat files, and as a complete, portable open source software system for handling genomes. All data are provided without restriction, and code is freely available. Ensembl's aims are to continue to "widen" this biological integration to include other model organisms relevant to understanding human biology as they become available; to "deepen" this integration to provide an ever more seamless linkage between equivalent components in different species; and to provide further classification of functional elements in the genome that have been previously elusive.

Entities:  

Mesh:

Year:  2004        PMID: 15078858      PMCID: PMC479121          DOI: 10.1101/gr.1860604

Source DB:  PubMed          Journal:  Genome Res        ISSN: 1088-9051            Impact factor:   9.043


  18 in total

1.  The UCSC Table Browser data retrieval tool.

Authors:  Donna Karolchik; Angela S Hinrichs; Terrence S Furey; Krishna M Roskin; Charles W Sugnet; David Haussler; W James Kent
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

2.  EnsMart: a generic system for fast and flexible access to biological data.

Authors:  Arek Kasprzyk; Damian Keefe; Damian Smedley; Darin London; William Spooner; Craig Melsopp; Martin Hammond; Philippe Rocca-Serra; Tony Cox; Ewan Birney
Journal:  Genome Res       Date:  2004-01       Impact factor: 9.043

3.  The Ensembl analysis pipeline.

Authors:  Simon C Potter; Laura Clarke; Val Curwen; Stephen Keenan; Emmanuel Mongin; Stephen M J Searle; Arne Stabenau; Roy Storey; Michele Clamp
Journal:  Genome Res       Date:  2004-05       Impact factor: 9.043

4.  The Ensembl Web site: mechanics of a genome browser.

Authors:  James Stalker; Brian Gibbins; Patrick Meidl; James Smith; William Spooner; Hans-Rudolf Hotz; Antony V Cox
Journal:  Genome Res       Date:  2004-05       Impact factor: 9.043

Review 5.  The Ensembl core software libraries.

Authors:  Arne Stabenau; Graham McVicker; Craig Melsopp; Glenn Proctor; Michele Clamp; Ewan Birney
Journal:  Genome Res       Date:  2004-05       Impact factor: 9.043

6.  The Ensembl automatic gene annotation system.

Authors:  Val Curwen; Eduardo Eyras; T Daniel Andrews; Laura Clarke; Emmanuel Mongin; Steven M J Searle; Michele Clamp
Journal:  Genome Res       Date:  2004-05       Impact factor: 9.043

7.  The Ensembl computing architecture.

Authors:  James A Cuff; Guy M P Coates; Tim J R Cutts; Mark Rae
Journal:  Genome Res       Date:  2004-05       Impact factor: 9.043

8.  WormBase: network access to the genome and biology of Caenorhabditis elegans.

Authors:  L Stein; P Sternberg; R Durbin; J Thierry-Mieg; J Spieth
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

9.  The otter annotation system.

Authors:  Stephen M J Searle; James Gilbert; Vivek Iyer; Michele Clamp
Journal:  Genome Res       Date:  2004-05       Impact factor: 9.043

Review 10.  The Anopheles gambiae genome: an update.

Authors:  Emmanuel Mongin; Christos Louis; Robert A Holt; Ewan Birney; Frank H Collins
Journal:  Trends Parasitol       Date:  2004-02
View more
  180 in total

1.  In silico identification of transcriptional regulators associated with c-Myc.

Authors:  Ran Elkon; Karen I Zeller; Chaim Linhart; Chi V Dang; Ron Shamir; Yosef Shiloh
Journal:  Nucleic Acids Res       Date:  2004-09-23       Impact factor: 16.971

2.  Patterns of gene divergence and VL promoter activity in immunoglobulin light chain clusters of the channel catfish.

Authors:  Julia Cay Jones; Seyed H Ghaffari; Craig J Lobb
Journal:  Immunogenetics       Date:  2004-09-03       Impact factor: 2.846

3.  Wobble base-pairing slows in vivo translation elongation in metazoans.

Authors:  Michael Stadler; Andrew Fire
Journal:  RNA       Date:  2011-11-01       Impact factor: 4.942

4.  Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage.

Authors:  Lukas Chavez; Justyna Jozefczuk; Christina Grimm; Jörn Dietrich; Bernd Timmermann; Hans Lehrach; Ralf Herwig; James Adjaye
Journal:  Genome Res       Date:  2010-08-27       Impact factor: 9.043

5.  Locus category based analysis of a large genome-wide association study of rheumatoid arthritis.

Authors:  Jan Freudenberg; Annette T Lee; Katherine A Siminovitch; Christopher I Amos; David Ballard; Wentian Li; Peter K Gregersen
Journal:  Hum Mol Genet       Date:  2010-07-16       Impact factor: 6.150

6.  A predicted interactome for Arabidopsis.

Authors:  Jane Geisler-Lee; Nicholas O'Toole; Ron Ammar; Nicholas J Provart; A Harvey Millar; Matt Geisler
Journal:  Plant Physiol       Date:  2007-08-03       Impact factor: 8.340

7.  EAnnot: a genome annotation tool using experimental evidence.

Authors:  Li Ding; Aniko Sabo; Nicolas Berkowicz; Rekha R Meyer; Yoram Shotland; Mark R Johnson; Kymberlie H Pepin; Richard K Wilson; John Spieth
Journal:  Genome Res       Date:  2004-12       Impact factor: 9.043

8.  The International HapMap Project Web site.

Authors:  Gudmundur A Thorisson; Albert V Smith; Lalitha Krishnan; Lincoln D Stein
Journal:  Genome Res       Date:  2005-11       Impact factor: 9.043

9.  Significant gene content variation characterizes the genomes of inbred mouse strains.

Authors:  Gene Cutler; Lisa A Marshall; Ni Chin; Helene Baribault; Paul D Kassner
Journal:  Genome Res       Date:  2007-11-07       Impact factor: 9.043

10.  Human self-protein CD8+ T-cell epitopes are both positively and negatively selected.

Authors:  Michal Almani; Shai Raffaeli; Tal Vider-Shalit; Lea Tsaban; Vered Fishbain; Yoram Louzoun
Journal:  Eur J Immunol       Date:  2009-04       Impact factor: 5.532

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.