EnsEMBL

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EnsEMBL (or Ensembl now I think), is the EBI-Sanger Centre Welcome Trust funded project for vertebrate genome annotation and comparative analyses. This extremely ambitious project has succeeded in dramatic form, providing a freely available annotation of the human genome while also making the software and data open source. The project continues to grow and improve as intraspecific polymorphism data is generated highlighting variation with a species and genome sequences of additional species providing key insight into the conservation and evolution of genomes. The Ensembl group provides a critical service of high quality annotation of these genome sequences in a both human browseable and programmatic form to allow biologist and bioinformatician alike to access the data.

Misc Trivia

BioPerl leader Ewan Birney helped conceive and lead Ensembl since its inception. Many other BioPerl contributors and users are based in this project.

References

  1. Birney E, Andrews D, Caccamo M, Chen Y, Clarke L, Coates G, Cox T, Cunningham F, Curwen V, Cutts T, Down T, Durbin R, Fernandez-Suarez XM, Flicek P, Gräf S, Hammond M, Herrero J, Howe K, Iyer V, Jekosch K, Kähäri A, Kasprzyk A, Keefe D, Kokocinski F, Kulesha E, London D, Longden I, Melsopp C, Meidl P, Overduin B, Parker A, Proctor G, Prlic A, Rae M, Rios D, Redmond S, Schuster M, Sealy I, Searle S, Severin J, Slater G, Smedley D, Smith J, Stabenau A, Stalker J, Trevanion S, Ureta-Vidal A, Vogel J, White S, Woodwark C, and Hubbard TJ. Ensembl 2006. Nucleic Acids Res 2006 Jan 1; 34(Database issue) D556-61. doi:10.1093/nar/gkj133 pmid:16381931. PubMed HubMed [nar2006]
  2. Hubbard T, Andrews D, Caccamo M, Cameron G, Chen Y, Clamp M, Clarke L, Coates G, Cox T, Cunningham F, Curwen V, Cutts T, Down T, Durbin R, Fernandez-Suarez XM, Gilbert J, Hammond M, Herrero J, Hotz H, Howe K, Iyer V, Jekosch K, Kahari A, Kasprzyk A, Keefe D, Keenan S, Kokocinsci F, London D, Longden I, McVicker G, Melsopp C, Meidl P, Potter S, Proctor G, Rae M, Rios D, Schuster M, Searle S, Severin J, Slater G, Smedley D, Smith J, Spooner W, Stabenau A, Stalker J, Storey R, Trevanion S, Ureta-Vidal A, Vogel J, White S, Woodwark C, and Birney E. Ensembl 2005. Nucleic Acids Res 2005 Jan 1; 33(Database issue) D447-53. doi:10.1093/nar/gki138 pmid:15608235. PubMed HubMed [nar2005]
  3. Birney E, Andrews D, Bevan P, Caccamo M, Cameron G, Chen Y, Clarke L, Coates G, Cox T, Cuff J, Curwen V, Cutts T, Down T, Durbin R, Eyras E, Fernandez-Suarez XM, Gane P, Gibbins B, Gilbert J, Hammond M, Hotz H, Iyer V, Kahari A, Jekosch K, Kasprzyk A, Keefe D, Keenan S, Lehvaslaiho H, McVicker G, Melsopp C, Meidl P, Mongin E, Pettett R, Potter S, Proctor G, Rae M, Searle S, Slater G, Smedley D, Smith J, Spooner W, Stabenau A, Stalker J, Storey R, Ureta-Vidal A, Woodwark C, Clamp M, and Hubbard T. Ensembl 2004. Nucleic Acids Res 2004 Jan 1; 32(Database issue) D468-70. doi:10.1093/nar/gkh038 pmid:14681459. PubMed HubMed [nar2004]
  4. Clamp M, Andrews D, Barker D, Bevan P, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Hubbard T, Kasprzyk A, Keefe D, Lehvaslaiho H, Iyer V, Melsopp C, Mongin E, Pettett R, Potter S, Rust A, Schmidt E, Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E, Ureta-Vidal A, Vastrik I, and Birney E. Ensembl 2002: accommodating comparative genomics. Nucleic Acids Res 2003 Jan 1; 31(1) 38-42. pmid:12519943. PubMed HubMed [nar2003]
  5. Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Huminiecki L, Kasprzyk A, Lehvaslaiho H, Lijnzaad P, Melsopp C, Mongin E, Pettett R, Pocock M, Potter S, Rust A, Schmidt E, Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E, Ureta-Vidal A, Vastrik I, and Clamp M. The Ensembl genome database project. Nucleic Acids Res 2002 Jan 1; 30(1) 38-41. pmid:11752248. PubMed HubMed [nar2002]
  6. Birney E. Ensembl: a genome infrastructure. Cold Spring Harb Symp Quant Biol 2003; 68 213-5. pmid:15338620. PubMed HubMed [cshsqb03]
  7. Hammond MP and Birney E. Genome information resources - developments at Ensembl. Trends Genet 2004 Jun; 20(6) 268-72. doi:10.1016/j.tig.2004.04.002 pmid:15145580. PubMed HubMed [tig04]
  8. Stabenau A, McVicker G, Melsopp C, Proctor G, Clamp M, and Birney E. The Ensembl core software libraries. Genome Res 2004 May; 14(5) 929-33. doi:10.1101/gr.1857204 pmid:15123588. PubMed HubMed [corelibs]
  9. Birney E, Andrews TD, Bevan P, Caccamo M, Chen Y, Clarke L, Coates G, Cuff J, Curwen V, Cutts T, Down T, Eyras E, Fernandez-Suarez XM, Gane P, Gibbins B, Gilbert J, Hammond M, Hotz HR, Iyer V, Jekosch K, Kahari A, Kasprzyk A, Keefe D, Keenan S, Lehvaslaiho H, McVicker G, Melsopp C, Meidl P, Mongin E, Pettett R, Potter S, Proctor G, Rae M, Searle S, Slater G, Smedley D, Smith J, Spooner W, Stabenau A, Stalker J, Storey R, Ureta-Vidal A, Woodwark KC, Cameron G, Durbin R, Cox A, Hubbard T, and Clamp M. An overview of Ensembl. Genome Res 2004 May; 14(5) 925-8. doi:10.1101/gr.1860604 pmid:15078858. PubMed HubMed [overview]
  10. Kasprzyk A, Keefe D, Smedley D, London D, Spooner W, Melsopp C, Hammond M, Rocca-Serra P, Cox T, and Birney E. EnsMart: a generic system for fast and flexible access to biological data. Genome Res 2004 Jan; 14(1) 160-9. doi:10.1101/gr.1645104 pmid:14707178. PubMed HubMed [ensmart]
  11. Birney E, Clamp M, and Hubbard T. Databases and tools for browsing genomes. Annu Rev Genomics Hum Genet 2002; 3 293-310. doi:10.1146/annurev.genom.3.030502.101529 pmid:12194990. PubMed HubMed [dbreview]
All Medline abstracts: PubMed HubMed

Also see the Ensembl publication page.

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