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 | PubMed ID:16381931 | 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 | PubMed ID:15608235 | 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 | PubMed ID:14681459 | 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. PubMed ID:12519943 | 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. PubMed ID:11752248 | HubMed [nar2002]
  6. Birney E and Ensembl Team. Ensembl: a genome infrastructure. Cold Spring Harb Symp Quant Biol. 2003;68:213-5. PubMed ID:15338620 | 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 | PubMed ID:15145580 | 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 | PubMed ID:15123588 | 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 | PubMed ID:15078858 | 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 | PubMed ID:14707178 | 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 | PubMed ID:12194990 | HubMed [dbreview]
All Medline abstracts: PubMed | HubMed

Also see the Ensembl publication page.

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