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Items: 1 to 20 of 151

1.

A database and API for variation, dense genotyping and resequencing data.

Rios D, McLaren WM, Chen Y, Birney E, Stabenau A, Flicek P, Cunningham F.

BMC Bioinformatics. 2010 May 11;11:238. doi: 10.1186/1471-2105-11-238.

2.

Ensembl variation resources.

Chen Y, Cunningham F, Rios D, McLaren WM, Smith J, Pritchard B, Spudich GM, Brent S, Kulesha E, Marin-Garcia P, Smedley D, Birney E, Flicek P.

BMC Genomics. 2010 May 11;11:293. doi: 10.1186/1471-2164-11-293.

3.

Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser.

Stenger JE, Xu H, Haynes C, Hauser ER, Pericak-Vance M, Goldschmidt-Clermont PJ, Vance JM.

BMC Bioinformatics. 2005 Apr 12;6:95.

4.

Ensembl 2002: accommodating comparative genomics.

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, Birney E.

Nucleic Acids Res. 2003 Jan 1;31(1):38-42.

5.

Ensembl's 10th year.

Flicek P, Aken BL, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Gräf S, Haider S, Hammond M, Howe K, Jenkinson A, Johnson N, Kähäri A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Koscielny G, Kulesha E, Lawson D, Longden I, Massingham T, McLaren W, Megy K, Overduin B, Pritchard B, Rios D, Ruffier M, Schuster M, Slater G, Smedley D, Spudich G, Tang YA, Trevanion S, Vilella A, Vogel J, White S, Wilder SP, Zadissa A, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Herrero J, Hubbard TJ, Parker A, Proctor G, Smith J, Searle SM.

Nucleic Acids Res. 2010 Jan;38(Database issue):D557-62. doi: 10.1093/nar/gkp972. Epub 2009 Nov 11.

6.

The Ensembl genome database project.

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, Clamp M.

Nucleic Acids Res. 2002 Jan 1;30(1):38-41.

7.

ArkMAP: integrating genomic maps across species and data sources.

Paterson T, Law A.

BMC Bioinformatics. 2013 Aug 13;14:246. doi: 10.1186/1471-2105-14-246.

8.

Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation.

Ruffier M, Kähäri A, Komorowska M, Keenan S, Laird M, Longden I, Proctor G, Searle S, Staines D, Taylor K, Vullo A, Yates A, Zerbino D, Flicek P.

Database (Oxford). 2017 Jan 1;2017(1). doi: 10.1093/database/bax020.

9.

Ensembl 2004.

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, Hubbard T.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D468-70.

10.

Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl.

Sand O, Thomas-Chollier M, van Helden J.

Bioinformatics. 2009 Oct 15;25(20):2739-40. doi: 10.1093/bioinformatics/btp519. Epub 2009 Aug 31.

PMID:
19720677
11.

Ensembl regulation resources.

Zerbino DR, Johnson N, Juetteman T, Sheppard D, Wilder SP, Lavidas I, Nuhn M, Perry E, Raffaillac-Desfosses Q, Sobral D, Keefe D, Gräf S, Ahmed I, Kinsella R, Pritchard B, Brent S, Amode R, Parker A, Trevanion S, Birney E, Dunham I, Flicek P.

Database (Oxford). 2016 Feb 17;2016. pii: bav119. doi: 10.1093/database/bav119. Print 2016.

12.

Ensembl comparative genomics resources.

Herrero J, Muffato M, Beal K, Fitzgerald S, Gordon L, Pignatelli M, Vilella AJ, Searle SM, Amode R, Brent S, Spooner W, Kulesha E, Yates A, Flicek P.

Database (Oxford). 2016 Feb 20;2016. pii: bav096. doi: 10.1093/database/bav096. Print 2016. Erratum in: Database (Oxford). 2016;2016. pii: baw053. doi: 10.1093/database/baw053.

13.
14.

Ensembl 2008.

Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Eyre T, Fitzgerald S, Fernandez-Banet J, Gräf S, Haider S, Hammond M, Holland R, Howe KL, Howe K, Johnson N, Jenkinson A, Kähäri A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Slater G, Smedley D, Spudich G, Trevanion S, Vilella AJ, Vogel J, White S, Wood M, Birney E, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Herrero J, Hubbard TJ, Kasprzyk A, Proctor G, Smith J, Ureta-Vidal A, Searle S.

Nucleic Acids Res. 2008 Jan;36(Database issue):D707-14. Epub 2007 Nov 13.

15.

Ensembl 2017.

Aken BL, Achuthan P, Akanni W, Amode MR, Bernsdorff F, Bhai J, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Juettemann T, Keenan S, Laird MR, Lavidas I, Maurel T, McLaren W, Moore B, Murphy DN, Nag R, Newman V, Nuhn M, Ong CK, Parker A, Patricio M, Riat HS, Sheppard D, Sparrow H, Taylor K, Thormann A, Vullo A, Walts B, Wilder SP, Zadissa A, Kostadima M, Martin FJ, Muffato M, Perry E, Ruffier M, Staines DM, Trevanion SJ, Cunningham F, Yates A, Zerbino DR, Flicek P.

Nucleic Acids Res. 2017 Jan 4;45(D1):D635-D642. doi: 10.1093/nar/gkw1104. Epub 2016 Nov 28.

16.

Ensembl 2009.

Hubbard TJ, Aken BL, Ayling S, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Clarke L, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Graf S, Haider S, Hammond M, Holland R, Howe K, Jenkinson A, Johnson N, Kahari A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Rios D, Schuster M, Slater G, Smedley D, Spooner W, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wilder S, Zadissa A, Birney E, Cunningham F, Curwen V, Durbin R, Fernandez-Suarez XM, Herrero J, Kasprzyk A, Proctor G, Smith J, Searle S, Flicek P.

Nucleic Acids Res. 2009 Jan;37(Database issue):D690-7. doi: 10.1093/nar/gkn828. Epub 2008 Nov 25.

17.

Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomics Data.

Bolser D, Staines DM, Pritchard E, Kersey P.

Methods Mol Biol. 2016;1374:115-40. doi: 10.1007/978-1-4939-3167-5_6.

PMID:
26519403
18.

Ensembl 2005.

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, Birney E.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D447-53.

19.

JEnsembl: a version-aware Java API to Ensembl data systems.

Paterson T, Law A.

Bioinformatics. 2012 Nov 1;28(21):2724-31. doi: 10.1093/bioinformatics/bts525. Epub 2012 Sep 3.

20.

An overview of Ensembl.

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, Clamp M.

Genome Res. 2004 May;14(5):925-8. Epub 2004 Apr 12. Review.

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