Scientific Publications

Citing Ensembl

If you would like to include a general reference to the Ensembl system in your work, we recommend citing the most recent overview article. For more specialised aspects of our system, further articles are listed below.

Citing Ensembl Data

Since release 25, all Ensembl releases are being archived as fully functional sites for about two years. This makes it possible to accurately cite data being referred to in a paper, even though the main Ensembl site is being continuously updated (currently release 50 - Jul 2008). For more information see http://archive.ensembl.org/.

The Ensembl Genome Browser and Annotation System

Genome Research Ensembl Special

The May 2004 issue of Genome Research includes an Ensembl special covering detailed aspects of the Ensembl web site, the underlying scalable database system for storing genome sequence and annotation information, as well as the automated genome analysis and annotation pipeline.

Ewan Birney, 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, and Michele Clamp
An Overview of Ensembl
Genome Res. 2004 May; 14(5):925-928.
[Abstract] [Full text]
Arne Stabenau, Graham McVicker, Craig Melsopp, Glenn Proctor, Michele Clamp, and Ewan Birney
The Ensembl Core Software Libraries
Genome Res. 2004 May; 14(5):929-933.
[Abstract] [Full text]
Simon C. Potter, Laura Clarke, Val Curwen, Stephen Keenan, Emmanuel Mongin, Stephen M.J. Searle, Arne Stabenau, Roy Storey, and Michele Clamp
The Ensembl Analysis Pipeline
Genome Res. 2004 May; 14(5):934-941.
[Abstract] [Full text]
Val Curwen, Eduardo Eyras, T. Daniel Andrews, Laura Clarke, Emmanuel Mongin, Steven M.J. Searle, and Michele Clamp
The Ensembl Automatic Gene Annotation System
Genome Res. 2004 May; 14(5):942-950.
[Abstract] [Full text]
James Stalker, Brian Gibbins, Patrick Meidl, James Smith, William Spooner, Hans-Rudolf Hotz, and Antony V. Cox
The Ensembl Web Site: Mechanics of a Genome Browser
Genome Res. 2004 May; 14(5):951-955.
[Abstract] [Full text]
Stephen B. Montgomery, Tamara Astakhova, Mikhail Bilenky, Ewan Birney, Tony Fu, Maik Hassel, Craig Melsopp, Marcin Rak, A. Gordon Robertson, Monica Sleumer, Asim S. Siddiqui, and Steven J.M. Jones
Sockeye: A 3D Environment for Comparative Genomics
Genome Res. 2004 May; 14(5):956-962.
[Abstract] [Full text]
Stephen M.J. Searle, James Gilbert, Vivek Iyer, and Michele Clamp
The Otter Annotation System
Genome Res. 2004 May; 14(5):963-970.
[Abstract] [Full text]
James A. Cuff, Guy M.P. Coates, Tim J.R. Cutts, and Mark Rae
The Ensembl Computing Architecture
Genome Res. 2004 May; 14(5):971-975.
[Abstract] [Full text]
Eduardo Eyras, Mario Caccamo, Val Curwen, and Michele Clamp
ESTGenes: Alternative Splicing From ESTs in Ensembl
Genome Res. 2004 May; 14(5):976-987.
[Abstract] [Full text]
Ewan Birney, Michele Clamp, and Richard Durbin GeneWise and Genomewise
Genome Res. 2004 May; 14(5):988-995.
[Abstract] [Full text]

Protocols to navigate Ensembl

Giulietta Spudich, Xosé M. Fernández-Suárez, and Ewan Birney
Genome Browsing with Ensembl: a practical overview
Brief Funct Genomic Proteomic, 2007 Sept; 6: 202-219
Xosé M. Fernández-Suárez and Michael K. Schuster
Using the Ensembl Genome Server to Browse Genomic Sequence Data.
UNIT 1.15 in Current Protocols in Bioinformatics, Supplement 16, January 2007.

Recent Developments

T. J. P. Hubbard, B. L. Aken, K. Beal1, B. Ballester1, M. Caccamo, Y. Chen, L. Clarke, G. Coates, F. Cunningham, T. Cutts, T. Down, S. C. Dyer, S. Fitzgerald, J. Fernandez-Banet, S. Graf, S. Haider, M. Hammond, J. Herrero, R. Holland, K. Howe, K. Howe, N. Johnson, A. Kahari, D. Keefe, F. Kokocinski, E. Kulesha, D. Lawson, I. Longden, C. Melsopp, K. Megy, P. Meidl, B. Overduin, A. Parker, A. Prlic, S. Rice, D. Rios, M. Schuster, I. Sealy, J. Severin, G. Slater, D. Smedley, G. Spudich, S. Trevanion, A. Vilella, J. Vogel, S. White, M. Wood, T. Cox, V. Curwen, R. Durbin, X. M. Fernandez-Suarez, P. Flicek, A. Kasprzyk, G. Proctor, S. Searle, J. Smith, A. Ureta-Vidal and E. Birney
Ensembl 2007
Nucleic Acids Res. 2007 Vol. 35, Database issue:D610-D617.
doi:10.1093/nar/gkl996
[Abstract] [Full text]
E. Birney, D. Andrews, M. Caccamo, Y. Chen, L. Clarke, G. Coates, T. Cox, F. Cunningham, V. Curwen, T. Cutts, T. Down, R. Durbin, X. M. Fernandez-Suarez, P. Flicek, S. Gräf, M. Hammond, J. Herrero, K. Howe, V. Iyer, K. Jekosch, A. Kähäri, A. Kasprzyk, D. Keefe, F. Kokocinski, E. Kulesha, D. London, I. Longden, C. Melsopp, P. Meidl, B. Overduin, A. Parker, G. Proctor, A. Prlic, M. Rae, D. Rios, S. Redmond, M. Schuster, I. Sealy, S. Searle, J. Severin, G. Slater, D. Smedley, J. Smith, A. Stabenau, J. Stalker, S. Trevanion, A. Ureta-Vidal, J. Vogel, S. White, C. Woodwark, and T. J. P. Hubbard
Ensembl 2006
Nucleic Acids Res. 2006 Jan 1;34 Database issue:D556-D561.
doi:10.1093/nar/gkj133
[Abstract] [Full text]
T. Hubbard, D. Andrews, M. Caccamo, G. Cameron, Y. Chen, M. Clamp, L. Clarke, G. Coates, T. Cox, F. Cunningham, V. Curwen, T. Cutts, T. Down, R. Durbin, X. M. Fernandez-Suarez, J. Gilbert, M. Hammond, J. Herrero, H. Hotz, K. Howe, V. Iyer, K. Jekosch, A. Kahari, A. Kasprzyk, D. Keefe, S. Keenan, F. Kokocinsci, D. London, I. Longden, G. McVicker, C. Melsopp, P. Meidl, S. Potter, G. Proctor, M. Rae, D. Rios, M. Schuster, S. Searle, J. Severin, G. Slater, D. Smedley, J. Smith, W. Spooner, A. Stabenau, J. Stalker, R. Storey, S. Trevanion, A. Ureta-Vidal, J. Vogel, S. White, C. Woodwark and E. Birney
Ensembl 2005
Nucleic Acids Res. 2005 Jan 1;33 Database issue:D447-D453.
doi:10.1093/nar/gki138
[Abstract] [Full text]
J. L. Ashurst, C.-K. Chen, J. G. R. Gilbert, K. Jekosch, S. Keenan, P. Meidl, S. M. Searle, J. Stalker, R. Storey, S. Trevanion, L. Wilming and T. Hubbard
The Vertebrate Genome Annotation (Vega) database.
Nucleic Acids Res. 2005 Jan 1;33 Database Issue:D459-D465.
doi:10.1093/nar/gki135
[Abstract] [Full text]
Martin P. Hammond and Ewan Birney
Genome information resources - developments at Ensembl
Trends Genet. 2004 Jun; 20(6):268-272.
doi:10.1016/j.tig.2004.04.002
E. Birney, D. Andrews, P. Bevan, M. Caccamo, G. Cameron, Y. Chen, L. Clarke, G. Coates, T. Cox, J. Cuff, V. Curwen, T. Cutts, T. Down, R. Durbin, E. Eyras, X. M. Fernandez-Suarez, P. Gane, B. Gibbins, J. Gilbert, M. Hammond, H. Hotz, V. Iyer, A. Kahari, K. Jekosch, A. Kasprzyk, D. Keefe, S. Keenan, H. Lehvaslaiho, G. McVicker, C. Melsopp, P. Meidl, E. Mongin, R. Pettett, S. Potter, G. Proctor, M. Rae, S. Searle, G. Slater, D. Smedley, J. Smith, W. Spooner, A. Stabenau, J. Stalker, R. Storey, A. Ureta-Vidal, C. Woodwark, M. Clamp and T. Hubbard
Ensembl 2004
Nucleic Acids Res. 2004 Jan 1;32 Database issue:D468-70.
[Abstract] [Full text]
M. Clamp, D. Andrews, D. Barker, P. Bevan, G. Cameron, Y. Chen, L. Clark, T. Cox, J. Cuff, V. Curwen, T. Down, R. Durbin, E. Eyras, J. Gilbert, M. Hammond, T. Hubbard, A. Kasprzyk, D. Keefe, H. Lehvaslaiho, V. Iyer, C. Melsopp, E. Mongin, R. Pettett, S. Potter, A. Rust, E. Schmidt, S. Searle, G. Slater, J. Smith, W. Spooner, A. Stabenau, J. Stalker, E. Stupka, A. Ureta-Vidal, I. Vastrik and E. Birney
Ensembl 2002: accommodating comparative genomics.
Nucleic Acids Res. 2003 Jan 1;31(1):38-42.
[Abstract] [Full text]
T. Hubbard, D. Barker, E. Birney, G. Cameron, Y. Chen, L. Clark, T. Cox, J. Cuff, V. Curwen, T. Down, R. Durbin, E. Eyras, J. Gilbert, M. Hammond, L. Huminiecki, A. Kasprzyk, H. Lehvaslaiho, P. Lijnzaad, C. Melsopp, E. Mongin, R. Pettett, M. Pocock, S. Potter, A. Rust, E. Schmidt, S. Searle, G. Slater, J. Smith, W. Spooner, A. Stabenau, J. Stalker, E. Stupka, A. Ureta-Vidal, I. Vastrik and M. Clamp.
The Ensembl genome database project.
Nucleic Acids Res. 2002 Jan 1; 30(1):38-41.
[Abstract] [Full text]

BioMart/EnsMart

A description of the BioMart and EnsMart data mining tools.

Arek Kasprzyk, Damian Keefe, Damian Smedley, Darin London, William Spooner, Craig Melsopp, Martin Hammond, Philippe Rocca-Serra, Tony Cox and Ewan Birney
EnsMart: A Generic System for Fast and Flexible Access to Biological Data.
Genome Res. 2004 Jan; 14(1):160-169.
[Full text]

Exonerate

A description of the generic tool for pairwise sequence comparison.

Guy St. C. Slater and Ewan Birney
Automated generation of heuristics for biological sequence comparison.
BMC Bioinformatics. 2005 Feb 15;6(1):31
doi:10.1186/1471-2105-6-31

Genome Analysis and Annotation Publications

International Human Genome Sequencing Consortium.
Finishing the euchromatic sequence of the human genome
Nature. 2004 Oct 21;431(7011):931-945.
doi:10.1038/nature03001
Mouse Genome Sequencing Consortium.
Initial sequencing and comparative analysis of the mouse genome.
Nature. 2002 Dec 5;420(6915):520-562.
doi:10.1038/nature01262
Rat Genome Sequencing Project Consortium.
Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
Nature. 2004 Apr 1;428(6982):493-521.
doi:10.1038/nature02426
International Chicken Genome Sequencing Consortium.
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.
Nature. 2004 Dec 9;432(7018):695-716.
doi:10.1038/nature03154
Emmanuel Mongin, Christos Louis, Robert A. Holt, Ewan Birney and Frank H. Collins
The Anopheles gambiae genome: an update.
Trends Parasitol. 2004 Feb; 20(2):49-52.
doi:10.1016/j.pt.2003.11.003

.