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.
Since release 25, all Ensembl releases have been archived as fully functional sites for about two years.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 [[SPECIESDEFS::ENSEMBL_VERSION]] - [[SPECIESDEFS::ENSEMBL_RELEASE_DATE]]). For more information see the list of current archives.
Paul Flicek, M. Ridwan Amode, Daniel Barrell, Kathryn Beal,
Simon Brent, Yuan Chen, Peter Clapham, Guy Coates, Susan Fairley,
Stephen Fitzgerald, Leo Gordon, Maurice Hendrix, Thibaut Hourlier,
Nathan Johnson, Andreas Kähäri, Damian Keefe, Stephen Keenan,
Rhoda Kinsella, Felix Kokocinski, Eugene Kulesha, Pontus Larsson,
Ian Longden, William McLaren, Bert Overduin, Bethan Pritchard,
Harpreet Singh Riat, Daniel Rios, Graham R. S. Ritchie, Magali Ruffier,
Michael Schuster, Daniel Sobral, Giulietta Spudich, Y. Amy Tang,
Stephen Trevanion, Jana Vandrovcova, Albert J. Vilella, Simon White,
Steven P. Wilder, Amonida Zadissa, Jorge Zamora, Bronwen L. Aken,
Ewan Birney, Fiona Cunningham, Ian Dunham, Richard Durbin,
Xosé M. Fernández-Suárez, Javier Herrero,
Tim J. P. Hubbard, Anne Parker, Glenn Proctor, Jan Vogel and
Stephen M. J. Searle
Ensembl 2011
Nucleic Acids Research 2011 39 Database issue:D800-D806
doi:10.1093/nar/gkq1064
Jessica Severin, Kathryn Beal, Albert J Vilella, Stephen Fitzgerald,
Michael Schuster, Leo Gordon, Abel Ureta-Vidal, Paul Flicek, Javier Herrero
eHive: An Artificial Intelligence workflow system for genomic analysis
BMC Bioinformatics 2010, 11:240 (11 May 2010)
[Abstract]
Yuan Chen, Fiona Cunningham, Daniel Rios, William M McLaren, James A Smith,
Bethan Pritchard, Giulietta M Spudich, Simon Brent, Eugene Kulesha, Pablo Marin-Garcia,
Damian Smedley, Ewan Birney, Paul Flicek
Ensembl variation resources
BMC Bioinformatics 2010, 11:293 (11 May 2010)
[Abstract]
Daniel Rios, William M McLaren, Yuan Chen, Ewan Birney, Arne Stabenau, Paul Flicek,
Fiona Cunningham
A database and API for variation, dense genotyping and resequencing data
BMC Bioinformatics 2010, 11:238 (11 May 2010)
[Abstract]
Benoît Ballester, Nathan Johnson, Glenn Proctor, Paul Flicek
Consistent annotation of gene expression arrays
BMC Bioinformatics 2010, 11:294 (11 May 2010)
[Abstract]
Giulietta M Spudich, Xosé M Fernández-Suárez
Touring Ensembl: A practical guide to genome browsing
BMC Bioinformatics 2010, 11:295 (11 May 2010)
[Abstract]
Anne Parker, Eugene Bragin, Simon Brent, Bethan Pritchard, James A Smith,
Stephen Trevanion
Using caching and optimization techniques to improve performance of the Ensembl website
BMC Bioinformatics 2010, 11:239 (11 May 2010)
[Abstract]
Paul Flicek, Bronwen L. Aken, Benoit Ballester, Kathryn Beal, Eugene
Bragin, Simon Brent, Yuan Chen, Peter Clapham, Guy Coates, Susan
Fairley, Stephen Fitzgerald, Julio Fernandez-Banet, Leo Gordon,
Stefan Gräf, Syed Haider, Martin Hammond, Kerstin Howe, Andrew
Jenkinson, Nathan Johnson, Andreas Kähäri Damian Keefe,
Stephen Keenan, Rhoda Kinsella, Felix Kokocinski, Gautier Koscielny,
Eugene Kulesha, Daniel Lawson, Ian Longden, Tim Massingham, William
McLaren, Karyn Megy, Bert Overduin, Bethan Pritchard, Daniel Rios,
Magali Ruffier, Michael Schuster, Guy Slater, Damian Smedley,
Giulietta Spudich, Y. Amy Tang, Stephen Trevanion, Albert Vilella,
Jan Vogel, Simon White, Steven P. Wilder, Amonida Zadissa, Ewan
Birney, Fiona Cunningham, Ian Dunham, Richard Durbin, Xosée M.
Fernández-Suarez, Javier Herrero ,Tim J. P. Hubbard, Anne
Parker, Glenn Proctor, James Smith, and Stephen M. J. Searle
Ensembl's 10th year
Nucleic Acids Research 2010 38 Database issue:D557-D562
doi:10.1093/nar/gkp972
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, Jun 2010.
www.ncbi.nlm.nih.gov/pubmed/20521244
Giulietta M Spudich and Xosé M Fernández-Suárez
Touring Ensembl: A practical guide to genome browsing
BMC Genomics 2010, 11:295 (11 May 2010)
www.biomedcentral.com/1471-2164/11/295
T. J. P. Hubbard, B. L. Aken, S. Ayling, B. Ballester, K. Beal, E.
Bragin, S. Brent, Y. Chen, P. Clapham, L. Clarke, G. Coates,
S. Fairley, S. Fitzgerald, J. Fernandez-Banet, L. Gordon,
S. Gräf, S. Haider, M. Hammond, R. Holland, K. Howe,
A. Jenkinson, N. Johnson, A. Kähäri, D. Keefe, S. Keenan,
R. Kinsella, F. Kokocinski, E. Kulesha, D. Lawson, I. Longden,
K. Megy, P. Meidl, B. Overduin, A. Parker, B. Pritchard, D. Rios,
M. Schuster, G. Slater, D. Smedley, W. Spooner, G. Spudich, S.
Trevanion, A. Vilella, J. Vogel, S. White, S. Wilder, A. Zadissa, E.
Birney, F. Cunningham, V. Curwen, R. Durbin, X. M. Fernandez-Suarez,
J. Herrero, A. Kasprzyk, G. Proctor, J. Smith, S. Searle and
P. Flicek
Ensembl 2009
Nucleic Acids Research 2009 37 Database issue:D690-D697
doi:10.1093/nar/gkn828
A.J. Vilella, J. Severin, A. Ureta-Vidal, R. Durbin, L. Heng and
E. Birney
EnsemblCompara GeneTrees: Analysis of complete,
duplication-aware phylogenetic trees in vertebrates.
Genome Research 2009 19:327-335
doi:10.1101/gr.073585.107
P. Flicek, B. L. Aken, K. Beal, B. Ballester, M. Caccamo, Y. Chen,
L. Clarke, G. Coates, F. Cunningham, T. Cutts, T. Down, S. C. Dyer,
T. Eyre, S. Fitzgerald, J. Fernandez-Banet, S. Gräf, S. Haider,
M. Hammond, R. Holland, K. L. Howe, K. Howe, N. Johnson, A. Jenkinson,
A. Kähäri, D. Keefe, F. Kokocinski, E. Kulesha, D. Lawson,
I. Longden, K. Megy, P. Meidl, B. Overduin, A. Parker, B. Pritchard,
A. Prlic, S. Rice, D. Rios, M. Schuster, I. Sealy, G. Slater,
D. Smedley, G. Spudich, S. Trevanion, A. J. Vilella, J. Vogel,
S. White, M. Wood, E. Birney, T. Cox, V. Curwen, R. Durbin,
X. M. Fernandez-Suarez, J. Herrero, T. J. P. Hubbard, A. Kasprzyk,
G. Proctor, J. Smith, A. Ureta-Vidal and S. Searle.
Ensembl 2008
Nucleic Acids Research 2008 36 Database issue:D707-14.
doi:10.1093/nar/gkm988
B. Paten, J. Herrero, S. Fitzgerald, K. Beal, P. Flicek, I. Holmes and
E. Birney
Genome-wide nucleotide-level mammalian ancestor
reconstruction
Genome Research 2008 18:1829-1843
doi:10.1101/gr.076521.108
B. Paten, J. Herrero, K. Beal, S. Fitzgerald and E. Birney
Enredo and Pecan: Genome-wide mammalian consistency-based
multiple alignment with paralogs
Genome Research 2008 18: 1814-1828
doi:10.1101/gr.076554.108
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
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 Research. 2007 Vol. 35, Database
issue:D610-D617.
doi:10.1093/nar/gkl996
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 Research 2006 Jan 1;34 Database
issue:D556-D561.
doi:10.1093/nar/gkj133
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
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 Research 2005 Jan 1;33 Database
issue:D447-D453.
doi:10.1093/nar/gki138
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
International Chicken Genome Sequencing Consortium.
Sequence and comparative analysis of the chicken genome
provide unique perspectives on vertebrate evolution.
Nature 2004 432(7018):695-716.
doi:10.1038/nature03154
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
Martin P. Hammond and Ewan Birney
Genome information resources - developments at
Ensembl
Trends Genetics 2004 20(6):268-272.
doi:10.1016/j.tig.2004.04.002
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 Research 2004 14(5):925-928.
doi:10.1101/gr.1860604
Arne Stabenau, Graham McVicker, Craig Melsopp, Glenn Proctor, Michele
Clamp and Ewan Birney
The Ensembl Core Software Libraries
Genome Research 2004 14(5):929-933.
doi:10.1101/gr.1857204
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 Research 2004 14(5):934-941.
doi:10.1101/gr.1859804
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 Research 2004 14(5):942-950.
doi:10.1101/gr.1858004
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 Research 2004 14(5):951-955.
doi:10.1101/gr.1863004
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 Research 2004 14(5):956-962.
doi:10.1101/gr.1890304
Stephen M.J. Searle, James Gilbert, Vivek Iyer and Michele Clamp
The Otter Annotation System
Genome Research 2004 14(5):963-970.
doi:10.1101/gr.1864804
James A. Cuff, Guy M.P. Coates, Tim J.R. Cutts and Mark Rae
The Ensembl Computing Architecture
Genome Research 2004 14(5):971-975.
doi:10.1101/gr.1866304
Eduardo Eyras, Mario Caccamo, Val Curwen and Michele Clamp
ESTGenes: Alternative Splicing From ESTs in
Ensembl
Genome Research 2004 14(5):976-987.
doi:10.1101/gr.1862204
Ewan Birney, Michele Clamp and Richard Durbin
GeneWise and Genomewise
Genome Research 2004 14(5):988-995.
doi:10.1101/gr.1865504
Rat Genome Sequencing Project Consortium.
Genome sequence of the Brown Norway rat yields insights into
mammalian evolution.
Nature. 2004 428(6982):493-521.
doi:10.1038/nature02426
Emmanuel Mongin, Christos Louis, Robert A. Holt, Ewan Birney and Frank
H. Collins
The Anopheles gambiae genome: an update.
Trends in Parasitology 2004 20(2):49-52.
doi:10.1016/j.pt.2003.11.003
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 Research 2004 14(1):160-169.
doi:10.1101/gr.1645104
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 Research 2004 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 Research 2003 31(1):38-42.
[Abstract]
[Full text]
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
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 Research 2002 30(1):38-41.
[Abstract]
[Full text]