Scientific PublicationsIn case you liked to include a general reference to the Ensembl system in your work, we would like to recommend citing the most recent overview article. For more specialised aspects of our system further articles would be available from the list below.
As Ensembl is continuously producing new website and data releases, it is also important to include the version and release date when citing Ensembl (currently v40 - Aug2006).
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]
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]
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]
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
International Human Genome Sequencing Consortium.
Finishing the euchromatic sequence of the human genome
Nature. 2004 Oct 21;431(7011):927-930.
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
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