Scientific Publications
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 pipeline.
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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.
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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.
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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.
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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.
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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.
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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.
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Stephen M.J. Searle, James Gilbert, Vivek Iyer, and Michele Clamp
The Otter Annotation System
Genome Res. 2004 May; 14(5):963-970.
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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.
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Eduardo Eyras, Mario Caccamo, Val Curwen, and Michele Clamp
ESTGenes: Alternative Splicing From ESTs in Ensembl
Genome Res. 2004 May; 14(5):976-987.
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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
A series of protocols to navigate Ensembl can be found in Current Protocols in Bioinformatics:
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Xose M. Fernandez Suarez 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.
An overview of recent developments
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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 Jan 1; Database issue
doi:10.1093/nar/gkl996
[Abstract] [Full text] -
Fiona Cunningham, Daniel Rios, Mark Griffiths, James Smith, Zemin Ning, Tony Cox, Paul Flicek, Pablo Marin-Garcin, Javier Herrero, Jane Rogers, Louise van der Weyden, Allan Bradley, Ewan Birney and David J Adams
TranscriptSNPView: a genome-wide catalog of mouse coding variation.
Nature Genetics. 2006 Aug; 38(8):853
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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.
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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 Res. 2005 Jan 1;33 Database issue:D447-D453.
doi:10.1093/nar/gki138
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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.
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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.
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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 'EnsMart' large-scale data retrieval tool.
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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]
An update on the Anopheles gambiae genome and Ensembl.
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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 -
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