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Ensembl References
Flicek P., Aken B.L., 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 Y.A., Trevanion S., Vilella A., Vogel J., White S., Wilder S.P., Zadissa A., Birney E., Cunningham F., Dunham I., Durbin R., Fernández-Suarez X.M., Herrero J., Hubbard T.J., Parker A., Proctor G., Smith J., Searle S.M. (2010)
Ensembl's 10th year.
Nucleic Acids Research 38: D557-D562.
abstract full-text PDF
Kersey P.J., Lawson D., Birney E., Derwent P.S., Haimel M., Herrero J., Keenan S., Kerhornou A., Koscielny G., Kähäri A., Kinsella R.J., Kulesha E., Maheswari U., Megy K., Nuhn M., Proctor G., Staines D., Valentin F., Vilella A.J., Yates A. (2010)
Ensembl genomes: Extending ensembl across the taxonomic space.
Nucleic Acids Research 38: D563-D569.
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Hubbard T.J., Aken B.L., 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 X.M.,
Herrero J., Kasprzyk A., Proctor G., Smith J., Searle S., Flicek P. (2009)
Ensembl 2009.
Nucleic Acids Research 37: D690-D697.
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Flicek P., Aken B.L., Beal K., Ballester B., Caccamo M., Chen Y., Clarke L., Coates G., Cunningham F.,
Cutts T., Down T., Dyer S.C., Eyre T., Fitzgerald S., Fernandez-Banet J., Gräf S., Haider S., Hammond M.,
Holland R., Howe K.L., 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 A.J., Vogel J., White S.,
Wood M., Birney E., Cox T., Curwen V., Durbin R., Fernandez-Suarez X.M., Herrero J., Hubbard T.J., Kasprzyk A.,
Proctor G., Smith J., Ureta-Vidal A., Searle S.
(2008)
Ensembl 2008.
Nucleic Acids Research 36 D707-D714.
abstract
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Reisinger F., Corpas M., Hancock J., Hermjakob H., Birney E. and Kahlem P. (2008)
ENFIN - An integrative structure for systems biology.
In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 132-143
abstract
full-text PDF [Subscription Required]
Fernandez Suarez X. M. and Schuster M. K. (2007)
Using the Ensembl Genome Server to Browse Genomic Sequence Data.
UNIT 1.15 in Current Protocols in Bioinformatics, Supplement 16, January 2007.
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Hoffman M.M., Birney E. (2007)
Estimating the neutral rate of nucleotide substitution using introns.
Molecular Biology and Evolution 24(2): 522-531.
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Hubbard T.J., Aken B.L., Beal K., Ballester B., Caccamo M., Chen Y., Clarke L., Coates G., Cunningham F., Cutts T., Down T., Dyer S.C., Fitzgerald S., Fernandez-Banet J., Graf S., Haider S., Hammond M., Herrero J., Holland R., Howe K., Howe K., Johnson N., Kahari A., Keefe D., Kokocinski F., Kulesha E., Lawson D., Longden I., Melsopp C., Megy K., Meidl P., Ouverdin B., Parker A., Prlic A., Rice S., Rios D., Schuster M., Sealy I., Severin J., Slater G., Smedley D., Spudich G., Trevanion S., Vilella A., Vogel J., White S., Wood M., Cox T., Curwen V., Durbin R., Fernandez-Suarez X.M., Flicek P., Kasprzyk A., Proctor G., Searle S., Smith J., Ureta-Vidal A., Birney E. (2007)
Ensembl 2007.
Nucleic Acids Research 35: D610-D617.
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Birney E., Andrews D., Caccamo M., Chen Y., Clarke L., Coates G., Cox T., Cunningham F., Curwen V., Cutts T., Down T., Durbin R., Fernandez-Suarez X.M., Flicek P., Gräf S., Hammond M., Herrero J., Howe K., Iyer V., Jekosch K., Kähäri A., Kasprzyk A., Keefe D., Kokocinski F., Kulesha E., London D., Longden I., Melsopp C., Meidl P., Overduin B., Parker A., Proctor G., Prlic A., Rae M., Rios D., Redmond S., Schuster M., Sealy I., Searle S., Severin J., Slater G., Smedley D., Smith J., Stabenau A., Stalker J., Trevanion S., Ureta-Vidal A., Vogel J., White S., Woodwark C., Hubbard T.J. (2006)
Ensembl 2006.
Nucleic Acids Research 34: D556-D561.
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Ashurst J. L. , Chen C.-K., Gilbert J. G. R., Jekosch K., Keenan S., Meidl P., Searle S. M., Stalker J., Storey R., Trevanion S., Wilming L. and Hubbard T. (2005)
The Vertebrate Genome Annotation (Vega) database.
Nucleic Acids Research 33: D459-D465.
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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 X. M., 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. and Birney E. (2005)
Ensembl 2005.
Nucleic Acids Research 33: D447-D453.
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Slater G. St. C. and Birney E. (2005)
Automated generation of heuristics for biological sequence comparison.
BMC Bioinformatics 6(1): 31-31.
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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 X.M., 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. (2004)
Ensembl 2004.
Nucleic Acids Research 32: D468-D470.
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Birney E., Andrews T.D., Bevan P., Caccamo M., Chen Y., Clarke L., Coates G., Cuff J., Curwen V., Cutts T., Down T., Eyras E., Fernandez-Suarez X.M., Gane P., Gibbins B., Gilbert J., Hammond M., Hotz H.R., 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 K.C., Cameron G., Durbin R., Cox A., Hubbard T., Clamp M. (2004)
An Overview of Ensembl.
Genome Research 14(5): 925-928.
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Birney E., Clamp M., and Durbin R. (2004)
GeneWise and Genomewise
Genome Research 14(5): 988-995.
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Cuff J. A., Coates G. M. P., Cutts T. J. R., and Rae M. (2004)
The Ensembl Computing Architecture.
Genome Research 14(5): 971-975.
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Curwen V., Eyras E., Andrews T.D., Clarke L., Mongin E., Searle S.M., Clamp M. (2004)
The Ensembl Automatic Gene Annotation System.
Genome Research 14(5): 942-950.
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Eyras E., Caccamo M., Curwen V., and Clamp M. (2004)
ESTGenes: Alternative Splicing From ESTs in Ensembl.
Genome Research 14(5): 976-987.
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Hammond M. P. and Birney E. (2004)
Genome information resources - developments at Ensembl.
Trends in Genetics 20(6): 268-272.
doi:10.1016/j.tig.2004.04.002
International Chicken Genome Sequencing Consortium. (2004)
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.
Nature 432(7018): 695-716.
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International Human Genome Sequencing Consortium. (2004)
Finishing the euchromatic sequence of the human genome.
Nature 431(7011): 931-945.
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Kasprzyk A., Keefe D., Smedley D., London D., Spooner W., Melsopp C., Hammond M., Rocca-Serra P., Cox T. and Birney E. (2004)
EnsMart: A Generic System for Fast and Flexible Access to Biological Data.
Genome Research 14(1): 160-169.
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Mongin E., Christos L., Holt, R. A., Birney E. and Collins F. H. (2004)
The Anopheles gambiae genome: an update.
Trends in Parasitology 20(2): 49-52.
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Montgomery S.B., Astakhova T., Bilenky M., Birney E., Fu T., Hassel M., Melsopp C., Rak M., Robertson A.G., Sleumer M., Siddiqui A.S., Jones S.J. (2004)
Sockeye: A 3D Environment for Comparative Genomics.
Genome Research 14(5): 956-962.
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Potter S.C., Clarke L., Curwen V., Keenan S., Mongin E., Searle S.M., Stabenau A., Storey R., Clamp M. (2004)
The Ensembl Analysis Pipeline.
Genome Research 14(5): 934-941.
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Rat Genome Sequencing Project Consortium, (2004)
Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
Nature 428(6982): 493-521.
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Searle S. M. J., Gilbert J., Iyer V., and Clamp M. (2004)
The Otter Annotation System.
Genome Research 14(5): 963-970.
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Stabenau A., McVicker G., Melsopp C., Proctor G., Clamp M., Birney E. (2004)
The Ensembl Core Software Libraries.
Genome Research 14(5): 929-933.
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Stalker J., Gibbins B., Meidl P., Smith J., Spooner W., Hotz H.R., Cox A.V. (2004)
The Ensembl Web Site: Mechanics of a Genome Browser.
Genome Research 14(5): 951-955.
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Clamp M. , Andrews D., Barker D., Bevan P., Cameron G., Chen Y., Clark L., Cox T., J Cuff ., 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. and Birney E. (2003)
Ensembl 2002: accommodating comparative genomics.
Nucleic Acids Research 31(1): 38-42.
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Hubbard T., Barker D., Birney E., Cameron G., Chen Y., Clark L., Cox T., Cuff J., Curwen V., Down T., Durbin R., E. Eyras, 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. and Clamp M. (2002)
The Ensembl genome database project.
Nucleic Acids Research 30(1): 38-41.
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Mouse Genome Sequencing Consortium (2002)
Initial sequencing and comparative analysis of the mouse genome.
Nature 420(6915): 520-562.
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