Ensembl 2009

Nucleic Acids Research

Volumn 37, Issue SUPPL. 1, 2009, Pages

  Hubbard, T J P ^a   Aken, B L ^a   Ayling, S ^a   Ballester, B ^b   Beal, K ^b   Bragin, E ^a   Brent, S ^a   Chen, Y ^b   Clapham, P ^a   Clarke, L ^a   Coates, G ^a   Fairley, S ^a   Fitzgerald, S ^b   Fernandez Banet, J ^a   Gordon, L ^b   Graf, S ^b   Haider, S ^b   Hammond, M ^b   Holland, R ^b   Howe, K ^a   Jenkinson, A ^b   Johnson, N ^b   Kahari, A ^b   Keefe, D ^b   Keenan, S ^b   Kinsella, R ^b   Kokocinski, F ^a   Kulesha, E ^b   Lawson, D ^b   Longden, I ^b   Megy, K ^b   Meidl, P ^b   Overduin, B ^b   Parker, A ^a   Pritchard, B ^a   Rios, D ^b   Schuster, M ^b   Slater, G ^b   Smedley, D ^b   Spooner, W ^b   Spudich, G ^b   Trevanion, S ^a   Vilella, A ^b   Vogel, J ^a   White, S ^a   Wilder, S ^b   Zadissa, A ^a   Birney, E ^b   Cunningham, F ^b   Curwen, V ^a   Durbin, R ^a   Fernandez Suarez, X M ^b   Herrero, J ^b   Kasprzyk, A ^b   Proctor, G ^b   Smith, J ^a   Searle, S ^a   Flicek, P ^b   more..

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHORDATA; COMPUTER INTERFACE; COMPUTER PROGRAM; ENSEMBL DATABASE; GENE VECTOR; GENETIC DATABASE; GENOME; HUMAN; HUMAN COMPUTER INTERACTION; INFORMATION SYSTEM; INTERNET; MAMMAL; NEW SPECIES; NONHUMAN; ORANG UTAN; PRIORITY JOURNAL;

ANIMALS; DATABASES, GENETIC; GENETIC VARIATION; GENOMICS; HUMANS; INTERNET; SEQUENCE ALIGNMENT;

CARYA ILLINOINENSIS; MAMMALIA; PONGO PYGMAEUS;

EID: 58149185123     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn828     Document Type: Article

References (38)

1. Karolchik,D., Kuhn,R.M., Baertsch,R., Barber,G.P., Clawson,H., Diekhans,M., Giardine,B., Harte,R.A., Hinrichs,A.S., Hsu,F. et al. (2008) The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res., 36, D773-D779.
2. Wheeler,D.L., Barrett,T., Benson,D.A., Bryant,S.H., Canese,K., Chetvernin,V., Church,D.M., Dicuccio,M., Edgar,R., Federhen,S. et al. (2008) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 36, D13-D21.
3. Dowell,R.D., Jokerst,R.M., Day,A., Eddy,S.R. and Stein,L. (2001) The Distributed Annotation System. BMC Bioinformatics, 2, 7.
4. Jenkinson,A.M., Albrecht,M., Birney,E., Blankenburg,H., Down,T., Finn,R.D., Hermjakob,H., Hubbard,T.J., Jimenez,R.C., Jones,P. et al. (2008) Integrating biological data - the Distributed Annotation System. BMC Bioinformatics, 9(Suppl 8), S3.
5. 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 Res., 14, 160-169.
6. The Star Consortium (2008) SNP and haplotype mapping for genetic analysis in the rat. Nat. Genet., 40, 560-566.
7. Twigger,S.N., Pruitt,K.D., Fernández-Suárez,X.M., Karolchik,D., Worley,K.C., Maglott,D.R., Brown,G., Weinstock,G., Gibbs,R.A., Kent,J. et al. (2008) What everybody should know about the rat genome and its online resources. Nat. Genet., 40, 523-527.
8. Aitman,T.J., Critser,J.K., Cuppen,E., Dominiczak,A., Fernandez-Suarez,X.M., Flint,J., Gauguier,D., Geurts,A.M., Gould,M., Harris,P.C. et al. (2008) Progress and prospects in rat genetics: a community view. Nat. Genet., 40, 516-522.
9. The ENCODE Project Consortium (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447, 799-816.
10. Gräf,S., Nielsen,F.G., Kurtz,S., Huynen,M.A., Birney,E., Stunnenberg,H. and Flicek,P. (2007) Optimized design and assessment of whole genome tiling arrays. Bioinformatics, 23, i195-i204.
11. Warren,W.C., Hillier,L.W., Marshall Graves,J.A., Birney,E., Ponting,C.P., Grutzner,F., Belov,K., Miller,W., Clarke,L., Chinwalla,A.T. et al. (2008) Genome analysis of the platypus reveals unique signatures of evolution. Nature, 453, 175-183.
12. Mikkelsen,T.S., Wake.eld,M.J., Aken,B., Amemiya,C.T., Chang,J.L., Duke,S., Garber,M., Gentles,A.J., Goodstadt,L., Heger,A. et al. (2007) Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature, 447, 167-177.
13. Rhesus Macaque Genome Sequencing and Analysis Consortium. (2007) Evolutionary and biomedical insights from the rhesus macaque genome. Science, 316, 222-234.
14. Flicek,P., Aken,B.L., Beal,K., Ballester,B., Caccamo,M., Chen,Y., Clarke,L., Coates,G., Cunningham,F., Cutts,T. et al. (2008) Ensembl 2008. Nucleic Acids Res., 36, D707-D714.
15. Spudich,G., Fernandez-Suarez,X.M. and Birney,E. (2007) Genome browsing with Ensembl: A practical overview. Briefings in functional genomics & proteomics, 6, 202-219.
16. Hubbard,T., Barker,D., Birney,E., Cameron,G., Chen,Y., Clark,L., Cox,T., Cu.,J., Curwen,V., Down,T. et al. (2002) The Ensembl genome database project. Nucleic Acids Res., 30, 38-41.
17. Cunningham,F., Rios,D., Gri.ths,M., Smith,J., Ning,Z., Cox,T., Flicek,P., Marin-Garcin,P., Herrero,J., Rogers,J. et al. (2006) TranscriptSNPView: A genome-wide catalog of mouse coding variation. Nat. Genet., 38, 853.
18. Hubbard,T.J., Aken,B.L., Beal,K., Ballester,B., Caccamo,M., Chen,Y., Clarke,L., Coates,G., Cunningham,F., Cutts,T. et al. (2007) Ensembl 2007. Nucleic Acids Res., 35, D610-D617.
19. Wilming,L.G., Gilbert,J.G., Howe,K., Trevanion,S., Hubbard,T. and Harrow,J.L. (2008) The vertebrate genome annotation (Vega) database. Nucleic Acids Res., 36, D753-D760.
20. Pruitt,K.D., Tatusova,T. and Maglott,D.R. (2007) NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 35, D61-D65.
21. Denoeud,F., Kapranov,P., Ucla,C., Frankish,A., Castelo,R., Drenkow,J., Lagarde,J., Alioto,T., Manzano,C., Chrast,J. et al. (2007) Prominent use of distal 50 transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res, 17, 746-759.
22. Harrow,J., Denoeud,F., Frankish,A., Reymond,A., Chen,C.K., Chrast,J., Lagarde,J., Gilbert,J.G., Storey,R., Swarbreck,D. et al. (2006) GENCODE: Producing a reference annotation for ENCODE. Genome Biol, 7(Suppl 1), S41-S49.
23. Guigó,R., Flicek,P., Abril,J.F., Reymond,A., Lagarde,J., Denoeud,F., Antonarakis,S., Ashburner,M., Bajic,V.B., Birney,B. et al. (2006) EGASP: The human ENCODE Genome Annotation Assessment Project. Genome Biology, 7, S2.
24. Tress,M.L., Martelli,P.L., Frankish,A., Reeves,G.A., Wesselink,J.J., Yeats,C., Olason,P.L., Albrecht,M., Hegyi,H., Giorgetti,A. et al. (2007) The implications of alternative splicing in the ENCODE protein complement. Proc. Natl Acad. Sci. USA, 104, 5495-5500.
25. Clamp,M., Fry,B., Kamal,M., Xie,X., Cu.,J., Lin,M.F., Kellis,M., Lindblad-Toh,K. and Lander,E.S. (2007) Distinguishing proteincoding and noncoding genes in the human genome. Proc. Natl Acad. Sci. USA., 104, 19428-19433.
26. The UniProt Consortium (2008) The universal protein resource (UniProt). Nucleic Acids Res., 36, D190-D195.
27. Bruford,E.A., Lush,M.J., Wright,M.W., Sneddon,T.P., Povey,S. and Birney,E. (2008) The HGNC Database in 2008: A resource for the human genome. Nucleic Acids Res., 36, D445-D448.
28. Paten,B., Herrero,J., Beal,K., Fitzgerald,S. and Birney,E. (2008) Enredo and Pecan: Genome-wide mammalian consistency based multiple alignment with paralogs. Genome Res., 18, 1814-1828.
29. Paten,B., Herrero,J., Fitzgerald,S., Beal,K., Flicek,P., Holmes,I. and Birney,E. (2008) Genome-wide nucleotide level mammalian ancestor reconstruction. Genome Res., 18, 1829-1843.
30. Cooper,G.M., Stone,E.A., Asimenos,G., Program,N.C.S., Green,E.D., Batzoglou,S. and Sidow,A. (2005) Distribution and intensity of constraint in mammalian genomic sequence. Genome Res., 15, 901-913.
31. Ruan,J., Li,H., Chen,Z., Coghlan,A., Coin,L.J., Guo,Y., Heriche,J.K., Hu,Y., Kristiansen,K., Li,R. et al. (2008) TreeFam: 2008 Update. Nucleic Acids Res., 36, D735-D740.
32. Massingham,T. and Goldman,N. (2005) Detecting amino acid sites under positive selection and purifying selection. Genetics, 169, 1753-1762.
33. Down,T.A., Rakyan,V.K., Turner,D.J., Flicek,P., Li,H., Kulesha,E., Graf,S., Johnson,N., Herrero,J., Tomazou,E.M. et al. (2008) A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat. Biotechnol., 26, 779-785.
34. Rakyan,V., Down,T., Thorne,N., Flicek,P., Kulesha,E., Graf,S., Tomazou,E., Backdahl,L., Johnson,N., Herberth,M. et al. (2008) An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Res., 18, 1518-1529.
35. Wang,Z., Zang,C., Rosenfeld,J.A., Schones,D.E., Barski,A., Cuddapah,S., Cui,K., Roh,T.Y., Peng,W., Zhang,M.Q. et al. (2008) Combinatorial patterns of histone acetylations and methylations in the human genome. Nat. Genet., 40, 897-903.
36. Barski,A., Cuddapah,S., Cui,K., Roh,T.Y., Schones,D.E., Wang,Z., Wei,G., Chepelev,I. and Zhao,K. (2007) High-resolution profiling of histone methylations in the human genome. Cell, 129, 823-837.
37. Stranger,B.E., Nica,A.C., Forrest,M.S., Dimas,A., Bird,C.P., Beazley,C., Ingle,C.E., Dunning,M., Flicek,P., Koller,D. et al. (2007) Population genomics of human gene expression. Nat. Genet., 39 1217-1224.
38. Wellcome Trust case control consortium (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature, 447, 661-678.