Literature DB >> 11752248

The Ensembl genome database project.

T Hubbard1, 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, M Clamp.   

Abstract

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of the human genome sequence, with confirmed gene predictions that have been integrated with external data sources, and is available as either an interactive web site or as flat files. It is also an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements from sequence analysis to data storage and visualisation. The Ensembl site is one of the leading sources of human genome sequence annotation and provided much of the analysis for publication by the international human genome project of the draft genome. The Ensembl system is being installed around the world in both companies and academic sites on machines ranging from supercomputers to laptops.

Entities:  

Mesh:

Year:  2002        PMID: 11752248      PMCID: PMC99161          DOI: 10.1093/nar/30.1.38

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  14 in total

1.  The DNA sequence of human chromosome 22.

Authors:  I Dunham; N Shimizu; B A Roe; S Chissoe; A R Hunt; J E Collins; R Bruskiewich; D M Beare; M Clamp; L J Smink; R Ainscough; J P Almeida; A Babbage; C Bagguley; J Bailey; K Barlow; K N Bates; O Beasley; C P Bird; S Blakey; A M Bridgeman; D Buck; J Burgess; W D Burrill; K P O'Brien
Journal:  Nature       Date:  1999-12-02       Impact factor: 49.962

2.  Protein interaction maps for complete genomes based on gene fusion events.

Authors:  A J Enright; I Iliopoulos; N C Kyrpides; C A Ouzounis
Journal:  Nature       Date:  1999-11-04       Impact factor: 49.962

3.  The InterPro database, an integrated documentation resource for protein families, domains and functional sites.

Authors:  R Apweiler; T K Attwood; A Bairoch; A Bateman; E Birney; M Biswas; P Bucher; L Cerutti; F Corpet; M D Croning; R Durbin; L Falquet; W Fleischmann; J Gouzy; H Hermjakob; N Hulo; I Jonassen; D Kahn; A Kanapin; Y Karavidopoulou; R Lopez; B Marx; N J Mulder; T M Oinn; M Pagni; F Servant; C J Sigrist; E M Zdobnov
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

4.  Open annotation offers a democratic solution to genome sequencing.

Authors:  T Hubbard; E Birney
Journal:  Nature       Date:  2000-02-24       Impact factor: 49.962

5.  OMIM passes the 1,000-disease-gene mark.

Authors:  S E Antonarakis; V A McKusick
Journal:  Nat Genet       Date:  2000-05       Impact factor: 38.330

6.  Initial sequencing and analysis of the human genome.

Authors:  E S Lander; L M Linton; B Birren; C Nusbaum; M C Zody; J Baldwin; K Devon; K Dewar; M Doyle; W FitzHugh; R Funke; D Gage; K Harris; A Heaford; J Howland; L Kann; J Lehoczky; R LeVine; P McEwan; K McKernan; J Meldrim; J P Mesirov; C Miranda; W Morris; J Naylor; C Raymond; M Rosetti; R Santos; A Sheridan; C Sougnez; Y Stange-Thomann; N Stojanovic; A Subramanian; D Wyman; J Rogers; J Sulston; R Ainscough; S Beck; D Bentley; J Burton; C Clee; N Carter; A Coulson; R Deadman; P Deloukas; A Dunham; I Dunham; R Durbin; L French; D Grafham; S Gregory; T Hubbard; S Humphray; A Hunt; M Jones; C Lloyd; A McMurray; L Matthews; S Mercer; S Milne; J C Mullikin; A Mungall; R Plumb; M Ross; R Shownkeen; S Sims; R H Waterston; R K Wilson; L W Hillier; J D McPherson; M A Marra; E R Mardis; L A Fulton; A T Chinwalla; K H Pepin; W R Gish; S L Chissoe; M C Wendl; K D Delehaunty; T L Miner; A Delehaunty; J B Kramer; L L Cook; R S Fulton; D L Johnson; P J Minx; S W Clifton; T Hawkins; E Branscomb; P Predki; P Richardson; S Wenning; T Slezak; N Doggett; J F Cheng; A Olsen; S Lucas; C Elkin; E Uberbacher; M Frazier; R A Gibbs; D M Muzny; S E Scherer; J B Bouck; E J Sodergren; K C Worley; C M Rives; J H Gorrell; M L Metzker; S L Naylor; R S Kucherlapati; D L Nelson; G M Weinstock; Y Sakaki; A Fujiyama; M Hattori; T Yada; A Toyoda; T Itoh; C Kawagoe; H Watanabe; Y Totoki; T Taylor; J Weissenbach; R Heilig; W Saurin; F Artiguenave; P Brottier; T Bruls; E Pelletier; C Robert; P Wincker; D R Smith; L Doucette-Stamm; M Rubenfield; K Weinstock; H M Lee; J Dubois; A Rosenthal; M Platzer; G Nyakatura; S Taudien; A Rump; H Yang; J Yu; J Wang; G Huang; J Gu; L Hood; L Rowen; A Madan; S Qin; R W Davis; N A Federspiel; A P Abola; M J Proctor; R M Myers; J Schmutz; M Dickson; J Grimwood; D R Cox; M V Olson; R Kaul; C Raymond; N Shimizu; K Kawasaki; S Minoshima; G A Evans; M Athanasiou; R Schultz; B A Roe; F Chen; H Pan; J Ramser; H Lehrach; R Reinhardt; W R McCombie; M de la Bastide; N Dedhia; H Blöcker; K Hornischer; G Nordsiek; R Agarwala; L Aravind; J A Bailey; A Bateman; S Batzoglou; E Birney; P Bork; D G Brown; C B Burge; L Cerutti; H C Chen; D Church; M Clamp; R R Copley; T Doerks; S R Eddy; E E Eichler; T S Furey; J Galagan; J G Gilbert; C Harmon; Y Hayashizaki; D Haussler; H Hermjakob; K Hokamp; W Jang; L S Johnson; T A Jones; S Kasif; A Kaspryzk; S Kennedy; W J Kent; P Kitts; E V Koonin; I Korf; D Kulp; D Lancet; T M Lowe; A McLysaght; T Mikkelsen; J V Moran; N Mulder; V J Pollara; C P Ponting; G Schuler; J Schultz; G Slater; A F Smit; E Stupka; J Szustakowki; D Thierry-Mieg; J Thierry-Mieg; L Wagner; J Wallis; R Wheeler; A Williams; Y I Wolf; K H Wolfe; S P Yang; R F Yeh; F Collins; M S Guyer; J Peterson; A Felsenfeld; K A Wetterstrand; A Patrinos; M J Morgan; P de Jong; J J Catanese; K Osoegawa; H Shizuya; S Choi; Y J Chen; J Szustakowki
Journal:  Nature       Date:  2001-02-15       Impact factor: 49.962

7.  The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000.

Authors:  A Bairoch; R Apweiler
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

8.  EST_GENOME: a program to align spliced DNA sequences to unspliced genomic DNA.

Authors:  R Mott
Journal:  Comput Appl Biosci       Date:  1997-08

9.  Using GeneWise in the Drosophila annotation experiment.

Authors:  E Birney; R Durbin
Journal:  Genome Res       Date:  2000-04       Impact factor: 9.043

10.  The distributed annotation system.

Authors:  R D Dowell; R M Jokerst; A Day; S R Eddy; L Stein
Journal:  BMC Bioinformatics       Date:  2001-10-10       Impact factor: 3.169

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  625 in total

1.  The EMBL Nucleotide Sequence Database.

Authors:  Guenter Stoesser; Wendy Baker; Alexandra van den Broek; Evelyn Camon; Maria Garcia-Pastor; Carola Kanz; Tamara Kulikova; Rasko Leinonen; Quan Lin; Vincent Lombard; Rodrigo Lopez; Nicole Redaschi; Peter Stoehr; Mary Ann Tuli; Katerina Tzouvara; Robert Vaughan
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

2.  Large-scale protein annotation through gene ontology.

Authors:  Hanqing Xie; Alon Wasserman; Zurit Levine; Amit Novik; Vladimir Grebinskiy; Avi Shoshan; Liat Mintz
Journal:  Genome Res       Date:  2002-05       Impact factor: 9.043

3.  Search and retrieve. Large-scale data generation is becoming increasingly important in biological research. But how good are the tools to make sense of the data?

Authors:  Alfonso Valencia
Journal:  EMBO Rep       Date:  2002-05       Impact factor: 8.807

4.  GALA, a database for genomic sequence alignments and annotations.

Authors:  Belinda Giardine; Laura Elnitski; Cathy Riemer; Izabela Makalowska; Scott Schwartz; Webb Miller; Ross C Hardison
Journal:  Genome Res       Date:  2003-04       Impact factor: 9.043

5.  Otubains: a new family of cysteine proteases in the ubiquitin pathway.

Authors:  Maxim Y Balakirev; Sergey O Tcherniuk; Michel Jaquinod; Jadwiga Chroboczek
Journal:  EMBO Rep       Date:  2003-05       Impact factor: 8.807

6.  The transcriptional activity of human Chromosome 22.

Authors:  John L Rinn; Ghia Euskirchen; Paul Bertone; Rebecca Martone; Nicholas M Luscombe; Stephen Hartman; Paul M Harrison; F Kenneth Nelson; Perry Miller; Mark Gerstein; Sherman Weissman; Michael Snyder
Journal:  Genes Dev       Date:  2003-02-15       Impact factor: 11.361

7.  HGVbase: a curated resource describing human DNA variation and phenotype relationships.

Authors:  D Fredman; G Munns; D Rios; F Sjöholm; M Siegfried; B Lenhard; H Lehväslaiho; A J Brookes
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

8.  The Centre for Modeling Human Disease Gene Trap resource.

Authors:  Christine To; Trevor Epp; Tammy Reid; Qing Lan; Mei Yu; Carol Y J Li; Minako Ohishi; Paula Hant; Nora Tsao; Guillermo Casallo; Janet Rossant; Lucy R Osborne; William L Stanford
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

9.  The mouse Gene Expression Database (GXD): updates and enhancements.

Authors:  David P Hill; Dale A Begley; Jacqueline H Finger; Terry F Hayamizu; Ingeborg J McCright; Constance M Smith; Jon S Beal; Lori E Corbani; Judith A Blake; Janan T Eppig; James A Kadin; Joel E Richardson; Martin Ringwald
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

10.  BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics.

Authors:  Wenming Zhao; Jing Wang; Ximiao He; Xiaobing Huang; Yongzhi Jiao; Mingtao Dai; Shulin Wei; Jian Fu; Ye Chen; Xiaoyu Ren; Yong Zhang; Peixiang Ni; Jianguo Zhang; Songgang Li; Jian Wang; Gane Ka-Shu Wong; Hongyu Zhao; Jun Yu; Huanming Yang; Jun Wang
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

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