Literature DB >> 14681459

Ensembl 2004.

E Birney1, 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, T Hubbard.   

Abstract

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organize biology around the sequences of large genomes. It is a comprehensive and integrated source of annotation of large genome sequences, available via interactive website, web services or flat files. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. The facilities of the system range from sequence analysis to data storage and visualization and installations exist around the world both in companies and at academic sites. With a total of nine genome sequences available from Ensembl and more genomes to follow, recent developments have focused mainly on closer integration between genomes and external data.

Mesh:

Year:  2004        PMID: 14681459      PMCID: PMC308772          DOI: 10.1093/nar/gkh038

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


  8 in total

1.  Initial sequencing and comparative analysis of the mouse genome.

Authors:  Robert H Waterston; Kerstin Lindblad-Toh; Ewan Birney; Jane Rogers; Josep F Abril; Pankaj Agarwal; Richa Agarwala; Rachel Ainscough; Marina Alexandersson; Peter An; Stylianos E Antonarakis; John Attwood; Robert Baertsch; Jonathon Bailey; Karen Barlow; Stephan Beck; Eric Berry; Bruce Birren; Toby Bloom; Peer Bork; Marc Botcherby; Nicolas Bray; Michael R Brent; Daniel G Brown; Stephen D Brown; Carol Bult; John Burton; Jonathan Butler; Robert D Campbell; Piero Carninci; Simon Cawley; Francesca Chiaromonte; Asif T Chinwalla; Deanna M Church; Michele Clamp; Christopher Clee; Francis S Collins; Lisa L Cook; Richard R Copley; Alan Coulson; Olivier Couronne; James Cuff; Val Curwen; Tim Cutts; Mark Daly; Robert David; Joy Davies; Kimberly D Delehaunty; Justin Deri; Emmanouil T Dermitzakis; Colin Dewey; Nicholas J Dickens; Mark Diekhans; Sheila Dodge; Inna Dubchak; Diane M Dunn; Sean R Eddy; Laura Elnitski; Richard D Emes; Pallavi Eswara; Eduardo Eyras; Adam Felsenfeld; Ginger A Fewell; Paul Flicek; Karen Foley; Wayne N Frankel; Lucinda A Fulton; Robert S Fulton; Terrence S Furey; Diane Gage; Richard A Gibbs; Gustavo Glusman; Sante Gnerre; Nick Goldman; Leo Goodstadt; Darren Grafham; Tina A Graves; Eric D Green; Simon Gregory; Roderic Guigó; Mark Guyer; Ross C Hardison; David Haussler; Yoshihide Hayashizaki; LaDeana W Hillier; Angela Hinrichs; Wratko Hlavina; Timothy Holzer; Fan Hsu; Axin Hua; Tim Hubbard; Adrienne Hunt; Ian Jackson; David B Jaffe; L Steven Johnson; Matthew Jones; Thomas A Jones; Ann Joy; Michael Kamal; Elinor K Karlsson; Donna Karolchik; Arkadiusz Kasprzyk; Jun Kawai; Evan Keibler; Cristyn Kells; W James Kent; Andrew Kirby; Diana L Kolbe; Ian Korf; Raju S Kucherlapati; Edward J Kulbokas; David Kulp; Tom Landers; J P Leger; Steven Leonard; Ivica Letunic; Rosie Levine; Jia Li; Ming Li; Christine Lloyd; Susan Lucas; Bin Ma; Donna R Maglott; Elaine R Mardis; Lucy Matthews; Evan Mauceli; John H Mayer; Megan McCarthy; W Richard McCombie; Stuart McLaren; Kirsten McLay; John D McPherson; Jim Meldrim; Beverley Meredith; Jill P Mesirov; Webb Miller; Tracie L Miner; Emmanuel Mongin; Kate T Montgomery; Michael Morgan; Richard Mott; James C Mullikin; Donna M Muzny; William E Nash; Joanne O Nelson; Michael N Nhan; Robert Nicol; Zemin Ning; Chad Nusbaum; Michael J O'Connor; Yasushi Okazaki; Karen Oliver; Emma Overton-Larty; Lior Pachter; Genís Parra; Kymberlie H Pepin; Jane Peterson; Pavel Pevzner; Robert Plumb; Craig S Pohl; Alex Poliakov; Tracy C Ponce; Chris P Ponting; Simon Potter; Michael Quail; Alexandre Reymond; Bruce A Roe; Krishna M Roskin; Edward M Rubin; Alistair G Rust; Ralph Santos; Victor Sapojnikov; Brian Schultz; Jörg Schultz; Matthias S Schwartz; Scott Schwartz; Carol Scott; Steven Seaman; Steve Searle; Ted Sharpe; Andrew Sheridan; Ratna Shownkeen; Sarah Sims; Jonathan B Singer; Guy Slater; Arian Smit; Douglas R Smith; Brian Spencer; Arne Stabenau; Nicole Stange-Thomann; Charles Sugnet; Mikita Suyama; Glenn Tesler; Johanna Thompson; David Torrents; Evanne Trevaskis; John Tromp; Catherine Ucla; Abel Ureta-Vidal; Jade P Vinson; Andrew C Von Niederhausern; Claire M Wade; Melanie Wall; Ryan J Weber; Robert B Weiss; Michael C Wendl; Anthony P West; Kris Wetterstrand; Raymond Wheeler; Simon Whelan; Jamey Wierzbowski; David Willey; Sophie Williams; Richard K Wilson; Eitan Winter; Kim C Worley; Dudley Wyman; Shan Yang; Shiaw-Pyng Yang; Evgeny M Zdobnov; Michael C Zody; Eric S Lander
Journal:  Nature       Date:  2002-12-05       Impact factor: 49.962

Review 2.  Databases and tools for browsing genomes.

Authors:  Ewan Birney; Michele Clamp; Tim Hubbard
Journal:  Annu Rev Genomics Hum Genet       Date:  2002-04-15       Impact factor: 8.929

3.  Ensembl 2002: accommodating comparative genomics.

Authors:  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; E Birney
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

4.  Biopipe: a flexible framework for protocol-based bioinformatics analysis.

Authors:  Shawn Hoon; Kiran Kumar Ratnapu; Jer-Ming Chia; Balamurugan Kumarasamy; Xiao Juguang; Michele Clamp; Arne Stabenau; Simon Potter; Laura Clarke; Elia Stupka
Journal:  Genome Res       Date:  2003-07-17       Impact factor: 9.043

5.  The genome sequence of the malaria mosquito Anopheles gambiae.

Authors:  Robert A Holt; G Mani Subramanian; Aaron Halpern; Granger G Sutton; Rosane Charlab; Deborah R Nusskern; Patrick Wincker; Andrew G Clark; José M C Ribeiro; Ron Wides; Steven L Salzberg; Brendan Loftus; Mark Yandell; William H Majoros; Douglas B Rusch; Zhongwu Lai; Cheryl L Kraft; Josep F Abril; Veronique Anthouard; Peter Arensburger; Peter W Atkinson; Holly Baden; Veronique de Berardinis; Danita Baldwin; Vladimir Benes; Jim Biedler; Claudia Blass; Randall Bolanos; Didier Boscus; Mary Barnstead; Shuang Cai; Angela Center; Kabir Chaturverdi; George K Christophides; Mathew A Chrystal; Michele Clamp; Anibal Cravchik; Val Curwen; Ali Dana; Art Delcher; Ian Dew; Cheryl A Evans; Michael Flanigan; Anne Grundschober-Freimoser; Lisa Friedli; Zhiping Gu; Ping Guan; Roderic Guigo; Maureen E Hillenmeyer; Susanne L Hladun; James R Hogan; Young S Hong; Jeffrey Hoover; Olivier Jaillon; Zhaoxi Ke; Chinnappa Kodira; Elena Kokoza; Anastasios Koutsos; Ivica Letunic; Alex Levitsky; Yong Liang; Jhy-Jhu Lin; Neil F Lobo; John R Lopez; Joel A Malek; Tina C McIntosh; Stephan Meister; Jason Miller; Clark Mobarry; Emmanuel Mongin; Sean D Murphy; David A O'Brochta; Cynthia Pfannkoch; Rong Qi; Megan A Regier; Karin Remington; Hongguang Shao; Maria V Sharakhova; Cynthia D Sitter; Jyoti Shetty; Thomas J Smith; Renee Strong; Jingtao Sun; Dana Thomasova; Lucas Q Ton; Pantelis Topalis; Zhijian Tu; Maria F Unger; Brian Walenz; Aihui Wang; Jian Wang; Mei Wang; Xuelan Wang; Kerry J Woodford; Jennifer R Wortman; Martin Wu; Alison Yao; Evgeny M Zdobnov; Hongyu Zhang; Qi Zhao; Shaying Zhao; Shiaoping C Zhu; Igor Zhimulev; Mario Coluzzi; Alessandra della Torre; Charles W Roth; Christos Louis; Francis Kalush; Richard J Mural; Eugene W Myers; Mark D Adams; Hamilton O Smith; Samuel Broder; Malcolm J Gardner; Claire M Fraser; Ewan Birney; Peer Bork; Paul T Brey; J Craig Venter; Jean Weissenbach; Fotis C Kafatos; Frank H Collins; Stephen L Hoffman
Journal:  Science       Date:  2002-10-04       Impact factor: 47.728

6.  The Jalview Java alignment editor.

Authors:  Michele Clamp; James Cuff; Stephen M Searle; Geoffrey J Barton
Journal:  Bioinformatics       Date:  2004-01-22       Impact factor: 6.937

7.  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

Review 8.  Apollo: a sequence annotation editor.

Authors:  S E Lewis; S M J Searle; N Harris; M Gibson; V Lyer; J Richter; C Wiel; L Bayraktaroglu; E Birney; M A Crosby; J S Kaminker; B B Matthews; S E Prochnik; C D Smithy; J L Tupy; G M Rubin; S Misra; C J Mungall; M E Clamp
Journal:  Genome Biol       Date:  2002-12-23       Impact factor: 13.583

  8 in total
  84 in total

1.  Testing computational prediction of missense mutation phenotypes: functional characterization of 204 mutations of human cystathionine beta synthase.

Authors:  Qiong Wei; Liqun Wang; Qiang Wang; Warren D Kruger; Roland L Dunbrack
Journal:  Proteins       Date:  2010-07

2.  MEROPS: the peptidase database.

Authors:  Neil D Rawlings; Dominic P Tolle; Alan J Barrett
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

3.  The Iccare web server: an attempt to merge sequence and mapping information for plant and animal species.

Authors:  Cédric Muller; Mathieu Denis; Laurent Gentzbittel; Thomas Faraut
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

4.  SNPbox: web-based high-throughput primer design from gene to genome.

Authors:  Stefan Weckx; Peter De Rijk; Christine Van Broeckhoven; Jurgen Del-Favero
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

5.  ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes.

Authors:  Ivan Ovcharenko; Marcelo A Nobrega; Gabriela G Loots; Lisa Stubbs
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

6.  MSCAN: identification of functional clusters of transcription factor binding sites.

Authors:  Wynand B L Alkema; Ojvind Johansson; Jens Lagergren; Wyeth W Wasserman
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

7.  Using Galaxy to perform large-scale interactive data analyses.

Authors:  Jennifer Hillman-Jackson; Dave Clements; Daniel Blankenberg; James Taylor; Anton Nekrutenko
Journal:  Curr Protoc Bioinformatics       Date:  2012-06

8.  PathEx: a novel multi factors based datasets selector web tool.

Authors:  Eric Bareke; Michael Pierre; Anthoula Gaigneaux; Bertrand De Meulder; Sophie Depiereux; Fabrice Berger; Naji Habra; Eric Depiereux
Journal:  BMC Bioinformatics       Date:  2010-10-22       Impact factor: 3.169

9.  Systematic recovery and analysis of full-ORF human cDNA clones.

Authors:  Agnes Baross; Yaron S N Butterfield; Shaun M Coughlin; Thomas Zeng; Malachi Griffith; Obi L Griffith; Anca S Petrescu; Duane E Smailus; Jaswinder Khattra; Helen L McDonald; Sheldon J McKay; Michelle Moksa; Robert A Holt; Marco A Marra
Journal:  Genome Res       Date:  2004-10       Impact factor: 9.043

10.  Comparative genomic analysis of human and chimpanzee indicates a key role for indels in primate evolution.

Authors:  Anna Wetterbom; Marie Sevov; Lucia Cavelier; Tomas F Bergström
Journal:  J Mol Evol       Date:  2006-10-29       Impact factor: 2.395

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