Literature DB >> 12519945

The UCSC Genome Browser Database.

D Karolchik1, R Baertsch, M Diekhans, T S Furey, A Hinrichs, Y T Lu, K M Roskin, M Schwartz, C W Sugnet, D J Thomas, R J Weber, D Haussler, W J Kent.   

Abstract

The University of California Santa Cruz (UCSC) Genome Browser Database is an up to date source for genome sequence data integrated with a large collection of related annotations. The database is optimized to support fast interactive performance with the web-based UCSC Genome Browser, a tool built on top of the database for rapid visualization and querying of the data at many levels. The annotations for a given genome are displayed in the browser as a series of tracks aligned with the genomic sequence. Sequence data and annotations may also be viewed in a text-based tabular format or downloaded as tab-delimited flat files. The Genome Browser Database, browsing tools and downloadable data files can all be found on the UCSC Genome Bioinformatics website (http://genome.ucsc.edu), which also contains links to documentation and related technical information.

Entities:  

Mesh：

Year:  2003        PMID： 12519945      PMCID： PMC165576          DOI： 10.1093/nar/gkg129

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


  11 in total

1.  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

2.  The Ensembl genome database project.

Authors:  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; M Clamp
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

3.  BLAT--the BLAST-like alignment tool.

Authors:  W James Kent
Journal:  Genome Res       Date:  2002-04       Impact factor: 9.043

4.  The human genome browser at UCSC.

Authors:  W James Kent; Charles W Sugnet; Terrence S Furey; Krishna M Roskin; Tom H Pringle; Alan M Zahler; David Haussler
Journal:  Genome Res       Date:  2002-06       Impact factor: 9.043

5.  Tandem repeats finder: a program to analyze DNA sequences.

Authors:  G Benson
Journal:  Nucleic Acids Res       Date:  1999-01-15       Impact factor: 16.971

6.  Ab initio gene finding in Drosophila genomic DNA.

Authors:  A A Salamov; V V Solovyev
Journal:  Genome Res       Date:  2000-04       Impact factor: 9.043

7.  Prediction of complete gene structures in human genomic DNA.

Authors:  C Burge; S Karlin
Journal:  J Mol Biol       Date:  1997-04-25       Impact factor: 5.469

Review 8.  Interspersed repeats and other mementos of transposable elements in mammalian genomes.

Authors:  A F Smit
Journal:  Curr Opin Genet Dev       Date:  1999-12       Impact factor: 5.578

9.  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

10.  Integration of cytogenetic landmarks into the draft sequence of the human genome.

Authors:  V G Cheung; N Nowak; W Jang; I R Kirsch; S Zhao; X N Chen; T S Furey; U J Kim; W L Kuo; M Olivier; J Conroy; A Kasprzyk; H Massa; R Yonescu; S Sait; C Thoreen; A Snijders; E Lemyre; J A Bailey; A Bruzel; W D Burrill; S M Clegg; S Collins; P Dhami; C Friedman; C S Han; S Herrick; J Lee; A H Ligon; S Lowry; M Morley; S Narasimhan; K Osoegawa; Z Peng; I Plajzer-Frick; B J Quade; D Scott; K Sirotkin; A A Thorpe; J W Gray; J Hudson; D Pinkel; T Ried; L Rowen; G L Shen-Ong; R L Strausberg; E Birney; D F Callen; J F Cheng; D R Cox; N A Doggett; N P Carter; E E Eichler; D Haussler; J R Korenberg; C C Morton; D Albertson; G Schuler; P J de Jong; B J Trask
Journal:  Nature       Date:  2001-02-15       Impact factor: 49.962
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  733 in total

1.  c-Myc regulates RNA splicing of the A-Raf kinase and its activation of the ERK pathway.

Authors:  Jens Rauch; Kim Moran-Jones; Valerie Albrecht; Thomas Schwarzl; Keith Hunter; Olivier Gires; Walter Kolch
Journal:  Cancer Res       Date:  2011-04-21       Impact factor: 12.701

Review 2.  Chlamydomonas reinhardtii at the crossroads of genomics.

Authors:  Arthur R Grossman; Elizabeth E Harris; Charles Hauser; Paul A Lefebvre; Diego Martinez; Dan Rokhsar; Jeff Shrager; Carolyn D Silflow; David Stern; Olivier Vallon; Zhaoduo Zhang
Journal:  Eukaryot Cell       Date:  2003-12

3.  Identification and characterization of multi-species conserved sequences.

Authors:  Elliott H Margulies; Mathieu Blanchette; David Haussler; Eric D Green
Journal:  Genome Res       Date:  2003-12       Impact factor: 9.043

4.  The UCSC Table Browser data retrieval tool.

Authors:  Donna Karolchik; Angela S Hinrichs; Terrence S Furey; Krishna M Roskin; Charles W Sugnet; David Haussler; W James Kent
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

5.  Hembase: browser and genome portal for hematology and erythroid biology.

Authors:  Sung-Ho Goh; Y Terry Lee; Gerard G Bouffard; Jeffery L Miller
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

6.  LIFEdb: a database for functional genomics experiments integrating information from external sources, and serving as a sample tracking system.

Authors:  Detlev Bannasch; Alexander Mehrle; Karl-Heinz Glatting; Rainer Pepperkok; Annemarie Poustka; Stefan Wiemann
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

7.  RTCGD: retroviral tagged cancer gene database.

Authors:  Keiko Akagi; Takeshi Suzuki; Robert M Stephens; Nancy A Jenkins; Neal G Copeland
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

8.  Mutation of l7Rn3 shows that Odz4 is required for mouse gastrulation.

Authors:  Amy C Lossie; Hisashi Nakamura; Sharon E Thomas; Monica J Justice
Journal:  Genetics       Date:  2004-10-16       Impact factor: 4.562

9.  Human ORFeome version 1.1: a platform for reverse proteomics.

Authors:  Jean-François Rual; Tomoko Hirozane-Kishikawa; Tong Hao; Nicolas Bertin; Siming Li; Amélie Dricot; Ning Li; Jennifer Rosenberg; Philippe Lamesch; Pierre-Olivier Vidalain; Tracey R Clingingsmith; James L Hartley; Dominic Esposito; David Cheo; Troy Moore; Blake Simmons; Reynaldo Sequerra; Stephanie Bosak; Lynn Doucette-Stamm; Christian Le Peuch; Jean Vandenhaute; Michael E Cusick; Joanna S Albala; David E Hill; Marc Vidal
Journal:  Genome Res       Date:  2004-10       Impact factor: 9.043

10.  1274 full-open reading frames of transcripts expressed in the developing mouse nervous system.

Authors:  Maria F Bonaldo; Thomas B Bair; Todd E Scheetz; Einat Snir; Ike Akabogu; Jennifer L Bair; Brian Berger; Keith Crouch; Aja Davis; Mari E Eyestone; Catherine Keppel; Tamara A Kucaba; Mark Lebeck; Jenny L Lin; Anna I R de Melo; Joshua Rehmann; Rebecca S Reiter; Kelly Schaefer; Christina Smith; Dylan Tack; Kurtis Trout; Val C Sheffield; Jim J-C Lin; Thomas L Casavant; Marcelo B Soares
Journal:  Genome Res       Date:  2004-10       Impact factor: 9.043
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