Literature DB >> 18606360

UCSC genome browser: deep support for molecular biomedical research.

Mary E Mangan1, Jennifer M Williams, Scott M Lathe, Donna Karolchik, Warren C Lathe.   

Abstract

The volume and complexity of genomic sequence data, and the additional experimental data required for annotation of the genomic context, pose a major challenge for display and access for biomedical researchers. Genome browsers organize this data and make it available in various ways to extract useful information to advance research projects. The UCSC Genome Browser is one of these resources. The official sequence data for a given species forms the framework to display many other types of data such as expression, variation, cross-species comparisons, and more. Visual representations of the data are available for exploration. Data can be queried with sequences. Complex database queries are also easily achieved with the Table Browser interface. Associated tools permit additional query types or access to additional data sources such as images of in situ localizations. Support for solving researcher's issues is provided with active discussion mailing lists and by providing updated training materials. The UCSC Genome Browser provides a source of deep support for a wide range of biomedical molecular research (http://genome.ucsc.edu).

Mesh:

Year:  2008        PMID: 18606360     DOI: 10.1016/S1387-2656(08)00003-3

Source DB:  PubMed          Journal:  Biotechnol Annu Rev        ISSN: 1387-2656


  13 in total

Review 1.  Annotating individual human genomes.

Authors:  Ali Torkamani; Ashley A Scott-Van Zeeland; Eric J Topol; Nicholas J Schork
Journal:  Genomics       Date:  2011-08-02       Impact factor: 5.736

2.  A pattern analysis of gene conversion literature.

Authors:  Mark J Lawson; Jian Jiao; Weiguo Fan; Liqing Zhang
Journal:  Comp Funct Genomics       Date:  2010-01-31

3.  Exploration of plant genomes in the FLAGdb++ environment.

Authors:  Sandra Dèrozier; Franck Samson; Jean-Philippe Tamby; Cécile Guichard; Véronique Brunaud; Philippe Grevet; Séverine Gagnot; Philippe Label; Jean-Charles Leplé; Alain Lecharny; Sébastien Aubourg
Journal:  Plant Methods       Date:  2011-03-29       Impact factor: 4.993

4.  Management of High-Throughput DNA Sequencing Projects: Alpheus.

Authors:  Neil A Miller; Stephen F Kingsmore; Andrew Farmer; Raymond J Langley; Joann Mudge; John A Crow; Alvaro J Gonzalez; Faye D Schilkey; Ryan J Kim; Jennifer van Velkinburgh; Gregory D May; C Forrest Black; M Kathy Myers; John P Utsey; Nicholas S Frost; David J Sugarbaker; Raphael Bueno; Stephen R Gullans; Susan M Baxter; Steve W Day; Ernest F Retzel
Journal:  J Comput Sci Syst Biol       Date:  2008-12-26

Review 5.  Analysis of complex disease association and linkage studies using the University of California Santa Cruz Genome Browser.

Authors:  Tianyuan Wang; Terrence S Furey
Journal:  Circ Cardiovasc Genet       Date:  2009-04

6.  GenoSets: visual analytic methods for comparative genomics.

Authors:  Aurora A Cain; Robert Kosara; Cynthia J Gibas
Journal:  PLoS One       Date:  2012-10-03       Impact factor: 3.240

7.  Genetic Association of NPY Gene Polymorphisms with Dampness-Phlegm Pattern in Korean Stroke Patients.

Authors:  Mi Mi Ko; Byoung Kab Kang; Ji Hye Lim; Myeong Soo Lee; Min Ho Cha
Journal:  Evid Based Complement Alternat Med       Date:  2011-10-29       Impact factor: 2.629

8.  Evolution of multiple phosphodiesterase isoforms in stickleback involved in cAMP signal transduction pathway.

Authors:  Yukuto Sato; Yasuyuki Hashiguchi; Mutsumi Nishida
Journal:  BMC Syst Biol       Date:  2009-02-20

9.  The database of experimentally supported targets: a functional update of TarBase.

Authors:  Giorgos L Papadopoulos; Martin Reczko; Victor A Simossis; Praveen Sethupathy; Artemis G Hatzigeorgiou
Journal:  Nucleic Acids Res       Date:  2008-10-27       Impact factor: 16.971

10.  Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API.

Authors:  Nobuaki Kono; Kazuharu Arakawa; Ryu Ogawa; Nobuhiro Kido; Kazuki Oshita; Keita Ikegami; Satoshi Tamaki; Masaru Tomita
Journal:  PLoS One       Date:  2009-11-11       Impact factor: 3.240

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