scholarly journals The UCSC Genome Browser Database: update 2009

2009 ◽  
Vol 37 (Database) ◽  
pp. D755-D761 ◽  
Author(s):  
R. M. Kuhn ◽  
D. Karolchik ◽  
A. S. Zweig ◽  
T. Wang ◽  
K. E. Smith ◽  
...  
Keyword(s):  
Ucsc Genome Browser ◽  
Genome Browser ◽  
Ucsc Genome Browser Database

scholarly journals The UCSC Genome Browser database: 2018 update

2017 ◽  
Vol 46 (D1) ◽  
pp. D762-D769 ◽  
Author(s):  
Jonathan Casper ◽  
Ann S Zweig ◽  
Chris Villarreal ◽  
Cath Tyner ◽  
Matthew L Speir ◽  
...  
Keyword(s):  
Ucsc Genome Browser ◽  
Genome Browser ◽  
Gene Interactions ◽  
Command Line ◽  
Web Interface ◽  
Variant Annotation ◽  
The Past ◽  
Ucsc Genome Browser Database ◽  
Genome Assemblies ◽  
Command Line Version

Abstract The UCSC Genome Browser (https://genome.ucsc.edu) provides a web interface for exploring annotated genome assemblies. The assemblies and annotation tracks are updated on an ongoing basis—12 assemblies and more than 28 tracks were added in the past year. Two recent additions are a display of CRISPR/Cas9 guide sequences and an interactive navigator for gene interactions. Other upgrades from the past year include a command-line version of the Variant Annotation Integrator, support for Human Genome Variation Society variant nomenclature input and output, and a revised highlighting tool that now supports multiple simultaneous regions and colors.

scholarly journals CruzDB: software for annotation of genomic intervals with UCSC genome-browser database

2013 ◽  
Vol 29 (23) ◽  
pp. 3003-3006 ◽  
Author(s):  
Brent S. Pedersen ◽  
Ivana V. Yang ◽  
Subhajyoti De
Keyword(s):  
Ucsc Genome Browser ◽  
Genome Browser ◽  
Ucsc Genome Browser Database

scholarly journals The UCSC Genome Browser database: 2015 update

2014 ◽  
Vol 43 (D1) ◽  
pp. D670-D681 ◽  
Author(s):  
Kate R. Rosenbloom ◽  
Joel Armstrong ◽  
Galt P. Barber ◽  
Jonathan Casper ◽  
Hiram Clawson ◽  
...  
Keyword(s):  
Ucsc Genome Browser ◽  
Genome Browser ◽  
Ucsc Genome Browser Database

scholarly journals The UCSC Genome Browser database: 2016 update

2015 ◽  
Vol 44 (D1) ◽  
pp. D717-D725 ◽  
Author(s):  
Matthew L. Speir ◽  
Ann S. Zweig ◽  
Kate R. Rosenbloom ◽  
Brian J. Raney ◽  
Benedict Paten ◽  
...  
Keyword(s):  
Ucsc Genome Browser ◽  
Genome Browser ◽  
Ucsc Genome Browser Database

scholarly journals The UCSC Genome Browser database: extensions and updates 2011

2011 ◽  
Vol 40 (D1) ◽  
pp. D918-D923 ◽  
Author(s):  
T. R. Dreszer ◽  
D. Karolchik ◽  
A. S. Zweig ◽  
A. S. Hinrichs ◽  
B. J. Raney ◽  
...  
Keyword(s):  
Ucsc Genome Browser ◽  
Genome Browser ◽  
Ucsc Genome Browser Database

scholarly journals The UCSC Genome Browser database: extensions and updates 2013

2012 ◽  
Vol 41 (D1) ◽  
pp. D64-D69 ◽  
Author(s):  
Laurence R. Meyer ◽  
Ann S. Zweig ◽  
Angie S. Hinrichs ◽  
Donna Karolchik ◽  
Robert M. Kuhn ◽  
...  
Keyword(s):  
Ucsc Genome Browser ◽  
Genome Browser ◽  
Ucsc Genome Browser Database

scholarly journals The UCSC Genome Browser database: update 2010

2009 ◽  
Vol 38 (Database) ◽  
pp. D613-D619 ◽  
Author(s):  
B. Rhead ◽  
D. Karolchik ◽  
R. M. Kuhn ◽  
A. S. Hinrichs ◽  
A. S. Zweig ◽  
...  
Keyword(s):  
Ucsc Genome Browser ◽  
Genome Browser ◽  
Ucsc Genome Browser Database

scholarly journals The UCSC Genome Browser database: 2021 update

2020 ◽  
Vol 49 (D1) ◽  
pp. D1046-D1057 ◽  
Author(s):  
Jairo Navarro Gonzalez ◽  
Ann S Zweig ◽  
Matthew L Speir ◽  
Daniel Schmelter ◽  
Kate R Rosenbloom ◽  
...  
Keyword(s):  
New Technologies ◽  
Ucsc Genome Browser ◽  
Regulatory Elements ◽  
Genome Browser ◽  
Eukaryotic Promoter ◽  
Ucsc Genome Browser Database ◽  
Eukaryotic Promoter Database ◽  
A Genome ◽  
Ncbi Refseq ◽  
Genome Annotations

Abstract For more than two decades, the UCSC Genome Browser database (https://genome.ucsc.edu) has provided high-quality genomics data visualization and genome annotations to the research community. As the field of genomics grows and more data become available, new modes of display are required to accommodate new technologies. New features released this past year include a Hi-C heatmap display, a phased family trio display for VCF files, and various track visualization improvements. Striving to keep data up-to-date, new updates to gene annotations include GENCODE Genes, NCBI RefSeq Genes, and Ensembl Genes. New data tracks added for human and mouse genomes include the ENCODE registry of candidate cis-regulatory elements, promoters from the Eukaryotic Promoter Database, and NCBI RefSeq Select and Matched Annotation from NCBI and EMBL-EBI (MANE). Within weeks of learning about the outbreak of coronavirus, UCSC released a genome browser, with detailed annotation tracks, for the SARS-CoV-2 RNA reference assembly.

scholarly journals The UCSC genome browser database: update 2007

2007 ◽  
Vol 35 (Database) ◽  
pp. D668-D673 ◽  
Author(s):  
R. M. Kuhn ◽  
D. Karolchik ◽  
A. S. Zweig ◽  
H. Trumbower ◽  
D. J. Thomas ◽  
...  
Keyword(s):  
Ucsc Genome Browser ◽  
Genome Browser ◽  
Ucsc Genome Browser Database
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