The UCSC Genome Browser database: 2015 update

By Kate R. Rosenbloom, J. Armstrong, Galt P. Barber, Jonathan Casper, Hiram Clawson, Mark Diekhans, Timothy R. Dreszer, Pauline A. Fujita, Luvina Guruvadoo, Maximilian Haeussler and 19 more. Nucleic Acids Res., 2014

993 citations recorded by the source corpus.

Launched in 2001 to showcase the draft human genome assembly, the UCSC Genome Browser database (http://genome.ucsc.edu) and associated tools continue to grow, providing a comprehensive resource of genome assemblies and annotations to scientists and students worldwide. Highlights of the past year include the release of a browser for the first new human genome reference assembly in 4 years in December 2013 (GRCh38, UCSC hg38), a watershed comparative genomics annotation (100-species multiple alignment and conservation) and a novel distribution mechanism for the browser (GBiB: Genome Browser in a Box). We created browsers for new species (Chinese hamster, elephant shark, minke whale), ‘mined the web’ for DNA sequences and expanded the browser display with stacked color graphs and region highlighting. As our user community increasingly adopts the UCSC track hub and assembly hub representations for sharing large-scale genomic annotation data sets and genome sequencing projects, our menu of public data hubs has tripled.

Subfields: Ecology, Molecular Biology

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Citations in the corpus

Ensembl 2016 (2015, methodology): “While acting as a hub of reference and baseline data similar to the UCSC Genome Browser (1) and RefSeq (2), we also distribute datasets we create and promote standards and interoperability between genomic resources.”
dbSUPER: a database of super-enhancers in mouse and human genome (2015, background): “Once a user clicks the visualization icon, dbSUPER will redirect user to UCSC Genome Browser and a custom track will be added to the UCSC genome browser session automatically.”
The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog) (2016, methodology): “GWAS Catalog data are also integrated into many bioinformatics resources including Ensembl (12), the UCSC Genome Browser (13), PheGenI (14), HuGE Navigator (15) and GWASdb (16).”
Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families (2017, methodology): “Valuable research outputs that are often locked up in figures and supplementary information files are encapsulated in Rfam entries and made accessible through the Rfam website and other resources that integrate the Rfam data, such as Ensembl (1) and UCSC (2) genome browsers.”
dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Non-synonymous and Splice Site SNVs (2016, methodology): “0. dbNSFP has gained popularity among human geneticists and has been adopted by mainstream annotation tools/resources, including the UCSC Genome Browser’s Variant Annotation Integrator (http://genome.ucsc.edu/cgi-bin/hgVai), Ensembl’s Variant Effect Predictor [McLaren et al., 2010], ANNOVAR [Wang et”
The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases (2015, background): “Each row is expandable by just one click to view the sequence alignment from the element, its details in the other species and a screenshot of the genomic location of the element from the UCSC genome browser (29).”
Tissue-specific mutation accumulation in human adult stem cells during life (2016, positive): “To generate a conserved DNA replication timing profile for the human genome, we downloaded 16 Repli-seq data sets from the ENCODE project 33 at the University of California, SantaCruz (UCSC) genome browser 34 (GRCh37/hg19).”
Ensembl 2017 (2016, methodology): “We collaborate with other informatics resources and tools including the Genome Reference Consortium (GRC) (15), the UCSC Genome Browser (16), UniProt (17), model organism databases (18,19) and relevant resources at the NCBI (20) to coordinate data presentation and standards.”
GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes (2015, methodology): “(A) Direct link to the genomic locus of the tRNA gene with the display of related data tracks in the UCSC Genome Browser (3) is provided when available.”
Next-generation diagnostics and disease-gene discovery with the Exomiser (2015, methodology): “49) and SIFT 50 , as provided by dbNSFP 51 ; variant annotations by Jannovar 27 ; and gene and transcript definitions by UCSC Genome Browser database 52 .”
A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease. (2016, methodology): “Conservation scores PhastCons and PhyloP 42 for 9 primates, 32 mammals, and 45 vertebrates multi-species alignments were derived from UCSC.”
Using the Neandertal genome to study the evolution of small insertions and deletions in modern humans (2017, methodology): “2001) (GhRch37/hg19) and six primates (chimpanzee [45] (panTro4), gorilla [46] (gorGor3), orangutan [47] (ponAbe2), gibbon [48] (nomLeu1), rhesus macaque [49] (rheMac3) and marmoset [50] (calJac3)) were downloaded from the UCSC genome browser [51] and converted into MAF format.”
WormBase 2016: expanding to enable helminth genomic research (2015, background): “org/about/ userguide/wormbasehubs) is updated with every WormBase release, and allows, for the first time, current WormBase genomes and annotations to be viewed in the UCSC genome browser (41).”