The UCSC Genome Browser database: 2017 update

By Cath Tyner, Galt P. Barber, Jonathan Casper, Hiram Clawson, Mark Diekhans, Christopher Eisenhart, Clay Fischer, David Gibson, Jairo Navarro Gonzalez, Luvina Guruvadoo and 16 more. Nucleic Acids Res., 2016

333 citations recorded by the source corpus.

Since its 2001 debut, the University of California, Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu/) team has provided continuous support to the international genomics and biomedical communities through a web-based, open source platform designed for the fast, scalable display of sequence alignments and annotations landscaped against a vast collection of quality reference genome assemblies. The browser's publicly accessible databases are the backbone of a rich, integrated bioinformatics tool suite that includes a graphical interface for data queries and downloads, alignment programs, command-line utilities and more. This year's highlights include newly designed home and gateway pages; a new ‘multi-region’ track display configuration for exon-only, gene-only and custom regions visualization; new genome browsers for three species (brown kiwi, crab-eating macaque and Malayan flying lemur); eight updated genome assemblies; extended support for new data types such as CRAM, RNA-seq expression data and long-range chromatin interaction pairs; and the unveiling of a new supported mirror site in Japan.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c02dda95d486c163d2f025126542aec4a76d6454

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In Molecular Biology

Citations in the corpus

Predicting the clinical impact of human mutation with deep neural networks (2018, unknown): “Canonical transcripts for protein-coding DNA sequence and multiple sequence alignments of 99 vertebrate genomes and branch length were downloaded from the UCSC genome browser 70,71 (see URLs).”
ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments (2017, methodology): “The content of the ReMap database can be browsed through four options: (i) across two mirror sites of the UCSC Genome Browser (22) where a public session has been created (Figure 2 and Supplementary Figure S3), (ii) across three Ensembl Genome Browser mirrors (16) (Supplementary Figure S4), (iii) us”
The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019 (2018, background): “Links to Ensembl (33) and the UCSC genome browser (34) provide genomic context.”
RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data (2017, methodology): “The genome sequences and annotations of all 13 species were downloaded from the UCSC genome browser (26), GENCODE (27) and Ensembl databases (28) (Supplementary Table S1).”
The UCSC Genome Browser database: 2018 update (2017, unknown): “The Genotype-Tissue Expression tracks on human assemblies involved a new form of display for the browser: bar charts within the Browser display (42).”
Supplementary Information for Predicting the clinical impact of human mutation with deep neural networks (2018, unknown): “2 Tyner, C. et al. The UCSC Genome Browser database: 2017 update. Nucleic Acids Res 45, D626-D634, doi:10.1093/nar/gkw1134 (2017). 3 Lek, M. et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature 536, 285-291, doi:10.1038/nature19057 (2016). 4 Prado-Martinez, J. et al. Great ap”