The UCSC Genome Browser database: 2019 update
By Maximilian Haeussler, Ann S. Zweig, Cath Tyner, Matthew L. Speir, Kate R. Rosenbloom, Brian J. Raney, Christopher M. Lee, Brian T. Lee, A. Hinrichs, Jairo Navarro Gonzalez and 8 more. Nucleic Acids Res., 2018
697 citations recorded by the source corpus.
Abstract The UCSC Genome Browser (https://genome.ucsc.edu) is a graphical viewer for exploring genome annotations. For almost two decades, the Browser has provided visualization tools for genetics and molecular biology and continues to add new data and features. This year, we added a new tool that lets users interactively arrange existing graphing tracks into new groups. Other software additions include new formats for chromosome interactions, a ChIP-Seq peak display for track hubs and improved support for HGVS. On the annotation side, we have added gnomAD, TCGA expression, RefSeq Functional elements, GTEx eQTLs, CRISPR Guides, SNPpedia and created a 30-way primate alignment on the human genome. Nine assemblies now have RefSeq-mapped gene models.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/e2ee014ca2c182585d8b3fc61e97141fe0a78a61
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Citations in the corpus
- The Application of Deep Learning in Cancer Prognosis Prediction (2020, methodology): “There are several public portals of TCGA, such as TCGA data portal [19], cBioPortal [20], the University of California, Santa Cruz cancer genome browser (UCSC Xena) [21] and FIREHOSE [22].”
- The ProteomeXchange consortium in 2020: enabling ‘big data’ approaches in proteomics (2019, background): “Figure 1 highlights some of those resources, including: (i) Protein knowledge bases (UniProt (19) and neXtProt (33)), to support information about each protein’s experimental evidence; (ii) Genome browsers (Ensembl (20) and UCSC Genome Browser (34)), where it is possible to integrate proteomics and ”
- Ensembl 2021 (2020, methodology): “We also display a collection of other tracks on the genome browser, including the annotation that was submitted to INSDC as part of the publication of the reference genome (38), and community annotation of sites and regions resulting from an effort coordinated by the UCSC genome browser (43).”
- Genomic basis for RNA alterations in cancer (2020, methodology): “Moreover, we looked at the overlap between somatic eQTL and 72,987 GeneHancer 89 enhancers-to-genes interactions, with at least two independent supporting methods (called ‘double-elite’), downloaded from the UCSC hg19 GeneHancer track 90 .”