The UCSC Genome Browser database: 2021 update.

Nucleic Acids Research
Jairo Navarro GonzalezW James Kent

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.

References

Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Jan 11, 2000·Nucleic Acids Research·S T SherryK Sirotkin
Jun 5, 2002·Genome Research·W James KentDavid Haussler
Dec 19, 2003·Nucleic Acids Research·Donna KarolchikW James Kent
Apr 7, 2009·American Journal of Human Genetics·Helen V FirthNigel P Carter
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jan 19, 2010·Bioinformatics·Heng Li, Richard Durbin
Apr 27, 2011·Human Mutation·Ivo F A C FokkemaJohan T den Dunnen
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Sep 8, 2012·Nature·UNKNOWN ENCODE Project Consortium
Nov 30, 2012·Nucleic Acids Research·Dennis A BensonEric W Sayers
Nov 30, 2012·Nucleic Acids Research·Ilkka LappalainenDeanna M Church
Nov 1, 2013·Nucleic Acids Research·Jeffrey R MacDonaldStephen W Scherer
Mar 29, 2014·Nature·Robin AnderssonAlbin Sandelin
Mar 29, 2014·Nature·Alistair R R ForrestYoshihide Hayashizaki
Nov 8, 2014·Nucleic Acids Research·René DreosPhilipp Bucher
Feb 20, 2015·Nature·UNKNOWN Roadmap Epigenomics ConsortiumManolis Kellis
Mar 10, 2015·Nature Methods·Daehwan KimSteven L Salzberg
May 28, 2015·The New England Journal of Medicine·Heidi L RehmUNKNOWN ClinGen
Jul 29, 2016·Cell Systems·Neva C DurandErez Lieberman Aiden
Dec 3, 2016·Nucleic Acids Research·René DreosPhilipp Bucher
Apr 7, 2017·Euro Surveillance : Bulletin Européen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin·Yuelong Shu, John McCauley
Nov 8, 2017·Nucleic Acids Research·Ioanna KalvariAnton I Petrov
Aug 26, 2018·Genome Biology·Peter KerpedjievNils Gehlenborg
Oct 12, 2018·Nucleic Acids Research·Bryony BraschiElspeth Bruford
Oct 26, 2018·Nucleic Acids Research·Adam FrankishPaul Flicek
Nov 6, 2018·Nucleic Acids Research·UNKNOWN UniProt Consortium
Jun 6, 2019·Nucleic Acids Research·Daofeng LiTing Wang
Aug 31, 2019·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Johannes BirgmeierGill Bejerano
Nov 30, 2019·Nucleic Acids Research·Melissa J LandrumBrandi L Kattman
Mar 28, 2020·Molecular Cell·Nils KrietensteinOliver J Rando
May 29, 2020·Nature·Konrad J KarczewskiDaniel G MacArthur
Jul 31, 2020·Nature·UNKNOWN ENCODE Project ConsortiumZhiping Weng
Sep 11, 2020·Nature Genetics·Jason D FernandesMaximilian Haeussler

❮ Previous
Next ❯

Citations

Apr 15, 2021·Proceedings of the National Academy of Sciences of the United States of America·Daniel AldeaYana G Kamberov
May 2, 2021·Trends in Genetics : TIG·Václav BrázdaRichard P Bowater
Apr 12, 2021·The European Journal of Neuroscience·Jacobus C BuurstedeOnno C Meijer
Jun 8, 2021·Current Opinion in Plant Biology·Elena V ZemlyanskayaVictoria Mironova
Jun 25, 2021·PLoS Genetics·Longhua GuoLeonid Kruglyak
Jul 16, 2021·Frontiers in Molecular Biosciences·Nanhong LiJian Huang
Jul 31, 2021·NAR Genomics and Bioinformatics·Enrique BlancoSergi Aranda
Jun 24, 2021·Angewandte Chemie·Sridhar SreeramuluHarald Schwalbe
Aug 1, 2021·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·Onur YilmazIbrahim Cemal
Aug 22, 2021·Nucleic Acids Research·Patricia P ChanTodd M Lowe
Aug 26, 2021·Nature Communications·Vikram AgarwalJay Shendure
Aug 28, 2021·Life Science Alliance·Melissa BotheSebastiaan H Meijsing
Aug 13, 2021·Genome Biology and Evolution·Andrea Talenti, James Prendergast
Sep 8, 2021·Frontiers in Cell and Developmental Biology·Oza ZaheedKellie Dean
Sep 21, 2021·ELife·Gabriela Santos-RodriguezRobert J Weatheritt
Oct 13, 2021·Molecular Cell·Sneha GopalanThomas G Fazzio
Oct 14, 2021·Briefings in Bioinformatics·Lihua JiaHuiyong Zhang
Nov 11, 2021·Nucleic Acids Research·Pora KimXiaobo Zhou
Nov 11, 2021·Nucleic Acids Research·Jose Manuel RodriguezMichael L Tress
Nov 16, 2021·Genome Biology·Yu ChenZechen Chong

❮ Previous
Next ❯

Methods Mentioned

BETA
RNA-seq
glycosylation
ChIP-seq
Hi-C
single-cell sequencing

Software Mentioned

bigDbSnp
Hisat2
JuiceBox
UCSC Genome Browser Basics
GISAID
DECIPHER
MySQL
Ensembl
Genome Browser
3D Genome Browser

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Current Protocols in Human Genetics
Donna KarolchikW James Kent
Current Protocols in Bioinformatics
Donna KarolchikW James Kent
Nucleic Acids Research
Donna KarolchikUniversity of California Santa Cruz
Cold Spring Harbor Protocols
Jui-Hung Hung, Zhiping Weng
Nature Genetics
Jason D FernandesMaximilian Haeussler
© 2021 Meta ULC. All rights reserved