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ready UCSC Genome Browser database

General Information
Genome assemblies and aligned annotations for a wide range of vertebrates and model organisms, along with an integrated tool set for visualizing, comparing, analyzing and sharing both publicly available and user-generated genomic datasets.

Homepage http://genome.ucsc.edu

Countries that developed this resource United States

Created in 2001

Taxonomic range





How to cite this record FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Nov 28 2021 2:32 a.m.


This record is maintained by BrianLee  ORCID

Record updated: June 30, 2021, 6:23 p.m. by BrianLee.

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Tools

Access / Retrieve Data

Conditions of Use

Applies to: General

Data Versioning

Data Release

Data Curation

Data Access




Publications

The UCSC Genome Browser database: extensions and updates 2013

Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, et al.
Nucleic Acids Res 2013

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The UCSC Table Browser data retrieval tool

Karolchik D., Hinrichs AS., Furey TS., Roskin KM., Sugnet CW., Haussler D., Kent WJ.,
Nucleic Acids Res. 2004

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The human genome browser at UCSC

Kent WJ., Sugnet CW., Furey TS., Roskin KM., Pringle TH., Zahler AM., Haussler D.,
Genome Res. 2002

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ENCODE data in the UCSC Genome Browser: year 5 update

Rosenbloom KR, Sloan CA, Malladi VS, Dreszer TR, Learned K, Kirkup VM, Wong MC, Maddren M, Fang R, Heitner SG, Lee BT, Barber GP, Harte RA, Diekhans M, Long JC, Wilder SP, Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ
Nucleic Acids Res. 2013

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BLAT--the BLAST-like alignment tool.

Kent WJ.,
Genome Res. 2002

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Exploring relationships and mining data with the UCSC Gene Sorter

Kent WJ, Hsu F, Karolchik D, Kuhn RM, Clawson H, Trumbower H, Haussler D
Genome Res. 2005

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The UCSC Genome Browser

Karolchik D, Hinrichs AS, Kent WJ
Curr Protoc Bioinformatics 2012

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Initial sequencing and analysis of the human genome

Lander ES., Linton LM., Birren B., Nusbaum C., Zody MC., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W., Funke R. et al.
Nature 2001

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Assembly of the working draft of the human genome with GigAssembler.

Kent WJ., Haussler D.,
Genome Res. 2001

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The UCSC Genome Browser database: 2016 update.

Speir ML,Zweig AS,Rosenbloom KR,Raney BJ,Paten B,Nejad P,Lee BT,Learned K,Karolchik D,Hinrichs AS,Heitner S,Harte RA,Haeussler M,Guruvadoo L,Fujita PA,Eisenhart C,Diekhans M,Clawson H,Casper J,Barber GP,Haussler D,Kuhn RM,Kent WJ
Nucleic Acids Res 2015

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The UCSC Genome Browser database: 2015 update.

Rosenbloom KR et al.
Nucleic Acids Res 2014

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The UCSC Genome Browser database: 2017 update.

Tyner C, et al.
Nucleic Acids Res 2016

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UCSC Genome Browser enters 20th year.

Lee CM, Barber GP, Casper J, Clawson H, Diekhans M, Gonzalez JN, Hinrichs AS, Lee BT, Nassar LR, Powell CC, Raney BJ, Rosenbloom KR, Schmelter D, Speir ML, Zweig AS, Haussler D, Haeussler M, Kuhn RM, Kent WJ.
Nucleic Acids Res. 2020

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The UCSC Genome Browser database: 2019 update

Haeussler M, Zweig AS, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Hinrichs AS, Gonzalez JN, Gibson D, Diekhans M, Clawson H, Casper J, Barber GP, Haussler D, Kuhn RM, Kent WJ.
Nucleic Acids Res. 2019

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The UCSC Genome Browser database: 2018 update.

Casper J, et al.
Nucleic Acids Res. 2018

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The UCSC Genome Browser database: 2021 update.

Navarro Gonzalez J,Zweig AS,Speir ML,Schmelter D,Rosenbloom KR,Raney BJ,Powell CC,Nassar LR,Maulding ND,Lee CM,Lee BT,Hinrichs AS,Fyfe AC,Fernandes JD,Diekhans M,Clawson H,Casper J,Benet-Pages A,Barber GP,Haussler D,Kuhn RM,Haeussler M,Kent WJ
Nucleic Acids Res 2020

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The UCSC SARS-CoV-2 Genome Browser.

Fernandes JD,Hinrichs AS,Clawson H,Gonzalez JN,Lee BT,Nassar LR,Raney BJ,Rosenbloom KR,Nerli S,Rao AA,Schmelter D,Fyfe A,Maulding N,Zweig AS,Lowe TM,Ares M Jr,Corbet-Detig R,Kent WJ,Haussler D,Haeussler M
Nat Genet 2020

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The UCSC repeat browser allows discovery and visualization of evolutionary conflict across repeat families.

Fernandes JD,Zamudio-Hurtado A,Clawson H,Kent WJ,Haussler D,Salama SR,Haeussler M
Mob DNA 2020

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Ultrafast Sample Placement on Existing Trees (UShER) Empowers Real-Time Phylogenetics for the SARS-CoV-2 Pandemic.

Turakhia Y,Thornlow B,Hinrichs AS,De Maio N,Gozashti L,Lanfear R,Haussler D,Corbett-Detig R
bioRxiv 2020

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