Follow these citation guidelines when
using applications from the Genome Browser tool suite or
data from the UCSC Genome Browser database in a research
work that will be published in a journal or on the
Internet. In addition to the relevant
paper, please include a reference to the Genome Browser
website in your manuscript: http://genome.ucsc.edu/. Be sure to
mention the release date of the genome assembly used in
your work to faciliate the examination of your data by
reviewers and the readers. Please do not include
references to our development servers (such as
genome-test.cse.ucsc.edu) in published links or URLs.
For an extended list of publications produced by the UCSC
Genome Bioinformatics group, see our
UCSC Genome Browser:
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler
AM, Haussler D.
The human genome browser at UCSC.
Genome Res. 2002 Jun;12(6):996-1006.
UCSC Genome Browser database/data:
Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M, Sloan CA, Rosenbloom KR,
Roe G, Rhead B, Raney BJ, Pohl A, Malladi VS, Li CH, Lee BT, Learned K, Kirkup V, Hsu F,
Heitner S, Harte RA, Haeussler M, Guruvadoo L, Goldman M, Giardine BM, Fujita PA, Dreszer TR,
Diekhans M, Cline MS, Clawson H, Barber GP, Haussler D, and Kent WJ.
The UCSC Genome Browser database: extensions and updates 2013.
Nucleic Acids Res. 2012 Nov 15. [Epub ahead of print]
paper for annotation data extracted from the Genome
Browser database. Annotation tracks should also be
credited according to their source, which can be found
on the track's description page or on the Genome Browser
UCSC ENCODE Browser/database:
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.
ENCODE Data in the UCSC Genome Browser: year 5 update.
Nucleic Acids Res. 2012; doi: 10.1093/nar/gks1172.
BLAT alignment tool:
BLAT - the BLAST-like alignment tool.
Genome Res. 2002 Apr;12(4):656-64.
UCSC Table Browser:
Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW,
Haussler D, Kent WJ.
The UCSC Table Browser data retrieval
Nucleic Acids Res. 2004 Jan 1;32(Database
Human genome assembly:
Work pertaining to the human genome assembly should cite
the Human Genome Consortium paper:
The Genome Sequencing Consortium.
Initial sequencing and analysis of the human
Nature. 2001 Feb 15;409(6822):860-921.
When publishing results pertaining to human genome
assemblies prior to the 22 Dec., 2001 assembly, also cite
Kent WJ, Haussler D.
Assembly of the working draft of the human
genome with gigAssembler.
Genome Res. 2001 Sep;11(9)1541-1548.
Other genome assemblies:
Manuscripts that include
the use of Genome Browser assembly data from organisms
other than H. sapiens should cite the relevant
initial sequencing paper. Most of these references can be
found on our
Publications web page.
Journal-quality screen shots of the
Genome Browser can be produced by using the PDF/PS
utility accessed via the top menu bar link on the tracks
display page. When including a screen shot in your
http://genome.ucsc.edu in the caption and cite
the Genome Browser paper in the manuscript. Don't forget
to mention the genome assembly used to produce the image.
When including a Genome Browser URL, please remove the
hgsid parameter. It is an internally-used
parameter that expires after about a day.