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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
Publications page.
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:
+
- Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M,
- Barber GP, Clawson H, Coelho A, Diekhans M, Dreszer TR, Giardine BM, Harte RA,
- Hillman-Jackson J, Hsu F, Kirkup V, Kuhn RM, Learned K, Li CH, Meyer LR, Pohl A,
- Raney BJ, Rosenbloom KR, Smith KE, Haussler D, Kent WJ.
- The UCSC Genome Browser database: update 2011.
- Nucleic Acids Res. 2010 Oct 18. [Epub ahead of print]
+ Dreszer TR, Karolchik D, Zweig AS, Hinrichs AS, Raney BJ, Kuhn RM, Meyer
+ LR, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, Pohl A, Malladi VS,
+ Li CH, Learned K, Kirkup V, Hsu F, Harte RA, Guruvadoo L, Goldman M,
+ Giardine BM, Fujita PA, Diekhans M, Cline MS, Clawson H, Barber GP,
+ Haussler D, Kent WJ.
+ The UCSC Genome Browser database: extensions and updates 2011.
+ Nucleic Acids Res. 2012 Jan;40(Database issue):D918-23.
+
+
Cite this
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
- Credits page.
+ Credits page.
+
+
UCSC ENCODE Browser/database:
+
- Rosenbloom KR, Dreszer TR, Pheasant M, Barber GP, Meyer
- LR, Pohl A, Raney BJ, Wang T, Hinrichs AS, Zweig AS,
- Fujita PA, Learned K, Rhead B, Smith KE, Kuhn RM,
- Karolchik D, Haussler D, Kent WJ.
- ENCODE whole-genome data in the UCSC Genome Browser.
- Nucleic Acids Res. 2010 Jan;38(Database issue):D620-5.
- Epub 2009 Nov 17.
+ Rosenbloom KR, Dreszer TR, Long JC, Malladi VS, Sloan CA, Raney BJ,
+ Cline MS, Karolchik D, Barber GP, Clawson H, Diekhans M, Fujita PA,
+ Goldman M, Gravell RC, Harte RA, Hinrichs AS, Kirkup VM, Kuhn RM,
+ Learned K, Maddren M, Meyer LR, Pohl A, Rhead B, Wong MC, Zweig AS,
+ Haussler D, Kent WJ.
+ ENCODE whole-genome data in the UCSC Genome Browser: update
+ 2012.
+ Nucleic Acids Res. 2012 Jan;40(Database issue):D912-7.
+
+
BLAT alignment tool:
Kent WJ.
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
tool.
Nucleic Acids Res. 2004 Jan 1;32(Database
issue):D493-6.
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
genome.
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
the GigAssembler:
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.
Screen shots:
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
manuscript, reference
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.
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