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  Citing the UCSC Browser in a Publication or Web Page
 

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:

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]

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.


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:

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.