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: 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.

UCSC Archaea Genome Browser

Chan P.P., Holmes A.D., Smith A.M., Tran D. and Lowe T.M. (2012) The UCSC Archaeal Genome Browser: 2012 update. Nucleic Acids Res. 40(1):D646-52.

Genome Browser Software and Website

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.

BLAT: 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.

BigWig and BigBed tools: Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed data sets. Bioinformatics. 2010 Sep 1;26(17):2204-7.

Track Data Hubs: Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, Nguyen N, Paten B, Zweig AS, Karolchik D, Kent WJ. Track Data Hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Bioinformatics. 2014 Apr 1;30(7):1003-5. Epub 2013 Nov 13.

UCSC Gene Sorter: Kent WJ, Hsu F, Karolchik D, Kuhn RM, Clawson H, Trumbower H, Haussler D. Exploring relationships and mining data with the UCSC Gene Sorter. Genome Res. 2005 May;15(5):737-41.

Genome Browser screen shots: Journal-quality screen shots of the Genome Browser can be produced by using the PDF/PS utility accessed via the View menu in the top navigation bar on the tracks display page. When including a screen shot in your manuscript, reference in the caption and cite the Genome Browser paper in the manuscript. When including a Genome Browser URL, please remove the hgsid parameter. It is an internally-used parameter that expires after about a day.