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.
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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.
@@ -59,31 +59,31 @@
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 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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Annotation data:
Rosenbloom KR, Armstrong J, Barber GP, Casper J, Clawson H, Diekhans M, Dreszer TR, Fujita PA,
Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hickey G, Hinrichs AS, Hubley R, Karolchik D,
Learned K, Lee BT, Li CH, Miga KH, Nguyen N, Paten B, Raney BJ, Smit AF, Speir ML, Zweig AS,
Haussler D, Kuhn RM, Kent WJ.
The UCSC Genome Browser database: 2015 update.
Nucleic Acids Res. 2015 Jan;43(Database issue):D670-81.
PMID: 25428374;
PMC: PMC4383971
(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.)