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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.
+
-
- Genome Browser Software and Website
+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.
@@ -96,32 +75,31 @@
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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- Genome Browser Data
+Genome Browser Data
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
@@ -154,26 +132,18 @@
Assembly of the working draft of the human genome with
gigAssembler.
Genome Res. 2001 Sep;11(9)1541-1548.
Cite this paper when publishing results pertaining to human genome
assemblies prior to the 22 Dec. 2001 assembly.
Other genome assemblies:
Manuscripts that include the use of Genome Browser assembly data from
organisms other than human should cite the relevant initial sequencing paper.
Often this information can be found on the Genome Browser
Credits page or on the GenBank BioProject
page for the organism.
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