-Follow these citation guidelines when using 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. Permission is granted for reuse of all graphics produced -by the UCSC Genome Browser website.
--Be sure to mention the release date of the genome -assembly used in your work to facilitate the examination of your data by reviewers and readers. -If you would like to add a URL to the Genome Browser displaying a specific location or -configuration, please use a Session URL. This will ensure -all data and settings remain fixed. Please do not include references -to our development servers (such as genome-test.soe.ucsc.edu) in published links or URLs.
+You are free to use all graphics produced by this website in your published work or on other websites, there +is no need to contact us to request permission, see the license page for details. +But the UCSC Genome Browser is exclusively funded by NIH and if research articles do +not cite or mention us, we cannot report the citations and it is harder for NIH to justify funding one of the +few long-term and stable resources in genomics. + +-We ask that authors cite our latest database update publications -alongside any specific tools used as described below. -For an extended list of publications produced by the UCSC Genome Browser group, see our -Publications page. It is worth noting that as of -April 1, 2020, Genome Browser papers have been cited 37,500 times in the literature. We -thank authors for the acknowledgement of our efforts.
+So you can do us a great favor if you cite the most recent NAR paper, the one +at the top of this . At the moment, the most recent paper has the PMID 36420891 and +the DOI 10.1093/nar/gkac1072. In addition, you can include a reference to the Genome +Browser website in your manuscript: http://genome.ucsc.edu or mention in the text that you used the "UCSC Genome Browser". +To cite just one of our computational tools, see the reference section below. + + +While doing this, you can check if the genome coordinates in your paper are +clear to the readers and if you specified the genome assembly that you used. +One cannot mention the genome assembly too often. Computational +biologists will appreciate if your supplemental files with genome annotations +include the genome assembly identifier directly in the file name. We try to +keep the identifiers short, currently they are "hg19" and "hg38". In a similar +vein, references to nucleotides ideally have the full chromosome position in +your publication text somewhere or in a supplemental table, and not only the +position on the transcript and or coding sequence, as transcript models can +change a lot. +
+ +To make this even easier, when refering to a gene or genomic location, you can +use the menu "My Data > My Sessions", to +generate a short, stable link to your current genome browser view for your +publication. In this way, readers can jump from your publication to this +genome location and get their view configured for your particular message. +You can even add your own annotations to the UCSC Genome Browser, either as +very simple text labels, by pasting a line like "chr1 1 1000 my_annotation" +into the box found under "My Data > Custom +Tracks" or by loading all genomics results into the browser via Track Hubs. +
-
-UCSC Genome Browser: +Original UCSC Genome Browser publication: 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.
Genome Browser screenshots: Journal-quality screenshots of the Genome Browser can be produced by using the View ->PDF utility in the top navigation bar from the tracks page. When including a screenshot in your manuscript, reference http://genome.ucsc.edu in the caption and cite -the Genome Browser paper in the manuscript. We recommend including a Session URL +the most recent Genome Browser paper in the manuscript. As mentioned above, we recommend including a My Data > My Sesssion URL of your screenshot to allow readers to interact with your data and get more information.
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.
@@ -75,61 +94,23 @@ 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.
UCSC SARS-CoV-2 Genome Browser Fernandes JD, Hinrichs AS, Clawson H, et al. The UCSC SARS-CoV-2 Genome Browser. Nat Genet. 2020 Sept 9; 52:991-998.
- - - --Annotation data: -Cite the most recent UCSC Genome Browser update in the Nucleic Acids Research -"Database" issue. A list of these papers can be found using this tailored -PubMed search. Be sure to sort the page by "Most Recent". -(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.) -
--ENCODE annotation data: -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. 2013 Jan;41(Database issue):D56-63.
--Human genome assembly: -The Genome Sequencing Consortium. -Initial -sequencing and analysis of the human genome. -Nature. 2001 Feb 15;409(6822):860-921.
-
-Very early human genome assemblies:
-Kent WJ, Haussler D.
-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.
+should, e.g. one of the thousands of GenArk assemblies that we provide, should cite the relevant sequencing paper. +Usually this information can be found on the +assembly description that appears when the genome is selected on our gateway page or on the NCBI GenBank BioProject +page of the assembly.