cad83b1193fe5487f19123b9ef2ffa9c0b96a3be donnak Wed Jan 15 15:06:29 2014 -0800 Redid the format of this page to shorten it and hopefully make it more usable. Added refs for big*, track hubs, and gene sorter, and updated a few of the other entries. diff --git src/hg/htdocs/cite.html src/hg/htdocs/cite.html index c39a369..a4e56bd 100755 --- src/hg/htdocs/cite.html +++ src/hg/htdocs/cite.html @@ -35,141 +35,140 @@ 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: + 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.

-

- UCSC Genome Browser database/data: - -

- Karolchik D, Barber GP, Casper J, Clawson H, Cline MS, Diekhans M, Dreszer TR, - Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hinrichs AS, - Learned K, Lee BT, Li CH, Raney BJ, Rhead B, Rosenbloom KR, Sloan CA, Speir ML, - Zweig AS, Haussler D, Kuhn RM, Kent WJ. - The UCSC Genome Browser database: 2014 update. - Nucleic Acids Res. 2013 Nov 21. [Epub ahead of print] - PMID: 24270787 -

- -

- 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: -

+ 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. 2013 Nov 30. [Epub ahead of print] +

+

+ 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. +

+

- Human genome assembly: + Genome Browser Data +

- Work pertaining to the human genome assembly should cite - the Human Genome Consortium paper: + Annotation data: + Karolchik D, Barber GP, Casper J, Clawson H, Cline MS, Diekhans M, Dreszer TR, + Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hinrichs AS, + Learned K, Lee BT, Li CH, Raney BJ, Rhead B, Rosenbloom KR, Sloan CA, Speir ML, + Zweig AS, Haussler D, Kuhn RM, Kent WJ. + The UCSC Genome Browser database: 2014 update. + Nucleic Acids Res. 2014 Jan 1;42(1):D764-70. +
+ 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. + TARGET=_blank>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: + 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. + TARGET=_blank>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 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. + 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.