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kate
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Merge branch 'staticPages' of hgwdev.sdsc.edu:/data/git/kent into staticPages

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  <h1>Citing the UCSC Browser in a Publication or Web Page</h1>
  <p>
- 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: <A HREF="index.html" 
- TARGET=_blank>http://genome.ucsc.edu/</A>. 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 <B>not</B> include
- references to our development servers (such as
- genome-test.cse.ucsc.edu) in published links or URLs.</P>
- <P>
- For an extended list of publications produced by the UCSC 
- Genome Bioinformatics group, see our 
- <A HREF="goldenPath/pubs.html">Publications</A> page.</P>
- <A NAME="ref"></A>
+ 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: <a href="index.html" target=_blank>http://genome.ucsc.edu/</a>. 
+ 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 <b>not</b> include references to 
+ our development servers (such as genome-test.cse.ucsc.edu) in published links or URLs.</p>
+ <p>
+ For an extended list of publications produced by the UCSC Genome Bioinformatics group, see our 
+ <a href="goldenPath/pubs.html">Publications</a> page.</p>
  
- <P>
+ <a name="ref"></a>
+ <p>
  <h2>Genome Browser Software and Website</h2>
- <P>
- <B>UCSC Genome Browser:</B>
- Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler 
- AM, Haussler D.  
- <A HREF="http://www.genome.org/cgi/content/abstract/12/6/996" 
- TARGET=_blank>The human genome browser at UCSC</A>. 
- <em>Genome Res.</em> 2002 Jun;12(6):996-1006. </P>
+ <p>
+ <b>UCSC Genome Browser:</b>
+ Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D.  
+ <a href="http://www.genome.org/cgi/content/abstract/12/6/996" 
+ target=_blank>The human genome browser at UCSC</a>. 
+ <em>Genome Res.</em> 2002 Jun;12(6):996-1006. </p>
  
- <P>
- <B>BLAT:</B> 
+ <p>
+ <b>BLAT:</b> 
  Kent WJ. 
- <A HREF="http://www.genome.org/cgi/content/abstract/12/4/656" 
- TARGET=_blank>BLAT - the BLAST-like alignment tool</A>. 
+ <a href="http://www.genome.org/cgi/content/abstract/12/4/656" 
+ target=_blank>BLAT - the BLAST-like alignment tool</a>. 
  <em>Genome Res.</em> 2002 Apr;12(4):656-64.
- </P>
+ </p>
  
- <P>
- <B>UCSC Table Browser:</B>
- Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, 
- Haussler D, Kent WJ. 
- <A HREF="http://nar.oupjournals.org/cgi/content/abstract/32/suppl_1/D493?ijkey=06tIQcBr2VZNz&keytype=ref" 
- TARGET=_blank>The UCSC Table Browser data retrieval 
- tool</A>. 
- <em>Nucleic Acids Res</em>. 2004 Jan 1;32(Database 
- issue):D493-6.
- </P>
- <P>
- <B>BigWig and BigBed tools:</B>
+ <p>
+ <b>UCSC Table Browser:</b>
+ Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ. 
+ <a href="http://nar.oupjournals.org/cgi/content/abstract/32/suppl_1/D493?ijkey=06tIQcBr2VZNz&keytype=ref" 
+ target=_blank>The UCSC Table Browser data retrieval 
+ tool</a>. 
+ <em>Nucleic Acids Res</em>. 2004 Jan 1;32(Database issue):D493-6.
+ </p>
+ <p>
+ <b>BigWig and BigBed tools:</b>
  Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D.  
- <A HREF="http://bioinformatics.oxfordjournals.org/content/26/17/2204.long"
- TARGET=_blank>BigWig and BigBed: enabling browsing of large distributed data 
- sets</A>.
+ <a href="http://bioinformatics.oxfordjournals.org/content/26/17/2204.long"
+ target=_blank>BigWig and BigBed: enabling browsing of large distributed data sets</a>.
  <em>Bioinformatics</em>. 2010 Sep 1;26(17):2204-7. 
- </P>
- <P>
- <B>Track Data Hubs:</B>
- Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, Nguyen N, Paten 
- B, Zweig AS, Karolchik D, Kent WJ.
+ </p>
+ <p>
+ <b>Track Data Hubs:</b>
+ Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, Nguyen N, Paten B, Zweig AS, 
+ Karolchik D, Kent WJ.
  <a href="http://bioinformatics.oxfordjournals.org/content/30/7/1003"
- target="_blank">Track Data Hubs enable visualization of user-defined genome-wide
-  annotations on the UCSC Genome Browser</a>.
+ target="_blank">Track Data Hubs enable visualization of user-defined genome-wide annotations on the 
+ UCSC Genome Browser</a>.
  <em>Bioinformatics</em>. 2014 Apr 1;30(7):1003-5. Epub 2013 Nov 13.
- </P>
- <P>
- <B>UCSC Gene Sorter:</B>
+ </p>
+ <p>
+ <b>UCSC Gene Sorter:</b>
  Kent WJ, Hsu F, Karolchik D, Kuhn RM, Clawson H, Trumbower H, Haussler D. 
- <A HREF="http://www.genome.org/cgi/content/abstract/15/5/737" 
- TARGET=_blank>Exploring relationships and mining data with the UCSC Gene 
- Sorter</A>.
+ <a href="http://www.genome.org/cgi/content/abstract/15/5/737" 
+ target=_blank>Exploring relationships and mining data with the UCSC Gene Sorter</a>.
  <em>Genome Res</em>. 2005 May;15(5):737-41.
- </P>
- <P>
- <B>Genome Browser screen shots:</B> 
+ </p>
+ <p>
+ <b>Genome Browser screen shots:</b> 
  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 
  <em>http://genome.ucsc.edu</em> 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
- <em>hgsid</em> parameter. It is an internally-used parameter that expires after 
- about a day.
- </P>
- <P>
+ <em>hgsid</em> parameter. It is an internally-used parameter that expires after about a day.
+ </p>
+ <p>
  <h2>Genome Browser Data</h2>
- </P>
- <P>
- <B>Annotation data:</B>
- 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,
+ </p>
+ <p>
+ <b>Annotation data:</b>
+ 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.
  <a href="http://nar.oxfordjournals.org/content/43/D1/D670.long"
  target="_blank"> The UCSC Genome Browser database: 2015 update</a>.
  <em>Nucleic Acids Res</em>. 2015 Jan;43(Database issue):D670-81.
- PMID: <a href="http://www.ncbi.nlm.nih.gov/pubmed/25428374"
- target="_blank">25428374</a>; PMC: <a
- href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383971/"
- target="_blank">PMC4383971</a>
+ PMID: <a href="http://www.ncbi.nlm.nih.gov/pubmed/25428374" target="_blank">25428374</a>; 
+ PMC: <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383971/" target="_blank">PMC4383971</a>
  <BR>
- <em>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 
- <A HREF="goldenPath/credits.html">Credits</A> page. </em>
- </P>
- <P>
- <B>ENCODE annotation data:</B> 
- 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.
- <A HREF="http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&amp;pmid=23193274" 
- TARGET="_blank">ENCODE data in the UCSC Genome Browser: year 5 update</A>.
+ <em>(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 <a href="goldenPath/credits.html">Credits</a> page.</em>)
+ </p>
+ <p>
+ <b>ENCODE annotation data:</b> 
+ 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.
+ <a href="http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&amp;pmid=23193274" 
+ target="_blank">ENCODE data in the UCSC Genome Browser: year 5 update</a>.
  <em>Nucleic Acids Res</em>. 2013 Jan;41(Database issue):D56-63.
- </P>
- <P>
- <B>Human genome assembly:</B> 
+ </p>
+ <p>
+ <b>Human genome assembly:</b> 
  The Genome Sequencing Consortium. 
- <A HREF="http://www.nature.com/nature/journal/v409/n6822/abs/409860a0.html"
- TARGET=_blank>Initial sequencing and analysis of the human genome</A>.  
+ <a href="http://www.nature.com/nature/journal/v409/n6822/abs/409860a0.html"
+ target=_blank>Initial sequencing and analysis of the human genome</a>.  
  <em>Nature</em>. 2001 Feb 15;409(6822):860-921.<BR>
- </P>
- <P>
- <B>Very early human genome assemblies:</B> 
+ </p>
+ <p>
+ <b>Very early human genome assemblies:</b> 
  Kent WJ, Haussler D. 
- <A HREF="http://www.genome.org/cgi/content/abstract/GR-1832Rv1" 
- TARGET=_blank>Assembly of the working draft of the human genome with 
- gigAssembler</A>. 
+ <a href="http://www.genome.org/cgi/content/abstract/GR-1832Rv1" 
+ target=_blank>Assembly of the working draft of the human genome with gigAssembler</a>. 
  <em>Genome Res</em>. 2001 Sep;11(9)1541-1548.<BR>
- <em> Cite this paper when publishing results pertaining to human genome 
- assemblies prior to the 22 Dec. 2001 assembly.</em> 
- </P>
- <P>
- <B>Other genome assemblies:</B> 
- 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 
- <A HREF="goldenPath/credits.html">Credits</A> page or on the GenBank BioProject
+ <em> Cite this paper when publishing results pertaining to human genome assemblies prior to the 
+ 22 Dec. 2001 assembly.</em> 
+ </p>
+ <p>
+ <b>Other genome assemblies:</b> 
+ 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 <a href="goldenPath/credits.html">Credits</a> page or on the GenBank BioProject
  page for the organism. 
- </P>
+ </p>
  
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