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donnak
  Wed Dec 28 23:39:25 2016 -0800
First pass at migration to new style sheet. Refs #18504

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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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