dedb2f285234e8e48ee012e0cf2d9dd7a3dd6cce kuhn Tue Oct 9 14:48:53 2012 -0700 changed refs to latest update diff --git src/hg/htdocs/cite.html src/hg/htdocs/cite.html index 33de8d1..79d171b 100755 --- src/hg/htdocs/cite.html +++ src/hg/htdocs/cite.html @@ -1,166 +1,176 @@ <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN"> <HTML> <HEAD> <META HTTP-EQUIV="Content-Type" CONTENT="text/html;CHARSET=iso-8859-1"> <TITLE>UCSC Genome Browser: Citing Us</TITLE> <LINK REL="STYLESHEET" HREF="style/HGStyle.css"> </HEAD> <BODY BGCOLOR="FFF9D2" LINK="0000CC" VLINK="#330066" ALINK="#330066"> <A NAME="TOP"></A> <TABLE BORDER=0 CELLPADDING=0 CELLSPACING=0 WIDTH="100%"> <TR><TH COLSPAN=2 ALIGN="left"><IMG SRC="images/title.jpg"></TH></TR> <TR><TD COLSPAN=2 HEIGHT=40><!--#include virtual="inc/topbar.html"--></TD></TR> <!--Content Tables-------------------------------------------------------> <TR><TD COLSPAN=2 CELLPADDING=10> <!--outer table is for border purposes--> <TABLE WIDTH="100%" BGCOLOR="#888888" BORDER="0" CELLSPACING="0" CELLPADDING="1"> <TR><TD> <TABLE BGCOLOR="fffee8" WIDTH="100%" BORDER="0" CELLSPACING="0" CELLPADDING="0"> <TR><TD> <TABLE BGCOLOR="D9E4F8" BACKGROUND="images/hr.gif" WIDTH=100%> <TR><TD> <FONT SIZE="4"><b> Citing the UCSC Browser in a Publication or Web Page</b></FONT> </TD></TR> </TABLE> <TABLE BGCOLOR="fffee8" WIDTH="100%" CELLPADDING=0> <TR><TH HEIGHT=10></TH></TR> <TR><TD WIDTH=10> </TD><TD> <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> <P> <HR> <B>UCSC Genome Browser:</B> <P> 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> <HR> <B>UCSC Genome Browser database/data:</B> + <P> - Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, - Barber GP, Clawson H, Coelho A, Diekhans M, Dreszer TR, Giardine BM, Harte RA, - Hillman-Jackson J, Hsu F, Kirkup V, Kuhn RM, Learned K, Li CH, Meyer LR, Pohl A, - Raney BJ, Rosenbloom KR, Smith KE, Haussler D, Kent WJ. - <a href="http://nar.oxfordjournals.org/content/early/2010/10/18/nar.gkq963.full.html? - ijkey=SAZMOkkaQEPBTSL&keytype=ref" TARGET=_blank>The UCSC Genome Browser database: update 2011</a>. - <em>Nucleic Acids Res</em>. 2010 Oct 18. [Epub ahead of print]</P> + Dreszer TR, Karolchik D, Zweig AS, Hinrichs AS, Raney BJ, Kuhn RM, Meyer + LR, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, Pohl A, Malladi VS, + Li CH, Learned K, Kirkup V, Hsu F, Harte RA, Guruvadoo L, Goldman M, + Giardine BM, Fujita PA, Diekhans M, Cline MS, Clawson H, Barber GP, + Haussler D, Kent WJ. + <A HREF="http://nar.oxfordjournals.org/content/40/D1/D918.long" + TARGET=_blank>The UCSC Genome Browser database: extensions and updates 2011</A>. + <em>Nucleic Acids Res</em>. 2012 Jan;40(Database issue):D918-23. + </p> + <P> 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. </P> + <A HREF="goldenPath/credits.html">Credits</A> page. + </P> + <P> <HR> <B>UCSC ENCODE Browser/database:</B> + <P> - Rosenbloom KR, Dreszer TR, Pheasant M, Barber GP, Meyer - LR, Pohl A, Raney BJ, Wang T, Hinrichs AS, Zweig AS, - Fujita PA, Learned K, Rhead B, Smith KE, Kuhn RM, - Karolchik D, Haussler D, Kent WJ. - <A HREF="http://nar.oxfordjournals.org/cgi/content/full/38/suppl_1/D620" - TARGET=_blank>ENCODE whole-genome data in the UCSC Genome Browser</A>. - <em>Nucleic Acids Res</em>. 2010 Jan;38(Database issue):D620-5. - Epub 2009 Nov 17.</P> + Rosenbloom KR, Dreszer TR, Long JC, Malladi VS, Sloan CA, Raney BJ, + Cline MS, Karolchik D, Barber GP, Clawson H, Diekhans M, Fujita PA, + Goldman M, Gravell RC, Harte RA, Hinrichs AS, Kirkup VM, Kuhn RM, + Learned K, Maddren M, Meyer LR, Pohl A, Rhead B, Wong MC, Zweig AS, + Haussler D, Kent WJ. + <A HREF="http://nar.oxfordjournals.org/content/40/D1/D912.long" + TARGET=_blank>ENCODE whole-genome data in the UCSC Genome Browser: update + 2012</A>. + <em>Nucleic Acids Res</em>. 2012 Jan;40(Database issue):D912-7. + </P> + <P> <HR> <B>BLAT alignment tool:</B> <P> Kent WJ. <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> <HR> <B>UCSC Table Browser:</B> <P> 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> <HR> <B>Human genome assembly:</B> <P> Work pertaining to the human genome assembly should cite the Human Genome Consortium paper: 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>. <em>Nature</em>. 2001 Feb 15;409(6822):860-921. </P> <P> When publishing results pertaining to human genome assemblies prior to the 22 Dec., 2001 assembly, also cite the GigAssembler: 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>. <em>Genome Res</em>. 2001 Sep;11(9)1541-1548. </P> <P> <HR> <B>Other genome assemblies:</B> <P>Manuscripts that include the use of Genome Browser assembly data from organisms other than <em>H. sapiens</em> should cite the relevant initial sequencing paper. Most of these references can be found on our <A HREF="goldenPath/pubs.html">Publications</A> web page. </P> <P> <HR> <B>Screen shots:</B> <P> 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 <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> </TD><TD WIDTH=15></TD></TR> </TABLE> <BR></TD></TR> </TABLE> </TD></TR> </TABLE> </TD></TR> </TABLE> </BODY> </HTML>