6a89c12dbd7cc73c93e8be489d4e7fedf8b06670
jnavarr5
  Mon Aug 3 16:25:26 2026 -0700
Fixing dead and unstable publisher links, refs #37986

diff --git src/hg/htdocs/cite.html src/hg/htdocs/cite.html
index bb907f75556..cad28564c84 100755
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@@ -58,157 +58,157 @@
 <li><b>Screenshots:</b> Journal-quality screenshots of the Genome Browser can be produced by using
 the View -&gt; PDF utility in the top navigation bar from the tracks page. When including a
 screenshot in your manuscript, reference <em>http://genome.ucsc.edu</em> in the caption and cite
 the most recent Genome Browser paper in the manuscript. As mentioned above, we recommend including
 a <a href="goldenPath/help/hgSessionHelp.html#Introduction">My Data &gt; My Session URL</a>
 of your screenshot to allow readers to interact with your data and get more information.</li>
 </ol>
 
 <a name="ref"></a>
 <h2>Genome Browser software and website references</h2>
 
 <p>
 <strong>Most recent UCSC Genome Browser publication:</strong><br>
 Casper J, Speir ML, Raney BJ, Perez G, Nassar LR, Lee CM, Hinrichs AS, Gonzalez JN, Fischer C,
 Diekhans M <em>et al</em>.
-<a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkaf1250" target="_blank">
+<a href="https://academic.oup.com/nar/article/54/D1/D1331/8326455" target="_blank">
 The UCSC Genome Browser database: 2026 update</a>.
 <em>Nucleic Acids Res</em>. 2026 Jan 6;54(D1):D1331-D1335.
 PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/41251146/" target="_blank">41251146</a>;
 DOI: <a href="https://doi.org/10.1093/nar/gkaf1250" target="_blank">10.1093/nar/gkaf1250</a>
 </p>
 
 <p>
 <strong>Original UCSC Genome Browser publication:</strong><br>
 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 
+<a href="https://genome.cshlp.org/content/12/6/996" target="_blank">The human genome
 browser at UCSC</a>.
 <em>Genome Res.</em> 2002 Jun;12(6):996-1006.
 PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/12045153/" target="_blank">12045153</a>;
 DOI: <a href="https://doi.org/10.1101/gr.229102" target="_blank">10.1101/gr.229102</a></p>
 
 <p>
 All present and past UCSC Genome Browser updates sorted by date can be shown with this 
 <a
     target=_blank href="https://pubmed.ncbi.nlm.nih.gov/?term=%28%28UCSC+Genome+Browser%5BTitle%5D%29+AND+%28update%5BTitle%5D+OR+updates%5BTitle%5D%29+AND+%22Nucleic+acids+research%22%5BJournal%5D%29+NOT+ENCODE%5BTitle%5D&sort=date">PubMed search</a>.
 </p>
 
 <hr>
 
 <p>
 <strong>BLAT:</strong><br>
 Kent WJ. 
-<a href="http://www.genome.org/cgi/content/abstract/12/4/656" target="_blank">BLAT - the BLAST-like 
+<a href="https://genome.cshlp.org/content/12/4/656" target="_blank">BLAT - the BLAST-like
 alignment tool</a>.
 <em>Genome Res.</em> 2002 Apr;12(4):656-64.
 PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/11932250/" target="_blank">11932250</a>;
 DOI: <a href="https://doi.org/10.1101/gr.229202" target="_blank">10.1101/gr.229202</a></p>
 
 <hr>
 
 <p>
 <strong>LiftOver:</strong><br>
 Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H, Diekhans M, Furey TS, Harte
 RA, Hsu F <em>et al</em>.
-<a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkj144" target="_blank">
+<a href="https://academic.oup.com/nar/article/34/suppl_1/D590/1133884" target="_blank">
 The UCSC Genome Browser Database: update 2006</a>.
 <em>Nucleic Acids Res</em>. 2006 Jan 1;34(Database issue):D590-8.
 PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/16381938/" target="_blank">16381938</a>;
 DOI: <a href="https://doi.org/10.1093/nar/gkj144" target="_blank">10.1093/nar/gkj144</a>
 </p>
 
 <hr>
 
 <p>
 <strong>UCSC Table Browser:</strong><br>
 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" 
+<a href="https://academic.oup.com/nar/article/32/suppl_1/D493/2505322"
 target="_blank">The UCSC Table Browser data retrieval tool</a>.
 <em>Nucleic Acids Res</em>. 2004 Jan 1;32(Database issue):D493-6.
 PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/14681465/" target="_blank">14681465</a>;
 DOI: <a href="https://doi.org/10.1093/nar/gkh103" target="_blank">10.1093/nar/gkh103</a></p>
 
 <hr>
 
 <p>
 <strong>UCSC Data Integrator and Variant Annotation Integrator:</strong><br>
 Hinrichs AS, Raney BJ, Speir ML, Rhead B, Casper J, Karolchik D, Kuhn RM, Rosenbloom KR, Zweig AS,
 Haussler D <em>et al</em>.
-<a href="https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btv766"
+<a href="https://academic.oup.com/bioinformatics/article/32/9/1430/1744314"
 target="_blank">
 UCSC Data Integrator and Variant Annotation Integrator</a>.
 <em>Bioinformatics</em>. 2016 May 1;32(9):1430-2.
 PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/26740527/" target="_blank">26740527</a>;
 DOI: <a href="https://doi.org/10.1093/bioinformatics/btv766" target="_blank">10.1093/bioinformatics/btv766</a>
 </p>
 
 <hr>
 
 <p>
 <strong>BigWig and BigBed tools:</strong><br>
 Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D.  
-<a href="http://bioinformatics.oxfordjournals.org/content/26/17/2204.long" target="_blank">BigWig 
+<a href="https://academic.oup.com/bioinformatics/article/26/17/2204/199001" target="_blank">BigWig
 and BigBed: enabling browsing of large distributed data sets</a>.
 <em>Bioinformatics</em>. 2010 Sep 1;26(17):2204-7.
 PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/20639541/" target="_blank">20639541</a>;
 DOI: <a href="https://doi.org/10.1093/bioinformatics/btq351" target="_blank">10.1093/bioinformatics/btq351</a></p>
 
 <hr>
 
 <p>
 <strong>RESTful API:</strong><br>
 Lee CM, Barber GP, Casper J, Clawson H, Diekhans M, Gonzalez JN, Hinrichs AS, Lee BT, Nassar LR,
 Powell CC <em>et al</em>.
-<a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkz1012" target="_blank">
+<a href="https://academic.oup.com/nar/article/48/D1/D756/5613680" target="_blank">
 UCSC Genome Browser enters 20th year</a>.
 <em>Nucleic Acids Res</em>. 2020 Jan 8;48(D1):D756-D761.
 PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/31691824/" target="_blank">31691824</a>;
 DOI: <a href="https://doi.org/10.1093/nar/gkz1012" target="_blank">10.1093/nar/gkz1012</a>
 </p>
 
 <hr>
 
 <p>
 <strong>Track Data Hubs:</strong><br>
 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"
+<a href="https://academic.oup.com/bioinformatics/article/30/7/1003/232409"
 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.
 PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/24227676/" target="_blank">24227676</a>;
 DOI: <a href="https://doi.org/10.1093/bioinformatics/btt637" target="_blank">10.1093/bioinformatics/btt637</a></p>
 
 <hr>
 
 <p>
 <strong>Genome Browser in a Box (GBiB):</strong><br>
 Haeussler M, Raney BJ, Hinrichs AS, Clawson H, Zweig AS, Karolchik D, Casper J, Speir ML, Haussler
 D, Kent WJ.
-<a href="https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btu712"
+<a href="https://academic.oup.com/bioinformatics/article/31/5/764/317854"
 target="_blank">
 Navigating protected genomics data with UCSC Genome Browser in a Box</a>.
 <em>Bioinformatics</em>. 2015 Mar 1;31(5):764-6.
 PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/25348212/" target="_blank">25348212</a>;
 DOI: <a href="https://doi.org/10.1093/bioinformatics/btu712" target="_blank">10.1093/bioinformatics/btu712</a></p>
 
 <hr>
 
 <p>
 <strong>UCSC Gene Sorter:</strong><br>
 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 
+<a href="https://genome.cshlp.org/content/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.
 PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/15867434/" target="_blank">15867434</a>;
 DOI: <a href="https://doi.org/10.1101/gr.3694705" target="_blank">10.1101/gr.3694705</a></p>
 
 <hr>
 
 <p>
 <strong>UCSC SARS-CoV-2 Genome Browser:</strong><br>
 Fernandes JD, Hinrichs AS, Clawson H, et al. 
 <a href="https://www.nature.com/articles/s41588-020-0700-8" 
 target="_blank">The UCSC SARS-CoV-2 Genome Browser</a>.
 <em>Nat Genet.</em> 2020 Oct;52(10):991-998.
 PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/32908258/" target="_blank">32908258</a>;
 DOI: <a href="https://doi.org/10.1038/s41588-020-0700-8" target="_blank">10.1038/s41588-020-0700-8</a></p>