67d52a65f28f7f85656b89616c6012501bbdbabc
markd
  Sun Sep 20 09:38:48 2026 -0700
Add DOI links to the ProCapNet and PRO-cap track references. refs #35528

Regenerated both reference sections with getTrackReferences --doi, keeping the
citation order each page already had rather than the tool's alphabetical order,
so the Cochran and Tome primary papers stay first.

Claude-Session: https://claude.ai/code/session_01LAB6jWshLvB7eNXQKWVuW5

diff --git src/hg/makeDb/trackDb/human/encode4ProCap.html src/hg/makeDb/trackDb/human/encode4ProCap.html
index f9adddd77a4..bc9dbff8ba0 100644
--- src/hg/makeDb/trackDb/human/encode4ProCap.html
+++ src/hg/makeDb/trackDb/human/encode4ProCap.html
@@ -120,41 +120,45 @@
 <p>
 PRO-cap data was generated as part of ENCODE by Sagar Shah and the Yu and Lis labs
 at Cornell University. Thanks to the ENCODE Consortium and the ENCODE production
 laboratories for making the data available.
 </p>
 
 <h2>References</h2>
 
 
 <p>
 Tome JM, Tippens ND, Lis JT.
 <a href="https://www.ncbi.nlm.nih.gov/pubmed/30349116" target="_blank">
 Single-molecule nascent RNA sequencing identifies regulatory domain architecture at promoters and
 enhancers</a>.
 <em>Nat Genet</em>. 2018 Nov;50(11):1533-1541.
-PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/30349116" target="_blank">30349116</a>; PMC: <a
+DOI: <a href="https://doi.org/10.1038/s41588-018-0234-5"
+target="_blank">10.1038/s41588-018-0234-5</a>; PMID: <a
+href="https://www.ncbi.nlm.nih.gov/pubmed/30349116" target="_blank">30349116</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6422046/" target="_blank">PMC6422046</a>
 </p>
 
 
 
 <p>
 Kwak H, Fuda NJ, Core LJ, Lis JT.
 <a href="https://www.ncbi.nlm.nih.gov/pubmed/23430654" target="_blank">
 Precise maps of RNA polymerase reveal how promoters direct initiation and pausing</a>.
 <em>Science</em>. 2013 Feb 22;339(6122):950-3.
+DOI: <a href="https://doi.org/10.1126/science.1229386" target="_blank">10.1126/science.1229386</a>;
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/23430654" target="_blank">23430654</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3974810/" target="_blank">PMC3974810</a>
 </p>
 
 
 
 <p>
 Luo Y, Hitz BC, Gabdank I, Hilton JA, Kagda MS, Lam B, Myers Z, Sud P, Jou J, Lin K <em>et al</em>.
 <a href="https://www.ncbi.nlm.nih.gov/pubmed/31713622" target="_blank">
 New developments on the Encyclopedia of DNA Elements (ENCODE) data portal</a>.
 <em>Nucleic Acids Res</em>. 2020 Jan 8;48(D1):D882-D889.
-PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/31713622" target="_blank">31713622</a>; PMC: <a
+DOI: <a href="https://doi.org/10.1093/nar/gkz1062" target="_blank">10.1093/nar/gkz1062</a>; PMID: <a
+href="https://www.ncbi.nlm.nih.gov/pubmed/31713622" target="_blank">31713622</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7061942/" target="_blank">PMC7061942</a>
 </p>