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/proCapNet.html src/hg/makeDb/trackDb/human/proCapNet.html
index 09ac9b6eb21..c5670d1a0d7 100644
--- src/hg/makeDb/trackDb/human/proCapNet.html
+++ src/hg/makeDb/trackDb/human/proCapNet.html
@@ -186,42 +186,47 @@
 <p>
 ProCapNet was developed by Kelly Cochran in the Kundaje lab at Stanford
 University. The genome-wide predictions and contribution scores were generated by
 Kelly Cochran in collaboration with the GENCODE consortium. Thanks to Kelly
 Cochran and Anshul Kundaje for making the data available.
 </p>
 
 <h2>References</h2>
 
 
 <p>
 Cochran K, Yin M, Mantripragada A, Schreiber J, Marinov GK, Shah SR, Yu H, Lis JT, Kundaje A.
 <a href="https://www.ncbi.nlm.nih.gov/pubmed/38853896" target="_blank">
 Dissecting the cis-regulatory syntax of transcription initiation with deep learning</a>.
 <em>bioRxiv</em>. 2024 Nov 21;.
-PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/38853896" target="_blank">38853896</a>; PMC: <a
+DOI: <a href="https://doi.org/10.1101/2024.05.28.596138"
+target="_blank">10.1101/2024.05.28.596138</a>; PMID: <a
+href="https://www.ncbi.nlm.nih.gov/pubmed/38853896" target="_blank">38853896</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11160661/" target="_blank">PMC11160661</a>
 </p>
 
 
 
 <p>
 Avsec Ž, Weilert M, Shrikumar A, Krueger S, Alexandari A, Dalal K, Fropf R, McAnany C, Gagneur J,
 Kundaje A <em>et al</em>.
 <a href="https://www.ncbi.nlm.nih.gov/pubmed/33603233" target="_blank">
 Base-resolution models of transcription-factor binding reveal soft motif syntax</a>.
 <em>Nat Genet</em>. 2021 Mar;53(3):354-366.
-PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/33603233" target="_blank">33603233</a>; PMC: <a
+DOI: <a href="https://doi.org/10.1038/s41588-021-00782-6"
+target="_blank">10.1038/s41588-021-00782-6</a>; PMID: <a
+href="https://www.ncbi.nlm.nih.gov/pubmed/33603233" target="_blank">33603233</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8812996/" target="_blank">PMC8812996</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>