0800aafe419bb4a252a0656a75b83e89ef27ec20
hiram
  Thu May 22 14:20:58 2025 -0700
use standard UCSC format for reference refs #34917

diff --git src/hg/makeDb/trackDb/contrib/tiberius/Tiberius.html src/hg/makeDb/trackDb/contrib/tiberius/Tiberius.html
index c8e28060d1c..317a4808d94 100644
--- src/hg/makeDb/trackDb/contrib/tiberius/Tiberius.html
+++ src/hg/makeDb/trackDb/contrib/tiberius/Tiberius.html
@@ -1,11 +1,23 @@
 <h2 id="description">UCSC Tiberius Track</h2>
 <p>The protein-coding genes were predicted with Tiberius in <i>ab initio</i> mode. The soft-masked genome was input only. The command was:</p>
 <code>tiberius.py --genome genome.fa --out tiberius.gtf</code>
 <p><a href="https://bioinf.uni-greifswald.de/bioinf/tiberius/genes/tib-tbl.html">Table with predicted coordinates, protein sequences and coding sequences of all mammals.</a></p>
 <p>Download code and see accuracy statistics on the <a href="https://github.com/Gaius-Augustus/Tiberius">Tiberius GitHub page</a>.</p>
 <p>Tiberius is a deep learning model that combines a HMM layer with other sequence-to-sequence models (convolutional neural networks, LSTM).</p>
 <p>Tiberius was trained on 32 mammalian genomes that did not include any <i>Hominidae</i> (see supplements of below preprint).</p>
 <h2 id="credits">Contact</h2>
 <p>Questions should be directed to <a href="mailto:lars.gabriel@uni-greifswald.de">Lars Gabriel</a> or <a href="mailto:mario.stanke@uni-greifswald.de">Mario Stanke</a>.</p>
+
 <h2 id="reference">Reference</h2>
-<a href="https://academic.oup.com/bioinformatics/article/40/12/btae685/7903281">Tiberius: End-to-End Deep Learning with an HMM for Gene Prediction. Lars Gabriel, Felix Becker, Katharina J. Hoff and Mario Stanke, <i>Bioinformatics</i> 2024;</a>, https://doi.org/10.1093/bioinformatics/btae685
+
+<p>
+Gabriel L, Becker F, Hoff KJ, Stanke M.
+<a href="https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btae685"
+target="_blank">
+Tiberius: end-to-end deep learning with an HMM for gene prediction</a>.
+<em>Bioinformatics</em>. 2024 Nov 28;40(12).
+DOI: <a href="https://doi.org/10.1093/bioinformatics/btae685"
+target="_blank">10.1093/bioinformatics/btae685</a>; PMID: <a
+href="https://www.ncbi.nlm.nih.gov/pubmed/39558581" target="_blank">39558581</a>; PMC: <a
+href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11645249/" target="_blank">PMC11645249</a>
+</p>