update maizecode to final version

Author: mschatz

index.html

@@ -37,27 +37,27 @@
 
 <tr>
   <td valign=top width=10>&raquo;</td>
-  <td valign=top><a href="https://www.biorxiv.org/content/10.1101/2024.12.23.629682v1">microGalaxy: A gateway to tools, workflows, and training for reproducible and FAIR analysis of microbial data </a><br>Dec 27, 2024<td> </tr> 
+  <td valign=top><a href="https://www.nature.com/articles/s41467-024-55195-w">MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication</a><br>Dec 30, 2024<td> </tr> 
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   <td valign=top width=10>&raquo;</td>
-  <td valign=top><a href="https://www.biorxiv.org/content/10.1101/2024.12.22.629724v1">Comparative genomics of the sexually transmitted parasite Trichomonas vaginalis reveals relaxed and convergent evolution and genes involved in spillover from birds to humans</a><br>Dec 25, 2024<td> </tr> 
+  <td valign=top><a href="https://www.biorxiv.org/content/10.1101/2024.12.23.629682v1">microGalaxy: A gateway to tools, workflows, and training for reproducible and FAIR analysis of microbial data </a><br>Dec 27, 2024<td> </tr> 
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   <td valign=top width=10>&raquo;</td>
-  <td valign=top><a href="https://clarivate.com/highly-cited-researchers/?action=clv_hcr_members_filter&clv-paged=1&clv-category=&clv-institution=&clv-region=&clv-name=schatz%2C%20michael">Schatz named among the most highly cited researchers in the world for 2024</a><br>Nov 19, 2024<td> </tr> 
+  <td valign=top><a href="https://www.biorxiv.org/content/10.1101/2024.12.22.629724v1">Comparative genomics of the sexually transmitted parasite Trichomonas vaginalis reveals relaxed and convergent evolution and genes involved in spillover from birds to humans</a><br>Dec 25, 2024<td> </tr> 
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   <td valign=top width=10>&raquo;</td>
-  <td valign=top><a href="https://genome.cshlp.org/content/early/2024/11/04/gr.279334.124">Gapless assembly of complete human and plant chromosomes using only nanopore sequencing</a><br>Nov 6, 2024<td> </tr> 
+  <td valign=top><a href="https://clarivate.com/highly-cited-researchers/?action=clv_hcr_members_filter&clv-paged=1&clv-category=&clv-institution=&clv-region=&clv-name=schatz%2C%20michael">Schatz named among the most highly cited researchers in the world for 2024</a><br>Nov 19, 2024<td> </tr> 
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   <td valign=top width=10>&raquo;</td>
-  <td valign=top><a href="https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btae590/7808857">BEATRICE: Bayesian Fine-mapping from Summary Data using Deep Variational Inference</a><br>Oct 3, 2024<td> </tr> 
+  <td valign=top><a href="https://genome.cshlp.org/content/early/2024/11/04/gr.279334.124">Gapless assembly of complete human and plant chromosomes using only nanopore sequencing</a><br>Nov 6, 2024<td> </tr> 
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 <tr><td colspan=2 align=right>(<a href="/news/">past news</a>)</td></tr>

news/index.html

@@ -9,6 +9,11 @@
 
 <tr><td colspan=2><br><h3>2024</h3><hr></td></tr
 
+<tr>
+  <td valign=top width=10>&raquo;</td>
+  <td valign=top><a href="https://www.nature.com/articles/s41467-024-55195-w">MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication</a><br>Dec 30, 2024<td> </tr> 
+<tr><td height=8 colspan=2></td></tr>
+
 <tr>
   <td valign=top width=10>&raquo;</td>
   <td valign=top><a href="https://www.biorxiv.org/content/10.1101/2024.12.23.629682v1">microGalaxy: A gateway to tools, workflows, and training for reproducible and FAIR analysis of microbial data </a><br>Dec 27, 2024<td> </tr> 

publications/index.html

@@ -20,54 +20,48 @@
 
 <tr><td colspan=3><h3>Preprints</h3><hr></td></tr>
 
-<tr><td valign=top align=right>P10.</td>
+<tr><td valign=top align=right>P9.</td>
 <td valign=top> <a href="https://www.biorxiv.org/content/10.1101/2024.12.22.629724v1">Comparative genomics of the sexually transmitted parasite Trichomonas vaginalis reveals relaxed and convergent evolution and genes involved in spillover from birds to humans</a><br>
 Sullivan et al (2024) <i>bioRxiv</i> https://doi.org/10.1101/2024.12.22.629724</td>
 <td valign=top> <a href="https://www.biorxiv.org/content/10.1101/2024.12.22.629724v1"><img width=50 height=70 src="thumb/2024-tvag.png"></a> </td> </tr>
 <tr><td></td></tr>
 
-<tr><td valign=top align=right>P9.</td>
+<tr><td valign=top align=right>P8.</td>
 <td valign=top> <a href="https://www.biorxiv.org/content/10.1101/2024.12.23.629682v1">microGalaxy: A gateway to tools, workflows, and training for reproducible and FAIR analysis of microbial data</a><br>
 Nasr et al (2024) <i>bioRxiv</i> https://doi.org/10.1101/2024.12.23.629682</td>
 <td valign=top> <a href="https://www.biorxiv.org/content/10.1101/2024.12.23.629682v1"><img width=50 height=70 src="thumb/2024-microgalaxy.png"></a> </td> </tr>
 <tr><td></td></tr>
 
-<tr><td valign=top align=right>P8.</td>
+<tr><td valign=top align=right>P7.</td>
 <td valign=top> <a href="https://www.biorxiv.org/content/10.1101/2024.09.10.612244v1">Solanum pan-genomics and pan-genetics reveal paralogs as contingencies in crop engineering</a><br>
 Benoit, Jenike et al (2024) <i>bioRxiv</i> https://doi.org/10.1101/2024.09.10.612244</td>
 <td valign=top> <a href="https://www.biorxiv.org/content/10.1101/2024.09.10.612244v1"><img width=50 height=70 src="thumb/2024-pansol.jpg"></a> </td> </tr>
 <tr><td></td></tr>
 
-<tr><td valign=top align=right>P7.</td>
+<tr><td valign=top align=right>P6.</td>
 <td valign=top> <a href="https://www.biorxiv.org/content/10.1101/2024.07.31.605654v1">Complete sequencing of ape genomes</a><br>
 Yoo et al (2024) <i>bioRxiv</i> doi:10.1101/2024.07.31.605654</td>
 <td valign=top> <a href="https://www.biorxiv.org/content/10.1101/2024.07.31.605654v1"><img width=50 height=70 src="thumb/2024-t2tape.jpg"></a> </td> </tr>
 <tr><td></td></tr>
 
-<tr><td valign=top align=right>P6.</td>
+<tr><td valign=top align=right>P5.</td>
 <td valign=top> <a href="https://arxiv.org/abs/2404.01519">Guide to k-mer approaches for genomics across the tree of life</a><br>
 Jenike et al. (2024) <i>arXiv</i> arXiv:2404.01519</td>
 <td valign=top> <a href="https://arxiv.org/abs/2404.01519"><img width=50 height=70 src="thumb/2024-kmer-guide.jpg"></a> </td> </tr>
 <tr><td></td></tr>
 
-<tr><td valign=top align=right>P5.</td>
+<tr><td valign=top align=right>P4.</td>
 <td valign=top> <a href="https://www.medrxiv.org/content/10.1101/2024.03.22.24304565v1">Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease</a><br>
 Jensen, Ni, et al. (2024) <i>medRxiv</i> doi: https://doi.org/10.1101/2024.03.22.24304565</td>
 <td valign=top> <a href="https://www.medrxiv.org/content/10.1101/2024.03.22.24304565v1"><img width=50 height=70 src="thumb/2024-watershed-sv.jpg"></a> </td> </tr>
 <tr><td></td></tr>
 
-<tr><td valign=top align=right>P4.</td>
+<tr><td valign=top align=right>P3.</td>
 <td valign=top> <a href="https://www.biorxiv.org/content/10.1101/2024.03.05.583511v1">Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment</a><br>
 Kovaka, S, Hook, PW, Jenike, KM, Shivakumar, V, Morina, LB, Razahhi, R, Timp, W, <b>Schatz, MC</b> (2024) <i>bioRxiv</i> doi: https://doi.org/10.1101/2024.03.05.583511</td>
 <td valign=top> <a href="https://www.biorxiv.org/content/10.1101/2024.03.05.583511v1"><img width=50 height=70 src="thumb/2024-uncalled4.jpg"></a> </td> </tr>
 <tr><td></td></tr>
 
-<tr><td valign=top align=right>P3.</td>
-<td valign=top> <a href="https://www.biorxiv.org/content/10.1101/2024.02.22.581585v1">MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication</a><br>
-Cahn et al. (2024) <i>bioRxiv</i> doi.org/10.1101/2024.02.22.581585</td>
-<td valign=top> <a href="https://www.biorxiv.org/content/10.1101/2024.02.22.581585v1"><img width=50 height=70 src="thumb/2024-maizecode.jpg"></a> </td> </tr>
-<tr><td></td></tr>
-
 <tr><td valign=top align=right>P2.</td>
 <td valign=top> <a href="https://www.biorxiv.org/content/10.1101/2023.08.24.554647v1">The genome of the Wollemi pine, a critically endangered living fossil unchanged since the Cretaceous, reveals extensive ancient transposon activity</a><br>
 Stevenson, DW, Ramakrishnan, S, de Santis Aleves, C et al.. (2023) <i>bioRxiv</i> doi: https://doi.org/10.1101/2023.08.24.554647 </td>
@@ -85,6 +79,12 @@
 
 <tr><td colspan=3><h3>2024</h3><hr></td></tr>
 
+<tr><td valign=top align=right>190.</td>
+<td valign=top> <a href="https://www.nature.com/articles/s41467-024-55195-w">MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication</a><br>
+Cahn et al. (2024) <i>Nature Communication</i> https://doi.org/10.1038/s41467-024-55195-w</td>
+<td valign=top> <a href="https://www.nature.com/articles/s41467-024-55195-w"><img width=50 height=70 src="thumb/2024-maizecode.jpg"></a> </td> </tr>
+<tr><td></td></tr>
+
 <tr><td valign=top align=right>189.</td>
 <td valign=top> <a href="https://genome.cshlp.org/content/early/2024/11/04/gr.279334.124">Gapless assembly of complete human and plant chromosomes using only nanopore sequencing </a><br>
 Koren et al. (2024) <i>Genome Research</i> doi: 10.1101/gr.279334.124 </td>