add pansol preprint and panedta final paper

Author: mschatz

index.html

@@ -37,27 +37,27 @@
 
 <tr>
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-  <td valign=top><a href="http://schatz-lab.org/people/">Welcome Nicole Brown to the lab!</a><br>Aug 26, 2024<td> </tr> 
+  <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>Sept 14, 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/btae493/7729118">ModDotPlot—rapid and interactive visualization of tandem repeats</a><br>Aug 7, 2024<td> </tr> 
+  <td valign=top><a href="https://genome.cshlp.org/content/early/2024/09/06/gr.278131.123.abstract">Differences in activity and stability drive transposable element variation in tropical and temperate maize</a><br>Sept 9, 2024<td> </tr> 
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   <td valign=top width=10>&raquo;</td>
-  <td valign=top><a href="https://www.science.org/doi/10.1126/science.ado1663">Convergent evolution of plant prickles by repeated gene co-option over deep time</a><br>Aug 6, 2024<td> </tr> 
+  <td valign=top><a href="http://schatz-lab.org/people/">Welcome Nicole Brown to the lab!</a><br>Aug 26, 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/10.1101/2024.07.31.605654v1">Complete sequencing of ape genomes</a><br>July 31, 2024<td> </tr> 
+  <td valign=top><a href="https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btae493/7729118">ModDotPlot—rapid and interactive visualization of tandem repeats</a><br>Aug 7, 2024<td> </tr> 
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 <tr>
   <td valign=top width=10>&raquo;</td>
-  <td valign=top><a href="https://genome.cshlp.org/content/early/2024/07/01/gr.277950.123.abstract">Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes</a><br>July 1, 2024<td> </tr> 
+  <td valign=top><a href="https://www.science.org/doi/10.1126/science.ado1663">Convergent evolution of plant prickles by repeated gene co-option over deep time</a><br>Aug 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 +9,16 @@
 
 <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.biorxiv.org/content/10.1101/2024.09.10.612244v1">Solanum pan-genomics and pan-genetics reveal paralogs as contingencies in crop engineering</a><br>Sept 14, 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://genome.cshlp.org/content/early/2024/09/06/gr.278131.123.abstract">Differences in activity and stability drive transposable element variation in tropical and temperate maize</a><br>Sept 9, 2024<td> </tr> 
+<tr><td height=8 colspan=2></td></tr>
+
 <tr>
   <td valign=top width=10>&raquo;</td>
   <td valign=top><a href="http://schatz-lab.org/people/">Welcome Nicole Brown to the lab!</a><br>Aug 26, 2024<td> </tr> 

publications/index.html

@@ -21,71 +21,71 @@
 <tr><td colspan=3><h3>Preprints</h3><hr></td></tr>
 
 <tr><td valign=top align=right>P12.</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>P11.</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>P11.</td>
+<tr><td valign=top align=right>P10.</td>
 <td valign=top> <a href="https://www.biorxiv.org/content/10.1101/2024.05.20.595044v1">MEM-based pangenome indexing for k-mer queries</a><br>
 Hwang et al (2024) <i>bioRxiv</i> doi:10.1101/2024.05.20.595044</td>
 <td valign=top> <a href="https://www.biorxiv.org/content/10.1101/2024.05.20.595044v1"><img width=50 height=70 src="thumb/2024-memo.jpg"></a> </td> </tr>
 <tr><td></td></tr>
 
-<tr><td valign=top align=right>P10.</td>
+<tr><td valign=top align=right>P9.</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>P9.</td>
+<tr><td valign=top align=right>P8.</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>P8.</td>
+<tr><td valign=top align=right>P7.</td>
 <td valign=top> <a href="https://www.biorxiv.org/content/10.1101/2024.03.15.585294v1">Gapless assembly of complete human and plant chromosomes using only nanopore sequencing</a><br>
 Koren et al. (2024) <i>bioRxiv</i> doi: https://doi.org/10.1101/2024.03.15.585294</td>
 <td valign=top> <a href="https://www.biorxiv.org/content/10.1101/2024.03.15.585294v1"><img width=50 height=70 src="thumb/2024-duplex.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/10.1101/2024.03.05.583511v1">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>P6.</td>
+<tr><td valign=top align=right>P5.</td>
 <td valign=top> <a href="https://www.medrxiv.org/content/10.1101/2024.03.05.24303792v1">Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation </a><br>
 Gustafson et al. (2024) <i>medRxiv</i> doi: https://doi.org/10.1101/2024.03.05.24303792</td>
 <td valign=top> <a href="https://www.medrxiv.org/content/10.1101/2024.03.05.24303792v1"><img width=50 height=70 src="thumb/2024-1kgp-ont.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.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>P4.</td>
+<tr><td valign=top align=right>P3.</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>
 <td valign=top> <a href="https://www.biorxiv.org/content/10.1101/2023.08.24.554647v1"><img width=50 height=70 src="thumb/2023-wolli.jpg"></a> </td> </tr>
 <tr><td></td></tr>
 
-<tr><td valign=top align=right>P3.</td>
+<tr><td valign=top align=right>P2.</td>
 <td valign=top> <a href="https://www.biorxiv.org/content/10.1101/2023.03.24.534116v1">BEATRICE: Bayesian Fine-mapping from Summary Data using Deep Variational Inference</a><br>
 Ghosal, S, <b>Schatz, M</b>, Venkataraman, A (2023) <i>bioRxiv</i> doi: https://doi.org/10.1101/2023.03.24.534116 </td>
 <td valign=top> <a href="https://www.biorxiv.org/content/10.1101/2023.03.24.534116v1"><img width=50 height=70 src="thumb/2023-beatrice.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/10.1101/2022.10.09.511471v1">Differences in activity and stability drive transposable element variation in tropical and temperate maize.</a><br>
-Ou, S, Collins, T, Qiu, Y, Seetharam, AS, Menard, CC, Manchanda, N, Gent, JI, <b>Schatz, MC</b>, Anderson, SN, Hufford, MB, Hirsch CN (2022) <i>bioRxiv</i> doi: https://doi.org/10.1101/2022.10.09.511471</td>
-<td valign=top> <a href="https://www.biorxiv.org/content/10.1101/2022.10.09.511471v1"><img width=50 height=70 src="thumb/2022-panedta.png"></a> </td> </tr>
-<tr><td></td></tr>
-
 <tr><td valign=top align=right>P1.</td>
 <td valign=top> <a href="https://www.biorxiv.org/content/10.1101/2022.07.07.499188v1">Modbamtools: Analysis of single-molecule epigenetic data for long-range profiling, heterogeneity, and clustering</a><br>
 Razaghi, R, Hook, PW, Ou, S, <b>Schatz, MC</b>, Hansen, KD, Jain, M, Timp, W (2022) <i>bioRxiv</i> doi: https://doi.org/10.1101/2022.07.07.499188</td>
@@ -97,6 +97,12 @@
 
 <tr><td colspan=3><h3>2024</h3><hr></td></tr>
 
+<tr><td valign=top align=right>185.</td>
+<td valign=top> <a href="https://genome.cshlp.org/content/early/2024/09/06/gr.278131.123.abstract">Differences in activity and stability drive transposable element variation in tropical and temperate maize.</a><br>
+Ou, S, Collins, T, Qiu, Y, Seetharam, AS, Menard, CC, Manchanda, N, Gent, JI, <b>Schatz, MC</b>, Anderson, SN, Hufford, MB, Hirsch CN (2024) <i>Genome Research</i> doi: 10.1101/gr.278131.123</td>
+<td valign=top> <a href="https://genome.cshlp.org/content/early/2024/09/06/gr.278131.123.abstract"><img width=50 height=70 src="thumb/2022-panedta.png"></a> </td> </tr>
+<tr><td></td></tr>
+
 <tr><td valign=top align=right>184.</td>
 <td valign=top> <a href="https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btae493/7729118">ModDotPlot - Rapid and interactive visualization of tandem repeats</a><br>
 Sweeten, AP, Schatz, MC, Phillippy, AM (2024) <i>Bioinformatics</i> doi:10.1093/bioinformatics/btae493</td>