new ppapers

Author: Alan Boyle

_includes/pub/pub.html

@@ -7,6 +7,32 @@
 
 <table>
 
+<tr valign="top">
+<td align="right" class="bibtexnumber">
+[<a name="kenney2025">81</a>]
+</td>
+<td class="bibtexitem">
+<b>SEMplR: an R package  for transcription factor binding prediction.</b>
+<br>Kinney G, Sherpa R, Burgess J, <b>Boyle AP</b>, Phanstiel D. <b><em>submitted</em></b>  2025.
+<br><a href="pub_bib.html#kenney2025"><img src="https://img.shields.io/badge/BibTeX--green.svg"></a>
+&nbsp;<div class='altmetric-embed' data-badge-type='2' data-doi='' data-badge-popover="bottom" data-hide-no-mentions="true" style="display: inline"></div>&nbsp;<span class="__dimensions_badge_embed__" data-doi="" data-style="small_rectangle" data-legend="hover-bottom" style="display:inline; vertical-align:baseline"></span><br>
+</td>
+</tr>
+
+
+<tr valign="top">
+<td align="right" class="bibtexnumber">
+[<a name="Li2025">80</a>]
+</td>
+<td class="bibtexitem">
+<b>The IGVF Catalog - from Genetic Variation to Function.</b>
+<br>Li D, Liu S, Assis P, Li M, <u>Dong S</u>, Whaling I, Jolanki O, Kagda M, Zhang W,  Macias-Velasco J, Liu T, Cody S, Antonacci-Fulton L, Huang Y, Liu J,  Montgomery M, Zeiberg D, Jain S, Pejaver V, Bergquist T, Chen Y, Radivojac P,  Gersbach C, Sherpa R, Castro C, <b>Boyle AP</b>, Starita L, Fowler D, Ahituv N, Dey  K, Majoros W, Reddy T, Craven M, Sinha R, Cai X, Nzima M, Calderwood M,  Rozowsky J, Gerstein M, Ma J, Yue F, Cherry JM, Love MI, Engreitz J, Hitz B,  Wang T.  <b><em>Accepted, Nucleic Acids Research</em></b> 2025.
+<br><a href="pub_bib.html#Li2025"><img src="https://img.shields.io/badge/BibTeX--green.svg"></a>
+&nbsp;<div class='altmetric-embed' data-badge-type='2' data-doi='' data-badge-popover="bottom" data-hide-no-mentions="true" style="display: inline"></div>&nbsp;<span class="__dimensions_badge_embed__" data-doi="" data-style="small_rectangle" data-legend="hover-bottom" style="display:inline; vertical-align:baseline"></span><br>
+</td>
+</tr>
+
+
 <tr valign="top">
 <td align="right" class="bibtexnumber">
 [<a name="SMaHT2025">79</a>]

_includes/pub/pub_bib.html

@@ -1,5 +1,24 @@
 {% raw %}
-<h1>pub.bib</h1><a name="SMaHT2025"></a><pre>
+<h1>pub.bib</h1><a name="kenney2025"></a><pre>
+@article{<a href="pub.html#kenney2025">kenney2025</a>,
+  author = {Grace Kinney and Rintsen Sherpa and Jeremy Burgess and Alan P Boyle and Douglas Phanstiel},
+  title = {{SEMplR: an R package for transcription factor binding prediction}},
+  year = {2025},
+  abstract = {{SEMplR is an R package that predicts transcription factor binding and variant effects using SNP Effect Matrices (SEMs), providing efficient, genome-wide scoring, enrichment testing, and visualization tools for comprehensive analysis of regulatory sequences.}},
+  journal = {submitted}
+}
+</pre>
+
+<a name="Li2025"></a><pre>
+@article{<a href="pub.html#Li2025">Li2025</a>,
+  author = {Li, Daofeng and Liu, Shane and Assis, Pedro and Li, Mingjie and Dong, Shengcheng and Whaling, Ian and Jolanki, Otto and Kagda, Meenakshi and Zhang, Wenjin and Macias-Velasco, Juan and Liu, Tianjie and Cody, Sarah and Antonacci-Fulton, Lucinda and Huang, Yuanhao and Liu, Jie and Montgomery, Michael and Zeiberg, Daniel and Jain, Shantanu and Pejaver, Vikas and Bergquist, Timothy and Chen, Yile and Radivojac, Predrag and Gersbach, Charles and Sherpa, Rintsen and Castro, Christopher and Boyle, Alan P and Starita, Lea and Fowler, Douglas and Ahituv, Nadav and Dey, Kushal and Majoros, William and Reddy, Tim and Craven, Mark and Sinha, Riya and Cai, Xiangmeng and Nzima, Mpathi and Calderwood, Mike and Rozowsky, Joel and Gerstein, Mark and Ma, Jian and Yue, Feng and Cherry, J Michael and Love, Michael I and Engreitz, Jesse and Hitz, Benjamin and Wang, Ting},
+  title = {{The IGVF Catalog - from Genetic Variation to Function}},
+  year = {2025},
+  journal = {Accepted, Nucleic Acids Research}
+}
+</pre>
+
+<a name="SMaHT2025"></a><pre>
 @article{<a href="pub.html#SMaHT2025">SMaHT2025</a>,
   author = {{The Somatic Mosaicism across Human Tissues Network (SMaHT)}},
   title = {Comprehensive benchmarking of somatic mutation detection by the SMaHT Network},