update to publications page

bergmanlab · Jul 18, 2024 · 1bae180 · 1bae180
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diff --git a/Publications/index.md b/Publications/index.md
@@ -8,10 +8,10 @@ Contributions from Bergman Lab members are underlined in the publication list be
 <span style="text-decoration: underline;">Chen, J.</span>, D.J. Garfinkel &amp; <span style="text-decoration: underline;">C.M. Bergman</span> (submitted) Horizontal transfer and recombination fuel Ty4 retrotransposon evolution in <em>Saccharomyces</em>. [<a href="https://www.biorxiv.org/content/10.1101/2023.12.20.572574v1">preprint</a>]
 
 ## 2024
-Hannon-Hatfield, J.A., <span style="text-decoration: underline;">Chen, J.</span>, <span style="text-decoration: underline;">C.M. Bergman</span> &amp;&nbsp; D.J. Garfinkel (in prep) Evolution of a restriction factor by domestication of a yeast retrotransposon.
+Hannon-Hatfield, J.A., <span style="text-decoration: underline;">Chen, J.</span>, <span style="text-decoration: underline;">C.M. Bergman</span> &amp;&nbsp; D.J. Garfinkel (2024) Evolution of a restriction factor by domestication of a yeast retrotransposon. <a href="https://academic.oup.com/mbe/article/41/3/msae050/7621844" rel="nofollow"><em>Mol. Biol. Evol.</em> <strong>41</strong>:msae050</a>.
 
 ## 2023
-<span style="text-decoration: underline;">Chen, J.</span> (2023) Bioinformatics and evolutionary genomics of transposable elements in yeast. Ph.D. Thesis, University of Georgia, USA.
+<span style="text-decoration: underline;">Chen, J.</span> (2023) <a href="https://www.proquest.com/docview/2917422789" rel="nofollow">Bioinformatics and evolutionary genomics of transposable elements in yeast.</a> Ph.D. Thesis, University of Georgia, USA.
 
 <span style="text-decoration: underline;">Chen, J.</span>, <span style="text-decoration: underline;">P.J. Basting</span>, <span style="text-decoration: underline;">S. Han</span>, D.J. Garfinkel &amp; <span style="text-decoration: underline;">C.M. Bergman</span> (2023) Reproducible evaluation of transposable element detectors with  McClintock 2 guides accurate inference of Ty insertion patterns in yeast. <a href="https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-023-00296-4" rel="nofollow"><em>Mobile DNA</em> <strong>14</strong>:8</a>.
 

diff --git a/_site/Blog/index.html b/_site/Blog/index.html
@@ -33,7 +33,7 @@
 
 
 
-  <meta name="twitter:site" content="@caseybergman">
+  <meta name="twitter:site" content="@bergmanlab">
   <meta name="twitter:title" content="Blog">
   <meta name="twitter:description" content="Department of Genetics &amp; Institute of Bioinformatics, UGA.">
   <meta name="twitter:url" content="http://localhost:4000/Blog/">
@@ -125,7 +125,7 @@
     <div class="masthead__menu">
       <nav id="site-nav" class="greedy-nav">
 
-          <a class="site-logo" href="/"><img src="/assets/images/casey_profile.jpg" alt="Bergman Lab"></a>
+          <a class="site-logo" href="/"><img src="/assets/images/slow-food-logo-redlarge.jpg" alt="Bergman Lab"></a>
 
         <a class="site-title" href="/">
           Bergman Lab
@@ -283,7 +283,7 @@ <h2 class="archive__item-title no_toc" itemprop="headline">
 
 
 
-          <li><a href="https://twitter.com/caseybergman" rel="nofollow noopener noreferrer"><i class="fab fa-fw fa-twitter-square" aria-hidden="true"></i> Twitter</a></li>
+          <li><a href="https://twitter.com/bergmanlab" rel="nofollow noopener noreferrer"><i class="fab fa-fw fa-twitter-square" aria-hidden="true"></i> Twitter</a></li>
 
 
 

diff --git a/_site/Join/index.html b/_site/Join/index.html
@@ -33,7 +33,7 @@
 
 
 
-  <meta name="twitter:site" content="@caseybergman">
+  <meta name="twitter:site" content="@bergmanlab">
   <meta name="twitter:title" content="Open lab positions">
   <meta name="twitter:description" content="Department of Genetics &amp; Institute of Bioinformatics, UGA.">
   <meta name="twitter:url" content="http://localhost:4000/Join/">
@@ -125,7 +125,7 @@
     <div class="masthead__menu">
       <nav id="site-nav" class="greedy-nav">
 
-          <a class="site-logo" href="/"><img src="/assets/images/casey_profile.jpg" alt="Bergman Lab"></a>
+          <a class="site-logo" href="/"><img src="/assets/images/slow-food-logo-redlarge.jpg" alt="Bergman Lab"></a>
 
         <a class="site-title" href="/">
           Bergman Lab
@@ -271,7 +271,7 @@ <h1 id="page-title" class="page__title" itemprop="headline">
 
 
 
-          <li><a href="https://twitter.com/caseybergman" rel="nofollow noopener noreferrer"><i class="fab fa-fw fa-twitter-square" aria-hidden="true"></i> Twitter</a></li>
+          <li><a href="https://twitter.com/bergmanlab" rel="nofollow noopener noreferrer"><i class="fab fa-fw fa-twitter-square" aria-hidden="true"></i> Twitter</a></li>
 
 
 

diff --git a/_site/People/index.html b/_site/People/index.html
@@ -33,7 +33,7 @@
 
 
 
-  <meta name="twitter:site" content="@caseybergman">
+  <meta name="twitter:site" content="@bergmanlab">
   <meta name="twitter:title" content="Lab Members">
   <meta name="twitter:description" content="Department of Genetics &amp; Institute of Bioinformatics, UGA.">
   <meta name="twitter:url" content="http://localhost:4000/People/">
@@ -125,7 +125,7 @@
     <div class="masthead__menu">
       <nav id="site-nav" class="greedy-nav">
 
-          <a class="site-logo" href="/"><img src="/assets/images/casey_profile.jpg" alt="Bergman Lab"></a>
+          <a class="site-logo" href="/"><img src="/assets/images/slow-food-logo-redlarge.jpg" alt="Bergman Lab"></a>
 
         <a class="site-title" href="/">
           Bergman Lab
@@ -342,7 +342,7 @@ <h3 class="name">Parisha Rahman</h3>
 
 
 
-          <li><a href="https://twitter.com/caseybergman" rel="nofollow noopener noreferrer"><i class="fab fa-fw fa-twitter-square" aria-hidden="true"></i> Twitter</a></li>
+          <li><a href="https://twitter.com/bergmanlab" rel="nofollow noopener noreferrer"><i class="fab fa-fw fa-twitter-square" aria-hidden="true"></i> Twitter</a></li>
 
 
 

diff --git a/_site/Publications/index.html b/_site/Publications/index.html
@@ -33,7 +33,7 @@
 
 
 
-  <meta name="twitter:site" content="@caseybergman">
+  <meta name="twitter:site" content="@bergmanlab">
   <meta name="twitter:title" content="Publications">
   <meta name="twitter:description" content="Department of Genetics &amp; Institute of Bioinformatics, UGA.">
   <meta name="twitter:url" content="http://localhost:4000/Publications/">
@@ -125,7 +125,7 @@
     <div class="masthead__menu">
       <nav id="site-nav" class="greedy-nav">
 
-          <a class="site-logo" href="/"><img src="/assets/images/casey_profile.jpg" alt="Bergman Lab"></a>
+          <a class="site-logo" href="/"><img src="/assets/images/slow-food-logo-redlarge.jpg" alt="Bergman Lab"></a>
 
         <a class="site-title" href="/">
           Bergman Lab
@@ -232,10 +232,10 @@ <h2 id="manuscripts">Manuscripts</h2>
 <p><span style="text-decoration: underline;">Chen, J.</span>, D.J. Garfinkel &amp; <span style="text-decoration: underline;">C.M. Bergman</span> (submitted) Horizontal transfer and recombination fuel Ty4 retrotransposon evolution in <em>Saccharomyces</em>. [<a href="https://www.biorxiv.org/content/10.1101/2023.12.20.572574v1">preprint</a>]</p>
 
 <h2 id="2024">2024</h2>
-<p>Hannon-Hatfield, J.A., <span style="text-decoration: underline;">Chen, J.</span>, <span style="text-decoration: underline;">C.M. Bergman</span> &amp;  D.J. Garfinkel (in prep) Evolution of a restriction factor by domestication of a yeast retrotransposon.</p>
+<p>Hannon-Hatfield, J.A., <span style="text-decoration: underline;">Chen, J.</span>, <span style="text-decoration: underline;">C.M. Bergman</span> &amp;  D.J. Garfinkel (2024) Evolution of a restriction factor by domestication of a yeast retrotransposon. <a href="https://academic.oup.com/mbe/article/41/3/msae050/7621844" rel="nofollow"><em>Mol. Biol. Evol.</em> <strong>41</strong>:msae050</a>.</p>
 
 <h2 id="2023">2023</h2>
-<p><span style="text-decoration: underline;">Chen, J.</span> (2023) Bioinformatics and evolutionary genomics of transposable elements in yeast. Ph.D. Thesis, University of Georgia, USA.</p>
+<p><span style="text-decoration: underline;">Chen, J.</span> (2023) <a href="https://www.proquest.com/docview/2917422789" rel="nofollow">Bioinformatics and evolutionary genomics of transposable elements in yeast.</a> Ph.D. Thesis, University of Georgia, USA.</p>
 
 <p><span style="text-decoration: underline;">Chen, J.</span>, <span style="text-decoration: underline;">P.J. Basting</span>, <span style="text-decoration: underline;">S. Han</span>, D.J. Garfinkel &amp; <span style="text-decoration: underline;">C.M. Bergman</span> (2023) Reproducible evaluation of transposable element detectors with  McClintock 2 guides accurate inference of Ty insertion patterns in yeast. <a href="https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-023-00296-4" rel="nofollow"><em>Mobile DNA</em> <strong>14</strong>:8</a>.</p>
 
@@ -516,7 +516,7 @@ <h2 id="2000">2000</h2>
 
 
 
-          <li><a href="https://twitter.com/caseybergman" rel="nofollow noopener noreferrer"><i class="fab fa-fw fa-twitter-square" aria-hidden="true"></i> Twitter</a></li>
+          <li><a href="https://twitter.com/bergmanlab" rel="nofollow noopener noreferrer"><i class="fab fa-fw fa-twitter-square" aria-hidden="true"></i> Twitter</a></li>
 
 
 

diff --git a/_site/Research/index.html b/_site/Research/index.html
@@ -33,7 +33,7 @@
 
 
 
-  <meta name="twitter:site" content="@caseybergman">
+  <meta name="twitter:site" content="@bergmanlab">
   <meta name="twitter:title" content="Research">
   <meta name="twitter:description" content="Department of Genetics &amp; Institute of Bioinformatics, UGA.">
   <meta name="twitter:url" content="http://localhost:4000/Research/">
@@ -125,7 +125,7 @@
     <div class="masthead__menu">
       <nav id="site-nav" class="greedy-nav">
 
-          <a class="site-logo" href="/"><img src="/assets/images/casey_profile.jpg" alt="Bergman Lab"></a>
+          <a class="site-logo" href="/"><img src="/assets/images/slow-food-logo-redlarge.jpg" alt="Bergman Lab"></a>
 
         <a class="site-title" href="/">
           Bergman Lab
@@ -273,7 +273,7 @@ <h2 id="genome-annotation-and-bioinformatics">Genome Annotation and Bioinformati
 
 
 
-          <li><a href="https://twitter.com/caseybergman" rel="nofollow noopener noreferrer"><i class="fab fa-fw fa-twitter-square" aria-hidden="true"></i> Twitter</a></li>
+          <li><a href="https://twitter.com/bergmanlab" rel="nofollow noopener noreferrer"><i class="fab fa-fw fa-twitter-square" aria-hidden="true"></i> Twitter</a></li>
 
 
 

diff --git a/_site/assets/images/index.html b/_site/assets/images/index.html
@@ -33,7 +33,7 @@
 
 
 
-  <meta name="twitter:site" content="@caseybergman">
+  <meta name="twitter:site" content="@bergmanlab">
   <meta name="twitter:title" content="Bergman Lab">
   <meta name="twitter:description" content="Department of Genetics &amp; Institute of Bioinformatics, UGA.">
   <meta name="twitter:url" content="http://localhost:4000/assets/images/">
@@ -125,7 +125,7 @@
     <div class="masthead__menu">
       <nav id="site-nav" class="greedy-nav">
 
-          <a class="site-logo" href="/"><img src="/assets/images/casey_profile.jpg" alt="Bergman Lab"></a>
+          <a class="site-logo" href="/"><img src="/assets/images/slow-food-logo-redlarge.jpg" alt="Bergman Lab"></a>
 
         <a class="site-title" href="/">
           Bergman Lab
@@ -269,7 +269,7 @@ <h1 id="page-title" class="page__title" itemprop="headline">
 
 
 
-          <li><a href="https://twitter.com/caseybergman" rel="nofollow noopener noreferrer"><i class="fab fa-fw fa-twitter-square" aria-hidden="true"></i> Twitter</a></li>
+          <li><a href="https://twitter.com/bergmanlab" rel="nofollow noopener noreferrer"><i class="fab fa-fw fa-twitter-square" aria-hidden="true"></i> Twitter</a></li>
 
 
 

diff --git a/_site/feed.xml b/_site/feed.xml
@@ -1 +1 @@
-<?xml version="1.0" encoding="utf-8"?><feed xmlns="http://www.w3.org/2005/Atom" ><generator uri="https://jekyllrb.com/" version="3.9.5">Jekyll</generator><link href="http://localhost:4000/feed.xml" rel="self" type="application/atom+xml" /><link href="http://localhost:4000/" rel="alternate" type="text/html" /><updated>2024-07-11T14:50:19-04:00</updated><id>http://localhost:4000/feed.xml</id><title type="html">Bergman Lab</title><subtitle>Department of Genetics &amp; Institute of Bioinformatics, UGA.</subtitle><author><name>Casey Bergman</name></author><entry><title type="html">Test</title><link href="http://localhost:4000/test/" rel="alternate" type="text/html" title="Test" /><published>2024-07-08T00:00:00-04:00</published><updated>2024-07-08T00:00:00-04:00</updated><id>http://localhost:4000/test</id><content type="html" xml:base="http://localhost:4000/test/"><![CDATA[<p>Testing a first post</p>]]></content><author><name>Casey Bergman</name></author><summary type="html"><![CDATA[Testing a first post]]></summary></entry></feed>
+<?xml version="1.0" encoding="utf-8"?><feed xmlns="http://www.w3.org/2005/Atom" ><generator uri="https://jekyllrb.com/" version="3.9.5">Jekyll</generator><link href="http://localhost:4000/feed.xml" rel="self" type="application/atom+xml" /><link href="http://localhost:4000/" rel="alternate" type="text/html" /><updated>2024-07-18T15:09:44-04:00</updated><id>http://localhost:4000/feed.xml</id><title type="html">Bergman Lab</title><subtitle>Department of Genetics &amp; Institute of Bioinformatics, UGA.</subtitle><author><name>Casey Bergman</name></author><entry><title type="html">Test</title><link href="http://localhost:4000/test/" rel="alternate" type="text/html" title="Test" /><published>2024-07-08T00:00:00-04:00</published><updated>2024-07-08T00:00:00-04:00</updated><id>http://localhost:4000/test</id><content type="html" xml:base="http://localhost:4000/test/"><![CDATA[<p>Testing a first post</p>]]></content><author><name>Casey Bergman</name></author><summary type="html"><![CDATA[Testing a first post]]></summary></entry></feed>
diff --git a/_site/index.html b/_site/index.html
@@ -33,7 +33,7 @@
 
 
 
-  <meta name="twitter:site" content="@caseybergman">
+  <meta name="twitter:site" content="@bergmanlab">
   <meta name="twitter:title" content="Welcome to the Bergman Lab">
   <meta name="twitter:description" content="Department of Genetics &amp; Institute of Bioinformatics, UGA.">
   <meta name="twitter:url" content="http://localhost:4000/">
@@ -70,8 +70,8 @@
   "name": "Bergman Lab",
   "description": "Department of Genetics & Institute of Bioinformatics, UGA.",
   "url": "http://localhost:4000",
-  "logo": "http://localhost:4000/assets/images/casey_profile.jpg",
-  "keywords": "Transposon,Mobile Elements,Yeast Genetics,Fly Genetics"
+  "logo": "http://localhost:4000/assets/images/slow-food-logo-redlarge.jpg",
+  "keywords": "Genome Informatics,Genome Evolution,Noncoding DNA,Mobile DNA,Genetics,Bioinformatics"
 }
 </script>
 
@@ -138,7 +138,7 @@
     <div class="masthead__menu">
       <nav id="site-nav" class="greedy-nav">
 
-          <a class="site-logo" href="/"><img src="/assets/images/casey_profile.jpg" alt="Bergman Lab"></a>
+          <a class="site-logo" href="/"><img src="/assets/images/slow-food-logo-redlarge.jpg" alt="Bergman Lab"></a>
 
         <a class="site-title" href="/">
           Bergman Lab
@@ -300,7 +300,7 @@ <h2 id="the-bergman-lab">The Bergman Lab</h2>
 
 
 
-          <li><a href="https://twitter.com/caseybergman" rel="nofollow noopener noreferrer"><i class="fab fa-fw fa-twitter-square" aria-hidden="true"></i> Twitter</a></li>
+          <li><a href="https://twitter.com/bergmanlab" rel="nofollow noopener noreferrer"><i class="fab fa-fw fa-twitter-square" aria-hidden="true"></i> Twitter</a></li>
 
 
 

diff --git a/_site/test/index.html b/_site/test/index.html
@@ -35,7 +35,7 @@
 
 
 
-  <meta name="twitter:site" content="@caseybergman">
+  <meta name="twitter:site" content="@bergmanlab">
   <meta name="twitter:title" content="Test">
   <meta name="twitter:description" content="Testing a first post">
   <meta name="twitter:url" content="http://localhost:4000/test/">
@@ -129,7 +129,7 @@
     <div class="masthead__menu">
       <nav id="site-nav" class="greedy-nav">
 
-          <a class="site-logo" href="/"><img src="/assets/images/casey_profile.jpg" alt="Bergman Lab"></a>
+          <a class="site-logo" href="/"><img src="/assets/images/slow-food-logo-redlarge.jpg" alt="Bergman Lab"></a>
 
         <a class="site-title" href="/">
           Bergman Lab
@@ -289,7 +289,7 @@ <h2 class="page__related-title">You May Also Enjoy</h2>
 
 
 
-          <li><a href="https://twitter.com/caseybergman" rel="nofollow noopener noreferrer"><i class="fab fa-fw fa-twitter-square" aria-hidden="true"></i> Twitter</a></li>
+          <li><a href="https://twitter.com/bergmanlab" rel="nofollow noopener noreferrer"><i class="fab fa-fw fa-twitter-square" aria-hidden="true"></i> Twitter</a></li>