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aboyleaboyle
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Convert index.html to templates
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‎_includes/footer.html

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</div>
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</div><!-- end container -->
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</div><!-- end main-wrap -->
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<div id="footer-wrap">
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<div class="container">
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<p>Alan P Boyle, PhD | <a href="mailto:[email protected]">[email protected]</a> | <a href="ABoyle_CV.pdf" onclick="var that=this;_gaq.push(['_trackEvent','Download','PDF',this.href]);setTimeout(function(){location.href=that.href;},500);return false;">CV</a> | Ann Arbor, MI</p>
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</div><!-- end container -->
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</div><!-- end footer-wrap -->
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</body>
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</html>

‎_includes/header.html

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<!DOCTYPE html>
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<html>
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<head>
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<title>{{page.title}} | The Boyle Lab</title>
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
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<link rel='stylesheet' type='text/css' href='main_style.css' />
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<link href='http://fonts.googleapis.com/css?family=Open+Sans:400,300,300italic,700,400italic,700italic' rel='stylesheet' type='text/css' />
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<script src='https://ajax.googleapis.com/ajax/libs/jquery/1.7.2/jquery.min.js'></script>
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<script type="text/javascript">
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var _gaq = _gaq || [];
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_gaq.push(['_setAccount', 'UA-33218724-1']);
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_gaq.push(['_trackPageview']);
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(function() {
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var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
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ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
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var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
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})();
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</script>
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</head>
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<body class='short-header-page'>
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<div id="header-wrap">
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<div class="container">
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<table id="header">
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<tr>
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<td id="header-right">
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<table>
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<tr>
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<td class="phone-number"><img src="images/U-M_2color-HorizontalReversed.30px.png" height=30></td>
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<td>
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<div style="text-align:left;">
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<span class="wsite-social">
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<a class='wsite-social-item wsite-social-flickr' href='http://scholar.google.com/citations?user=yAqEpxMAAAAJ' target='_blank'></a><a class='wsite-social-item wsite-social-plus' href='ABoyle_CV.pdf' target='_blank' onclick="var that=this;_gaq.push(['_trackEvent','Download','PDF',this.href]);setTimeout(function(){location.href=that.href;},500);return false;"></a><a class='wsite-social-item wsite-social-twitter' href='http://twitter.com/ap_boyle' target='_blank'></a><a class='wsite-social-item wsite-social-linkedin' href='http://www.linkedin.com/profile/view?id=38624939' target='_blank'></a><a class='wsite-social-item wsite-social-mail' href='mailto:[email protected]' target='_blank'></a>
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</span>
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</div>
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</td>
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</tr>
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</table>
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</td>
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</tr>
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</table>
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</div><!-- end container -->
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</div><!-- end header-wrap -->

‎_includes/nav.html

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{% assign current = page.url | downcase | split: '/' %}
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<div id="nav-wrap">
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<div class="container">
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<table>
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<tr>
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<td><span id="wsite-title">The Boyle Lab</span></td>
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<td id="nav">
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<div id="navigation">
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<ul class='wsite-menu-default'>
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<li {% if current[1] == 'index.html' $}id='active'{% endif %}><a href='index.html'>Home</a></li>
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<li {% if current[1] == 'research.html' $}id='active'{% endif %}><a href='research.html'>Research</a></li>
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<li {% if current[1] == 'software.html' $}id='active'{% endif %}><a href='software.html'>Software</a></li>
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<li {% if current[1] == 'publications.html' $}id='active'{% endif %}><a href='publications.html'>Publications</a></li>
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<li {% if current[1] == 'jobs.html' $}id='active'{% endif %}><a href='jobs.html'>Jobs</a></li>
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</ul>
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</div>
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</td>
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</tr>
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</table>
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</div><!-- end container -->
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</div><!-- end nav-wrap -->

‎_layouts/default.html

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{% include header.html %}
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{% include nav.html %}
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<div id="banner-wrap">
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<div class="container">
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<div id="banner">
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<div class="wsite-header"></div>
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<div style="clear:both;"></div>
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</div><!-- end banner -->
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</div><!-- end container -->
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</div><!-- end banner-wrap -->
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<div id="main-wrap">
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<div class="container">
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<div class="wsite-content">
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{{content}}
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</div>
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</div><!-- end container -->
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</div><!-- end main-wrap -->
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{% include footer.html %}

‎index.html

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‎index.md

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---
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title: Home
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layout: default
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---
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<table width=100%>
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<tr>
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<td>
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<p>
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</p>
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<br>
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<p>
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I am an Associate Professor in the Department of Computational Medicine & Bioinformatics in the University of Michigian Medical School. Previously I was a postdoctoral scholar in the Department of Genetics in the Stanford University School of Medicine working under <a href="http://snyderlab.stanford.edu/">Dr. Michael Snyder</a>.
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I obtained my Ph.D. in Computational Biology & Bioinformatics from the Duke University Institute for Genome Sciences and Policy in December of 2009. There I was co-advised by <a href="http://fureylab.web.unc.edu/">Dr. Terry Furey</a> and <a href="http://www.genome.duke.edu/labs/crawford/">Dr. Greg Crawford</a>.
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</p>
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<br>
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<p>
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In the modern era of genomics, high-throughput experiments provide molecular biology data that has completely changed how we are able to explore biological systems.
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We can apply computational tools to help answer biological problems that were previously intractable.
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We aim to combine computational approaches with high-throughput biological assays to better understand the whole human transcriptional regulatory system.
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</p>
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<br>
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<p>
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Understanding gene regulation at the transcriptional level is critical to understanding complex biological systems and human disease. In virtually all organisms gene regulation is mediated by a “regulatory code” in which distinct combinations of specific transcription factors collaborate to regulate the expression of individual genes.
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This code is complex and not readily obvious from sequences alone.
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It likely involves many cis-regulatory modules that exist both upstream and within genes.
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In addition, mounting evidence suggests that major differences between individuals and species lie at the level of gene regulation and that changes in cis-regulatory sequences are responsible for these effects.
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</p>
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<br>
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<p>
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My research aims to explore this regulatory code by examining the non-coding regulatory elements in the human genome.
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I have actively participated in the ENCODE project since 2007 as a member of the analysis working group (AWG) and as a member of both the Snyder and the Furey/Crawford labs. I have more recently been involved in the modENCODE and mouse ENCODE projects. I have had the opportunity to lead a collaborative effort by the modENCODE consortium to perform a final round of regulatory analysis and publish the concluding findings of the project.
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</p>
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</td>
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<td width=200px>
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<a href="DNA_Cloud.png"><img src="images/DNA_Cloud_small.png" style="margin:0px 10px 0px 10px"></a>
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</td>
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</tr>
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</table>
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