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feed.xml

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-<?xml version="1.0" encoding="utf-8"?><feed xmlns="http://www.w3.org/2005/Atom" xml:lang="en"><generator uri="https://jekyllrb.com/" version="4.3.3">Jekyll</generator><link href="/feed.xml" rel="self" type="application/atom+xml"/><link href="/" rel="alternate" type="text/html" hreflang="en"/><updated>2024-09-04T17:06:47+00:00</updated><id>/feed.xml</id><title type="html">Treangen lab at Rice University</title><subtitle>Treangen lab website. </subtitle><entry><title type="html">Bryce Kille now a Ph.D. candidate!</title><link href="/blog/2024/bryce/" rel="alternate" type="text/html" title="Bryce Kille now a Ph.D. candidate!"/><published>2024-08-30T15:32:13+00:00</published><updated>2024-08-30T15:32:13+00:00</updated><id>/blog/2024/bryce</id><content type="html" xml:base="/blog/2024/bryce/"><![CDATA[<p>Bryce passed his Thesis propsoal defense with flying colors, congrats Bryce!</p> <p>Committee members:</p> <ul> <li>Dr. Adam Phillippy (NIH NHGRI)</li> <li>Dr. Caleb Bashor (Rice BIOE)</li> <li>Dr. Fritz Sedlazeck (BCM HGSC)</li> <li>Dr. Vladimir Braverman (Rice CS)</li> <li>Dr. Todd Treangen (Rice CS)</li> </ul>]]></content><author><name></name></author><category term="sample-posts"/><category term="formatting"/><category term="code"/><summary type="html"><![CDATA[Thesis proposal defense]]></summary></entry><entry><title type="html">Google Gemini updates: Flash 1.5, Gemma 2 and Project Astra</title><link href="/blog/2024/google-gemini-updates-flash-15-gemma-2-and-project-astra/" rel="alternate" type="text/html" title="Google Gemini updates: Flash 1.5, Gemma 2 and Project Astra"/><published>2024-05-14T00:00:00+00:00</published><updated>2024-05-14T00:00:00+00:00</updated><id>/blog/2024/google-gemini-updates-flash-15-gemma-2-and-project-astra</id><content type="html" xml:base="/blog/2024/google-gemini-updates-flash-15-gemma-2-and-project-astra/"><![CDATA[]]></content><author><name></name></author><summary type="html"><![CDATA[We’re sharing updates across our Gemini family of models and a glimpse of Project Astra, our vision for the future of AI assistants.]]></summary></entry><entry><title type="html">Displaying External Posts on Your al-folio Blog</title><link href="/blog/2022/displaying-external-posts-on-your-al-folio-blog/" rel="alternate" type="text/html" title="Displaying External Posts on Your al-folio Blog"/><published>2022-04-23T23:20:09+00:00</published><updated>2022-04-23T23:20:09+00:00</updated><id>/blog/2022/displaying-external-posts-on-your-al-folio-blog</id><content type="html" xml:base="/blog/2022/displaying-external-posts-on-your-al-folio-blog/"><![CDATA[]]></content><author><name></name></author></entry></feed>
+<?xml version="1.0" encoding="utf-8"?><feed xmlns="http://www.w3.org/2005/Atom" xml:lang="en"><generator uri="https://jekyllrb.com/" version="4.3.3">Jekyll</generator><link href="/feed.xml" rel="self" type="application/atom+xml"/><link href="/" rel="alternate" type="text/html" hreflang="en"/><updated>2024-09-04T17:19:01+00:00</updated><id>/feed.xml</id><title type="html">Treangen lab at Rice University</title><subtitle>Treangen lab website. </subtitle><entry><title type="html">Bryce Kille now a Ph.D. candidate!</title><link href="/blog/2024/bryce/" rel="alternate" type="text/html" title="Bryce Kille now a Ph.D. candidate!"/><published>2024-08-30T15:32:13+00:00</published><updated>2024-08-30T15:32:13+00:00</updated><id>/blog/2024/bryce</id><content type="html" xml:base="/blog/2024/bryce/"><![CDATA[<p>Bryce passed his Thesis propsoal defense with flying colors, congrats Bryce!</p> <p>Committee members:</p> <ul> <li>Dr. Adam Phillippy (NIH NHGRI)</li> <li>Dr. Caleb Bashor (Rice BIOE)</li> <li>Dr. Fritz Sedlazeck (BCM HGSC)</li> <li>Dr. Vladimir Braverman (Rice CS)</li> <li>Dr. Todd Treangen (Rice CS)</li> </ul>]]></content><author><name></name></author><category term="sample-posts"/><category term="formatting"/><category term="code"/><summary type="html"><![CDATA[Thesis proposal defense]]></summary></entry><entry><title type="html">Google Gemini updates: Flash 1.5, Gemma 2 and Project Astra</title><link href="/blog/2024/google-gemini-updates-flash-15-gemma-2-and-project-astra/" rel="alternate" type="text/html" title="Google Gemini updates: Flash 1.5, Gemma 2 and Project Astra"/><published>2024-05-14T00:00:00+00:00</published><updated>2024-05-14T00:00:00+00:00</updated><id>/blog/2024/google-gemini-updates-flash-15-gemma-2-and-project-astra</id><content type="html" xml:base="/blog/2024/google-gemini-updates-flash-15-gemma-2-and-project-astra/"><![CDATA[]]></content><author><name></name></author><summary type="html"><![CDATA[We’re sharing updates across our Gemini family of models and a glimpse of Project Astra, our vision for the future of AI assistants.]]></summary></entry><entry><title type="html">Displaying External Posts on Your al-folio Blog</title><link href="/blog/2022/displaying-external-posts-on-your-al-folio-blog/" rel="alternate" type="text/html" title="Displaying External Posts on Your al-folio Blog"/><published>2022-04-23T23:20:09+00:00</published><updated>2022-04-23T23:20:09+00:00</updated><id>/blog/2022/displaying-external-posts-on-your-al-folio-blog</id><content type="html" xml:base="/blog/2022/displaying-external-posts-on-your-al-folio-blog/"><![CDATA[]]></content><author><name></name></author></entry></feed>

profiles/rdoughty/index.html

@@ -1,4 +1,4 @@
-<!DOCTYPE html> <html lang="en"> <head> <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> <title> Ryan Doughty | Treangen lab at Rice University </title> <meta name="author" content="Treangen J. Treangen"> <meta name="description" content="1st Year Compter Science Ph.D. student, interested in metagenomics and virome analysis."> <meta name="keywords" content="jekyll, jekyll-theme, academic-website, portfolio-website"> <link rel="stylesheet" href="/assets/css/bootstrap.min.css?a4b3f509e79c54a512b890d73235ef04"> <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/css/mdb.min.css" integrity="sha256-jpjYvU3G3N6nrrBwXJoVEYI/0zw8htfFnhT9ljN3JJw=" crossorigin="anonymous"> <link defer rel="stylesheet" href="/assets/css/academicons.min.css?f0b7046b84e425c55f3463ac249818f5"> <link defer rel="stylesheet" type="text/css" href="https://fonts.googleapis.com/css?family=Roboto:300,400,500,700|Roboto+Slab:100,300,400,500,700|Material+Icons&amp;display=swap"> <link defer rel="stylesheet" href="/assets/css/jekyll-pygments-themes-github.css?591dab5a4e56573bf4ef7fd332894c99" media="" id="highlight_theme_light"> <link rel="shortcut icon" href="data:image/svg+xml,&lt;svg%20xmlns=%22http://www.w3.org/2000/svg%22%20viewBox=%220%200%20100%20100%22&gt;&lt;text%20y=%22.9em%22%20font-size=%2290%22&gt;%E2%9A%9B%EF%B8%8F&lt;/text&gt;&lt;/svg&gt;"> <link rel="stylesheet" href="/assets/css/main.css?d41d8cd98f00b204e9800998ecf8427e"> <link rel="canonical" href="/profiles/rdoughty/"> <script src="/assets/js/theme.js?9a0c749ec5240d9cda97bc72359a72c0"></script> <link defer rel="stylesheet" href="/assets/css/jekyll-pygments-themes-native.css?5847e5ed4a4568527aa6cfab446049ca" media="none" id="highlight_theme_dark"> <script>initTheme();</script> </head> <body class="fixed-top-nav "> <header> <nav id="navbar" class="navbar navbar-light navbar-expand-sm fixed-top" role="navigation"> <div class="container"> <a class="navbar-brand title font-weight-lighter" href="/"> Treangen lab at Rice University </a> <button class="navbar-toggler collapsed ml-auto" type="button" data-toggle="collapse" data-target="#navbarNav" aria-controls="navbarNav" aria-expanded="false" aria-label="Toggle navigation"> <span class="sr-only">Toggle navigation</span> <span class="icon-bar top-bar"></span> <span class="icon-bar middle-bar"></span> <span class="icon-bar bottom-bar"></span> </button> <div class="collapse navbar-collapse text-right" id="navbarNav"> <ul class="navbar-nav ml-auto flex-nowrap"> <li class="nav-item "> <a class="nav-link" href="/">lab </a> </li> <li class="nav-item "> <a class="nav-link" href="/people/">people </a> </li> <li class="nav-item "> <a class="nav-link" href="/publications/">publications </a> </li> <li class="nav-item "> <a class="nav-link" href="/repositories/">github </a> </li> <li class="nav-item "> <a class="nav-link" href="/cv/">cv </a> </li> <li class="nav-item "> <a class="nav-link" href="/teaching/">teaching </a> </li> <li class="nav-item"> <button id="search-toggle" title="Search" onclick="openSearchModal()"> <span class="nav-link">ctrl k <i class="ti ti-search"></i></span> </button> </li> <li class="toggle-container"> <button id="light-toggle" title="Change theme"> <i class="ti ti-sun-moon" id="light-toggle-system"></i> <i class="ti ti-moon-filled" id="light-toggle-dark"></i> <i class="ti ti-sun-filled" id="light-toggle-light"></i> </button> </li> </ul> </div> </div> </nav> <progress id="progress" value="0"> <div class="progress-container"> <span class="progress-bar"></span> </div> </progress> </header> <div class="container mt-5" role="main"> <div class="post"> <header class="post-header"> <h1 class="post-title">Ryan Doughty</h1> <p class="post-description">1st Year Compter Science Ph.D. student, interested in metagenomics and virome analysis.</p> </header> <article> <p>Ryan (1st year PhD student, Computer Science), obtained his BS in Computer Science from Case Western Reserve University. During his undergraduate studies, he worked with Dr. Treangen on large-scale wastewater analyses and targeted metagenomic sequencing methods. He also spent six months in Vigo, Spain, working in Dr. David Posada’s lab, focusing on gut-virome biomarkers in colorectal cancer. Additionally, he interned at Intellia Therapeutics for a summer, where he contributed to developing machine learning methods for CRISPR Cas-9 guide design. Ryan’s current research interests center around comprehending the global virosphere through viral genomic analyses.</p> <p>A few of Ryan’s recent publications: <a class="citation" href="#mccall2023targeted">(McCall et al., 2023)</a>.</p> </article> <h2>References</h2> <div class="publications"> <h2 class="bibliography">2023</h2> <ol class="bibliography"><li> <div class="row"> <div id="mccall2023targeted" class="col-sm-10"> <div class="title">Targeted metagenomic sequencing for detection of vertebrate viruses in wastewater for public health surveillance</div> <div class="author"> Camille McCall, Ryan A Leo Elworth, Kristine M Wylie, and <span class="more-authors" title="click to view 7 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '7 more authors' ? 'Todd N Wylie, Katherine Dyson, Ryan Doughty, Todd J Treangen, Loren Hopkins, Katherine Ensor, Lauren B Stadler' : '7 more authors'; var cursorPosition=0; var textAdder=setInterval(function(){ element.html(more_authors_text.substring(0, cursorPosition + 1)); if (++cursorPosition == more_authors_text.length){ clearInterval(textAdder); } }, '10'); ">7 more authors</span> </div> <div class="periodical"> <em>ACS ES&amp;T Water</em>, 2023 </div> <div class="periodical"> </div> <div class="links"> <a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a> </div> <div class="bibtex hidden"> <figure class="highlight"><pre><code class="language-bibtex" data-lang="bibtex"><span class="nc">@article</span><span class="p">{</span><span class="nl">mccall2023targeted</span><span class="p">,</span>
+<!DOCTYPE html> <html lang="en"> <head> <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> <title> Ryan Doughty | Treangen lab at Rice University </title> <meta name="author" content="Treangen J. Treangen"> <meta name="description" content="1st Year Compter Science Ph.D. student, interested in metagenomics and virome analysis."> <meta name="keywords" content="jekyll, jekyll-theme, academic-website, portfolio-website"> <link rel="stylesheet" href="/assets/css/bootstrap.min.css?a4b3f509e79c54a512b890d73235ef04"> <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/css/mdb.min.css" integrity="sha256-jpjYvU3G3N6nrrBwXJoVEYI/0zw8htfFnhT9ljN3JJw=" crossorigin="anonymous"> <link defer rel="stylesheet" href="/assets/css/academicons.min.css?f0b7046b84e425c55f3463ac249818f5"> <link defer rel="stylesheet" type="text/css" href="https://fonts.googleapis.com/css?family=Roboto:300,400,500,700|Roboto+Slab:100,300,400,500,700|Material+Icons&amp;display=swap"> <link defer rel="stylesheet" href="/assets/css/jekyll-pygments-themes-github.css?591dab5a4e56573bf4ef7fd332894c99" media="" id="highlight_theme_light"> <link rel="shortcut icon" href="data:image/svg+xml,&lt;svg%20xmlns=%22http://www.w3.org/2000/svg%22%20viewBox=%220%200%20100%20100%22&gt;&lt;text%20y=%22.9em%22%20font-size=%2290%22&gt;%E2%9A%9B%EF%B8%8F&lt;/text&gt;&lt;/svg&gt;"> <link rel="stylesheet" href="/assets/css/main.css?d41d8cd98f00b204e9800998ecf8427e"> <link rel="canonical" href="/profiles/rdoughty/"> <script src="/assets/js/theme.js?9a0c749ec5240d9cda97bc72359a72c0"></script> <link defer rel="stylesheet" href="/assets/css/jekyll-pygments-themes-native.css?5847e5ed4a4568527aa6cfab446049ca" media="none" id="highlight_theme_dark"> <script>initTheme();</script> </head> <body class="fixed-top-nav "> <header> <nav id="navbar" class="navbar navbar-light navbar-expand-sm fixed-top" role="navigation"> <div class="container"> <a class="navbar-brand title font-weight-lighter" href="/"> Treangen lab at Rice University </a> <button class="navbar-toggler collapsed ml-auto" type="button" data-toggle="collapse" data-target="#navbarNav" aria-controls="navbarNav" aria-expanded="false" aria-label="Toggle navigation"> <span class="sr-only">Toggle navigation</span> <span class="icon-bar top-bar"></span> <span class="icon-bar middle-bar"></span> <span class="icon-bar bottom-bar"></span> </button> <div class="collapse navbar-collapse text-right" id="navbarNav"> <ul class="navbar-nav ml-auto flex-nowrap"> <li class="nav-item "> <a class="nav-link" href="/">lab </a> </li> <li class="nav-item "> <a class="nav-link" href="/people/">people </a> </li> <li class="nav-item "> <a class="nav-link" href="/publications/">publications </a> </li> <li class="nav-item "> <a class="nav-link" href="/repositories/">github </a> </li> <li class="nav-item "> <a class="nav-link" href="/cv/">cv </a> </li> <li class="nav-item "> <a class="nav-link" href="/teaching/">teaching </a> </li> <li class="nav-item"> <button id="search-toggle" title="Search" onclick="openSearchModal()"> <span class="nav-link">ctrl k <i class="ti ti-search"></i></span> </button> </li> <li class="toggle-container"> <button id="light-toggle" title="Change theme"> <i class="ti ti-sun-moon" id="light-toggle-system"></i> <i class="ti ti-moon-filled" id="light-toggle-dark"></i> <i class="ti ti-sun-filled" id="light-toggle-light"></i> </button> </li> </ul> </div> </div> </nav> <progress id="progress" value="0"> <div class="progress-container"> <span class="progress-bar"></span> </div> </progress> </header> <div class="container mt-5" role="main"> <div class="post"> <header class="post-header"> <h1 class="post-title">Ryan Doughty</h1> <p class="post-description">1st Year Compter Science Ph.D. student, interested in metagenomics and virome analysis.</p> </header> <article> <p>Ryan (1st year PhD student, Computer Science), obtained his BS in Computer Science from Case Western Reserve University. During his undergraduate studies, he worked with Dr. Treangen on large-scale wastewater analyses and targeted metagenomic sequencing methods. He also spent six months in Vigo, Spain, working in Dr. David Posada’s lab, focusing on gut-virome biomarkers in colorectal cancer. Additionally, he interned at Intellia Therapeutics for a summer, where he contributed to developing machine learning methods for CRISPR Cas-9 guide design. Ryan’s current research interests center around comprehending the global virosphere through viral genomic analyses. Ryan is supported by CS departmental support and NIH NIAID GCID (U19AI144297)</p> <p>A few of Ryan’s recent publications: <a class="citation" href="#mccall2023targeted">(McCall et al., 2023)</a>.</p> </article> <h2>References</h2> <div class="publications"> <h2 class="bibliography">2023</h2> <ol class="bibliography"><li> <div class="row"> <div id="mccall2023targeted" class="col-sm-10"> <div class="title">Targeted metagenomic sequencing for detection of vertebrate viruses in wastewater for public health surveillance</div> <div class="author"> Camille McCall, Ryan A Leo Elworth, Kristine M Wylie, and <span class="more-authors" title="click to view 7 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '7 more authors' ? 'Todd N Wylie, Katherine Dyson, Ryan Doughty, Todd J Treangen, Loren Hopkins, Katherine Ensor, Lauren B Stadler' : '7 more authors'; var cursorPosition=0; var textAdder=setInterval(function(){ element.html(more_authors_text.substring(0, cursorPosition + 1)); if (++cursorPosition == more_authors_text.length){ clearInterval(textAdder); } }, '10'); ">7 more authors</span> </div> <div class="periodical"> <em>ACS ES&amp;T Water</em>, 2023 </div> <div class="periodical"> </div> <div class="links"> <a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a> </div> <div class="bibtex hidden"> <figure class="highlight"><pre><code class="language-bibtex" data-lang="bibtex"><span class="nc">@article</span><span class="p">{</span><span class="nl">mccall2023targeted</span><span class="p">,</span>
   <span class="na">title</span> <span class="p">=</span> <span class="s">{Targeted metagenomic sequencing for detection of vertebrate viruses in wastewater for public health surveillance}</span><span class="p">,</span>
   <span class="na">author</span> <span class="p">=</span> <span class="s">{McCall, Camille and Leo Elworth, Ryan A and Wylie, Kristine M and Wylie, Todd N and Dyson, Katherine and Doughty, Ryan and Treangen, Todd J and Hopkins, Loren and Ensor, Katherine and Stadler, Lauren B}</span><span class="p">,</span>
   <span class="na">year</span> <span class="p">=</span> <span class="s">{2023}</span><span class="p">,</span>