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-<!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> Treangen lab at Rice University </title> <meta name="author" content="Treangen J. Treangen"> <meta name="description" content="Treangen lab website. "> <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="/assets/img/icon.png?1402e11f70634aa41af40aa7fea75a5e"> <link rel="stylesheet" href="/assets/css/main.css?d41d8cd98f00b204e9800998ecf8427e"> <link rel="canonical" href="/"> <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"> <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 active"> <a class="nav-link" href="/">about <span class="sr-only">(current)</span> </a> </li> <li class="nav-item "> <a class="nav-link" href="/people/">people </a> </li> <li class="nav-item "> <a class="nav-link" href="/blog/">blog </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/">Code </a> </li> <li class="nav-item "> <a class="nav-link" href="/cv/">Lab PI </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"> Treangen lab at Rice University </h1> <p class="desc"><a href="https://csweb.rice.edu" rel="external nofollow noopener" target="_blank">Department of Computer Science, Rice University </a>.</p> </header> <article> <div class="profile float-right"> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/labphoto_new.JPG-480.webp 480w,/assets/img/labphoto_new.JPG-800.webp 800w,/assets/img/labphoto_new.JPG-1400.webp 1400w," sizes="(min-width: 930px) 270.0px, (min-width: 576px) 30vw, 95vw" type="image/webp"> <img src="/assets/img/labphoto_new.JPG?9a46427ded805673d0daed3ac9e807ed" class="img-fluid z-depth-1 rounded" width="100%" height="auto" alt="labphoto_new.JPG" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"> </source></picture> </figure> <div class="more-info"> <p>Treangen Lab, September 2024</p> <p>Rice University, Houston, TX</p> </div> </div> <div class="clearfix"> <p>Welcome to the Treangen lab website, a bioinformatics and computational biology research group at Rice University, led by Dr. Todd J. Treangen (Associate Professor in the Department of Computer Science and affiliated Associate Professor in the Department of Bioengineering).</p> <p>Since launching in 2018, the Treangen lab has focused on developing scalable and accurate computational algorithms, methods, and open-source software tools to answer research questions specific to: (i) identifying and characterizing known and novel microbial pathogens, (ii) population scale microbial genome variation and evolution, and (iii) studying microbial communities across time and space in the environment and human-host-associated microbiomes.</p> <p>The Treangen lab is actively funded by CDC, NIH (NIA, NIAID), and NSF (EF, IIS, SHF). Prior support from: c3.ai DTI, DHS, IARPA, and NIH.</p> <div class="row"> <div class="col-sm mt-3 mt-md-0"> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/CDC_logo-480.webp 480w,/assets/img/CDC_logo-800.webp 800w,/assets/img/CDC_logo-1400.webp 1400w," sizes="95vw" type="image/webp"></source> <img src="/assets/img/CDC_logo.png" class="img-fluid rounded z-depth-1" width="100%" height="auto" title="CDC" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"> </picture> </figure> </div> <div class="col-sm mt-3 mt-md-0"> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/NIAID_logo-480.webp 480w,/assets/img/NIAID_logo-800.webp 800w,/assets/img/NIAID_logo-1400.webp 1400w," sizes="95vw" type="image/webp"></source> <img src="/assets/img/NIAID_logo.png" class="img-fluid rounded z-depth-1" width="100%" height="auto" title="NIH" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"> </picture> </figure> </div> <div class="col-sm mt-3 mt-md-0"> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/NSF_logo-480.webp 480w,/assets/img/NSF_logo-800.webp 800w,/assets/img/NSF_logo-1400.webp 1400w," sizes="95vw" type="image/webp"></source> <img src="/assets/img/NSF_logo.png" class="img-fluid rounded z-depth-1" width="100%" height="auto" title="NSF" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"> </picture> </figure> </div> </div> </div> <h2> <a href="/news/" style="color: inherit">news</a> </h2> <div class="news"> <div class="table-responsive"> <table class="table table-sm table-borderless"> <tr> <th scope="row" style="width: 20%">Aug 30, 2024</th> <td> Bryce Kille successfully passed his Thesis Proposal Defense, now a Ph.D. candidate! </td> </tr> <tr> <th scope="row" style="width: 20%">Aug 29, 2024</th> <td> Fall’24 semester COMP 416/519 kicks off </td> </tr> <tr> <th scope="row" style="width: 20%">Aug 01, 2024</th> <td> Genome Sleuths’24 has concluded, huge thanks to all of the undergrad participants and grad student mentors </td> </tr> </table> </div> </div> <h2> <a href="/publications/" style="color: inherit">selected publications</a> </h2> <div class="publications"> <ol class="bibliography"> <li> <div class="row"> <div id="balaji2022seqscreen" class="col-sm-10"> <div class="title">SeqScreen: accurate and sensitive functional screening of pathogenic sequences via ensemble learning</div> <div class="author"> Advait Balaji, Bryce Kille, Anthony D Kappell, and <span class="more-authors" title="click to view 8 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '8 more authors' ? 'Gene D Godbold, Madeline Diep, RA Leo Elworth, Zhiqin Qian, Dreycey Albin, Daniel J Nasko, Nidhi Shah, others' : '8 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'); ">8 more authors</span> </div> <div class="periodical"> <em>Genome biology</em>, 2022 </div> <div class="periodical"> </div> <div class="links"> <a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a> </div> <div class="badges"> <span class="altmetric-embed" data-badge-type="2" data-badge-popover="right" data-altmetric-id="130006025"></span> <a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;user=N5irv88AAAAJ&amp;citation_for_view=N5irv88AAAAJ:CHSYGLWDkRkC" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-32-4285F4?logo=googlescholar&amp;labelColor=beige" alt="32 Google Scholar citations"> </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">balaji2022seqscreen</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> Treangen lab at Rice University </title> <meta name="author" content="Treangen J. Treangen"> <meta name="description" content="Treangen lab website. "> <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="/assets/img/icon.png?1402e11f70634aa41af40aa7fea75a5e"> <link rel="stylesheet" href="/assets/css/main.css?d41d8cd98f00b204e9800998ecf8427e"> <link rel="canonical" href="/"> <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"> <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 active"> <a class="nav-link" href="/">about <span class="sr-only">(current)</span> </a> </li> <li class="nav-item "> <a class="nav-link" href="/people/">people </a> </li> <li class="nav-item "> <a class="nav-link" href="/blog/">blog </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/">Code </a> </li> <li class="nav-item "> <a class="nav-link" href="/cv/">Lab PI </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"> Treangen lab at Rice University </h1> <p class="desc"><a href="https://csweb.rice.edu" rel="external nofollow noopener" target="_blank">Department of Computer Science, Rice University </a>.</p> </header> <article> <div class="profile float-right"> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/labphoto_new-480.webp 480w,/assets/img/labphoto_new-800.webp 800w,/assets/img/labphoto_new-1400.webp 1400w," sizes="(min-width: 930px) 270.0px, (min-width: 576px) 30vw, 95vw" type="image/webp"> <img src="/assets/img/labphoto_new.png?e55002fc90d8fc24420700902314134b" class="img-fluid z-depth-1 rounded" width="100%" height="auto" alt="labphoto_new.png" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"> </source></picture> </figure> <div class="more-info"> <p>Treangen Lab, September 2024</p> <p>Rice University, Houston, TX</p> </div> </div> <div class="clearfix"> <p>Welcome to the Treangen lab website, a bioinformatics and computational biology research group at Rice University, led by Dr. Todd J. Treangen (Associate Professor in the Department of Computer Science and affiliated Associate Professor in the Department of Bioengineering).</p> <p>Since launching in 2018, the Treangen lab has focused on developing scalable and accurate computational algorithms, methods, and open-source software tools to answer research questions specific to: (i) identifying and characterizing known and novel microbial pathogens, (ii) population scale microbial genome variation and evolution, and (iii) studying microbial communities across time and space in the environment and human-host-associated microbiomes.</p> <p>The Treangen lab is actively funded by CDC, NIH (NIA, NIAID), and NSF (EF, IIS, SHF). Prior support from: c3.ai DTI, DHS, IARPA, and NIH.</p> <div class="row"> <div class="col-sm mt-3 mt-md-0"> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/CDC_logo-480.webp 480w,/assets/img/CDC_logo-800.webp 800w,/assets/img/CDC_logo-1400.webp 1400w," sizes="95vw" type="image/webp"></source> <img src="/assets/img/CDC_logo.png" class="img-fluid rounded z-depth-1" width="100%" height="auto" title="CDC" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"> </picture> </figure> </div> <div class="col-sm mt-3 mt-md-0"> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/NIAID_logo-480.webp 480w,/assets/img/NIAID_logo-800.webp 800w,/assets/img/NIAID_logo-1400.webp 1400w," sizes="95vw" type="image/webp"></source> <img src="/assets/img/NIAID_logo.png" class="img-fluid rounded z-depth-1" width="100%" height="auto" title="NIH" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"> </picture> </figure> </div> <div class="col-sm mt-3 mt-md-0"> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/NSF_logo-480.webp 480w,/assets/img/NSF_logo-800.webp 800w,/assets/img/NSF_logo-1400.webp 1400w," sizes="95vw" type="image/webp"></source> <img src="/assets/img/NSF_logo.png" class="img-fluid rounded z-depth-1" width="100%" height="auto" title="NSF" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"> </picture> </figure> </div> </div> </div> <h2> <a href="/news/" style="color: inherit">news</a> </h2> <div class="news"> <div class="table-responsive"> <table class="table table-sm table-borderless"> <tr> <th scope="row" style="width: 20%">Aug 30, 2024</th> <td> Bryce Kille successfully passed his Thesis Proposal Defense, now a Ph.D. candidate! </td> </tr> <tr> <th scope="row" style="width: 20%">Aug 29, 2024</th> <td> Fall’24 semester COMP 416/519 kicks off </td> </tr> <tr> <th scope="row" style="width: 20%">Aug 01, 2024</th> <td> Genome Sleuths’24 has concluded, huge thanks to all of the undergrad participants and grad student mentors </td> </tr> </table> </div> </div> <h2> <a href="/publications/" style="color: inherit">selected publications</a> </h2> <div class="publications"> <ol class="bibliography"> <li> <div class="row"> <div id="balaji2022seqscreen" class="col-sm-10"> <div class="title">SeqScreen: accurate and sensitive functional screening of pathogenic sequences via ensemble learning</div> <div class="author"> Advait Balaji, Bryce Kille, Anthony D Kappell, and <span class="more-authors" title="click to view 8 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '8 more authors' ? 'Gene D Godbold, Madeline Diep, RA Leo Elworth, Zhiqin Qian, Dreycey Albin, Daniel J Nasko, Nidhi Shah, others' : '8 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'); ">8 more authors</span> </div> <div class="periodical"> <em>Genome biology</em>, 2022 </div> <div class="periodical"> </div> <div class="links"> <a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a> </div> <div class="badges"> <span class="altmetric-embed" data-badge-type="2" data-badge-popover="right" data-altmetric-id="130006025"></span> <a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;user=N5irv88AAAAJ&amp;citation_for_view=N5irv88AAAAJ:CHSYGLWDkRkC" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-32-4285F4?logo=googlescholar&amp;labelColor=beige" alt="32 Google Scholar citations"> </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">balaji2022seqscreen</span><span class="p">,</span>
   <span class="na">title</span> <span class="p">=</span> <span class="s">{SeqScreen: accurate and sensitive functional screening of pathogenic sequences via ensemble learning}</span><span class="p">,</span>
   <span class="na">author</span> <span class="p">=</span> <span class="s">{Balaji, Advait and Kille, Bryce and Kappell, Anthony D and Godbold, Gene D and Diep, Madeline and Elworth, RA Leo and Qian, Zhiqin and Albin, Dreycey and Nasko, Daniel J and Shah, Nidhi and others}</span><span class="p">,</span>
   <span class="na">year</span> <span class="p">=</span> <span class="s">{2022}</span><span class="p">,</span>