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diff --git a/cv/index.html b/cv/index.html
index 7d8320a4..c6e248a2 100644
--- a/cv/index.html
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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> Lab PI | Treangen lab at Rice University </title> <meta name="author" content="Treangen J. Treangen"> <meta name="description" content="Treangen Lab PI (Dr. Todd J. 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Treangen)</p> </header> <article> <div class="cv"> <a class="anchor" id="CV (updated September 2024)"></a> <div class="card mt-3 p-3"> <h3 class="card-title font-weight-medium">CV (updated September 2024)</h3> <div> <table class="table table-cv table-sm table-borderless table-responsive"> <tr> <td class="p-1 pr-2 font-weight-bold"> <b>Full Name</b> </td> <td class="p-1 pl-2 font-weight-light text">Todd J. Treangen</td> </tr> <tr> <td class="p-1 pr-2 font-weight-bold"> <b>Languages</b> </td> <td class="p-1 pl-2 font-weight-light text">English, Galician (fluent), Spanish (fluent), Portugues, French</td> </tr> </table> </div> </div> <a class="anchor" id="Education"></a> <div class="card mt-3 p-3"> <h3 class="card-title font-weight-medium">Education</h3> <div> <ul class="card-text font-weight-light list-group list-group-flush"> <li class="list-group-item"> <div class="row"> <div class="col-xs-2 cl-sm-2 col-md-2 text-center" style="width: 75px"> <table class="table-cv"> <tbody> <tr> <td> <span class="badge font-weight-bold danger-color-dark text-uppercase align-middle" style="min-width: 75px">2008</span> </td> </tr> </tbody> </table> </div> <div class="col-xs-10 cl-sm-10 col-md-10 mt-2 mt-md-0"> <h6 class="title font-weight-bold ml-1 ml-md-4">Ph.D. in Computer Science</h6> <table class="table-cv ml-1 ml-md-4 institution"> <tbody> <tr> <td style="vertical-align: top; text-align: center" class="institution"> <i class="fa-solid fa-building-columns iconinstitution"></i> </td> <td class="institution">Polytechnic University of Catalonia, Barcelona, Spain</td> </tr> </tbody> </table> <ul class="items"> <li> <span class="item">Focus on bioinformatics and computational biology.</span> </li> <li> <span class="item">Research involved the development of algorithms for genome analysis.</span> </li> <li> <span class="item-title">Dissertation</span> <ul class="subitems"> <li> <span class="subitem">{"Title"=&gt;"Novel Computational Methods for Large Scale Genome Comparison"}</span> </li> <li> <span class="subitem">{"Advisor"=&gt;"Dr. Xavier Messeguer"}</span> </li> </ul> </li> </ul> </div> </div> </li> <li class="list-group-item"> <div class="row"> <div class="col-xs-2 cl-sm-2 col-md-2 text-center" style="width: 75px"> <table class="table-cv"> <tbody> <tr> <td> <span class="badge font-weight-bold danger-color-dark text-uppercase align-middle" style="min-width: 75px">2004</span> </td> </tr> </tbody> </table> </div> <div class="col-xs-10 cl-sm-10 col-md-10 mt-2 mt-md-0"> <h6 class="title font-weight-bold ml-1 ml-md-4">MS in Computer Science</h6> <table class="table-cv ml-1 ml-md-4 institution"> <tbody> <tr> <td style="vertical-align: top; text-align: center" class="institution"> <i class="fa-solid fa-building-columns iconinstitution"></i> </td> <td class="institution">Polytechnic University of Catalonia, Barcelona, Spain</td> </tr> </tbody> </table> <ul class="items"> <li> <span class="item">Specialized in algorithm development for large-scale genomic data.</span> </li> <li> <span class="item">Completed a thesis on "Efficient Methods for Genome Alignment."</span> </li> </ul> </div> </div> </li> </ul> </div> </div> <a class="anchor" id="Experience"></a> <div class="card mt-3 p-3"> <h3 class="card-title font-weight-medium">Experience</h3> <div> <ul class="card-text font-weight-light list-group list-group-flush"> <li class="list-group-item"> <div class="row"> <div class="col-xs-2 cl-sm-2 col-md-2 text-center" style="width: 75px"> <table class="table-cv"> <tbody> <tr> <td> <span class="badge font-weight-bold danger-color-dark text-uppercase align-middle" style="min-width: 75px">2023 - present</span> </td> </tr> </tbody> </table> </div> <div class="col-xs-10 cl-sm-10 col-md-10 mt-2 mt-md-0"> <h6 class="title font-weight-bold ml-1 ml-md-4">Associate Professor, Computer Science</h6> <table class="table-cv ml-1 ml-md-4 institution"> <tbody> <tr> <td style="vertical-align: top; text-align: center" class="institution"> <i class="fa-solid fa-building-columns iconinstitution"></i> </td> <td class="institution">Rice University, Houston, Texas, USA</td> </tr> </tbody> </table> <ul class="items"> <li> <span class="item">Affiliate faculty in Department of Bioengineering</span> </li> <li> <span class="item">Leads the Treangen Lab, focusing on bioinformatics, genomics, and metagenomics.</span> </li> <li> <span class="item">Developed tools for microbial detection and outbreak tracking.</span> </li> <li> <span class="item-title">Research</span> <ul class="subitems"> <li> <span class="subitem">Focus on AI-driven approaches for genomic data analysis.</span> </li> <li> <span class="subitem">Developed algorithms for rapid pathogen detection.</span> </li> </ul> </li> </ul> </div> </div> </li> <li class="list-group-item"> <div class="row"> <div class="col-xs-2 cl-sm-2 col-md-2 text-center" style="width: 75px"> <table class="table-cv"> <tbody> <tr> <td> <span class="badge font-weight-bold danger-color-dark text-uppercase align-middle" style="min-width: 75px">2018 - 2023</span> </td> </tr> </tbody> </table> </div> <div class="col-xs-10 cl-sm-10 col-md-10 mt-2 mt-md-0"> <h6 class="title font-weight-bold ml-1 ml-md-4">Assistant Professor, Computer Science</h6> <table class="table-cv ml-1 ml-md-4 institution"> <tbody> <tr> <td style="vertical-align: top; text-align: center" class="institution"> <i class="fa-solid fa-building-columns iconinstitution"></i> </td> <td class="institution">Rice University, Houston, Texas, USA</td> </tr> </tbody> </table> <ul class="items"> <li> <span class="item">Leads the Treangen Lab, focusing on bioinformatics, genomics, and metagenomics.</span> </li> <li> <span class="item">Developed tools for microbial detection and outbreak tracking.</span> </li> <li> <span class="item-title">Research</span> <ul class="subitems"> <li> <span class="subitem">Focus on AI-driven approaches for genomic data analysis.</span> </li> <li> <span class="subitem">Developed algorithms for rapid pathogen detection.</span> </li> </ul> </li> </ul> </div> </div> </li> <li class="list-group-item"> <div class="row"> <div class="col-xs-2 cl-sm-2 col-md-2 text-center" style="width: 75px"> <table class="table-cv"> <tbody> <tr> <td> <span class="badge font-weight-bold danger-color-dark text-uppercase align-middle" style="min-width: 75px">2016 - 2018</span> </td> </tr> </tbody> </table> </div> <div class="col-xs-10 cl-sm-10 col-md-10 mt-2 mt-md-0"> <h6 class="title font-weight-bold ml-1 ml-md-4">Research Assistant Professor, UMIACS</h6> <table class="table-cv ml-1 ml-md-4 institution"> <tbody> <tr> <td style="vertical-align: top; text-align: center" class="institution"> <i class="fa-solid fa-building-columns iconinstitution"></i> </td> <td class="institution">University of Maryland, College Park, Maryland, USA</td> </tr> </tbody> </table> <ul class="items"> <li> <span class="item">Conducted research on genome assembly and metagenomics.</span> </li> <li> <span class="item">Collaborated on the development of scalable bioinformatics tools.</span> </li> </ul> </div> </div> </li> <li class="list-group-item"> <div class="row"> <div class="col-xs-2 cl-sm-2 col-md-2 text-center" style="width: 75px"> <table class="table-cv"> <tbody> <tr> <td> <span class="badge font-weight-bold danger-color-dark text-uppercase align-middle" style="min-width: 75px">2012 - 2016</span> </td> </tr> </tbody> </table> </div> <div class="col-xs-10 cl-sm-10 col-md-10 mt-2 mt-md-0"> <h6 class="title font-weight-bold ml-1 ml-md-4">PI and Bioinformatics Scientist</h6> <table class="table-cv ml-1 ml-md-4 institution"> <tbody> <tr> <td style="vertical-align: top; text-align: center" class="institution"> <i class="fa-solid fa-building-columns iconinstitution"></i> </td> <td class="institution">National Biodefense Analysis and Countermeasures Center (NBACC)</td> </tr> </tbody> </table> <ul class="items"> <li> <span class="item">Focused on pathogen detection and large scale genome comparison of microbes</span> </li> </ul> </div> </div> </li> <li class="list-group-item"> <div class="row"> <div class="col-xs-2 cl-sm-2 col-md-2 text-center" style="width: 75px"> <table class="table-cv"> <tbody> <tr> <td> <span class="badge font-weight-bold danger-color-dark text-uppercase align-middle" style="min-width: 75px">2011 - 2012</span> </td> </tr> </tbody> </table> </div> <div class="col-xs-10 cl-sm-10 col-md-10 mt-2 mt-md-0"> <h6 class="title font-weight-bold ml-1 ml-md-4">Postdoctoral Scientist, School of Public Health</h6> <table class="table-cv ml-1 ml-md-4 institution"> <tbody> <tr> <td style="vertical-align: top; text-align: center" class="institution"> <i class="fa-solid fa-building-columns iconinstitution"></i> </td> <td class="institution">Johns Hopkins University (Salzberg lab)</td> </tr> </tbody> </table> <ul class="items"> <li> <span class="item">Focused on genome assembly</span> </li> </ul> </div> </div> </li> <li class="list-group-item"> <div class="row"> <div class="col-xs-2 cl-sm-2 col-md-2 text-center" style="width: 75px"> <table class="table-cv"> <tbody> <tr> <td> <span class="badge font-weight-bold danger-color-dark text-uppercase align-middle" style="min-width: 75px">2010 - 2011</span> </td> </tr> </tbody> </table> </div> <div class="col-xs-10 cl-sm-10 col-md-10 mt-2 mt-md-0"> <h6 class="title font-weight-bold ml-1 ml-md-4">Postdoctoral Scientist, CBCB</h6> <table class="table-cv ml-1 ml-md-4 institution"> <tbody> <tr> <td style="vertical-align: top; text-align: center" class="institution"> <i class="fa-solid fa-building-columns iconinstitution"></i> </td> <td class="institution">University of Maryland College Park (Pop and Salzberg labs)</td> </tr> </tbody> </table> <ul class="items"> <li> <span class="item">Focused on genome and metagenome assembly</span> </li> </ul> </div> </div> </li> <li class="list-group-item"> <div class="row"> <div class="col-xs-2 cl-sm-2 col-md-2 text-center" style="width: 75px"> <table class="table-cv"> <tbody> <tr> <td> <span class="badge font-weight-bold danger-color-dark text-uppercase align-middle" style="min-width: 75px">2008 - 2010</span> </td> </tr> </tbody> </table> </div> <div class="col-xs-10 cl-sm-10 col-md-10 mt-2 mt-md-0"> <h6 class="title font-weight-bold ml-1 ml-md-4">Postdoctoral Scientist</h6> <table class="table-cv ml-1 ml-md-4 institution"> <tbody> <tr> <td style="vertical-align: top; text-align: center" class="institution"> <i class="fa-solid fa-building-columns iconinstitution"></i> </td> <td class="institution">Institut Pasteur, Paris, France (Rocha lab)</td> </tr> </tbody> </table> <ul class="items"> <li> <span class="item">Focused on evolutionary microbial genomics (GEM)</span> </li> </ul> </div> </div> </li> </ul> </div> </div> <a class="anchor" id="Open Source Projects"></a> <div class="card mt-3 p-3"> <h3 class="card-title font-weight-medium">Open Source Projects</h3> <div> <ul class="card-text font-weight-light list-group list-group-flush"> <li class="list-group-item"> <div class="row"> <div class="col-xs-2 cl-sm-2 col-md-2 text-center" style="width: 75px"> <table class="table-cv"> <tbody> <tr> <td> <span class="badge font-weight-bold danger-color-dark text-uppercase align-middle" style="min-width: 75px">2010-2015</span> </td> </tr> </tbody> </table> </div> <div class="col-xs-10 cl-sm-10 col-md-10 mt-2 mt-md-0"> <h6 class="title font-weight-bold ml-1 ml-md-4"><a href="https://github.com/marbl/metamos" rel="external nofollow noopener" target="_blank">MetAMOS</a></h6> <ul class="items"> <li> <span class="item">An open-source metagenomic assembly and analysis pipeline.</span> </li> </ul> </div> </div> </li> <li class="list-group-item"> <div class="row"> <div class="col-xs-2 cl-sm-2 col-md-2 text-center" style="width: 75px"> <table class="table-cv"> <tbody> <tr> <td> <span class="badge font-weight-bold danger-color-dark text-uppercase align-middle" style="min-width: 75px">2010-2015</span> </td> </tr> </tbody> </table> </div> <div class="col-xs-10 cl-sm-10 col-md-10 mt-2 mt-md-0"> <h6 class="title font-weight-bold ml-1 ml-md-4"><a href="https://github.com/marbl/parsnp" rel="external nofollow noopener" target="_blank">ParSNP</a></h6> <ul class="items"> <li> <span class="item">An open-source microbial core genome alignment tool.</span> </li> </ul> </div> </div> </li> <li class="list-group-item"> <div class="row"> <div class="col-xs-2 cl-sm-2 col-md-2 text-center" style="width: 75px"> <table class="table-cv"> <tbody> <tr> <td> <span class="badge font-weight-bold danger-color-dark text-uppercase align-middle" style="min-width: 75px">2013-2018</span> </td> </tr> </tbody> </table> </div> <div class="col-xs-10 cl-sm-10 col-md-10 mt-2 mt-md-0"> <h6 class="title font-weight-bold ml-1 ml-md-4"><a href="https://github.com/marbl/mash" rel="external nofollow noopener" target="_blank">Mash</a></h6> <ul class="items"> <li> <span class="item">Fast genome and metagenome distance estimation using MinHash.</span> </li> </ul> </div> </div> </li> <li class="list-group-item"> <div class="row"> <div class="col-xs-2 cl-sm-2 col-md-2 text-center" style="width: 75px"> <table class="table-cv"> <tbody> <tr> <td> <span class="badge font-weight-bold danger-color-dark text-uppercase align-middle" style="min-width: 75px">2018-2024</span> </td> </tr> </tbody> </table> </div> <div class="col-xs-10 cl-sm-10 col-md-10 mt-2 mt-md-0"> <h6 class="title font-weight-bold ml-1 ml-md-4"><a href="https://github.com/treangenlab" rel="external nofollow noopener" target="_blank">Treangen lab software</a></h6> <ul class="items"> <li> <span class="item">Variety of open-source tools for microbial genomics and metagenomics</span> </li> </ul> </div> </div> </li> </ul> </div> </div> <a class="anchor" id="Honors and Awards"></a> <div class="card mt-3 p-3"> <h3 class="card-title font-weight-medium">Honors and Awards</h3> <div> <ul class="card-text font-weight-light list-group list-group-flush"> <li class="list-group-item"> <div class="row"> <div class="col-xs-2 cl-sm-2 col-md-2 text-center" style="width: 75px"> <table class="table-cv"> <tbody> <tr> <td> <span class="badge font-weight-bold danger-color-dark text-uppercase align-middle" style="min-width: 75px">2008</span> </td> </tr> </tbody> </table> </div> <div class="col-xs-10 cl-sm-10 col-md-10 mt-2 mt-md-0"> <ul class="items"> <li> <span class="item">Europeus Doctor</span> </li> </ul> </div> </div> </li> <li class="list-group-item"> <div class="row"> <div class="col-xs-2 cl-sm-2 col-md-2 text-center" style="width: 75px"> <table class="table-cv"> <tbody> <tr> <td> <span class="badge font-weight-bold danger-color-dark text-uppercase align-middle" style="min-width: 75px">2023</span> </td> </tr> </tbody> </table> </div> <div class="col-xs-10 cl-sm-10 col-md-10 mt-2 mt-md-0"> <ul class="items"> <li> <span class="item">NSF CAREER Award</span> </li> </ul> </div> </div> </li> <li class="list-group-item"> <div class="row"> <div class="col-xs-2 cl-sm-2 col-md-2 text-center" style="width: 75px"> <table class="table-cv"> <tbody> <tr> <td> <span class="badge font-weight-bold danger-color-dark text-uppercase align-middle" style="min-width: 75px">2024</span> </td> </tr> </tbody> </table> </div> <div class="col-xs-10 cl-sm-10 col-md-10 mt-2 mt-md-0"> <ul class="items"> <li> <span class="item">Rice School of Engineering (SoE) University Research and Teaching Award</span> </li> </ul> </div> </div> </li> </ul> </div> </div> <a class="anchor" id="Academic Interests"></a> <div class="card mt-3 p-3"> <h3 class="card-title font-weight-medium">Academic Interests</h3> <div> <ul class="card-text font-weight-light list-group list-group-flush"> <li class="list-group-item"> <h5 class="font-italic">Microbial genomics</h5> <ul class="subitems"> <li> <span class="subitem">Development of algorithms for microbial genome assembly, alignment analysis.</span> </li> <li> <span class="subitem">Comparative genomics of bacterial pathogens.</span> </li> </ul> </li> <li class="list-group-item"> <h5 class="font-italic">Metagenomics</h5> <ul class="subitems"> <li> <span class="subitem">Computational methods for studying microbial communities.</span> </li> <li> <span class="subitem">Metagenomics and the study of microbial diversity.</span> </li> </ul> </li> </ul> </div> </div> <a class="anchor" id="Other Interests"></a> <div class="card mt-3 p-3"> <h3 class="card-title font-weight-medium">Other Interests</h3> <div> <ul class="card-text font-weight-light list-group list-group-flush"> <li class="list-group-item"> <u>Hobbies:</u> Website design and maintenance, metagenomic workshops, Fishing for percebes</li> </ul> </div> </div> </div> </article> </div> </div> </div> </div> <footer class="fixed-bottom" role="contentinfo"> <div class="container mt-0"> © Copyright 2024 Treangen J. 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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> Lab PI | Treangen lab at Rice University </title> <meta name="author" content="Treangen J. Treangen"> <meta name="description" content="Treangen Lab PI (Dr. Todd J. 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Treangen)</p> </header> <article> <div class="cv"> <a class="anchor" id="CV (updated September 2024)"></a> <div class="card mt-3 p-3"> <h3 class="card-title font-weight-medium">CV (updated September 2024)</h3> <div> <table class="table table-cv table-sm table-borderless table-responsive"> <tr> <td class="p-1 pr-2 font-weight-bold"> <b>Full Name</b> </td> <td class="p-1 pl-2 font-weight-light text">Todd J. Treangen</td> </tr> <tr> <td class="p-1 pr-2 font-weight-bold"> <b>Languages</b> </td> <td class="p-1 pl-2 font-weight-light text">English, Galician, Spanish</td> </tr> </table> </div> </div> <a class="anchor" id="Education"></a> <div class="card mt-3 p-3"> <h3 class="card-title font-weight-medium">Education</h3> <div> <ul class="card-text font-weight-light list-group list-group-flush"> <li class="list-group-item"> <div class="row"> <div class="col-xs-2 cl-sm-2 col-md-2 text-center" style="width: 75px"> <table class="table-cv"> <tbody> <tr> <td> <span class="badge font-weight-bold danger-color-dark text-uppercase align-middle" style="min-width: 75px">2008</span> </td> </tr> </tbody> </table> </div> <div class="col-xs-10 cl-sm-10 col-md-10 mt-2 mt-md-0"> <h6 class="title font-weight-bold ml-1 ml-md-4">Ph.D. in Computer Science</h6> <table class="table-cv ml-1 ml-md-4 institution"> <tbody> <tr> <td style="vertical-align: top; text-align: center" class="institution"> <i class="fa-solid fa-building-columns iconinstitution"></i> </td> <td class="institution">Polytechnic University of Catalonia, Barcelona, Spain</td> </tr> </tbody> </table> <ul class="items"> <li> <span class="item">Focus on bioinformatics and computational biology.</span> </li> <li> <span class="item">Research involved the development of algorithms for genome analysis.</span> </li> <li> <span class="item-title">Dissertation</span> <ul class="subitems"> <li> <span class="subitem">{"Title"=&gt;"Novel Computational Methods for Large Scale Genome Comparison"}</span> </li> <li> <span class="subitem">{"Advisor"=&gt;"Dr. Xavier Messeguer"}</span> </li> </ul> </li> </ul> </div> </div> </li> <li class="list-group-item"> <div class="row"> <div class="col-xs-2 cl-sm-2 col-md-2 text-center" style="width: 75px"> <table class="table-cv"> <tbody> <tr> <td> <span class="badge font-weight-bold danger-color-dark text-uppercase align-middle" style="min-width: 75px">2004</span> </td> </tr> </tbody> </table> </div> <div class="col-xs-10 cl-sm-10 col-md-10 mt-2 mt-md-0"> <h6 class="title font-weight-bold ml-1 ml-md-4">MS in Computer Science</h6> <table class="table-cv ml-1 ml-md-4 institution"> <tbody> <tr> <td style="vertical-align: top; text-align: center" class="institution"> <i class="fa-solid fa-building-columns iconinstitution"></i> </td> <td class="institution">Polytechnic University of Catalonia, Barcelona, Spain</td> </tr> </tbody> </table> <ul class="items"> <li> <span class="item">Specialized in algorithm development for large-scale genomic data.</span> </li> <li> <span class="item">Completed a thesis on "Efficient Methods for Genome Alignment."</span> </li> </ul> </div> </div> </li> </ul> </div> </div> <a class="anchor" id="Experience"></a> <div class="card mt-3 p-3"> <h3 class="card-title font-weight-medium">Experience</h3> <div> <ul class="card-text font-weight-light list-group list-group-flush"> <li class="list-group-item"> <div class="row"> <div class="col-xs-2 cl-sm-2 col-md-2 text-center" style="width: 75px"> <table class="table-cv"> <tbody> <tr> <td> <span class="badge font-weight-bold danger-color-dark text-uppercase align-middle" style="min-width: 75px">2023 - present</span> </td> </tr> </tbody> </table> </div> <div class="col-xs-10 cl-sm-10 col-md-10 mt-2 mt-md-0"> <h6 class="title font-weight-bold ml-1 ml-md-4">Associate Professor, Computer Science</h6> <table class="table-cv ml-1 ml-md-4 institution"> <tbody> <tr> <td style="vertical-align: top; text-align: center" class="institution"> <i class="fa-solid fa-building-columns iconinstitution"></i> </td> <td class="institution">Rice University, Houston, Texas, USA</td> </tr> </tbody> </table> <ul class="items"> <li> <span class="item">Affiliate faculty in Department of Bioengineering</span> </li> <li> <span class="item">Leads the Treangen Lab, focusing on bioinformatics, genomics, and metagenomics.</span> </li> <li> <span class="item">Developed tools for microbial detection and outbreak tracking.</span> </li> <li> <span class="item-title">Research</span> <ul class="subitems"> <li> <span class="subitem">Focus on AI-driven approaches for genomic data analysis.</span> </li> <li> <span class="subitem">Developed algorithms for rapid pathogen detection.</span> </li> </ul> </li> </ul> </div> </div> </li> <li class="list-group-item"> <div class="row"> <div class="col-xs-2 cl-sm-2 col-md-2 text-center" style="width: 75px"> <table class="table-cv"> <tbody> <tr> <td> <span class="badge font-weight-bold danger-color-dark text-uppercase align-middle" style="min-width: 75px">2018 - 2023</span> </td> </tr> </tbody> </table> </div> <div class="col-xs-10 cl-sm-10 col-md-10 mt-2 mt-md-0"> <h6 class="title font-weight-bold ml-1 ml-md-4">Assistant Professor, Computer Science</h6> <table class="table-cv ml-1 ml-md-4 institution"> <tbody> <tr> <td style="vertical-align: top; text-align: center" class="institution"> <i class="fa-solid fa-building-columns iconinstitution"></i> </td> <td class="institution">Rice University, Houston, Texas, USA</td> </tr> </tbody> </table> <ul class="items"> <li> <span class="item">Leads the Treangen Lab, focusing on bioinformatics, genomics, and metagenomics.</span> </li> <li> <span class="item">Developed tools for microbial detection and outbreak tracking.</span> </li> <li> <span class="item-title">Research</span> <ul class="subitems"> <li> <span class="subitem">Focus on AI-driven approaches for genomic data analysis.</span> </li> <li> <span class="subitem">Developed algorithms for rapid pathogen detection.</span> </li> </ul> </li> </ul> </div> </div> </li> <li class="list-group-item"> <div class="row"> <div class="col-xs-2 cl-sm-2 col-md-2 text-center" style="width: 75px"> <table class="table-cv"> <tbody> <tr> <td> <span class="badge font-weight-bold danger-color-dark text-uppercase align-middle" style="min-width: 75px">2016 - 2018</span> </td> </tr> </tbody> </table> </div> <div class="col-xs-10 cl-sm-10 col-md-10 mt-2 mt-md-0"> <h6 class="title font-weight-bold ml-1 ml-md-4">Research Assistant Professor, UMIACS</h6> <table class="table-cv ml-1 ml-md-4 institution"> <tbody> <tr> <td style="vertical-align: top; text-align: center" class="institution"> <i class="fa-solid fa-building-columns iconinstitution"></i> </td> <td class="institution">University of Maryland, College Park, Maryland, USA</td> </tr> </tbody> </table> <ul class="items"> <li> <span class="item">Conducted research on genome assembly and metagenomics.</span> </li> <li> <span class="item">Collaborated on the development of scalable bioinformatics tools.</span> </li> </ul> </div> </div> </li> <li class="list-group-item"> <div class="row"> <div class="col-xs-2 cl-sm-2 col-md-2 text-center" style="width: 75px"> <table class="table-cv"> <tbody> <tr> <td> <span class="badge font-weight-bold danger-color-dark text-uppercase align-middle" style="min-width: 75px">2012 - 2016</span> </td> </tr> </tbody> </table> </div> <div class="col-xs-10 cl-sm-10 col-md-10 mt-2 mt-md-0"> <h6 class="title font-weight-bold ml-1 ml-md-4">PI and Bioinformatics Scientist</h6> <table class="table-cv ml-1 ml-md-4 institution"> <tbody> <tr> <td style="vertical-align: top; text-align: center" class="institution"> <i class="fa-solid fa-building-columns iconinstitution"></i> </td> <td class="institution">National Biodefense Analysis and Countermeasures Center (NBACC)</td> </tr> </tbody> </table> <ul class="items"> <li> <span class="item">Focused on pathogen detection and large scale genome comparison of microbes</span> </li> </ul> </div> </div> </li> <li class="list-group-item"> <div class="row"> <div class="col-xs-2 cl-sm-2 col-md-2 text-center" style="width: 75px"> <table class="table-cv"> <tbody> <tr> <td> <span class="badge font-weight-bold danger-color-dark text-uppercase align-middle" style="min-width: 75px">2011 - 2012</span> </td> </tr> </tbody> </table> </div> <div class="col-xs-10 cl-sm-10 col-md-10 mt-2 mt-md-0"> <h6 class="title font-weight-bold ml-1 ml-md-4">Postdoctoral Scientist, School of Public Health</h6> <table class="table-cv ml-1 ml-md-4 institution"> <tbody> <tr> <td style="vertical-align: top; text-align: center" class="institution"> <i class="fa-solid fa-building-columns iconinstitution"></i> </td> <td class="institution">Johns Hopkins University (Salzberg lab)</td> </tr> </tbody> </table> <ul class="items"> <li> <span class="item">Focused on genome assembly</span> </li> </ul> </div> </div> </li> <li class="list-group-item"> <div class="row"> <div class="col-xs-2 cl-sm-2 col-md-2 text-center" style="width: 75px"> <table class="table-cv"> <tbody> <tr> <td> <span class="badge font-weight-bold danger-color-dark text-uppercase align-middle" style="min-width: 75px">2010 - 2011</span> </td> </tr> </tbody> </table> </div> <div class="col-xs-10 cl-sm-10 col-md-10 mt-2 mt-md-0"> <h6 class="title font-weight-bold ml-1 ml-md-4">Postdoctoral Scientist, CBCB</h6> <table class="table-cv ml-1 ml-md-4 institution"> <tbody> <tr> <td style="vertical-align: top; text-align: center" class="institution"> <i class="fa-solid fa-building-columns iconinstitution"></i> </td> <td class="institution">University of Maryland College Park (Pop and Salzberg labs)</td> </tr> </tbody> </table> <ul class="items"> <li> <span class="item">Focused on genome and metagenome assembly</span> </li> </ul> </div> </div> </li> <li class="list-group-item"> <div class="row"> <div class="col-xs-2 cl-sm-2 col-md-2 text-center" style="width: 75px"> <table class="table-cv"> <tbody> <tr> <td> <span class="badge font-weight-bold danger-color-dark text-uppercase align-middle" style="min-width: 75px">2008 - 2010</span> </td> </tr> </tbody> </table> </div> <div class="col-xs-10 cl-sm-10 col-md-10 mt-2 mt-md-0"> <h6 class="title font-weight-bold ml-1 ml-md-4">Postdoctoral Scientist</h6> <table class="table-cv ml-1 ml-md-4 institution"> <tbody> <tr> <td style="vertical-align: top; text-align: center" class="institution"> <i class="fa-solid fa-building-columns iconinstitution"></i> </td> <td class="institution">Institut Pasteur, Paris, France (Rocha lab)</td> </tr> </tbody> </table> <ul class="items"> <li> <span class="item">Focused on evolutionary microbial genomics (GEM)</span> </li> </ul> </div> </div> </li> </ul> </div> </div> <a class="anchor" id="Open Source Projects"></a> <div class="card mt-3 p-3"> <h3 class="card-title font-weight-medium">Open Source Projects</h3> <div> <ul class="card-text font-weight-light list-group list-group-flush"> <li class="list-group-item"> <div class="row"> <div class="col-xs-2 cl-sm-2 col-md-2 text-center" style="width: 75px"> <table class="table-cv"> <tbody> <tr> <td> <span class="badge font-weight-bold danger-color-dark text-uppercase align-middle" style="min-width: 75px">2010-2015</span> </td> </tr> </tbody> </table> </div> <div class="col-xs-10 cl-sm-10 col-md-10 mt-2 mt-md-0"> <h6 class="title font-weight-bold ml-1 ml-md-4"><a href="https://github.com/marbl/metamos" rel="external nofollow noopener" target="_blank">MetAMOS</a></h6> <ul class="items"> <li> <span class="item">An open-source metagenomic assembly and analysis pipeline.</span> </li> </ul> </div> </div> </li> <li class="list-group-item"> <div class="row"> <div class="col-xs-2 cl-sm-2 col-md-2 text-center" style="width: 75px"> <table class="table-cv"> <tbody> <tr> <td> <span class="badge font-weight-bold danger-color-dark text-uppercase align-middle" style="min-width: 75px">2010-2015</span> </td> </tr> </tbody> </table> </div> <div class="col-xs-10 cl-sm-10 col-md-10 mt-2 mt-md-0"> <h6 class="title font-weight-bold ml-1 ml-md-4"><a href="https://github.com/marbl/parsnp" rel="external nofollow noopener" target="_blank">ParSNP</a></h6> <ul class="items"> <li> <span class="item">An open-source microbial core genome alignment tool.</span> </li> </ul> </div> </div> </li> <li class="list-group-item"> <div class="row"> <div class="col-xs-2 cl-sm-2 col-md-2 text-center" style="width: 75px"> <table class="table-cv"> <tbody> <tr> <td> <span class="badge font-weight-bold danger-color-dark text-uppercase align-middle" style="min-width: 75px">2013-2018</span> </td> </tr> </tbody> </table> </div> <div class="col-xs-10 cl-sm-10 col-md-10 mt-2 mt-md-0"> <h6 class="title font-weight-bold ml-1 ml-md-4"><a href="https://github.com/marbl/mash" rel="external nofollow noopener" target="_blank">Mash</a></h6> <ul class="items"> <li> <span class="item">Fast genome and metagenome distance estimation using MinHash.</span> </li> </ul> </div> </div> </li> <li class="list-group-item"> <div class="row"> <div class="col-xs-2 cl-sm-2 col-md-2 text-center" style="width: 75px"> <table class="table-cv"> <tbody> <tr> <td> <span class="badge font-weight-bold danger-color-dark text-uppercase align-middle" style="min-width: 75px">2018-2024</span> </td> </tr> </tbody> </table> </div> <div class="col-xs-10 cl-sm-10 col-md-10 mt-2 mt-md-0"> <h6 class="title font-weight-bold ml-1 ml-md-4"><a href="https://github.com/treangenlab" rel="external nofollow noopener" target="_blank">Treangen lab software</a></h6> <ul class="items"> <li> <span class="item">Variety of open-source tools for microbial genomics and metagenomics</span> </li> </ul> </div> </div> </li> </ul> </div> </div> <a class="anchor" id="Honors and Awards"></a> <div class="card mt-3 p-3"> <h3 class="card-title font-weight-medium">Honors and Awards</h3> <div> <ul class="card-text font-weight-light list-group list-group-flush"> <li class="list-group-item"> <div class="row"> <div class="col-xs-2 cl-sm-2 col-md-2 text-center" style="width: 75px"> <table class="table-cv"> <tbody> <tr> <td> <span class="badge font-weight-bold danger-color-dark text-uppercase align-middle" style="min-width: 75px">2008</span> </td> </tr> </tbody> </table> </div> <div class="col-xs-10 cl-sm-10 col-md-10 mt-2 mt-md-0"> <ul class="items"> <li> <span class="item">Europeus Doctor</span> </li> </ul> </div> </div> </li> <li class="list-group-item"> <div class="row"> <div class="col-xs-2 cl-sm-2 col-md-2 text-center" style="width: 75px"> <table class="table-cv"> <tbody> <tr> <td> <span class="badge font-weight-bold danger-color-dark text-uppercase align-middle" style="min-width: 75px">2023</span> </td> </tr> </tbody> </table> </div> <div class="col-xs-10 cl-sm-10 col-md-10 mt-2 mt-md-0"> <ul class="items"> <li> <span class="item">NSF CAREER Award</span> </li> </ul> </div> </div> </li> <li class="list-group-item"> <div class="row"> <div class="col-xs-2 cl-sm-2 col-md-2 text-center" style="width: 75px"> <table class="table-cv"> <tbody> <tr> <td> <span class="badge font-weight-bold danger-color-dark text-uppercase align-middle" style="min-width: 75px">2024</span> </td> </tr> </tbody> </table> </div> <div class="col-xs-10 cl-sm-10 col-md-10 mt-2 mt-md-0"> <ul class="items"> <li> <span class="item">Rice School of Engineering (SoE) University Research and Teaching Award</span> </li> </ul> </div> </div> </li> </ul> </div> </div> <a class="anchor" id="Academic Interests"></a> <div class="card mt-3 p-3"> <h3 class="card-title font-weight-medium">Academic Interests</h3> <div> <ul class="card-text font-weight-light list-group list-group-flush"> <li class="list-group-item"> <h5 class="font-italic">Microbial genomics</h5> <ul class="subitems"> <li> <span class="subitem">Development of algorithms for microbial genome assembly, alignment analysis.</span> </li> <li> <span class="subitem">Comparative genomics of bacterial pathogens.</span> </li> </ul> </li> <li class="list-group-item"> <h5 class="font-italic">Metagenomics</h5> <ul class="subitems"> <li> <span class="subitem">Computational methods for studying microbial communities.</span> </li> <li> <span class="subitem">Metagenomics and the study of microbial diversity.</span> </li> </ul> </li> </ul> </div> </div> </div> </article> </div> </div> </div> </div> <footer class="fixed-bottom" role="contentinfo"> <div class="container mt-0"> © Copyright 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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="4.3.4">Jekyll</generator><link href="/feed.xml" rel="self" type="application/atom+xml"/><link href="/" rel="alternate" type="text/html" hreflang="en"/><updated>2024-11-17T01:37:51+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">Reflections from Lake Arrowhead Microbial Genomics 2024</title><link href="/blog/2024/LAMG_conference/" rel="alternate" type="text/html" title="Reflections from Lake Arrowhead Microbial Genomics 2024"/><published>2024-10-17T00:00:00+00:00</published><updated>2024-10-17T00:00:00+00:00</updated><id>/blog/2024/LAMG_conference</id><content type="html" xml:base="/blog/2024/LAMG_conference/"><![CDATA[<h2 id="introduction">Introduction</h2> <p>I am excited to share my experiences at the <a href="https://www.lamg.info/conference-site">Lake Arrowhead Microbial Genomes (LAMG), 2024 Conference</a>, held from September 15th to 19th at the beautiful Lake Arrowhead. Presenting my poster on two computational tools, Lemur and Magnet, developed by Treangen lab alumni; <a href="https://scholar.google.com/citations?user=HEwzrPEAAAAJ&amp;hl=en">Dr. Nicolae Sapoval</a> and <a href="https://scholar.google.com/citations?user=v39CxLgAAAAJ&amp;hl=zh-CN">Dr. Yunxi Liu</a> respectively, was a privilege. Lemur is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets and Magnet is a computational tool that uses reference based method to refine taxonomic assignment and provide accurate abundance estimations. Find more details about these projects <a href="https://github.com/treangenlab/lemur">here</a></p> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/posterLAMG-480.webp 480w,/assets/img/posterLAMG-800.webp 800w,/assets/img/posterLAMG-1400.webp 1400w," sizes="95vw" type="image/webp"/> <img src="/assets/img/posterLAMG.jpeg" class="img-fluid rounded z-depth-1" width="100%" height="auto" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"/> </picture> </figure> <h3 id="first-impressions">First Impressions</h3> <p>The setting was stunning! We stayed in lakeside cabins with a serene, scenic view, and the perfect California weather made it easy to unwind, enjoy nature, and dive into productive networking and science.</p> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/LakeArrowhead-480.webp 480w,/assets/img/LakeArrowhead-800.webp 800w,/assets/img/LakeArrowhead-1400.webp 1400w," sizes="95vw" type="image/webp"/> <img src="/assets/img/LakeArrowhead.jpeg" class="img-fluid rounded z-depth-1" width="100%" height="auto" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"/> </picture> </figure> <p>As a computational biology and bioinformatics student, it was exciting to be among a predominantly wet-lab audience, sharing insights and learning what biologists value in computational tools. I liked how there was a good mix of students and PIs and Biotech companies as well. This gave me the industry and academia interplay which I really like to see. The diverse talks were inspiring, and two stood out to me in particular.</p> <hr/> <h2 id="highlights-of-the-talks">Highlights of the Talks</h2> <p>One of the standout talks for me was <a href="https://djschwartzlab.wustl.edu/">Dr. Drew Schwartz’s</a>(https://scholar.google.com/citations?user=_eybPZYAAAAJ&amp;hl=en) presentation titled, “Pediatric Gut Microbiome Development and Disruption.” Dr. Schwartz’s work dives deep into the potential of the microbiome to inform personalized medicine—especially for vulnerable pediatric patients.Dr. Schwartz raised an interesting question: Can the composition of a newborn’s microbiome predict their risk of bloodstream infections? The goal is to explore the use of rapid long-read sequencing combined with advanced computational algorithms to conduct personalized risk assessments and support antibiotic stewardship. This approach could significantly reduce unnecessary antibiotic treatments for infants, which is a crucial step toward optimizing neonatal care.</p> <p>Another great talk “Into the Unknown: Genome-resolved Metagenomics of Soil using HiFi Sequencing,” <a href="https://scholar.google.com/citations?user=xZFaH9oAAAAJ&amp;hl=en">Dan Portik</a> delved into the complexities of soil metagenome assembly and the potential of long-read sequencing to improve it. Using the latest Revio PacBio sequencer, Portik and his team tested HiFi-MAG-Pipeline to generate metagenome-assembled genomes (MAGs) with high accuracy, overcoming the long-standing challenges of soil metagenome assembly. He demonstrated how short-read sequencing struggles with MAGs, whereas PacBio HiFi’s long reads can deliver transformative, scalable assemblies, marking a significant advancement in metagenomics research.</p> <hr/> <h2 id="poster-presentation-feedback">Poster Presentation feedback</h2> <p>I received positive feedback on my poster, with a lot of interest in Lemur and Magnet’s efficiency and precision. Participants appreciated how lightweight the tools were, and many were impressed by Magnet’s capability as a quality check and abundance estimation tool. There was also interest in expanding the tools to detect viral species. The networking opportunities were invaluable, especially as a “bio-heavy” conference where I could learn directly from biologists, the primary users of the tools our lab develops. Hearing from researchers who had already used Lemur was a gratifying highlight, especially when they shared how straightforward and effective it was for their analyses.</p> <hr/> <h2 id="overall-experience">Overall Experience</h2> <p>Overall, my first trip to Lake Arrowhead was a memorable experience, surrounded by beautiful mountains and lakes. Beyond the picturesque setting, this conference was a rich environment for networking and sparking new ideas. It highlights for me the collaborative nature of the microbial genomics field and the importance of continuous interactions between computational and biological perspectives. I’m excited to bring back these insights to our lab and continue contributing to the dynamic world of microbial genomics! This is a conference that anyone with an interest in microbiome studies should attend, the diverse work being done across the world in this field is mindblowing and very innovative. The remote location of Lake Arrowhead also gave me time to focus on science with no distraction.</p> <hr/>]]></content><author><name>Natalie Kokroko</name></author><category term="workshops"/><summary type="html"><![CDATA[Natalie's first experience and takeaways from the Lake Arrowhead Microbial Genomes Conference, 2024.]]></summary></entry><entry><title type="html">Reflections from MBL STAMPS 2024</title><link href="/blog/2024/stampsblog/" rel="alternate" type="text/html" title="Reflections from MBL STAMPS 2024"/><published>2024-09-28T00:00:00+00:00</published><updated>2024-09-28T00:00:00+00:00</updated><id>/blog/2024/stampsblog</id><content type="html" xml:base="/blog/2024/stampsblog/"><![CDATA[<h2 id="introduction">Introduction</h2> <p>Hey there, I’m Austin Marshall, a first year postdoctoral fellow in the <a href="https://villapol.hmailabs.org/">Villapol</a> and <a href="https://treangenlab.github.io/">Treangen</a> Labs where I work on trimming the knowledge gap between microbiologists and computer scientists. This blog will be related to my experience of the Strategies and Techniques for Analyzing Microbial Population Structures (STAMPS) workshop that I attended this past July.</p> <hr/> <h2 id="venue">Venue</h2> <h3 id="location">Location</h3> <p>The STAMPS workshop is held at the University of Chicago, Marine Biological Laboratory. The Marine Biological Laboratory (<strong>MBL</strong>) is located in <a href="https://www.google.com/maps/place/Woods+Hole,+Falmouth,+MA/@41.5300117,-70.6892765,14z/data=!3m1!4b1!4m6!3m5!1s0x89e4d87731d3bb2b:0x6057f1e3e2336b81!8m2!3d41.5264977!4d-70.6730857!16zL20vMHR5N2I?entry=ttu&amp;g_ep=EgoyMDI0MDkyNS4wIKXMDSoASAFQAw%3D%3D">Wood’s Hole, Massachusetts</a> and is the closest mainland town to <a href="https://www.google.com/maps/place/Martha's+Vineyard/@41.3923525,-70.817379,11z/data=!3m1!4b1!4m14!1m7!3m6!1s0x89e525890034153b:0xf5d72dfce4b4bc43!2sMartha's+Vineyard!8m2!3d41.3804981!4d-70.645473!16zL20vMGd0cmc!3m5!1s0x89e525890034153b:0xf5d72dfce4b4bc43!8m2!3d41.3804981!4d-70.645473!16zL20vMGd0cmc?entry=ttu&amp;g_ep=EgoyMDI0MDkyNS4wIKXMDSoASAFQAw%3D%3D">Martha’s Vineyard.</a></p> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/crabs_mbl-480.webp 480w,/assets/img/crabs_mbl-800.webp 800w,/assets/img/crabs_mbl-1400.webp 1400w," sizes="95vw" type="image/webp"/> <img src="/assets/img/crabs_mbl.jpg" class="img-fluid rounded z-depth-1" width="100%" height="auto" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"/> </picture> </figure> <h3 id="history">History</h3> <p>I was unaware of the immensely deep research history that the Woods Hole Oceanographic Institute and Marine Biology Laboratory have until I was tired of having my thinking cap on one evening and started looking around the amazing displays where I stumbled upon this.</p> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/thm_nobel-480.webp 480w,/assets/img/thm_nobel-800.webp 800w,/assets/img/thm_nobel-1400.webp 1400w," sizes="95vw" type="image/webp"/> <img src="/assets/img/thm_nobel.jpg" class="img-fluid rounded z-depth-1" width="100%" height="auto" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"/> </picture> </figure> <p>Check out this awesome Nobel prize they have on display near the Lillie Library, it was awarded to Thomas Hunt Morgan for his discovery of the role chromosomes play in heredity. Countless nobel laureates, defining figures in biology, and just amazing researchers had walked through these same halls that I was fortunate enough to have the opportunity to as well. For a wild list of nobel laureates affiliated with the MBL check out <a href="https://www.mbl.edu/about/history-archives/nobel-laureates">this page.</a></p> <hr/> <h2 id="topics-and-presenters">Topics and Presenters</h2> <p>The <a href="https://www.mbl.edu/education/advanced-research-training-courses/course-offerings/strategies-and-techniques-analyzing-microbial-population-structures">course description</a> of the STAMPS workshop is pretty spot-on. (<em>nanopore sequencing pun</em>) We went through the analysis of short-read and long-read amplicon sequencing analysis as well as metagenomic sequence analysis. Personally, I believe the <em>Stats Day</em> was the most useful part for me but this could be due to my background and experience level.</p> <p>The speaker lineup for the STAMPS workshop is pretty insane. The lectures began with an introduction into sequencing modalities and 16S sequence analysis by <a href="https://scholar.google.com/citations?user=zGifBvwAAAAJ&amp;hl=en">Dr. Ben Callahan.</a> Following Dr. Callahan, we were introduced into metagenomics and kmer based analyses by <a href="https://scholar.google.com/citations?user=O4rYanMAAAAJ&amp;hl=en">Dr. C. Titus Brown</a> who is definitely a leader in this field as his group is responsible for the creation and maintenance of <a href="https://github.com/sourmash-bio/sourmash">sourmash</a>, <a href="https://github.com/dib-lab/khmer">khmer</a>, and <a href="https://github.com/spacegraphcats/spacegraphcats/">spacegraphcats</a>.</p> <p>After Dr. Brown gave the basis of metagenomic asequencing and analysis it was time for my group to step up to the plate. My co-PI <a href="https://scholar.google.com/citations?user=N5irv88AAAAJ&amp;hl=en">Dr. Todd J. Treangen</a> and STAMPS alumni / research scientist in the Treangen Lab <a href="https://scholar.google.com/citations?hl=en&amp;user=E1v2MBUAAAAJ">Dr. Michael G. Nute</a> gave a very in-depth look into metagenomic assembly including a hands on demonstration of reference-based vs. de-novo assembly methods and also gave some insight into multiprocessing and how we as a class only ran our assembly on one core…</p> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/agm_assembler-480.webp 480w,/assets/img/agm_assembler-800.webp 800w,/assets/img/agm_assembler-1400.webp 1400w," sizes="95vw" type="image/webp"/> <img src="/assets/img/agm_assembler.jpg" class="img-fluid rounded z-depth-1" width="100%" height="auto" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"/> </picture> </figure> <p>Behind the scenes of the metagenomic assembly tutorial, shown above a cinnamon bun powered window size estimator.</p> <p>The next day we were introduced to the fascinating research of <a href="https://scholar.google.com/citations?user=yFncM6AAAAAJ&amp;hl=en">Dr. Curtis Huttenhower.</a> If you are in the world of microbiome research you should be familiar with this name. Dr. Huttenhower covered a broad overview of his group’s research but dove in-depth with a few of the Biobakery’s newer tools including <a href="https://github.com/biobakery/anpan">anpan</a>, <a href="https://github.com/biobakery/halla">HAllA</a>, and <a href="https://github.com/biobakery/maaslin3">MaAsLin3</a>. This was probably one of the more intense lab sessions we had and we certainly put those Rstudio VM’s to good use.</p> <p>On the third to last day we had our <em>Stats Day</em>, led by the wonderful and talented <a href="https://scholar.google.com/citations?hl=en&amp;user=pFlAtDsAAAAJ">Dr. Amy Willis.</a> Dr. Willis walked the class through arguably some of the most complex and misunderstood areas of microbiome sequence analysis including relative abundances, alpha and beta diversity, as well as differential abundance analyses. Her research is certainly at the top of the field and if you are performing any microbiome analysis you should check out the <a href="https://github.com/statdivlab">StatDivLab’s github</a> for their plethora of programs that will help give you <em>confidence</em> in your results. I also want to shoutout her wonderful PhD students <a href="https://github.com/svteichman">Sarah</a>, <a href="https://github.com/shirmath">Shirley</a>, and <a href="https://github.com/MariaAVC">Maria</a> who are the next generation of microbiome stats wizards.</p> <p>My last full day was focused on metagenomic binning, with a little added flavor of strain level analysis and phylogenetics thanks to Mike Nute’s background and PhD with <a href="https://scholar.google.com/citations?hl=en&amp;user=pPB_WK0AAAAJ">Dr. Tandy Warnow.</a> During this lecture and lab, we walked through the steps of using common binning tools (and what they are doing) as well as ran a multiple sequence alignment using <a href="https://github.com/marbl/parsnp">parsnp2</a> with a <a href="https://github.com/marbl/gingr">gingr</a> visualization!</p> <p>One of the speakers who was unable to come because of the dang C*VID was <a href="https://scholar.google.com/citations?user=-ONw6lsAAAAJ&amp;hl=en">Dr. Mike Lee.</a> Dr. Lee was still involved in this workshop as he was kind of our tech guy behind the scenes, as he had setup all our own individual compute instances (JupyterLab and Rstudio) and installed all the dependencies for the workshop labs to run smoothly. Mike Lee is someone I had really looked forward to meeting, as his website <a href="https://astrobiomike.github.io/">Happy Belly Bioinformatics</a>, was one of the main resources I used to begin my bioinformatics journey, also we worked in the same field at different NASA facilities for a while. Mike if you’re reading this <strong>hmu!</strong></p> <hr/> <h2 id="overall-experience">Overall experience</h2> <p>I think this was a great learning experience and it was hosted at a fantastic institution that has a remarkable past. Proabably my biggest gripe about this conference was the lack of air conditioning in the housing. Coming from Houston Texas, where the AC is on so much that there is a 40 degree temperature difference between inside and outside this was a bit of a challenge but it should not defer <strong>anyone</strong> from attending this workshop, it’s part of the experience.</p> <hr/> <h2 id="should-you-go">Should you go?</h2> <p><strong>Yes</strong>. If you are a biologist working on any microbiome analysis this would be a very beneficial experience for you and even if you are slightly seasoned in microbial sequence analysis like myself, I was still able to find it quite useful and gave me some more confidence to help get over the ever present <a href="https://en.wikipedia.org/wiki/Impostor_syndrome">imposter syndrome.</a> If you have any questions on the STAMPS workshop or on more aspects of my time at STAMPS feel free to reach out via my contact info and check out the <a href="https://github.com/mblstamps/stamps2024">STAMPS 2024 github!</a></p> <hr/>]]></content><author><name>Austin Marshall</name></author><category term="workshops"/><summary type="html"><![CDATA[Austin's experience and recap of the STAMPS 2024 workshop]]></summary></entry><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></feed>
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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="4.3.4">Jekyll</generator><link href="/feed.xml" rel="self" type="application/atom+xml"/><link href="/" rel="alternate" type="text/html" hreflang="en"/><updated>2024-11-17T17:33:41+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">Reflections from Lake Arrowhead Microbial Genomics 2024</title><link href="/blog/2024/LAMG_conference/" rel="alternate" type="text/html" title="Reflections from Lake Arrowhead Microbial Genomics 2024"/><published>2024-10-17T00:00:00+00:00</published><updated>2024-10-17T00:00:00+00:00</updated><id>/blog/2024/LAMG_conference</id><content type="html" xml:base="/blog/2024/LAMG_conference/"><![CDATA[<h2 id="introduction">Introduction</h2> <p>I am excited to share my experiences at the <a href="https://www.lamg.info/conference-site">Lake Arrowhead Microbial Genomes (LAMG), 2024 Conference</a>, held from September 15th to 19th at the beautiful Lake Arrowhead. Presenting my poster on two computational tools, Lemur and Magnet, developed by Treangen lab alumni; <a href="https://scholar.google.com/citations?user=HEwzrPEAAAAJ&amp;hl=en">Dr. Nicolae Sapoval</a> and <a href="https://scholar.google.com/citations?user=v39CxLgAAAAJ&amp;hl=zh-CN">Dr. Yunxi Liu</a> respectively, was a privilege. Lemur is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets and Magnet is a computational tool that uses reference based method to refine taxonomic assignment and provide accurate abundance estimations. Find more details about these projects <a href="https://github.com/treangenlab/lemur">here</a></p> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/posterLAMG-480.webp 480w,/assets/img/posterLAMG-800.webp 800w,/assets/img/posterLAMG-1400.webp 1400w," sizes="95vw" type="image/webp"/> <img src="/assets/img/posterLAMG.jpeg" class="img-fluid rounded z-depth-1" width="100%" height="auto" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"/> </picture> </figure> <h3 id="first-impressions">First Impressions</h3> <p>The setting was stunning! We stayed in lakeside cabins with a serene, scenic view, and the perfect California weather made it easy to unwind, enjoy nature, and dive into productive networking and science.</p> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/LakeArrowhead-480.webp 480w,/assets/img/LakeArrowhead-800.webp 800w,/assets/img/LakeArrowhead-1400.webp 1400w," sizes="95vw" type="image/webp"/> <img src="/assets/img/LakeArrowhead.jpeg" class="img-fluid rounded z-depth-1" width="100%" height="auto" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"/> </picture> </figure> <p>As a computational biology and bioinformatics student, it was exciting to be among a predominantly wet-lab audience, sharing insights and learning what biologists value in computational tools. I liked how there was a good mix of students and PIs and Biotech companies as well. This gave me the industry and academia interplay which I really like to see. The diverse talks were inspiring, and two stood out to me in particular.</p> <hr/> <h2 id="highlights-of-the-talks">Highlights of the Talks</h2> <p>One of the standout talks for me was <a href="https://djschwartzlab.wustl.edu/">Dr. Drew Schwartz’s</a>(https://scholar.google.com/citations?user=_eybPZYAAAAJ&amp;hl=en) presentation titled, “Pediatric Gut Microbiome Development and Disruption.” Dr. Schwartz’s work dives deep into the potential of the microbiome to inform personalized medicine—especially for vulnerable pediatric patients.Dr. Schwartz raised an interesting question: Can the composition of a newborn’s microbiome predict their risk of bloodstream infections? The goal is to explore the use of rapid long-read sequencing combined with advanced computational algorithms to conduct personalized risk assessments and support antibiotic stewardship. This approach could significantly reduce unnecessary antibiotic treatments for infants, which is a crucial step toward optimizing neonatal care.</p> <p>Another great talk “Into the Unknown: Genome-resolved Metagenomics of Soil using HiFi Sequencing,” <a href="https://scholar.google.com/citations?user=xZFaH9oAAAAJ&amp;hl=en">Dan Portik</a> delved into the complexities of soil metagenome assembly and the potential of long-read sequencing to improve it. Using the latest Revio PacBio sequencer, Portik and his team tested HiFi-MAG-Pipeline to generate metagenome-assembled genomes (MAGs) with high accuracy, overcoming the long-standing challenges of soil metagenome assembly. He demonstrated how short-read sequencing struggles with MAGs, whereas PacBio HiFi’s long reads can deliver transformative, scalable assemblies, marking a significant advancement in metagenomics research.</p> <hr/> <h2 id="poster-presentation-feedback">Poster Presentation feedback</h2> <p>I received positive feedback on my poster, with a lot of interest in Lemur and Magnet’s efficiency and precision. Participants appreciated how lightweight the tools were, and many were impressed by Magnet’s capability as a quality check and abundance estimation tool. There was also interest in expanding the tools to detect viral species. The networking opportunities were invaluable, especially as a “bio-heavy” conference where I could learn directly from biologists, the primary users of the tools our lab develops. Hearing from researchers who had already used Lemur was a gratifying highlight, especially when they shared how straightforward and effective it was for their analyses.</p> <hr/> <h2 id="overall-experience">Overall Experience</h2> <p>Overall, my first trip to Lake Arrowhead was a memorable experience, surrounded by beautiful mountains and lakes. Beyond the picturesque setting, this conference was a rich environment for networking and sparking new ideas. It highlights for me the collaborative nature of the microbial genomics field and the importance of continuous interactions between computational and biological perspectives. I’m excited to bring back these insights to our lab and continue contributing to the dynamic world of microbial genomics! This is a conference that anyone with an interest in microbiome studies should attend, the diverse work being done across the world in this field is mindblowing and very innovative. The remote location of Lake Arrowhead also gave me time to focus on science with no distraction.</p> <hr/>]]></content><author><name>Natalie Kokroko</name></author><category term="workshops"/><summary type="html"><![CDATA[Natalie's first experience and takeaways from the Lake Arrowhead Microbial Genomes Conference, 2024.]]></summary></entry><entry><title type="html">Reflections from MBL STAMPS 2024</title><link href="/blog/2024/stampsblog/" rel="alternate" type="text/html" title="Reflections from MBL STAMPS 2024"/><published>2024-09-28T00:00:00+00:00</published><updated>2024-09-28T00:00:00+00:00</updated><id>/blog/2024/stampsblog</id><content type="html" xml:base="/blog/2024/stampsblog/"><![CDATA[<h2 id="introduction">Introduction</h2> <p>Hey there, I’m Austin Marshall, a first year postdoctoral fellow in the <a href="https://villapol.hmailabs.org/">Villapol</a> and <a href="https://treangenlab.github.io/">Treangen</a> Labs where I work on trimming the knowledge gap between microbiologists and computer scientists. This blog will be related to my experience of the Strategies and Techniques for Analyzing Microbial Population Structures (STAMPS) workshop that I attended this past July.</p> <hr/> <h2 id="venue">Venue</h2> <h3 id="location">Location</h3> <p>The STAMPS workshop is held at the University of Chicago, Marine Biological Laboratory. The Marine Biological Laboratory (<strong>MBL</strong>) is located in <a href="https://www.google.com/maps/place/Woods+Hole,+Falmouth,+MA/@41.5300117,-70.6892765,14z/data=!3m1!4b1!4m6!3m5!1s0x89e4d87731d3bb2b:0x6057f1e3e2336b81!8m2!3d41.5264977!4d-70.6730857!16zL20vMHR5N2I?entry=ttu&amp;g_ep=EgoyMDI0MDkyNS4wIKXMDSoASAFQAw%3D%3D">Wood’s Hole, Massachusetts</a> and is the closest mainland town to <a href="https://www.google.com/maps/place/Martha's+Vineyard/@41.3923525,-70.817379,11z/data=!3m1!4b1!4m14!1m7!3m6!1s0x89e525890034153b:0xf5d72dfce4b4bc43!2sMartha's+Vineyard!8m2!3d41.3804981!4d-70.645473!16zL20vMGd0cmc!3m5!1s0x89e525890034153b:0xf5d72dfce4b4bc43!8m2!3d41.3804981!4d-70.645473!16zL20vMGd0cmc?entry=ttu&amp;g_ep=EgoyMDI0MDkyNS4wIKXMDSoASAFQAw%3D%3D">Martha’s Vineyard.</a></p> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/crabs_mbl-480.webp 480w,/assets/img/crabs_mbl-800.webp 800w,/assets/img/crabs_mbl-1400.webp 1400w," sizes="95vw" type="image/webp"/> <img src="/assets/img/crabs_mbl.jpg" class="img-fluid rounded z-depth-1" width="100%" height="auto" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"/> </picture> </figure> <h3 id="history">History</h3> <p>I was unaware of the immensely deep research history that the Woods Hole Oceanographic Institute and Marine Biology Laboratory have until I was tired of having my thinking cap on one evening and started looking around the amazing displays where I stumbled upon this.</p> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/thm_nobel-480.webp 480w,/assets/img/thm_nobel-800.webp 800w,/assets/img/thm_nobel-1400.webp 1400w," sizes="95vw" type="image/webp"/> <img src="/assets/img/thm_nobel.jpg" class="img-fluid rounded z-depth-1" width="100%" height="auto" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"/> </picture> </figure> <p>Check out this awesome Nobel prize they have on display near the Lillie Library, it was awarded to Thomas Hunt Morgan for his discovery of the role chromosomes play in heredity. Countless nobel laureates, defining figures in biology, and just amazing researchers had walked through these same halls that I was fortunate enough to have the opportunity to as well. For a wild list of nobel laureates affiliated with the MBL check out <a href="https://www.mbl.edu/about/history-archives/nobel-laureates">this page.</a></p> <hr/> <h2 id="topics-and-presenters">Topics and Presenters</h2> <p>The <a href="https://www.mbl.edu/education/advanced-research-training-courses/course-offerings/strategies-and-techniques-analyzing-microbial-population-structures">course description</a> of the STAMPS workshop is pretty spot-on. (<em>nanopore sequencing pun</em>) We went through the analysis of short-read and long-read amplicon sequencing analysis as well as metagenomic sequence analysis. Personally, I believe the <em>Stats Day</em> was the most useful part for me but this could be due to my background and experience level.</p> <p>The speaker lineup for the STAMPS workshop is pretty insane. The lectures began with an introduction into sequencing modalities and 16S sequence analysis by <a href="https://scholar.google.com/citations?user=zGifBvwAAAAJ&amp;hl=en">Dr. Ben Callahan.</a> Following Dr. Callahan, we were introduced into metagenomics and kmer based analyses by <a href="https://scholar.google.com/citations?user=O4rYanMAAAAJ&amp;hl=en">Dr. C. Titus Brown</a> who is definitely a leader in this field as his group is responsible for the creation and maintenance of <a href="https://github.com/sourmash-bio/sourmash">sourmash</a>, <a href="https://github.com/dib-lab/khmer">khmer</a>, and <a href="https://github.com/spacegraphcats/spacegraphcats/">spacegraphcats</a>.</p> <p>After Dr. Brown gave the basis of metagenomic asequencing and analysis it was time for my group to step up to the plate. My co-PI <a href="https://scholar.google.com/citations?user=N5irv88AAAAJ&amp;hl=en">Dr. Todd J. Treangen</a> and STAMPS alumni / research scientist in the Treangen Lab <a href="https://scholar.google.com/citations?hl=en&amp;user=E1v2MBUAAAAJ">Dr. Michael G. Nute</a> gave a very in-depth look into metagenomic assembly including a hands on demonstration of reference-based vs. de-novo assembly methods and also gave some insight into multiprocessing and how we as a class only ran our assembly on one core…</p> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/agm_assembler-480.webp 480w,/assets/img/agm_assembler-800.webp 800w,/assets/img/agm_assembler-1400.webp 1400w," sizes="95vw" type="image/webp"/> <img src="/assets/img/agm_assembler.jpg" class="img-fluid rounded z-depth-1" width="100%" height="auto" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"/> </picture> </figure> <p>Behind the scenes of the metagenomic assembly tutorial, shown above a cinnamon bun powered window size estimator.</p> <p>The next day we were introduced to the fascinating research of <a href="https://scholar.google.com/citations?user=yFncM6AAAAAJ&amp;hl=en">Dr. Curtis Huttenhower.</a> If you are in the world of microbiome research you should be familiar with this name. Dr. Huttenhower covered a broad overview of his group’s research but dove in-depth with a few of the Biobakery’s newer tools including <a href="https://github.com/biobakery/anpan">anpan</a>, <a href="https://github.com/biobakery/halla">HAllA</a>, and <a href="https://github.com/biobakery/maaslin3">MaAsLin3</a>. This was probably one of the more intense lab sessions we had and we certainly put those Rstudio VM’s to good use.</p> <p>On the third to last day we had our <em>Stats Day</em>, led by the wonderful and talented <a href="https://scholar.google.com/citations?hl=en&amp;user=pFlAtDsAAAAJ">Dr. Amy Willis.</a> Dr. Willis walked the class through arguably some of the most complex and misunderstood areas of microbiome sequence analysis including relative abundances, alpha and beta diversity, as well as differential abundance analyses. Her research is certainly at the top of the field and if you are performing any microbiome analysis you should check out the <a href="https://github.com/statdivlab">StatDivLab’s github</a> for their plethora of programs that will help give you <em>confidence</em> in your results. I also want to shoutout her wonderful PhD students <a href="https://github.com/svteichman">Sarah</a>, <a href="https://github.com/shirmath">Shirley</a>, and <a href="https://github.com/MariaAVC">Maria</a> who are the next generation of microbiome stats wizards.</p> <p>My last full day was focused on metagenomic binning, with a little added flavor of strain level analysis and phylogenetics thanks to Mike Nute’s background and PhD with <a href="https://scholar.google.com/citations?hl=en&amp;user=pPB_WK0AAAAJ">Dr. Tandy Warnow.</a> During this lecture and lab, we walked through the steps of using common binning tools (and what they are doing) as well as ran a multiple sequence alignment using <a href="https://github.com/marbl/parsnp">parsnp2</a> with a <a href="https://github.com/marbl/gingr">gingr</a> visualization!</p> <p>One of the speakers who was unable to come because of the dang C*VID was <a href="https://scholar.google.com/citations?user=-ONw6lsAAAAJ&amp;hl=en">Dr. Mike Lee.</a> Dr. Lee was still involved in this workshop as he was kind of our tech guy behind the scenes, as he had setup all our own individual compute instances (JupyterLab and Rstudio) and installed all the dependencies for the workshop labs to run smoothly. Mike Lee is someone I had really looked forward to meeting, as his website <a href="https://astrobiomike.github.io/">Happy Belly Bioinformatics</a>, was one of the main resources I used to begin my bioinformatics journey, also we worked in the same field at different NASA facilities for a while. Mike if you’re reading this <strong>hmu!</strong></p> <hr/> <h2 id="overall-experience">Overall experience</h2> <p>I think this was a great learning experience and it was hosted at a fantastic institution that has a remarkable past. Proabably my biggest gripe about this conference was the lack of air conditioning in the housing. Coming from Houston Texas, where the AC is on so much that there is a 40 degree temperature difference between inside and outside this was a bit of a challenge but it should not defer <strong>anyone</strong> from attending this workshop, it’s part of the experience.</p> <hr/> <h2 id="should-you-go">Should you go?</h2> <p><strong>Yes</strong>. If you are a biologist working on any microbiome analysis this would be a very beneficial experience for you and even if you are slightly seasoned in microbial sequence analysis like myself, I was still able to find it quite useful and gave me some more confidence to help get over the ever present <a href="https://en.wikipedia.org/wiki/Impostor_syndrome">imposter syndrome.</a> If you have any questions on the STAMPS workshop or on more aspects of my time at STAMPS feel free to reach out via my contact info and check out the <a href="https://github.com/mblstamps/stamps2024">STAMPS 2024 github!</a></p> <hr/>]]></content><author><name>Austin Marshall</name></author><category term="workshops"/><summary type="html"><![CDATA[Austin's experience and recap of the STAMPS 2024 workshop]]></summary></entry><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></feed>
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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> Bryce Kille | Treangen lab at Rice University </title> <meta name="author" content="Treangen J. Treangen"> <meta name="description" content="4th Year Ph.D. student, big fan all things sequence analysis, high-performance computing, and discrete algorithms."> <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/mdbootstrap@4.20.0/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="/profiles/bkille/"> <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="/">about </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">Bryce Kille</h1> <p class="post-description">4th Year Ph.D. student, big fan all things sequence analysis, high-performance computing, and discrete algorithms.</p> </header> <article> <p>Bryce (4th year PhD student, Computer Science) received his MS in Bioinformatics and BS in Computer Science + Chemistry from the University of Illinois at Urbana-Champaign. As an undergraduate, he worked at Dow Agrosciences in both the computational biology and cheminformatics groups. His projects included developing software for phylogeny analysis and creating models for compound activity prediction. During his Master’s program, Bryce worked in a biochemistry lab developing software for genome mining <a class="citation" href="#schwalen2018bioinformatic">(Schwalen et al., 2018)</a> as well as a on research project for creating bit-wise algorithms for the C++ STL (<a href="https://github.com/bkille/BitLib" rel="external nofollow noopener" target="_blank">BitLib</a>). One of his main interests is casting biological and chemical problems into theoretical computer science questions.</p> <p>As a PhD student, Bryce has worked on a range of sequence-analysis applications, such as genome alignment <a class="citation" href="#kille2023minmers">(Kille et al., 2023; Kille et al., 2024)</a> and variant calling <a class="citation" href="#kille2021accelerating">(Kille et al., 2021)</a>. Bryce is currently a <a href="https://www.gulfcoastconsortia.org/home/training/bmi-nlm/" rel="external nofollow noopener" target="_blank">NLM Biomedical Informatics predoctoral fellow</a> (NIH grant T15LM007093).</p> </article> <h2>References</h2> <div class="publications"> <h2 class="bibliography">2024</h2> <ol class="bibliography"><li> <div class="row"> <div id="kille2024parsnp" class="col-sm-10"> <div class="title">Parsnp 2.0: scalable core-genome alignment for massive microbial datasets</div> <div class="author"> Bryce Kille, Michael G Nute, Victor Huang, and <span class="more-authors" title="click to view 3 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '3 more authors' ? 'Eddie Kim, Adam M Phillippy, Todd J Treangen' : '3 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'); ">3 more authors</span> </div> <div class="periodical"> <em>Bioinformatics</em>, 2024 </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"> <a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;user=EUtkB0sAAAAJ&amp;citation_for_view=EUtkB0sAAAAJ:K3LRdlH-MEoC" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-4-4285F4?logo=googlescholar&amp;labelColor=beige" alt="4 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">kille2024parsnp</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> Bryce Kille | Treangen lab at Rice University </title> <meta name="author" content="Treangen J. Treangen"> <meta name="description" content="4th Year Ph.D. student, big fan all things sequence analysis, high-performance computing, and discrete algorithms."> <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/mdbootstrap@4.20.0/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="/profiles/bkille/"> <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="/">about </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">Bryce Kille</h1> <p class="post-description">4th Year Ph.D. student, big fan all things sequence analysis, high-performance computing, and discrete algorithms.</p> </header> <article> <p>Bryce (4th year PhD student, Computer Science) received his MS in Bioinformatics and BS in Computer Science + Chemistry from the University of Illinois at Urbana-Champaign. As an undergraduate, he worked at Dow Agrosciences in both the computational biology and cheminformatics groups. His projects included developing software for phylogeny analysis and creating models for compound activity prediction. During his Master’s program, Bryce worked in a biochemistry lab developing software for genome mining <a class="citation" href="#schwalen2018bioinformatic">(Schwalen et al., 2018)</a> as well as a on research project for creating bit-wise algorithms for the C++ STL (<a href="https://github.com/bkille/BitLib" rel="external nofollow noopener" target="_blank">BitLib</a>). One of his main interests is casting biological and chemical problems into theoretical computer science questions.</p> <p>As a PhD student, Bryce has worked on a range of sequence-analysis applications, such as genome alignment <a class="citation" href="#kille2023minmers">(Kille et al., 2023; Kille et al., 2024)</a> and variant calling <a class="citation" href="#kille2021accelerating">(Kille et al., 2021)</a>. Bryce is currently a <a href="https://www.gulfcoastconsortia.org/home/training/bmi-nlm/" rel="external nofollow noopener" target="_blank">NLM Biomedical Informatics predoctoral fellow</a> (NIH grant T15LM007093).</p> </article> <h2>References</h2> <div class="publications"> <h2 class="bibliography">2024</h2> <ol class="bibliography"><li> <div class="row"> <div id="kille2024parsnp" class="col-sm-10"> <div class="title">Parsnp 2.0: scalable core-genome alignment for massive microbial datasets</div> <div class="author"> Bryce Kille, Michael G Nute, Victor Huang, and <span class="more-authors" title="click to view 3 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '3 more authors' ? 'Eddie Kim, Adam M Phillippy, Todd J Treangen' : '3 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'); ">3 more authors</span> </div> <div class="periodical"> <em>Bioinformatics</em>, 2024 </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"> <a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;user=EUtkB0sAAAAJ&amp;citation_for_view=EUtkB0sAAAAJ:K3LRdlH-MEoC" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-5-4285F4?logo=googlescholar&amp;labelColor=beige" alt="5 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">kille2024parsnp</span><span class="p">,</span>
   <span class="na">title</span> <span class="p">=</span> <span class="s">{Parsnp 2.0: scalable core-genome alignment for massive microbial datasets}</span><span class="p">,</span>
   <span class="na">author</span> <span class="p">=</span> <span class="s">{Kille, Bryce and Nute, Michael G and Huang, Victor and Kim, Eddie and Phillippy, Adam M and Treangen, Todd J}</span><span class="p">,</span>
   <span class="na">year</span> <span class="p">=</span> <span class="s">{2024}</span><span class="p">,</span>
diff --git a/profiles/mnute/index.html b/profiles/mnute/index.html
index 912e50fd..6acd63dc 100644
--- a/profiles/mnute/index.html
+++ b/profiles/mnute/index.html
@@ -5,7 +5,7 @@
   <span class="na">journal</span> <span class="p">=</span> <span class="s">{bioRxiv}</span><span class="p">,</span>
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   <span class="na">pages</span> <span class="p">=</span> <span class="s">{2024--06}</span>
-<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> <li> <div class="row"> <div id="kille2024parsnp" class="col-sm-10"> <div class="title">Parsnp 2.0: scalable core-genome alignment for massive microbial datasets</div> <div class="author"> Bryce Kille, Michael G Nute, Victor Huang, and <span class="more-authors" title="click to view 3 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '3 more authors' ? 'Eddie Kim, Adam M Phillippy, Todd J Treangen' : '3 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'); ">3 more authors</span> </div> <div class="periodical"> <em>Bioinformatics</em>, 2024 </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"> <a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;user=EUtkB0sAAAAJ&amp;citation_for_view=EUtkB0sAAAAJ:K3LRdlH-MEoC" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-4-4285F4?logo=googlescholar&amp;labelColor=beige" alt="4 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">kille2024parsnp</span><span class="p">,</span>
+<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> <li> <div class="row"> <div id="kille2024parsnp" class="col-sm-10"> <div class="title">Parsnp 2.0: scalable core-genome alignment for massive microbial datasets</div> <div class="author"> Bryce Kille, Michael G Nute, Victor Huang, and <span class="more-authors" title="click to view 3 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '3 more authors' ? 'Eddie Kim, Adam M Phillippy, Todd J Treangen' : '3 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'); ">3 more authors</span> </div> <div class="periodical"> <em>Bioinformatics</em>, 2024 </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"> <a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;user=EUtkB0sAAAAJ&amp;citation_for_view=EUtkB0sAAAAJ:K3LRdlH-MEoC" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-5-4285F4?logo=googlescholar&amp;labelColor=beige" alt="5 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">kille2024parsnp</span><span class="p">,</span>
   <span class="na">title</span> <span class="p">=</span> <span class="s">{Parsnp 2.0: scalable core-genome alignment for massive microbial datasets}</span><span class="p">,</span>
   <span class="na">author</span> <span class="p">=</span> <span class="s">{Kille, Bryce and Nute, Michael G and Huang, Victor and Kim, Eddie and Phillippy, Adam M and Treangen, Todd J}</span><span class="p">,</span>
   <span class="na">year</span> <span class="p">=</span> <span class="s">{2024}</span><span class="p">,</span>
diff --git a/publications/index.html b/publications/index.html
index 55c6f03b..356f6ff4 100644
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+++ b/publications/index.html
@@ -55,7 +55,7 @@
   <span class="na">year</span> <span class="p">=</span> <span class="s">{2024}</span><span class="p">,</span>
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-<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> <li> <div class="row"> <div id="kille2024parsnp" class="col-sm-10"> <div class="title">Parsnp 2.0: scalable core-genome alignment for massive microbial datasets</div> <div class="author"> Bryce Kille, Michael G Nute, Victor Huang, and <span class="more-authors" title="click to view 3 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '3 more authors' ? 'Eddie Kim, Adam M Phillippy, Todd J Treangen' : '3 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'); ">3 more authors</span> </div> <div class="periodical"> <em>Bioinformatics</em>, 2024 </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"> <a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;user=EUtkB0sAAAAJ&amp;citation_for_view=EUtkB0sAAAAJ:K3LRdlH-MEoC" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-4-4285F4?logo=googlescholar&amp;labelColor=beige" alt="4 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">kille2024parsnp</span><span class="p">,</span>
+<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> <li> <div class="row"> <div id="kille2024parsnp" class="col-sm-10"> <div class="title">Parsnp 2.0: scalable core-genome alignment for massive microbial datasets</div> <div class="author"> Bryce Kille, Michael G Nute, Victor Huang, and <span class="more-authors" title="click to view 3 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '3 more authors' ? 'Eddie Kim, Adam M Phillippy, Todd J Treangen' : '3 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'); ">3 more authors</span> </div> <div class="periodical"> <em>Bioinformatics</em>, 2024 </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"> <a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;user=EUtkB0sAAAAJ&amp;citation_for_view=EUtkB0sAAAAJ:K3LRdlH-MEoC" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-5-4285F4?logo=googlescholar&amp;labelColor=beige" alt="5 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">kille2024parsnp</span><span class="p">,</span>
   <span class="na">title</span> <span class="p">=</span> <span class="s">{Parsnp 2.0: scalable core-genome alignment for massive microbial datasets}</span><span class="p">,</span>
   <span class="na">author</span> <span class="p">=</span> <span class="s">{Kille, Bryce and Nute, Michael G and Huang, Victor and Kim, Eddie and Phillippy, Adam M and Treangen, Todd J}</span><span class="p">,</span>
   <span class="na">year</span> <span class="p">=</span> <span class="s">{2024}</span><span class="p">,</span>
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