From 7420335ac8522833c5488ab6961b1af3a6175381 Mon Sep 17 00:00:00 2001
From: Natalie-koks <137814633+Natalie-koks@users.noreply.github.com>
Date: Thu, 17 Oct 2024 21:58:18 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20treangen?=
 =?UTF-8?q?lab/treangenlab.github.io@e2fe84a08d94920040b8c6c12e714151ae177?=
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MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 404.html                              |  2 +-
 _pages/dropdown/index.html            |  2 +-
 assets/jupyter/blog.ipynb.html        |  2 +-
 blog/2024/bryce/index.html            |  2 +-
 blog/2024/index.html                  |  2 +-
 blog/2024/stampsblog/index.html       |  2 +-
 blog/category/sample-posts/index.html |  2 +-
 blog/index.html                       |  2 +-
 blog/tag/code/index.html              |  2 +-
 blog/tag/formatting/index.html        |  2 +-
 blog/tag/workshops/index.html         |  2 +-
 cv/index.html                         |  2 +-
 feed.xml                              |  2 +-
 index.html                            |  6 +++---
 news/announcement_3/index.html        |  2 +-
 news/bryce_tpd/index.html             |  2 +-
 news/fall_semester_2024/index.html    |  2 +-
 news/index.html                       |  2 +-
 people/index.html                     |  2 +-
 profiles/amarshall/index.html         |  2 +-
 profiles/apatel/index.html            |  2 +-
 profiles/bkille/index.html            |  4 ++--
 profiles/dongwei/index.html           |  2 +-
 profiles/ehuang/index.html            |  2 +-
 profiles/fquinanta/index.html         |  2 +-
 profiles/mnute/index.html             |  8 ++++----
 profiles/nkokroko/index.html          |  2 +-
 profiles/rdoughty/index.html          |  2 +-
 profiles/xwang/index.html             |  6 +++---
 projects/1_project/index.html         |  2 +-
 projects/2_project/index.html         |  2 +-
 projects/3_project/index.html         |  2 +-
 projects/4_project/index.html         |  2 +-
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 projects/6_project/index.html         |  2 +-
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 projects/8_project/index.html         |  2 +-
 projects/9_project/index.html         |  2 +-
 projects/index.html                   |  2 +-
 publications/index.html               | 14 +++++++-------
 repositories/index.html               |  2 +-
 sitemap.xml                           |  2 +-
 teaching/index.html                   |  2 +-
 43 files changed, 57 insertions(+), 57 deletions(-)
diff --git a/404.html b/404.html
index 7d200a70..a53796e2 100644
--- a/404.html
+++ b/404.html
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-    </script> </d-front-matter> <header> <nav id="navbar" class="navbar navbar-light navbar-expand-sm fixed-top" role="navigation"> <div class="container"> <a class="navbar-brand title font-weight-lighter" href="/"> Treangen lab at Rice University </a> <button class="navbar-toggler collapsed ml-auto" type="button" data-toggle="collapse" data-target="#navbarNav" aria-controls="navbarNav" aria-expanded="false" aria-label="Toggle navigation"> <span class="sr-only">Toggle navigation</span> <span class="icon-bar top-bar"></span> <span class="icon-bar middle-bar"></span> <span class="icon-bar bottom-bar"></span> </button> <div class="collapse navbar-collapse text-right" id="navbarNav"> <ul class="navbar-nav ml-auto flex-nowrap"> <li class="nav-item "> <a class="nav-link" href="/">lab </a> </li> <li class="nav-item "> <a class="nav-link" href="/people/">people </a> </li> <li class="nav-item active"> <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/">github </a> </li> <li class="nav-item "> <a class="nav-link" href="/cv/">cv </a> </li> <li class="nav-item "> <a class="nav-link" href="/teaching/">teaching </a> </li> <li class="nav-item"> <button id="search-toggle" title="Search" onclick="openSearchModal()"> <span class="nav-link">ctrl k <i class="ti ti-search"></i></span> </button> </li> <li class="toggle-container"> <button id="light-toggle" title="Change theme"> <i class="ti ti-sun-moon" id="light-toggle-system"></i> <i class="ti ti-moon-filled" id="light-toggle-dark"></i> <i class="ti ti-sun-filled" id="light-toggle-light"></i> </button> </li> </ul> </div> </div> </nav> <progress id="progress" value="0"> <div class="progress-container"> <span class="progress-bar"></span> </div> </progress> </header> <div class="post distill"> <d-title> <h1>Austin's STAMPS 2024 Experience</h1> <p>Experience and recap of the STAMPS 2024 workshop</p> </d-title> <d-byline></d-byline> <d-article> <d-contents> <nav class="l-text figcaption"> <h3>Contents</h3> <div> <a href="#introduction">Introduction</a> </div> <div> <a href="#venue">Venue</a> </div> <div> <a href="#topics-and-presenters">Topics and Presenters</a> </div> <div> <a href="#overall-experience">Overall experience</a> </div> <div> <a href="#should-you-go">Should you go?</a> </div> </nav> </d-contents> <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/" rel="external nofollow noopener" target="_blank">Villapol</a> and <a href="https://treangenlab.github.io/" rel="external nofollow noopener" target="_blank">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" rel="external nofollow noopener" target="_blank">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" rel="external nofollow noopener" target="_blank">Martha’s Vineyard.</a></p> <div class="text-align: center;"> <img src="https://treangenlab.github.io/assets/img/crabs_mbl.jpg" alt="horseshoe crabs at MBL"> </div> <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> <div class="text-align: center;"> <img src="https://treangenlab.github.io/assets/img/thm_nobel.jpg" alt="Thomas Hunt Morgan Nobel Prize"> </div> <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" rel="external nofollow noopener" target="_blank">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" rel="external nofollow noopener" target="_blank">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" rel="external nofollow noopener" target="_blank">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" rel="external nofollow noopener" target="_blank">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" rel="external nofollow noopener" target="_blank">sourmash</a>, <a href="https://github.com/dib-lab/khmer" rel="external nofollow noopener" target="_blank">khmer</a>, and <a href="https://github.com/spacegraphcats/spacegraphcats/" rel="external nofollow noopener" target="_blank">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" rel="external nofollow noopener" target="_blank">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" rel="external nofollow noopener" target="_blank">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> <div class="text-align: center;"> <img src="https://treangenlab.github.io/assets/img/agm_assembler.jpg" alt="cinnamon bun powered genome assembler"> </div> <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" rel="external nofollow noopener" target="_blank">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" rel="external nofollow noopener" target="_blank">anpan</a>, <a href="https://github.com/biobakery/halla" rel="external nofollow noopener" target="_blank">HAllA</a>, and <a href="https://github.com/biobakery/maaslin3" rel="external nofollow noopener" target="_blank">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" rel="external nofollow noopener" target="_blank">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" rel="external nofollow noopener" target="_blank">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" rel="external nofollow noopener" target="_blank">Sarah</a>, <a href="https://github.com/shirmath" rel="external nofollow noopener" target="_blank">Shirley</a>, and <a href="https://github.com/MariaAVC" rel="external nofollow noopener" target="_blank">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" rel="external nofollow noopener" target="_blank">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" rel="external nofollow noopener" target="_blank">parsnp2</a> with a <a href="https://github.com/marbl/gingr" rel="external nofollow noopener" target="_blank">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" rel="external nofollow noopener" target="_blank">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/" rel="external nofollow noopener" target="_blank">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" rel="external nofollow noopener" target="_blank">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" rel="external nofollow noopener" target="_blank">STAMPS 2024 github!</a></p> <hr> </d-article> <d-appendix> <d-footnote-list></d-footnote-list> <d-citation-list></d-citation-list> </d-appendix> <d-bibliography src="/assets/bibliography/"></d-bibliography> </div> <footer class="fixed-bottom" role="contentinfo"> <div class="container mt-0"> © Copyright 2024 Treangen J. 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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" rel="external nofollow noopener" target="_blank">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" rel="external nofollow noopener" target="_blank">Martha’s Vineyard.</a></p> <div class="text-align: center;"> <img src="https://treangenlab.github.io/assets/img/crabs_mbl.jpg" alt="horseshoe crabs at MBL"> </div> <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> <div class="text-align: center;"> <img src="https://treangenlab.github.io/assets/img/thm_nobel.jpg" alt="Thomas Hunt Morgan Nobel Prize"> </div> <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" rel="external nofollow noopener" target="_blank">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" rel="external nofollow noopener" target="_blank">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" rel="external nofollow noopener" target="_blank">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" rel="external nofollow noopener" target="_blank">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" rel="external nofollow noopener" target="_blank">sourmash</a>, <a href="https://github.com/dib-lab/khmer" rel="external nofollow noopener" target="_blank">khmer</a>, and <a href="https://github.com/spacegraphcats/spacegraphcats/" rel="external nofollow noopener" target="_blank">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" rel="external nofollow noopener" target="_blank">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" rel="external nofollow noopener" target="_blank">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> <div class="text-align: center;"> <img src="https://treangenlab.github.io/assets/img/agm_assembler.jpg" alt="cinnamon bun powered genome assembler"> </div> <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" rel="external nofollow noopener" target="_blank">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" rel="external nofollow noopener" target="_blank">anpan</a>, <a href="https://github.com/biobakery/halla" rel="external nofollow noopener" target="_blank">HAllA</a>, and <a href="https://github.com/biobakery/maaslin3" rel="external nofollow noopener" target="_blank">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" rel="external nofollow noopener" target="_blank">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" rel="external nofollow noopener" target="_blank">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" rel="external nofollow noopener" target="_blank">Sarah</a>, <a href="https://github.com/shirmath" rel="external nofollow noopener" target="_blank">Shirley</a>, and <a href="https://github.com/MariaAVC" rel="external nofollow noopener" target="_blank">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" rel="external nofollow noopener" target="_blank">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" rel="external nofollow noopener" target="_blank">parsnp2</a> with a <a href="https://github.com/marbl/gingr" rel="external nofollow noopener" target="_blank">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" rel="external nofollow noopener" target="_blank">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/" rel="external nofollow noopener" target="_blank">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" rel="external nofollow noopener" target="_blank">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" rel="external nofollow noopener" target="_blank">STAMPS 2024 github!</a></p> <hr> </d-article> <d-appendix> <d-footnote-list></d-footnote-list> <d-citation-list></d-citation-list> </d-appendix> <d-bibliography src="/assets/bibliography/"></d-bibliography> </div> <footer class="fixed-bottom" role="contentinfo"> <div class="container mt-0"> © Copyright 2024 Treangen 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 (um pouco), French (un peu)</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> cv | Treangen lab at Rice University </title> <meta name="author" content="Treangen J. Treangen"> <meta name="description" content="CV of Treangen Lab PI (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 (um pouco), French (un peu)</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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-<?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>2024-10-10T15:21:56+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">Austin’s STAMPS 2024 Experience</title><link href="/blog/2024/stampsblog/" rel="alternate" type="text/html" title="Austin’s STAMPS 2024 Experience"/><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> <div class="text-align: center;"> <img src="https://treangenlab.github.io/assets/img/crabs_mbl.jpg" alt="horseshoe crabs at MBL"/> </div> <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> <div class="text-align: center;"> <img src="https://treangenlab.github.io/assets/img/thm_nobel.jpg" alt="Thomas Hunt Morgan Nobel Prize"/> </div> <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> <div class="text-align: center;"> <img src="https://treangenlab.github.io/assets/img/agm_assembler.jpg" alt="cinnamon bun powered genome assembler"/> </div> <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[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>2024-10-17T21:53:48+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">Austin’s STAMPS 2024 Experience</title><link href="/blog/2024/stampsblog/" rel="alternate" type="text/html" title="Austin’s STAMPS 2024 Experience"/><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> <div class="text-align: center;"> <img src="https://treangenlab.github.io/assets/img/crabs_mbl.jpg" alt="horseshoe crabs at MBL"/> </div> <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> <div class="text-align: center;"> <img src="https://treangenlab.github.io/assets/img/thm_nobel.jpg" alt="Thomas Hunt Morgan Nobel Prize"/> </div> <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> <div class="text-align: center;"> <img src="https://treangenlab.github.io/assets/img/agm_assembler.jpg" alt="cinnamon bun powered genome assembler"/> </div> <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[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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   <span class="na">volume</span> <span class="p">=</span> <span class="s">{23}</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="curry2022emu" class="col-sm-10"> <div class="title">Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data</div> <div class="author"> Kristen D Curry, Qi Wang, Michael G Nute, and <span class="more-authors" title="click to view 8 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '8 more authors' ? 'Alona Tyshaieva, Elizabeth Reeves, Sirena Soriano, Qinglong Wu, Enid Graeber, Patrick Finzer, Werner Mendling, others' : '8 more authors'; var cursorPosition=0; var textAdder=setInterval(function(){ element.html(more_authors_text.substring(0, cursorPosition + 1)); if (++cursorPosition == more_authors_text.length){ clearInterval(textAdder); } }, '10'); ">8 more authors</span> </div> <div class="periodical"> <em>Nature methods</em>, 2022 </div> <div class="periodical"> </div> <div class="links"> <a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a> </div> <div class="badges"> <span class="altmetric-embed" data-badge-type="2" data-badge-popover="right" data-altmetric-id="130469175"></span> <a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;user=N5irv88AAAAJ&amp;citation_for_view=N5irv88AAAAJ:1sJd4Hv_s6UC" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-130-4285F4?logo=googlescholar&amp;labelColor=beige" alt="130 Google Scholar citations"> </a> </div> <div class="bibtex hidden"> <figure class="highlight"><pre><code class="language-bibtex" data-lang="bibtex"><span class="nc">@article</span><span class="p">{</span><span class="nl">curry2022emu</span><span class="p">,</span>
+<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> <li> <div class="row"> <div id="curry2022emu" class="col-sm-10"> <div class="title">Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data</div> <div class="author"> Kristen D Curry, Qi Wang, Michael G Nute, and <span class="more-authors" title="click to view 8 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '8 more authors' ? 'Alona Tyshaieva, Elizabeth Reeves, Sirena Soriano, Qinglong Wu, Enid Graeber, Patrick Finzer, Werner Mendling, others' : '8 more authors'; var cursorPosition=0; var textAdder=setInterval(function(){ element.html(more_authors_text.substring(0, cursorPosition + 1)); if (++cursorPosition == more_authors_text.length){ clearInterval(textAdder); } }, '10'); ">8 more authors</span> </div> <div class="periodical"> <em>Nature methods</em>, 2022 </div> <div class="periodical"> </div> <div class="links"> <a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a> </div> <div class="badges"> <span class="altmetric-embed" data-badge-type="2" data-badge-popover="right" data-altmetric-id="130469175"></span> <a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;user=N5irv88AAAAJ&amp;citation_for_view=N5irv88AAAAJ:1sJd4Hv_s6UC" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-140-4285F4?logo=googlescholar&amp;labelColor=beige" alt="140 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">curry2022emu</span><span class="p">,</span>
   <span class="na">title</span> <span class="p">=</span> <span class="s">{Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data}</span><span class="p">,</span>
   <span class="na">author</span> <span class="p">=</span> <span class="s">{Curry, Kristen D and Wang, Qi and Nute, Michael G and Tyshaieva, Alona and Reeves, Elizabeth and Soriano, Sirena and Wu, Qinglong and Graeber, Enid and Finzer, Patrick and Mendling, Werner and others}</span><span class="p">,</span>
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@@ -16,7 +16,7 @@
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   <span class="na">pages</span> <span class="p">=</span> <span class="s">{845--853}</span>
-<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> <li> <div class="row"> <div id="sapoval2022current" class="col-sm-10"> <div class="title">Current progress and open challenges for applying deep learning across the biosciences</div> <div class="author"> Nicolae Sapoval, Amirali Aghazadeh, Michael G Nute, and <span class="more-authors" title="click to view 8 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '8 more authors' ? 'Dinler A Antunes, Advait Balaji, Richard Baraniuk, CJ Barberan, Ruth Dannenfelser, Chen Dun, Mohammadamin Edrisi, others' : '8 more authors'; var cursorPosition=0; var textAdder=setInterval(function(){ element.html(more_authors_text.substring(0, cursorPosition + 1)); if (++cursorPosition == more_authors_text.length){ clearInterval(textAdder); } }, '10'); ">8 more authors</span> </div> <div class="periodical"> <em>Nature Communications</em>, 2022 </div> <div class="periodical"> </div> <div class="links"> <a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a> </div> <div class="badges"> <span class="altmetric-embed" data-badge-type="2" data-badge-popover="right" data-altmetric-id="125736934"></span> <a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;user=N5irv88AAAAJ&amp;citation_for_view=N5irv88AAAAJ:1qzjygNMrQYC" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-210-4285F4?logo=googlescholar&amp;labelColor=beige" alt="210 Google Scholar citations"> </a> </div> <div class="bibtex hidden"> <figure class="highlight"><pre><code class="language-bibtex" data-lang="bibtex"><span class="nc">@article</span><span class="p">{</span><span class="nl">sapoval2022current</span><span class="p">,</span>
+<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> <li> <div class="row"> <div id="sapoval2022current" class="col-sm-10"> <div class="title">Current progress and open challenges for applying deep learning across the biosciences</div> <div class="author"> Nicolae Sapoval, Amirali Aghazadeh, Michael G Nute, and <span class="more-authors" title="click to view 8 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '8 more authors' ? 'Dinler A Antunes, Advait Balaji, Richard Baraniuk, CJ Barberan, Ruth Dannenfelser, Chen Dun, Mohammadamin Edrisi, others' : '8 more authors'; var cursorPosition=0; var textAdder=setInterval(function(){ element.html(more_authors_text.substring(0, cursorPosition + 1)); if (++cursorPosition == more_authors_text.length){ clearInterval(textAdder); } }, '10'); ">8 more authors</span> </div> <div class="periodical"> <em>Nature Communications</em>, 2022 </div> <div class="periodical"> </div> <div class="links"> <a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a> </div> <div class="badges"> <span class="altmetric-embed" data-badge-type="2" data-badge-popover="right" data-altmetric-id="125736934"></span> <a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;user=N5irv88AAAAJ&amp;citation_for_view=N5irv88AAAAJ:1qzjygNMrQYC" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-220-4285F4?logo=googlescholar&amp;labelColor=beige" alt="220 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">sapoval2022current</span><span class="p">,</span>
   <span class="na">title</span> <span class="p">=</span> <span class="s">{Current progress and open challenges for applying deep learning across the biosciences}</span><span class="p">,</span>
   <span class="na">author</span> <span class="p">=</span> <span class="s">{Sapoval, Nicolae and Aghazadeh, Amirali and Nute, Michael G and Antunes, Dinler A and Balaji, Advait and Baraniuk, Richard and Barberan, CJ and Dannenfelser, Ruth and Dun, Chen and Edrisi, Mohammadamin and others}</span><span class="p">,</span>
   <span class="na">year</span> <span class="p">=</span> <span class="s">{2022}</span><span class="p">,</span>
@@ -25,4 +25,4 @@
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-<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> </ol> </div> <div class="social"> <div class="contact-icons"> <a href="mailto:%74%72%65%61%6E%67%65%6E@%72%69%63%65.%65%64%75" title="email"><i class="fa-solid fa-envelope"></i></a> <a href="https://orcid.org/0000-0002-3760-564X" title="ORCID" rel="external nofollow noopener" target="_blank"><i class="ai ai-orcid"></i></a> <a href="https://scholar.google.com/citations?user=N5irv88AAAAJ" title="Google Scholar" rel="external nofollow noopener" target="_blank"><i class="ai ai-google-scholar"></i></a> <a href="https://osf.io/5etvy/" title="Open Science Framework" rel="external nofollow noopener" target="_blank"><i class="ai ai-osf"></i></a> <a href="https://github.com/treangen" title="GitHub" rel="external nofollow noopener" target="_blank"><i class="fa-brands fa-github"></i></a> <a href="https://www.linkedin.com/in/tjtreangen" title="LinkedIn" rel="external nofollow noopener" target="_blank"><i class="fa-brands fa-linkedin"></i></a> <a href="https://gitlab.com/treangen" title="GitLab" rel="external nofollow noopener" target="_blank"><i class="fa-brands fa-gitlab"></i></a> <a href="https://bsky.app/profile/treangen.bsky.social" title="Bluesky" rel="external nofollow noopener" target="_blank"><i class="fa-brands fa-bluesky"></i></a> </div> <div class="contact-note">Email is the best way to reach us. </div> </div> </article> </div> </div> <footer class="fixed-bottom" role="contentinfo"> <div class="container mt-0"> © Copyright 2024 Treangen J. 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$('.responsive-img-srcset').remove();"> </picture> </figure> <div class="card-body"> <h2 class="card-title">Ryan Doughty</h2> <p class="card-text">1st Year Compter Science Ph.D. student, interested in metagenomics and virome analysis.</p> <div class="row ml-1 mr-1 p-0"> </div> </div> </div> </a> </div> <div class="col"> <a href="/profiles/ehuang/"> <div class="card h-100 hoverable"> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/ehuang-480.webp 480w,/assets/img/ehuang-800.webp 800w,/assets/img/ehuang-1400.webp 1400w," sizes="50px" type="image/webp"></source> <img src="/assets/img/ehuang.png" class="card-img-top" width="100%" height="auto" alt="project thumbnail" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"> </picture> </figure> <div class="card-body"> <h2 class="card-title">Eddy Huang</h2> <p class="card-text">3rd Year Ph.D. student, interested in Microbiome Analysis, Metagenomics Database, High Performance Computing, and Deep Learning</p> <div class="row ml-1 mr-1 p-0"> </div> </div> </div> </a> </div> <div class="col"> <a href="/profiles/bkille/"> <div class="card h-100 hoverable"> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/bkille-480.webp 480w,/assets/img/bkille-800.webp 800w,/assets/img/bkille-1400.webp 1400w," sizes="50px" type="image/webp"></source> <img src="/assets/img/bkille.png" class="card-img-top" width="100%" height="auto" alt="project thumbnail" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"> </picture> </figure> <div class="card-body"> <h2 class="card-title">Bryce Kille</h2> <p class="card-text">4th Year Ph.D. student, big fan all things sequence analysis, high-performance computing, and discrete algorithms.</p> <div class="row ml-1 mr-1 p-0"> </div> </div> </div> </a> </div> <div class="col"> <a href="/profiles/nkokroko/"> <div class="card h-100 hoverable"> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/nkokroko-480.webp 480w,/assets/img/nkokroko-800.webp 800w,/assets/img/nkokroko-1400.webp 1400w," sizes="50px" type="image/webp"></source> <img src="/assets/img/nkokroko.png" class="card-img-top" width="100%" height="auto" alt="project thumbnail" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"> </picture> </figure> <div class="card-body"> <h2 class="card-title">Natalie Kokroko</h2> <p class="card-text">2nd Year Computer Science Ph.D. student, interested in microbiome analysis and metagenomics.</p> <div class="row ml-1 mr-1 p-0"> </div> </div> </div> </a> </div> <div class="col"> <a href="/profiles/dongwei/"> <div class="card h-100 hoverable"> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/dongwei-480.webp 480w,/assets/img/dongwei-800.webp 800w,/assets/img/dongwei-1400.webp 1400w," sizes="50px" type="image/webp"></source> <img src="/assets/img/dongwei.png" class="card-img-top" width="100%" height="auto" alt="project thumbnail" loading="eager" onerror="this.onerror=null; 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$('.responsive-img-srcset').remove();"> </picture> </figure> <div class="card-body"> <h2 class="card-title">Ryan Doughty</h2> <p class="card-text">1st Year Compter Science Ph.D. student, interested in metagenomics and virome analysis.</p> <div class="row ml-1 mr-1 p-0"> </div> </div> </div> </a> </div> <div class="col"> <a href="/profiles/ehuang/"> <div class="card h-100 hoverable"> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/ehuang-480.webp 480w,/assets/img/ehuang-800.webp 800w,/assets/img/ehuang-1400.webp 1400w," sizes="50px" type="image/webp"></source> <img src="/assets/img/ehuang.png" class="card-img-top" width="100%" height="auto" alt="project thumbnail" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"> </picture> </figure> <div class="card-body"> <h2 class="card-title">Eddy Huang</h2> <p class="card-text">3rd Year Ph.D. student, interested in Microbiome Analysis, Metagenomics Database, High Performance Computing, and Deep Learning</p> <div class="row ml-1 mr-1 p-0"> </div> </div> </div> </a> </div> <div class="col"> <a href="/profiles/bkille/"> <div class="card h-100 hoverable"> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/bkille-480.webp 480w,/assets/img/bkille-800.webp 800w,/assets/img/bkille-1400.webp 1400w," sizes="50px" type="image/webp"></source> <img src="/assets/img/bkille.png" class="card-img-top" width="100%" height="auto" alt="project thumbnail" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"> </picture> </figure> <div class="card-body"> <h2 class="card-title">Bryce Kille</h2> <p class="card-text">4th Year Ph.D. student, big fan all things sequence analysis, high-performance computing, and discrete algorithms.</p> <div class="row ml-1 mr-1 p-0"> </div> </div> </div> </a> </div> <div class="col"> <a href="/profiles/nkokroko/"> <div class="card h-100 hoverable"> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/nkokroko-480.webp 480w,/assets/img/nkokroko-800.webp 800w,/assets/img/nkokroko-1400.webp 1400w," sizes="50px" type="image/webp"></source> <img src="/assets/img/nkokroko.png" class="card-img-top" width="100%" height="auto" alt="project thumbnail" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"> </picture> </figure> <div class="card-body"> <h2 class="card-title">Natalie Kokroko</h2> <p class="card-text">2nd Year Computer Science Ph.D. student, interested in microbiome analysis and metagenomics.</p> <div class="row ml-1 mr-1 p-0"> </div> </div> </div> </a> </div> <div class="col"> <a href="/profiles/dongwei/"> <div class="card h-100 hoverable"> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/dongwei-480.webp 480w,/assets/img/dongwei-800.webp 800w,/assets/img/dongwei-1400.webp 1400w," sizes="50px" type="image/webp"></source> <img src="/assets/img/dongwei.png" class="card-img-top" width="100%" height="auto" alt="project thumbnail" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"> </picture> </figure> <div class="card-body"> <h2 class="card-title">Dongwei Li</h2> <p class="card-text">1st Year Ph.D. student, interested in machine learning and computational biology.</p> <div class="row ml-1 mr-1 p-0"> </div> </div> </div> </a> </div> <div class="col"> <a href="/profiles/fquinanta/"> <div class="card h-100 hoverable"> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/fquintana-480.webp 480w,/assets/img/fquintana-800.webp 800w,/assets/img/fquintana-1400.webp 1400w," sizes="50px" type="image/webp"></source> <img src="/assets/img/fquintana.png" class="card-img-top" width="100%" height="auto" alt="project thumbnail" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"> </picture> </figure> <div class="card-body"> <h2 class="card-title">Felix Quintana</h2> <p class="card-text">3rd Year Ph.D. student interested in protein function prediction and model assessment.</p> <div class="row ml-1 mr-1 p-0"> </div> </div> </div> </a> </div> <div class="col"> <a href="/profiles/xwang/"> <div class="card h-100 hoverable"> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/xwang-480.webp 480w,/assets/img/xwang-800.webp 800w,/assets/img/xwang-1400.webp 1400w," sizes="50px" type="image/webp"></source> <img src="/assets/img/xwang.png" class="card-img-top" width="100%" height="auto" alt="project thumbnail" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"> </picture> </figure> <div class="card-body"> <h2 class="card-title">Michael X. Wang</h2> <p class="card-text">6th Year Bioengineering Ph.D. student. Lead developer of Olivar.</p> <div class="row ml-1 mr-1 p-0"> </div> </div> </div> </a> </div> </div> <a id="Senior Personnel" href=".#Senior%20Personnel"> <h2 class="category">Senior Personnel</h2> </a> <div class="row row-cols-1 row-cols-md-3"> <div class="col"> <a href="/profiles/mnute/"> <div class="card h-100 hoverable"> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/mnute-480.webp 480w,/assets/img/mnute-800.webp 800w,/assets/img/mnute-1400.webp 1400w," sizes="50px" type="image/webp"></source> <img src="/assets/img/mnute.png" class="card-img-top" width="100%" height="auto" alt="project thumbnail" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"> </picture> </figure> <div class="card-body"> <h2 class="card-title">Dr. Michael Nute</h2> <p class="card-text">Research Scientist, Department of Computer Science, Rice University</p> <div class="row ml-1 mr-1 p-0"> </div> </div> </div> </a> </div> <div class="col"> <a href="/profiles/amarshall/"> <div class="card h-100 hoverable"> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/amarshall-480.webp 480w,/assets/img/amarshall-800.webp 800w,/assets/img/amarshall-1400.webp 1400w," sizes="50px" type="image/webp"></source> <img src="/assets/img/amarshall.png" class="card-img-top" width="100%" height="auto" alt="project thumbnail" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"> </picture> </figure> <div class="card-body"> <h2 class="card-title">Dr. Austin Marshall</h2> <p class="card-text">NLM BMI postdoctoral fellow interested in applying novel bioinformatic practices to microbiome studies</p> <div class="row ml-1 mr-1 p-0"> </div> </div> </div> </a> </div> </div> <a id="Visiting Students" href=".#Visiting%20Students"> <h2 class="category">Visiting Students</h2> </a> <div class="row row-cols-1 row-cols-md-3"> <div class="col"> <a href="/profiles/apatel/"> <div class="card h-100 hoverable"> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/apatel-480.webp 480w,/assets/img/apatel-800.webp 800w,/assets/img/apatel-1400.webp 1400w," sizes="50px" type="image/webp"></source> <img src="/assets/img/apatel.png" class="card-img-top" width="100%" height="auto" alt="project thumbnail" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"> </picture> </figure> <div class="card-body"> <h2 class="card-title">Anika Patel</h2> <p class="card-text">Undergraduate</p> <div class="row ml-1 mr-1 p-0"> </div> </div> </div> </a> </div> </div> </div> </article> </div> </div> <footer class="fixed-bottom" role="contentinfo"> <div class="container mt-0"> © Copyright 2024 Treangen J. 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diff --git a/profiles/amarshall/index.html b/profiles/amarshall/index.html
index c08bff82..243e5db5 100644
--- a/profiles/amarshall/index.html
+++ b/profiles/amarshall/index.html
@@ -19,4 +19,4 @@
   <span class="na">year</span> <span class="p">=</span> <span class="s">{2024}</span><span class="p">,</span>
   <span class="na">journal</span> <span class="p">=</span> <span class="s">{Research Square}</span><span class="p">,</span>
   <span class="na">publisher</span> <span class="p">=</span> <span class="s">{American Journal Experts}</span>
-<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> </ol> </div> </div> </div> <footer class="fixed-bottom" role="contentinfo"> <div class="container mt-0"> © Copyright 2024 Treangen J. Treangen. Powered by <a href="https://jekyllrb.com/" target="_blank" rel="external nofollow noopener">Jekyll</a> with <a href="https://github.com/alshedivat/al-folio" rel="external nofollow noopener" target="_blank">al-folio</a> theme. Hosted by <a href="https://pages.github.com/" target="_blank" rel="external nofollow noopener">GitHub Pages</a>. 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diff --git a/profiles/apatel/index.html b/profiles/apatel/index.html
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Since joining the Treangen lab in the Spring semester of 2024, she has been working on characterizing gut microbiome samples using an autoencoder. She hopes to continue working on computational biology research after graduation. Outside of academics, Anika enjoys photography!</p> </article> </div> </div> <footer class="fixed-bottom" role="contentinfo"> <div class="container mt-0"> © Copyright 2024 Treangen J. Treangen. Powered by <a href="https://jekyllrb.com/" target="_blank" rel="external nofollow noopener">Jekyll</a> with <a href="https://github.com/alshedivat/al-folio" rel="external nofollow noopener" target="_blank">al-folio</a> theme. Hosted by <a href="https://pages.github.com/" target="_blank" rel="external nofollow noopener">GitHub Pages</a>. 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diff --git a/profiles/bkille/index.html b/profiles/bkille/index.html
index 8fb8f510..e5debc13 100644
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+++ b/profiles/bkille/index.html
@@ -7,7 +7,7 @@
   <span class="na">volume</span> <span class="p">=</span> <span class="s">{40}</span><span class="p">,</span>
   <span class="na">number</span> <span class="p">=</span> <span class="s">{5}</span><span class="p">,</span>
   <span class="na">pages</span> <span class="p">=</span> <span class="s">{btae311}</span>
-<span class="p">}</span></code></pre></figure> </div> </div> </div> </li></ol> <h2 class="bibliography">2023</h2> <ol class="bibliography"><li> <div class="row"> <div id="kille2023minmers" class="col-sm-10"> <div class="title">Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation</div> <div class="author"> Bryce Kille, Erik Garrison, Todd J Treangen, and <span class="more-authors" title="click to view 1 more author" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '1 more author' ? 'Adam M Phillippy' : '1 more author'; 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'); ">1 more author</span> </div> <div class="periodical"> <em>Bioinformatics</em>, 2023 </div> <div class="periodical"> </div> <div class="links"> <a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a> </div> <div class="badges"> <a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;user=EUtkB0sAAAAJ&amp;citation_for_view=EUtkB0sAAAAJ:p2g8aNsByqUC" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-9-4285F4?logo=googlescholar&amp;labelColor=beige" alt="9 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">kille2023minmers</span><span class="p">,</span>
+<span class="p">}</span></code></pre></figure> </div> </div> </div> </li></ol> <h2 class="bibliography">2023</h2> <ol class="bibliography"><li> <div class="row"> <div id="kille2023minmers" class="col-sm-10"> <div class="title">Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation</div> <div class="author"> Bryce Kille, Erik Garrison, Todd J Treangen, and <span class="more-authors" title="click to view 1 more author" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '1 more author' ? 'Adam M Phillippy' : '1 more author'; 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'); ">1 more author</span> </div> <div class="periodical"> <em>Bioinformatics</em>, 2023 </div> <div class="periodical"> </div> <div class="links"> <a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a> </div> <div class="badges"> <a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;user=EUtkB0sAAAAJ&amp;citation_for_view=EUtkB0sAAAAJ:p2g8aNsByqUC" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-10-4285F4?logo=googlescholar&amp;labelColor=beige" alt="10 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">kille2023minmers</span><span class="p">,</span>
   <span class="na">title</span> <span class="p">=</span> <span class="s">{Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation}</span><span class="p">,</span>
   <span class="na">author</span> <span class="p">=</span> <span class="s">{Kille, Bryce and Garrison, Erik and Treangen, Todd J and Phillippy, Adam M}</span><span class="p">,</span>
   <span class="na">year</span> <span class="p">=</span> <span class="s">{2023}</span><span class="p">,</span>
@@ -32,4 +32,4 @@
   <span class="na">pages</span> <span class="p">=</span> <span class="s">{9494--9501}</span><span class="p">,</span>
   <span class="na">year</span> <span class="p">=</span> <span class="s">{2018}</span><span class="p">,</span>
   <span class="na">publisher</span> <span class="p">=</span> <span class="s">{ACS Publications}</span>
-<span class="p">}</span></code></pre></figure> </div> </div> </div> </li></ol> </div> </div> </div> <footer class="fixed-bottom" role="contentinfo"> <div class="container mt-0"> © Copyright 2024 Treangen J. Treangen. Powered by <a href="https://jekyllrb.com/" target="_blank" rel="external nofollow noopener">Jekyll</a> with <a href="https://github.com/alshedivat/al-folio" rel="external nofollow noopener" target="_blank">al-folio</a> theme. Hosted by <a href="https://pages.github.com/" target="_blank" rel="external nofollow noopener">GitHub Pages</a>. 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diff --git a/profiles/dongwei/index.html b/profiles/dongwei/index.html
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Dongwei holds a Bachelor’s degree in Computer Science from Shandong University and a Master of Computer Science (MCS) from Rice University. Prior to her doctoral studies, Dongwei worked as a bioinformatics programmer at Baylor College of Medicine, where she focused on research involving large language models (LLMs), graph neural networks (GNNs), and single-cell data analysis. Her primary research interests lie in computational biology, with a particular emphasis on genomics. Dongwei’s research is funded by the Department of Computer Science at Rice University.</p> <p>Outside of lab, she enjoys watching movies with her cat, Disco.</p> </article> <h2>References</h2> <div class="publications"> </div> </div> </div> <footer class="fixed-bottom" role="contentinfo"> <div class="container mt-0"> © Copyright 2024 Treangen J. Treangen. 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Dongwei holds a Bachelor’s degree in Computer Science from Shandong University and a Master of Computer Science (MCS) from Rice University. Prior to her doctoral studies, Dongwei worked as a bioinformatics programmer at Baylor College of Medicine, where she focused on research involving large language models (LLMs), graph neural networks (GNNs), and single-cell data analysis. Her primary research interests lie in computational biology, with a particular emphasis on genomics. Dongwei’s research is funded by the Department of Computer Science at Rice University.</p> <p>Outside of lab, she enjoys watching movies with her cat, Disco.</p> </article> <h2>References</h2> <div class="publications"> </div> </div> </div> <footer class="fixed-bottom" role="contentinfo"> <div class="container mt-0"> © Copyright 2024 Treangen J. Treangen. 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   <span class="na">year</span> <span class="p">=</span> <span class="s">{2023}</span><span class="p">,</span>
   <span class="na">journal</span> <span class="p">=</span> <span class="s">{bioRxiv}</span><span class="p">,</span>
   <span class="na">publisher</span> <span class="p">=</span> <span class="s">{Cold Spring Harbor Laboratory}</span>
-<span class="p">}</span></code></pre></figure> </div> </div> </div> </li></ol> </div> </div> </div> <footer class="fixed-bottom" role="contentinfo"> <div class="container mt-0"> © Copyright 2024 Treangen J. Treangen. Powered by <a href="https://jekyllrb.com/" target="_blank" rel="external nofollow noopener">Jekyll</a> with <a href="https://github.com/alshedivat/al-folio" rel="external nofollow noopener" target="_blank">al-folio</a> theme. Hosted by <a href="https://pages.github.com/" target="_blank" rel="external nofollow noopener">GitHub Pages</a>. 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+<span class="p">}</span></code></pre></figure> </div> </div> </div> </li></ol> </div> </div> </div> <footer class="fixed-bottom" role="contentinfo"> <div class="container mt-0"> © Copyright 2024 Treangen J. Treangen. Powered by <a href="https://jekyllrb.com/" target="_blank" rel="external nofollow noopener">Jekyll</a> with <a href="https://github.com/alshedivat/al-folio" rel="external nofollow noopener" target="_blank">al-folio</a> theme. Hosted by <a href="https://pages.github.com/" target="_blank" rel="external nofollow noopener">GitHub Pages</a>. 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diff --git a/profiles/fquinanta/index.html b/profiles/fquinanta/index.html
index 66d98613..9d1d352e 100644
--- a/profiles/fquinanta/index.html
+++ b/profiles/fquinanta/index.html
@@ -4,4 +4,4 @@
   <span class="na">year</span> <span class="p">=</span> <span class="s">{2023}</span><span class="p">,</span>
   <span class="na">booktitle</span> <span class="p">=</span> <span class="s">{Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics}</span><span class="p">,</span>
   <span class="na">pages</span> <span class="p">=</span> <span class="s">{1--6}</span>
-<span class="p">}</span></code></pre></figure> </div> </div> </div> </li></ol> </div> </div> </div> <footer class="fixed-bottom" role="contentinfo"> <div class="container mt-0"> © Copyright 2024 Treangen J. Treangen. Powered by <a href="https://jekyllrb.com/" target="_blank" rel="external nofollow noopener">Jekyll</a> with <a href="https://github.com/alshedivat/al-folio" rel="external nofollow noopener" target="_blank">al-folio</a> theme. Hosted by <a href="https://pages.github.com/" target="_blank" rel="external nofollow noopener">GitHub Pages</a>. 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+<span class="p">}</span></code></pre></figure> </div> </div> </div> </li></ol> </div> </div> </div> <footer class="fixed-bottom" role="contentinfo"> <div class="container mt-0"> © Copyright 2024 Treangen J. Treangen. Powered by <a href="https://jekyllrb.com/" target="_blank" rel="external nofollow noopener">Jekyll</a> with <a href="https://github.com/alshedivat/al-folio" rel="external nofollow noopener" target="_blank">al-folio</a> theme. Hosted by <a href="https://pages.github.com/" target="_blank" rel="external nofollow noopener">GitHub Pages</a>. 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diff --git a/profiles/mnute/index.html b/profiles/mnute/index.html
index 45b8c90e..7529b30c 100644
--- a/profiles/mnute/index.html
+++ b/profiles/mnute/index.html
@@ -29,7 +29,7 @@
   <span class="na">year</span> <span class="p">=</span> <span class="s">{2023}</span><span class="p">,</span>
   <span class="na">booktitle</span> <span class="p">=</span> <span class="s">{Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics}</span><span class="p">,</span>
   <span class="na">pages</span> <span class="p">=</span> <span class="s">{1--10}</span>
-<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> </ol> <h2 class="bibliography">2022</h2> <ol class="bibliography"> <li> <div class="row"> <div id="curry2022emu" class="col-sm-10"> <div class="title">Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data</div> <div class="author"> Kristen D Curry, Qi Wang, Michael G Nute, and <span class="more-authors" title="click to view 8 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '8 more authors' ? 'Alona Tyshaieva, Elizabeth Reeves, Sirena Soriano, Qinglong Wu, Enid Graeber, Patrick Finzer, Werner Mendling, others' : '8 more authors'; var cursorPosition=0; var textAdder=setInterval(function(){ element.html(more_authors_text.substring(0, cursorPosition + 1)); if (++cursorPosition == more_authors_text.length){ clearInterval(textAdder); } }, '10'); ">8 more authors</span> </div> <div class="periodical"> <em>Nature methods</em>, 2022 </div> <div class="periodical"> </div> <div class="links"> <a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a> </div> <div class="badges"> <span class="altmetric-embed" data-badge-type="2" data-badge-popover="right" data-altmetric-id="130469175"></span> <a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;user=N5irv88AAAAJ&amp;citation_for_view=N5irv88AAAAJ:1sJd4Hv_s6UC" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-130-4285F4?logo=googlescholar&amp;labelColor=beige" alt="130 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">curry2022emu</span><span class="p">,</span>
+<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> </ol> <h2 class="bibliography">2022</h2> <ol class="bibliography"> <li> <div class="row"> <div id="curry2022emu" class="col-sm-10"> <div class="title">Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data</div> <div class="author"> Kristen D Curry, Qi Wang, Michael G Nute, and <span class="more-authors" title="click to view 8 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '8 more authors' ? 'Alona Tyshaieva, Elizabeth Reeves, Sirena Soriano, Qinglong Wu, Enid Graeber, Patrick Finzer, Werner Mendling, others' : '8 more authors'; var cursorPosition=0; var textAdder=setInterval(function(){ element.html(more_authors_text.substring(0, cursorPosition + 1)); if (++cursorPosition == more_authors_text.length){ clearInterval(textAdder); } }, '10'); ">8 more authors</span> </div> <div class="periodical"> <em>Nature methods</em>, 2022 </div> <div class="periodical"> </div> <div class="links"> <a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a> </div> <div class="badges"> <span class="altmetric-embed" data-badge-type="2" data-badge-popover="right" data-altmetric-id="130469175"></span> <a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;user=N5irv88AAAAJ&amp;citation_for_view=N5irv88AAAAJ:1sJd4Hv_s6UC" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-140-4285F4?logo=googlescholar&amp;labelColor=beige" alt="140 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">curry2022emu</span><span class="p">,</span>
   <span class="na">title</span> <span class="p">=</span> <span class="s">{Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data}</span><span class="p">,</span>
   <span class="na">author</span> <span class="p">=</span> <span class="s">{Curry, Kristen D and Wang, Qi and Nute, Michael G and Tyshaieva, Alona and Reeves, Elizabeth and Soriano, Sirena and Wu, Qinglong and Graeber, Enid and Finzer, Patrick and Mendling, Werner and others}</span><span class="p">,</span>
   <span class="na">year</span> <span class="p">=</span> <span class="s">{2022}</span><span class="p">,</span>
@@ -46,7 +46,7 @@
   <span class="na">publisher</span> <span class="p">=</span> <span class="s">{Elsevier}</span><span class="p">,</span>
   <span class="na">volume</span> <span class="p">=</span> <span class="s">{21}</span><span class="p">,</span>
   <span class="na">pages</span> <span class="p">=</span> <span class="s">{100438}</span>
-<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> <li> <div class="row"> <div id="kille2022multiple" class="col-sm-10"> <div class="title">Multiple genome alignment in the telomere-to-telomere assembly era</div> <div class="author"> Bryce Kille, Advait Balaji, Fritz J Sedlazeck, and <span class="more-authors" title="click to view 2 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '2 more authors' ? 'Michael Nute, Todd J Treangen' : '2 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'); ">2 more authors</span> </div> <div class="periodical"> <em>Genome Biology</em>, 2022 </div> <div class="periodical"> </div> <div class="links"> <a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a> </div> <div class="badges"> <a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;user=EUtkB0sAAAAJ&amp;citation_for_view=EUtkB0sAAAAJ:nb7KW1ujOQ8C" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-25-4285F4?logo=googlescholar&amp;labelColor=beige" alt="25 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">kille2022multiple</span><span class="p">,</span>
+<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> <li> <div class="row"> <div id="kille2022multiple" class="col-sm-10"> <div class="title">Multiple genome alignment in the telomere-to-telomere assembly era</div> <div class="author"> Bryce Kille, Advait Balaji, Fritz J Sedlazeck, and <span class="more-authors" title="click to view 2 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '2 more authors' ? 'Michael Nute, Todd J Treangen' : '2 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'); ">2 more authors</span> </div> <div class="periodical"> <em>Genome Biology</em>, 2022 </div> <div class="periodical"> </div> <div class="links"> <a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a> </div> <div class="badges"> <a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;user=EUtkB0sAAAAJ&amp;citation_for_view=EUtkB0sAAAAJ:nb7KW1ujOQ8C" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-26-4285F4?logo=googlescholar&amp;labelColor=beige" alt="26 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">kille2022multiple</span><span class="p">,</span>
   <span class="na">title</span> <span class="p">=</span> <span class="s">{Multiple genome alignment in the telomere-to-telomere assembly era}</span><span class="p">,</span>
   <span class="na">author</span> <span class="p">=</span> <span class="s">{Kille, Bryce and Balaji, Advait and Sedlazeck, Fritz J and Nute, Michael and Treangen, Todd J}</span><span class="p">,</span>
   <span class="na">year</span> <span class="p">=</span> <span class="s">{2022}</span><span class="p">,</span>
@@ -55,7 +55,7 @@
   <span class="na">volume</span> <span class="p">=</span> <span class="s">{23}</span><span class="p">,</span>
   <span class="na">number</span> <span class="p">=</span> <span class="s">{1}</span><span class="p">,</span>
   <span class="na">pages</span> <span class="p">=</span> <span class="s">{182}</span>
-<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> <li> <div class="row"> <div id="sapoval2022current" class="col-sm-10"> <div class="title">Current progress and open challenges for applying deep learning across the biosciences</div> <div class="author"> Nicolae Sapoval, Amirali Aghazadeh, Michael G Nute, and <span class="more-authors" title="click to view 8 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '8 more authors' ? 'Dinler A Antunes, Advait Balaji, Richard Baraniuk, CJ Barberan, Ruth Dannenfelser, Chen Dun, Mohammadamin Edrisi, others' : '8 more authors'; var cursorPosition=0; var textAdder=setInterval(function(){ element.html(more_authors_text.substring(0, cursorPosition + 1)); if (++cursorPosition == more_authors_text.length){ clearInterval(textAdder); } }, '10'); ">8 more authors</span> </div> <div class="periodical"> <em>Nature Communications</em>, 2022 </div> <div class="periodical"> </div> <div class="links"> <a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a> </div> <div class="badges"> <span class="altmetric-embed" data-badge-type="2" data-badge-popover="right" data-altmetric-id="125736934"></span> <a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;user=N5irv88AAAAJ&amp;citation_for_view=N5irv88AAAAJ:1qzjygNMrQYC" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-210-4285F4?logo=googlescholar&amp;labelColor=beige" alt="210 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">sapoval2022current</span><span class="p">,</span>
+<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> <li> <div class="row"> <div id="sapoval2022current" class="col-sm-10"> <div class="title">Current progress and open challenges for applying deep learning across the biosciences</div> <div class="author"> Nicolae Sapoval, Amirali Aghazadeh, Michael G Nute, and <span class="more-authors" title="click to view 8 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '8 more authors' ? 'Dinler A Antunes, Advait Balaji, Richard Baraniuk, CJ Barberan, Ruth Dannenfelser, Chen Dun, Mohammadamin Edrisi, others' : '8 more authors'; var cursorPosition=0; var textAdder=setInterval(function(){ element.html(more_authors_text.substring(0, cursorPosition + 1)); if (++cursorPosition == more_authors_text.length){ clearInterval(textAdder); } }, '10'); ">8 more authors</span> </div> <div class="periodical"> <em>Nature Communications</em>, 2022 </div> <div class="periodical"> </div> <div class="links"> <a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a> </div> <div class="badges"> <span class="altmetric-embed" data-badge-type="2" data-badge-popover="right" data-altmetric-id="125736934"></span> <a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;user=N5irv88AAAAJ&amp;citation_for_view=N5irv88AAAAJ:1qzjygNMrQYC" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-220-4285F4?logo=googlescholar&amp;labelColor=beige" alt="220 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">sapoval2022current</span><span class="p">,</span>
   <span class="na">title</span> <span class="p">=</span> <span class="s">{Current progress and open challenges for applying deep learning across the biosciences}</span><span class="p">,</span>
   <span class="na">author</span> <span class="p">=</span> <span class="s">{Sapoval, Nicolae and Aghazadeh, Amirali and Nute, Michael G and Antunes, Dinler A and Balaji, Advait and Baraniuk, Richard and Barberan, CJ and Dannenfelser, Ruth and Dun, Chen and Edrisi, Mohammadamin and others}</span><span class="p">,</span>
   <span class="na">year</span> <span class="p">=</span> <span class="s">{2022}</span><span class="p">,</span>
@@ -80,4 +80,4 @@
   <span class="na">journal</span> <span class="p">=</span> <span class="s">{bioRxiv}</span><span class="p">,</span>
   <span class="na">publisher</span> <span class="p">=</span> <span class="s">{Cold Spring Harbor Laboratory}</span><span class="p">,</span>
   <span class="na">pages</span> <span class="p">=</span> <span class="s">{2020--05}</span>
-<span class="p">}</span></code></pre></figure> </div> </div> </div> </li></ol> </div> </div> </div> <footer class="fixed-bottom" role="contentinfo"> <div class="container mt-0"> © Copyright 2024 Treangen J. Treangen. Powered by <a href="https://jekyllrb.com/" target="_blank" rel="external nofollow noopener">Jekyll</a> with <a href="https://github.com/alshedivat/al-folio" rel="external nofollow noopener" target="_blank">al-folio</a> theme. Hosted by <a href="https://pages.github.com/" target="_blank" rel="external nofollow noopener">GitHub Pages</a>. 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+<span class="p">}</span></code></pre></figure> </div> </div> </div> </li></ol> </div> </div> </div> <footer class="fixed-bottom" role="contentinfo"> <div class="container mt-0"> © Copyright 2024 Treangen J. Treangen. Powered by <a href="https://jekyllrb.com/" target="_blank" rel="external nofollow noopener">Jekyll</a> with <a href="https://github.com/alshedivat/al-folio" rel="external nofollow noopener" target="_blank">al-folio</a> theme. Hosted by <a href="https://pages.github.com/" target="_blank" rel="external nofollow noopener">GitHub Pages</a>. 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diff --git a/profiles/nkokroko/index.html b/profiles/nkokroko/index.html
index bff27db9..3a2b9311 100644
--- a/profiles/nkokroko/index.html
+++ b/profiles/nkokroko/index.html
@@ -5,4 +5,4 @@
   <span class="na">journal</span> <span class="p">=</span> <span class="s">{bioRxiv}</span><span class="p">,</span>
   <span class="na">publisher</span> <span class="p">=</span> <span class="s">{Cold Spring Harbor Laboratory}</span><span class="p">,</span>
   <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> </ol> </div> </div> </div> <footer class="fixed-bottom" role="contentinfo"> <div class="container mt-0"> © Copyright 2024 Treangen J. Treangen. Powered by <a href="https://jekyllrb.com/" target="_blank" rel="external nofollow noopener">Jekyll</a> with <a href="https://github.com/alshedivat/al-folio" rel="external nofollow noopener" target="_blank">al-folio</a> theme. Hosted by <a href="https://pages.github.com/" target="_blank" rel="external nofollow noopener">GitHub Pages</a>. 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+<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> </ol> </div> </div> </div> <footer class="fixed-bottom" role="contentinfo"> <div class="container mt-0"> © Copyright 2024 Treangen J. Treangen. Powered by <a href="https://jekyllrb.com/" target="_blank" rel="external nofollow noopener">Jekyll</a> with <a href="https://github.com/alshedivat/al-folio" rel="external nofollow noopener" target="_blank">al-folio</a> theme. Hosted by <a href="https://pages.github.com/" target="_blank" rel="external nofollow noopener">GitHub Pages</a>. 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index 6f835976..a2b0bee5 100644
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   <span class="na">volume</span> <span class="p">=</span> <span class="s">{3}</span><span class="p">,</span>
   <span class="na">number</span> <span class="p">=</span> <span class="s">{9}</span><span class="p">,</span>
   <span class="na">pages</span> <span class="p">=</span> <span class="s">{2955--2965}</span>
-<span class="p">}</span></code></pre></figure> </div> </div> </div> </li></ol> </div> </div> </div> <footer class="fixed-bottom" role="contentinfo"> <div class="container mt-0"> © Copyright 2024 Treangen J. Treangen. Powered by <a href="https://jekyllrb.com/" target="_blank" rel="external nofollow noopener">Jekyll</a> with <a href="https://github.com/alshedivat/al-folio" rel="external nofollow noopener" target="_blank">al-folio</a> theme. Hosted by <a href="https://pages.github.com/" target="_blank" rel="external nofollow noopener">GitHub Pages</a>. 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diff --git a/profiles/xwang/index.html b/profiles/xwang/index.html
index e3912448..6765a0e3 100644
--- a/profiles/xwang/index.html
+++ b/profiles/xwang/index.html
@@ -1,4 +1,4 @@
-<!DOCTYPE html> <html lang="en"> <head> <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> <title> Michael X. Wang | Treangen lab at Rice University </title> <meta name="author" content="Treangen J. Treangen"> <meta name="description" content="6th Year Bioengineering Ph.D. student. Lead developer of Olivar."> <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="data:image/svg+xml,&lt;svg%20xmlns=%22http://www.w3.org/2000/svg%22%20viewBox=%220%200%20100%20100%22&gt;&lt;text%20y=%22.9em%22%20font-size=%2290%22&gt;%E2%9A%9B%EF%B8%8F&lt;/text&gt;&lt;/svg&gt;"> <link rel="stylesheet" href="/assets/css/main.css?d41d8cd98f00b204e9800998ecf8427e"> <link rel="canonical" href="/profiles/xwang/"> <script src="/assets/js/theme.js?9a0c749ec5240d9cda97bc72359a72c0"></script> <link defer rel="stylesheet" href="/assets/css/jekyll-pygments-themes-native.css?5847e5ed4a4568527aa6cfab446049ca" media="none" id="highlight_theme_dark"> <script>initTheme();</script> </head> <body class="fixed-top-nav "> <header> <nav id="navbar" class="navbar navbar-light navbar-expand-sm fixed-top" role="navigation"> <div class="container"> <a class="navbar-brand title font-weight-lighter" href="/"> Treangen lab at Rice University </a> <button class="navbar-toggler collapsed ml-auto" type="button" data-toggle="collapse" data-target="#navbarNav" aria-controls="navbarNav" aria-expanded="false" aria-label="Toggle navigation"> <span class="sr-only">Toggle navigation</span> <span class="icon-bar top-bar"></span> <span class="icon-bar middle-bar"></span> <span class="icon-bar bottom-bar"></span> </button> <div class="collapse navbar-collapse text-right" id="navbarNav"> <ul class="navbar-nav ml-auto flex-nowrap"> <li class="nav-item "> <a class="nav-link" href="/">lab </a> </li> <li class="nav-item "> <a class="nav-link" href="/people/">people </a> </li> <li class="nav-item "> <a class="nav-link" href="/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/">github </a> </li> <li class="nav-item "> <a class="nav-link" href="/cv/">cv </a> </li> <li class="nav-item "> <a class="nav-link" href="/teaching/">teaching </a> </li> <li class="nav-item"> <button id="search-toggle" title="Search" onclick="openSearchModal()"> <span class="nav-link">ctrl k <i class="ti ti-search"></i></span> </button> </li> <li class="toggle-container"> <button id="light-toggle" title="Change theme"> <i class="ti ti-sun-moon" id="light-toggle-system"></i> <i class="ti ti-moon-filled" id="light-toggle-dark"></i> <i class="ti ti-sun-filled" id="light-toggle-light"></i> </button> </li> </ul> </div> </div> </nav> <progress id="progress" value="0"> <div class="progress-container"> <span class="progress-bar"></span> </div> </progress> </header> <div class="container mt-5" role="main"> <div class="post"> <header class="post-header"> <h1 class="post-title">Michael X. Wang</h1> <p class="post-description">6th Year Bioengineering Ph.D. student. Lead developer of Olivar.</p> </header> <article> <p>Michael (6th year PhD candidate, Bioengineering) obtained a B.E. degree in Biomedical Engineering from Tsinghua University in 2019. During his undergraduate, he did research in developing multiplexed droplet digital PCR (ddPCR) assays with Dr. Yong Guo. Before joining the Treangen Lab in 2022, he worked on design and optimization of multiplexed NGS assays with Dr. David Y. Zhang <a class="citation" href="#xie2022designing">(Xie et al., 2022; Wu et al., 2022; Zhang et al., 2021)</a>. His primary research interest is algorithms for multiplexed primer and probe design, under the setting of wastewater pathogen surveillance <a class="citation" href="#wang2024olivar">(Wang et al., 2024; Wu et al., 2024; Wolken et al., 2024)</a>. Michael likes playing all kinds of sports and loves music.</p> <p>Michael is supported by CDC award (75D30122C14709) and NSF CAREER (IIS 2239114).</p> </article> <h2>References</h2> <div class="publications"> <h2 class="bibliography">2024</h2> <ol class="bibliography"> <li> <div class="row"> <div id="wang2024olivar" class="col-sm-10"> <div class="title">Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens</div> <div class="author"> Michael X Wang, Esther G Lou, Nicolae Sapoval, and <span class="more-authors" title="click to view 8 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '8 more authors' ? 'Eddie Kim, Prashant Kalvapalle, Bryce Kille, RA Leo Elworth, Yunxi Liu, Yilei Fu, Lauren B Stadler, others' : '8 more authors'; var cursorPosition=0; var textAdder=setInterval(function(){ element.html(more_authors_text.substring(0, cursorPosition + 1)); if (++cursorPosition == more_authors_text.length){ clearInterval(textAdder); } }, '10'); ">8 more authors</span> </div> <div class="periodical"> <em>Nature Communications</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=C1dcx88AAAAJ&amp;citation_for_view=C1dcx88AAAAJ:hqOjcs7Dif8C" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-0-4285F4?logo=googlescholar&amp;labelColor=beige" alt="0 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">wang2024olivar</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> Michael X. Wang | Treangen lab at Rice University </title> <meta name="author" content="Treangen J. Treangen"> <meta name="description" content="6th Year Bioengineering Ph.D. student. Lead developer of Olivar."> <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="data:image/svg+xml,&lt;svg%20xmlns=%22http://www.w3.org/2000/svg%22%20viewBox=%220%200%20100%20100%22&gt;&lt;text%20y=%22.9em%22%20font-size=%2290%22&gt;%E2%9A%9B%EF%B8%8F&lt;/text&gt;&lt;/svg&gt;"> <link rel="stylesheet" href="/assets/css/main.css?d41d8cd98f00b204e9800998ecf8427e"> <link rel="canonical" href="/profiles/xwang/"> <script src="/assets/js/theme.js?9a0c749ec5240d9cda97bc72359a72c0"></script> <link defer rel="stylesheet" href="/assets/css/jekyll-pygments-themes-native.css?5847e5ed4a4568527aa6cfab446049ca" media="none" id="highlight_theme_dark"> <script>initTheme();</script> </head> <body class="fixed-top-nav "> <header> <nav id="navbar" class="navbar navbar-light navbar-expand-sm fixed-top" role="navigation"> <div class="container"> <a class="navbar-brand title font-weight-lighter" href="/"> Treangen lab at Rice University </a> <button class="navbar-toggler collapsed ml-auto" type="button" data-toggle="collapse" data-target="#navbarNav" aria-controls="navbarNav" aria-expanded="false" aria-label="Toggle navigation"> <span class="sr-only">Toggle navigation</span> <span class="icon-bar top-bar"></span> <span class="icon-bar middle-bar"></span> <span class="icon-bar bottom-bar"></span> </button> <div class="collapse navbar-collapse text-right" id="navbarNav"> <ul class="navbar-nav ml-auto flex-nowrap"> <li class="nav-item "> <a class="nav-link" href="/">lab </a> </li> <li class="nav-item "> <a class="nav-link" href="/people/">people </a> </li> <li class="nav-item "> <a class="nav-link" href="/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/">github </a> </li> <li class="nav-item "> <a class="nav-link" href="/cv/">cv </a> </li> <li class="nav-item "> <a class="nav-link" href="/teaching/">teaching </a> </li> <li class="nav-item"> <button id="search-toggle" title="Search" onclick="openSearchModal()"> <span class="nav-link">ctrl k <i class="ti ti-search"></i></span> </button> </li> <li class="toggle-container"> <button id="light-toggle" title="Change theme"> <i class="ti ti-sun-moon" id="light-toggle-system"></i> <i class="ti ti-moon-filled" id="light-toggle-dark"></i> <i class="ti ti-sun-filled" id="light-toggle-light"></i> </button> </li> </ul> </div> </div> </nav> <progress id="progress" value="0"> <div class="progress-container"> <span class="progress-bar"></span> </div> </progress> </header> <div class="container mt-5" role="main"> <div class="post"> <header class="post-header"> <h1 class="post-title">Michael X. Wang</h1> <p class="post-description">6th Year Bioengineering Ph.D. student. Lead developer of Olivar.</p> </header> <article> <p>Michael (6th year PhD candidate, Bioengineering) obtained a B.E. degree in Biomedical Engineering from Tsinghua University in 2019. During his undergraduate, he did research in developing multiplexed droplet digital PCR (ddPCR) assays with Dr. Yong Guo. Before joining the Treangen Lab in 2022, he worked on design and optimization of multiplexed NGS assays with Dr. David Y. Zhang <a class="citation" href="#xie2022designing">(Xie et al., 2022; Wu et al., 2022; Zhang et al., 2021)</a>. His primary research interest is algorithms for multiplexed primer and probe design, under the setting of wastewater pathogen surveillance <a class="citation" href="#wang2024olivar">(Wang et al., 2024; Wu et al., 2024; Wolken et al., 2024)</a>. Michael likes playing all kinds of sports and loves music.</p> <p>Michael is supported by CDC award (75D30122C14709) and NSF CAREER (IIS 2239114).</p> </article> <h2>References</h2> <div class="publications"> <h2 class="bibliography">2024</h2> <ol class="bibliography"> <li> <div class="row"> <div id="wang2024olivar" class="col-sm-10"> <div class="title">Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens</div> <div class="author"> Michael X Wang, Esther G Lou, Nicolae Sapoval, and <span class="more-authors" title="click to view 8 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '8 more authors' ? 'Eddie Kim, Prashant Kalvapalle, Bryce Kille, RA Leo Elworth, Yunxi Liu, Yilei Fu, Lauren B Stadler, others' : '8 more authors'; var cursorPosition=0; var textAdder=setInterval(function(){ element.html(more_authors_text.substring(0, cursorPosition + 1)); if (++cursorPosition == more_authors_text.length){ clearInterval(textAdder); } }, '10'); ">8 more authors</span> </div> <div class="periodical"> <em>Nature Communications</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=C1dcx88AAAAJ&amp;citation_for_view=C1dcx88AAAAJ:hqOjcs7Dif8C" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-2-4285F4?logo=googlescholar&amp;labelColor=beige" alt="2 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">wang2024olivar</span><span class="p">,</span>
   <span class="na">title</span> <span class="p">=</span> <span class="s">{Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens}</span><span class="p">,</span>
   <span class="na">author</span> <span class="p">=</span> <span class="s">{Wang, Michael X and Lou, Esther G and Sapoval, Nicolae and Kim, Eddie and Kalvapalle, Prashant and Kille, Bryce and Elworth, RA Leo and Liu, Yunxi and Fu, Yilei and Stadler, Lauren B and others}</span><span class="p">,</span>
   <span class="na">year</span> <span class="p">=</span> <span class="s">{2024}</span><span class="p">,</span>
@@ -40,7 +40,7 @@
   <span class="na">pages</span> <span class="p">=</span> <span class="s">{1791}</span><span class="p">,</span>
   <span class="na">year</span> <span class="p">=</span> <span class="s">{2022}</span><span class="p">,</span>
   <span class="na">publisher</span> <span class="p">=</span> <span class="s">{Nature Publishing Group UK London}</span>
-<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> </ol> <h2 class="bibliography">2021</h2> <ol class="bibliography"><li> <div class="row"> <div id="zhang2021deep" class="col-sm-10"> <div class="title">A deep learning model for predicting next-generation sequencing depth from DNA sequence</div> <div class="author"> Jinny X Zhang, Boyan Yordanov, Alexander Gaunt, and <span class="more-authors" title="click to view 8 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '8 more authors' ? 'Michael X Wang, Peng Dai, Yuan-Jyue Chen, Kerou Zhang, John Z Fang, Neil Dalchau, Jiaming Li, others' : '8 more authors'; var cursorPosition=0; var textAdder=setInterval(function(){ element.html(more_authors_text.substring(0, cursorPosition + 1)); if (++cursorPosition == more_authors_text.length){ clearInterval(textAdder); } }, '10'); ">8 more authors</span> </div> <div class="periodical"> <em>Nature communications</em>, 2021 </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=C1dcx88AAAAJ&amp;citation_for_view=C1dcx88AAAAJ:UeHWp8X0CEIC" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-64-4285F4?logo=googlescholar&amp;labelColor=beige" alt="64 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">zhang2021deep</span><span class="p">,</span>
+<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> </ol> <h2 class="bibliography">2021</h2> <ol class="bibliography"><li> <div class="row"> <div id="zhang2021deep" class="col-sm-10"> <div class="title">A deep learning model for predicting next-generation sequencing depth from DNA sequence</div> <div class="author"> Jinny X Zhang, Boyan Yordanov, Alexander Gaunt, and <span class="more-authors" title="click to view 8 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '8 more authors' ? 'Michael X Wang, Peng Dai, Yuan-Jyue Chen, Kerou Zhang, John Z Fang, Neil Dalchau, Jiaming Li, others' : '8 more authors'; var cursorPosition=0; var textAdder=setInterval(function(){ element.html(more_authors_text.substring(0, cursorPosition + 1)); if (++cursorPosition == more_authors_text.length){ clearInterval(textAdder); } }, '10'); ">8 more authors</span> </div> <div class="periodical"> <em>Nature communications</em>, 2021 </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=C1dcx88AAAAJ&amp;citation_for_view=C1dcx88AAAAJ:UeHWp8X0CEIC" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-66-4285F4?logo=googlescholar&amp;labelColor=beige" alt="66 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">zhang2021deep</span><span class="p">,</span>
   <span class="na">title</span> <span class="p">=</span> <span class="s">{A deep learning model for predicting next-generation sequencing depth from DNA sequence}</span><span class="p">,</span>
   <span class="na">author</span> <span class="p">=</span> <span class="s">{Zhang, Jinny X and Yordanov, Boyan and Gaunt, Alexander and Wang, Michael X and Dai, Peng and Chen, Yuan-Jyue and Zhang, Kerou and Fang, John Z and Dalchau, Neil and Li, Jiaming and others}</span><span class="p">,</span>
   <span class="na">journal</span> <span class="p">=</span> <span class="s">{Nature communications}</span><span class="p">,</span>
@@ -49,4 +49,4 @@
   <span class="na">pages</span> <span class="p">=</span> <span class="s">{4387}</span><span class="p">,</span>
   <span class="na">year</span> <span class="p">=</span> <span class="s">{2021}</span><span class="p">,</span>
   <span class="na">publisher</span> <span class="p">=</span> <span class="s">{Nature Publishing Group UK London}</span>
-<span class="p">}</span></code></pre></figure> </div> </div> </div> </li></ol> </div> </div> </div> <footer class="fixed-bottom" role="contentinfo"> <div class="container mt-0"> © Copyright 2024 Treangen J. Treangen. Powered by <a href="https://jekyllrb.com/" target="_blank" rel="external nofollow noopener">Jekyll</a> with <a href="https://github.com/alshedivat/al-folio" rel="external nofollow noopener" target="_blank">al-folio</a> theme. Hosted by <a href="https://pages.github.com/" target="_blank" rel="external nofollow noopener">GitHub Pages</a>. 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-</code></pre></div></div> </article> <h2>References</h2> <div class="publications"> </div> </div> </div> <footer class="fixed-bottom" role="contentinfo"> <div class="container mt-0"> © Copyright 2024 Treangen J. Treangen. Powered by <a href="https://jekyllrb.com/" target="_blank" rel="external nofollow noopener">Jekyll</a> with <a href="https://github.com/alshedivat/al-folio" rel="external nofollow noopener" target="_blank">al-folio</a> theme. Hosted by <a href="https://pages.github.com/" target="_blank" rel="external nofollow noopener">GitHub Pages</a>. 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index bfd75403..94fd8e44 100644
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-</code></pre></div></div> </article> <h2>References</h2> <div class="publications"> </div> </div> </div> <footer class="fixed-bottom" role="contentinfo"> <div class="container mt-0"> © Copyright 2024 Treangen J. Treangen. Powered by <a href="https://jekyllrb.com/" target="_blank" rel="external nofollow noopener">Jekyll</a> with <a href="https://github.com/alshedivat/al-folio" rel="external nofollow noopener" target="_blank">al-folio</a> theme. Hosted by <a href="https://pages.github.com/" target="_blank" rel="external nofollow noopener">GitHub Pages</a>. 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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> projects | Treangen lab at Rice University </title> <meta name="author" content="Treangen J. 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$('.responsive-img-srcset').remove();"> </picture> </figure> <div class="card-body"> <h2 class="card-title">project 1</h2> <p class="card-text">with background image</p> <div class="row ml-1 mr-1 p-0"> </div> </div> </div> </a> </div> <div class="col"> <a href="/projects/7_project/"> <div class="card h-100 hoverable"> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/4-480.webp 480w,/assets/img/4-800.webp 800w,/assets/img/4-1400.webp 1400w," sizes="50px" type="image/webp"></source> <img src="/assets/img/4.jpg" class="card-img-top" width="100%" height="auto" alt="project thumbnail" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"> </picture> </figure> <div class="card-body"> <h2 class="card-title">project 7</h2> <p class="card-text">with background image</p> <div class="row ml-1 mr-1 p-0"> </div> </div> </div> </a> </div> <div class="col"> <a href="/projects/2_project/"> <div class="card h-100 hoverable"> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/3-480.webp 480w,/assets/img/3-800.webp 800w,/assets/img/3-1400.webp 1400w," sizes="50px" type="image/webp"></source> <img src="/assets/img/3.jpg" class="card-img-top" width="100%" height="auto" alt="project thumbnail" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"> </picture> </figure> <div class="card-body"> <h2 class="card-title">project 2</h2> <p class="card-text">a project with a background image and giscus comments</p> <div class="row ml-1 mr-1 p-0"> </div> </div> </div> </a> </div> <div class="col"> <a href="/projects/8_project/"> <div class="card h-100 hoverable"> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/9-480.webp 480w,/assets/img/9-800.webp 800w,/assets/img/9-1400.webp 1400w," sizes="50px" type="image/webp"></source> <img src="/assets/img/9.jpg" class="card-img-top" width="100%" height="auto" alt="project thumbnail" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"> </picture> </figure> <div class="card-body"> <h2 class="card-title">project 8</h2> <p class="card-text">an other project with a background image and giscus comments</p> <div class="row ml-1 mr-1 p-0"> </div> </div> </div> </a> </div> <div class="col"> <a href="https://unsplash.com" rel="external nofollow noopener" target="_blank"> <div class="card h-100 hoverable"> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/7-480.webp 480w,/assets/img/7-800.webp 800w,/assets/img/7-1400.webp 1400w," sizes="50px" type="image/webp"></source> <img src="/assets/img/7.jpg" class="card-img-top" width="100%" height="auto" alt="project thumbnail" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"> </picture> </figure> <div class="card-body"> <h2 class="card-title">project 3 with very long name</h2> <p class="card-text">a project that redirects to another website</p> <div class="row ml-1 mr-1 p-0"> </div> </div> </div> </a> </div> </div> <a id="fun" href=".#fun"> <h2 class="category">fun</h2> </a> <div class="row row-cols-1 row-cols-md-3"> <div class="col"> <a href="/projects/4_project/"> <div class="card h-100 hoverable"> <div class="card-body"> <h2 class="card-title">project 4</h2> <p class="card-text">another without an image</p> <div class="row ml-1 mr-1 p-0"> </div> </div> </div> </a> </div> <div class="col"> <a href="/projects/5_project/"> <div class="card h-100 hoverable"> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/1-480.webp 480w,/assets/img/1-800.webp 800w,/assets/img/1-1400.webp 1400w," sizes="50px" type="image/webp"></source> <img src="/assets/img/1.jpg" class="card-img-top" width="100%" height="auto" alt="project thumbnail" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"> </picture> </figure> <div class="card-body"> <h2 class="card-title">project 5</h2> <p class="card-text">a project with a background image</p> <div class="row ml-1 mr-1 p-0"> </div> </div> </div> </a> </div> <div class="col"> <a href="/projects/6_project/"> <div class="card h-100 hoverable"> <div class="card-body"> <h2 class="card-title">project 6</h2> <p class="card-text">a project with no image</p> <div class="row ml-1 mr-1 p-0"> </div> </div> </div> </a> </div> <div class="col"> <a href="/projects/9_project/"> <div class="card h-100 hoverable"> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/6-480.webp 480w,/assets/img/6-800.webp 800w,/assets/img/6-1400.webp 1400w," sizes="50px" type="image/webp"></source> <img src="/assets/img/6.jpg" class="card-img-top" width="100%" height="auto" alt="project thumbnail" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"> </picture> </figure> <div class="card-body"> <h2 class="card-title">project 9</h2> <p class="card-text">another project with an image 🎉</p> <div class="row ml-1 mr-1 p-0"> </div> </div> </div> </a> </div> </div> </div> </article> </div> </div> <footer class="fixed-bottom" role="contentinfo"> <div class="container mt-0"> © Copyright 2024 Treangen J. 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$('.responsive-img-srcset').remove();"> </picture> </figure> <div class="card-body"> <h2 class="card-title">project 1</h2> <p class="card-text">with background image</p> <div class="row ml-1 mr-1 p-0"> </div> </div> </div> </a> </div> <div class="col"> <a href="/projects/7_project/"> <div class="card h-100 hoverable"> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/4-480.webp 480w,/assets/img/4-800.webp 800w,/assets/img/4-1400.webp 1400w," sizes="50px" type="image/webp"></source> <img src="/assets/img/4.jpg" class="card-img-top" width="100%" height="auto" alt="project thumbnail" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"> </picture> </figure> <div class="card-body"> <h2 class="card-title">project 7</h2> <p class="card-text">with background image</p> <div class="row ml-1 mr-1 p-0"> </div> </div> </div> </a> </div> <div class="col"> <a href="/projects/2_project/"> <div class="card h-100 hoverable"> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/3-480.webp 480w,/assets/img/3-800.webp 800w,/assets/img/3-1400.webp 1400w," sizes="50px" type="image/webp"></source> <img src="/assets/img/3.jpg" class="card-img-top" width="100%" height="auto" alt="project thumbnail" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"> </picture> </figure> <div class="card-body"> <h2 class="card-title">project 2</h2> <p class="card-text">a project with a background image and giscus comments</p> <div class="row ml-1 mr-1 p-0"> </div> </div> </div> </a> </div> <div class="col"> <a href="/projects/8_project/"> <div class="card h-100 hoverable"> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/9-480.webp 480w,/assets/img/9-800.webp 800w,/assets/img/9-1400.webp 1400w," sizes="50px" type="image/webp"></source> <img src="/assets/img/9.jpg" class="card-img-top" width="100%" height="auto" alt="project thumbnail" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"> </picture> </figure> <div class="card-body"> <h2 class="card-title">project 8</h2> <p class="card-text">an other project with a background image and giscus comments</p> <div class="row ml-1 mr-1 p-0"> </div> </div> </div> </a> </div> <div class="col"> <a href="https://unsplash.com" rel="external nofollow noopener" target="_blank"> <div class="card h-100 hoverable"> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/7-480.webp 480w,/assets/img/7-800.webp 800w,/assets/img/7-1400.webp 1400w," sizes="50px" type="image/webp"></source> <img src="/assets/img/7.jpg" class="card-img-top" width="100%" height="auto" alt="project thumbnail" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"> </picture> </figure> <div class="card-body"> <h2 class="card-title">project 3 with very long name</h2> <p class="card-text">a project that redirects to another website</p> <div class="row ml-1 mr-1 p-0"> </div> </div> </div> </a> </div> </div> <a id="fun" href=".#fun"> <h2 class="category">fun</h2> </a> <div class="row row-cols-1 row-cols-md-3"> <div class="col"> <a href="/projects/4_project/"> <div class="card h-100 hoverable"> <div class="card-body"> <h2 class="card-title">project 4</h2> <p class="card-text">another without an image</p> <div class="row ml-1 mr-1 p-0"> </div> </div> </div> </a> </div> <div class="col"> <a href="/projects/5_project/"> <div class="card h-100 hoverable"> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/1-480.webp 480w,/assets/img/1-800.webp 800w,/assets/img/1-1400.webp 1400w," sizes="50px" type="image/webp"></source> <img src="/assets/img/1.jpg" class="card-img-top" width="100%" height="auto" alt="project thumbnail" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"> </picture> </figure> <div class="card-body"> <h2 class="card-title">project 5</h2> <p class="card-text">a project with a background image</p> <div class="row ml-1 mr-1 p-0"> </div> </div> </div> </a> </div> <div class="col"> <a href="/projects/6_project/"> <div class="card h-100 hoverable"> <div class="card-body"> <h2 class="card-title">project 6</h2> <p class="card-text">a project with no image</p> <div class="row ml-1 mr-1 p-0"> </div> </div> </div> </a> </div> <div class="col"> <a href="/projects/9_project/"> <div class="card h-100 hoverable"> <figure> <picture> <source class="responsive-img-srcset" srcset="/assets/img/6-480.webp 480w,/assets/img/6-800.webp 800w,/assets/img/6-1400.webp 1400w," sizes="50px" type="image/webp"></source> <img src="/assets/img/6.jpg" class="card-img-top" width="100%" height="auto" alt="project thumbnail" loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"> </picture> </figure> <div class="card-body"> <h2 class="card-title">project 9</h2> <p class="card-text">another project with an image 🎉</p> <div class="row ml-1 mr-1 p-0"> </div> </div> </div> </a> </div> </div> </div> </article> </div> </div> <footer class="fixed-bottom" role="contentinfo"> <div class="container mt-0"> © Copyright 2024 Treangen J. 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Wang",description:"6th Year Bioengineering Ph.D. student. Lead developer of Olivar.",section:"Profiles",handler:()=>{window.location.href="/profiles/xwang/"}},{id:"projects-project-1",title:"project 1",description:"with background image",section:"Projects",handler:()=>{window.location.href="/projects/1_project/"}},{id:"projects-project-2",title:"project 2",description:"a project with a background image and giscus comments",section:"Projects",handler:()=>{window.location.href="/projects/2_project/"}},{id:"projects-project-3-with-very-long-name",title:"project 3 with very long name",description:"a project that redirects to another website",section:"Projects",handler:()=>{window.location.href="/projects/3_project/"}},{id:"projects-project-4",title:"project 4",description:"another without an image",section:"Projects",handler:()=>{window.location.href="/projects/4_project/"}},{id:"projects-project-5",title:"project 5",description:"a project with a background image",section:"Projects",handler:()=>{window.location.href="/projects/5_project/"}},{id:"projects-project-6",title:"project 6",description:"a project with no image",section:"Projects",handler:()=>{window.location.href="/projects/6_project/"}},{id:"projects-project-7",title:"project 7",description:"with background image",section:"Projects",handler:()=>{window.location.href="/projects/7_project/"}},{id:"projects-project-8",title:"project 8",description:"an other project with a background image and giscus comments",section:"Projects",handler:()=>{window.location.href="/projects/8_project/"}},{id:"projects-project-9",title:"project 9",description:"another project with an image \ud83c\udf89",section:"Projects",handler:()=>{window.location.href="/projects/9_project/"}},{id:"socials-email",title:"Send email",section:"Socials",handler:()=>{window.open("mailto:%74%72%65%61%6E%67%65%6E@%72%69%63%65.%65%64%75","_blank")}},{id:"socials-orcid",title:"ORCID",section:"Socials",handler:()=>{window.open("https://orcid.org/0000-0002-3760-564X","_blank")}},{id:"socials-google-scholar",title:"Google Scholar",section:"Socials",handler:()=>{window.open("https://scholar.google.com/citations?user=N5irv88AAAAJ","_blank")}},{id:"socials-open-science-framework",title:"Open Science Framework",section:"Socials",handler:()=>{window.open("https://osf.io/5etvy/","_blank")}},{id:"socials-github",title:"GitHub",section:"Socials",handler:()=>{window.open("https://github.com/treangen","_blank")}},{id:"socials-linkedin",title:"LinkedIn",section:"Socials",handler:()=>{window.open("https://www.linkedin.com/in/tjtreangen","_blank")}},{id:"socials-gitlab",title:"GitLab",section:"Socials",handler:()=>{window.open("https://gitlab.com/treangen","_blank")}},{id:"socials-bluesky",title:"Bluesky",section:"Socials",handler:()=>{window.open("https://bsky.app/profile/treangen.bsky.social","_blank")}},{id:"light-theme",title:"Change theme to light",description:"Change the theme of the site to Light",section:"Theme",handler:()=>{setThemeSetting("light")}},{id:"dark-theme",title:"Change theme to dark",description:"Change the theme of the site to Dark",section:"Theme",handler:()=>{setThemeSetting("dark")}},{id:"system-theme",title:"Use system default theme",description:"Change the theme of the site to System Default",section:"Theme",handler:()=>{setThemeSetting("system")}}];</script> <script src="/assets/js/shortcut-key.js?6f508d74becd347268a7f822bca7309d"></script> </body> </html>
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diff --git a/publications/index.html b/publications/index.html
index 15d91b50..18888924 100644
--- a/publications/index.html
+++ b/publications/index.html
@@ -121,7 +121,7 @@
   <span class="na">year</span> <span class="p">=</span> <span class="s">{2024}</span><span class="p">,</span>
   <span class="na">journal</span> <span class="p">=</span> <span class="s">{arXiv e-prints}</span><span class="p">,</span>
   <span class="na">pages</span> <span class="p">=</span> <span class="s">{arXiv--2403}</span>
-<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> <li> <div class="row"> <div id="wang2024olivar" class="col-sm-10"> <div class="title">Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens</div> <div class="author"> Michael X Wang, Esther G Lou, Nicolae Sapoval, and <span class="more-authors" title="click to view 8 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '8 more authors' ? 'Eddie Kim, Prashant Kalvapalle, Bryce Kille, RA Leo Elworth, Yunxi Liu, Yilei Fu, Lauren B Stadler, others' : '8 more authors'; var cursorPosition=0; var textAdder=setInterval(function(){ element.html(more_authors_text.substring(0, cursorPosition + 1)); if (++cursorPosition == more_authors_text.length){ clearInterval(textAdder); } }, '10'); ">8 more authors</span> </div> <div class="periodical"> <em>Nature Communications</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=C1dcx88AAAAJ&amp;citation_for_view=C1dcx88AAAAJ:hqOjcs7Dif8C" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-0-4285F4?logo=googlescholar&amp;labelColor=beige" alt="0 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">wang2024olivar</span><span class="p">,</span>
+<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> <li> <div class="row"> <div id="wang2024olivar" class="col-sm-10"> <div class="title">Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens</div> <div class="author"> Michael X Wang, Esther G Lou, Nicolae Sapoval, and <span class="more-authors" title="click to view 8 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '8 more authors' ? 'Eddie Kim, Prashant Kalvapalle, Bryce Kille, RA Leo Elworth, Yunxi Liu, Yilei Fu, Lauren B Stadler, others' : '8 more authors'; var cursorPosition=0; var textAdder=setInterval(function(){ element.html(more_authors_text.substring(0, cursorPosition + 1)); if (++cursorPosition == more_authors_text.length){ clearInterval(textAdder); } }, '10'); ">8 more authors</span> </div> <div class="periodical"> <em>Nature Communications</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=C1dcx88AAAAJ&amp;citation_for_view=C1dcx88AAAAJ:hqOjcs7Dif8C" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-2-4285F4?logo=googlescholar&amp;labelColor=beige" alt="2 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">wang2024olivar</span><span class="p">,</span>
   <span class="na">title</span> <span class="p">=</span> <span class="s">{Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens}</span><span class="p">,</span>
   <span class="na">author</span> <span class="p">=</span> <span class="s">{Wang, Michael X and Lou, Esther G and Sapoval, Nicolae and Kim, Eddie and Kalvapalle, Prashant and Kille, Bryce and Elworth, RA Leo and Liu, Yunxi and Fu, Yilei and Stadler, Lauren B and others}</span><span class="p">,</span>
   <span class="na">year</span> <span class="p">=</span> <span class="s">{2024}</span><span class="p">,</span>
@@ -196,7 +196,7 @@
   <span class="na">year</span> <span class="p">=</span> <span class="s">{2023}</span><span class="p">,</span>
   <span class="na">journal</span> <span class="p">=</span> <span class="s">{bioRxiv}</span><span class="p">,</span>
   <span class="na">publisher</span> <span class="p">=</span> <span class="s">{Cold Spring Harbor Laboratory}</span>
-<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> <li> <div class="row"> <div id="kille2023minmers" class="col-sm-10"> <div class="title">Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation</div> <div class="author"> Bryce Kille, Erik Garrison, Todd J Treangen, and <span class="more-authors" title="click to view 1 more author" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '1 more author' ? 'Adam M Phillippy' : '1 more author'; 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'); ">1 more author</span> </div> <div class="periodical"> <em>Bioinformatics</em>, 2023 </div> <div class="periodical"> </div> <div class="links"> <a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a> </div> <div class="badges"> <a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;user=EUtkB0sAAAAJ&amp;citation_for_view=EUtkB0sAAAAJ:p2g8aNsByqUC" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-9-4285F4?logo=googlescholar&amp;labelColor=beige" alt="9 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">kille2023minmers</span><span class="p">,</span>
+<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> <li> <div class="row"> <div id="kille2023minmers" class="col-sm-10"> <div class="title">Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation</div> <div class="author"> Bryce Kille, Erik Garrison, Todd J Treangen, and <span class="more-authors" title="click to view 1 more author" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '1 more author' ? 'Adam M Phillippy' : '1 more author'; 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'); ">1 more author</span> </div> <div class="periodical"> <em>Bioinformatics</em>, 2023 </div> <div class="periodical"> </div> <div class="links"> <a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a> </div> <div class="badges"> <a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;user=EUtkB0sAAAAJ&amp;citation_for_view=EUtkB0sAAAAJ:p2g8aNsByqUC" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-10-4285F4?logo=googlescholar&amp;labelColor=beige" alt="10 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">kille2023minmers</span><span class="p">,</span>
   <span class="na">title</span> <span class="p">=</span> <span class="s">{Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation}</span><span class="p">,</span>
   <span class="na">author</span> <span class="p">=</span> <span class="s">{Kille, Bryce and Garrison, Erik and Treangen, Todd J and Phillippy, Adam M}</span><span class="p">,</span>
   <span class="na">year</span> <span class="p">=</span> <span class="s">{2023}</span><span class="p">,</span>
@@ -302,7 +302,7 @@
   <span class="na">booktitle</span> <span class="p">=</span> <span class="s">{International Conference on Machine Learning}</span><span class="p">,</span>
   <span class="na">pages</span> <span class="p">=</span> <span class="s">{4202--4218}</span><span class="p">,</span>
   <span class="na">organization</span> <span class="p">=</span> <span class="s">{PMLR}</span>
-<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> <li> <div class="row"> <div id="curry2022emu" class="col-sm-10"> <div class="title">Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data</div> <div class="author"> Kristen D Curry, Qi Wang, Michael G Nute, and <span class="more-authors" title="click to view 8 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '8 more authors' ? 'Alona Tyshaieva, Elizabeth Reeves, Sirena Soriano, Qinglong Wu, Enid Graeber, Patrick Finzer, Werner Mendling, others' : '8 more authors'; var cursorPosition=0; var textAdder=setInterval(function(){ element.html(more_authors_text.substring(0, cursorPosition + 1)); if (++cursorPosition == more_authors_text.length){ clearInterval(textAdder); } }, '10'); ">8 more authors</span> </div> <div class="periodical"> <em>Nature methods</em>, 2022 </div> <div class="periodical"> </div> <div class="links"> <a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a> </div> <div class="badges"> <span class="altmetric-embed" data-badge-type="2" data-badge-popover="right" data-altmetric-id="130469175"></span> <a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;user=N5irv88AAAAJ&amp;citation_for_view=N5irv88AAAAJ:1sJd4Hv_s6UC" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-130-4285F4?logo=googlescholar&amp;labelColor=beige" alt="130 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">curry2022emu</span><span class="p">,</span>
+<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> <li> <div class="row"> <div id="curry2022emu" class="col-sm-10"> <div class="title">Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data</div> <div class="author"> Kristen D Curry, Qi Wang, Michael G Nute, and <span class="more-authors" title="click to view 8 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '8 more authors' ? 'Alona Tyshaieva, Elizabeth Reeves, Sirena Soriano, Qinglong Wu, Enid Graeber, Patrick Finzer, Werner Mendling, others' : '8 more authors'; var cursorPosition=0; var textAdder=setInterval(function(){ element.html(more_authors_text.substring(0, cursorPosition + 1)); if (++cursorPosition == more_authors_text.length){ clearInterval(textAdder); } }, '10'); ">8 more authors</span> </div> <div class="periodical"> <em>Nature methods</em>, 2022 </div> <div class="periodical"> </div> <div class="links"> <a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a> </div> <div class="badges"> <span class="altmetric-embed" data-badge-type="2" data-badge-popover="right" data-altmetric-id="130469175"></span> <a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;user=N5irv88AAAAJ&amp;citation_for_view=N5irv88AAAAJ:1sJd4Hv_s6UC" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-140-4285F4?logo=googlescholar&amp;labelColor=beige" alt="140 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">curry2022emu</span><span class="p">,</span>
   <span class="na">title</span> <span class="p">=</span> <span class="s">{Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data}</span><span class="p">,</span>
   <span class="na">author</span> <span class="p">=</span> <span class="s">{Curry, Kristen D and Wang, Qi and Nute, Michael G and Tyshaieva, Alona and Reeves, Elizabeth and Soriano, Sirena and Wu, Qinglong and Graeber, Enid and Finzer, Patrick and Mendling, Werner and others}</span><span class="p">,</span>
   <span class="na">year</span> <span class="p">=</span> <span class="s">{2022}</span><span class="p">,</span>
@@ -338,7 +338,7 @@
   <span class="na">volume</span> <span class="p">=</span> <span class="s">{12}</span><span class="p">,</span>
   <span class="na">number</span> <span class="p">=</span> <span class="s">{1}</span><span class="p">,</span>
   <span class="na">pages</span> <span class="p">=</span> <span class="s">{21125}</span>
-<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> <li> <div class="row"> <div id="kille2022multiple" class="col-sm-10"> <div class="title">Multiple genome alignment in the telomere-to-telomere assembly era</div> <div class="author"> Bryce Kille, Advait Balaji, Fritz J Sedlazeck, and <span class="more-authors" title="click to view 2 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '2 more authors' ? 'Michael Nute, Todd J Treangen' : '2 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'); ">2 more authors</span> </div> <div class="periodical"> <em>Genome Biology</em>, 2022 </div> <div class="periodical"> </div> <div class="links"> <a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a> </div> <div class="badges"> <a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;user=EUtkB0sAAAAJ&amp;citation_for_view=EUtkB0sAAAAJ:nb7KW1ujOQ8C" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-25-4285F4?logo=googlescholar&amp;labelColor=beige" alt="25 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">kille2022multiple</span><span class="p">,</span>
+<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> <li> <div class="row"> <div id="kille2022multiple" class="col-sm-10"> <div class="title">Multiple genome alignment in the telomere-to-telomere assembly era</div> <div class="author"> Bryce Kille, Advait Balaji, Fritz J Sedlazeck, and <span class="more-authors" title="click to view 2 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '2 more authors' ? 'Michael Nute, Todd J Treangen' : '2 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'); ">2 more authors</span> </div> <div class="periodical"> <em>Genome Biology</em>, 2022 </div> <div class="periodical"> </div> <div class="links"> <a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a> </div> <div class="badges"> <a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;user=EUtkB0sAAAAJ&amp;citation_for_view=EUtkB0sAAAAJ:nb7KW1ujOQ8C" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-26-4285F4?logo=googlescholar&amp;labelColor=beige" alt="26 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">kille2022multiple</span><span class="p">,</span>
   <span class="na">title</span> <span class="p">=</span> <span class="s">{Multiple genome alignment in the telomere-to-telomere assembly era}</span><span class="p">,</span>
   <span class="na">author</span> <span class="p">=</span> <span class="s">{Kille, Bryce and Balaji, Advait and Sedlazeck, Fritz J and Nute, Michael and Treangen, Todd J}</span><span class="p">,</span>
   <span class="na">year</span> <span class="p">=</span> <span class="s">{2022}</span><span class="p">,</span>
@@ -387,7 +387,7 @@
   <span class="na">volume</span> <span class="p">=</span> <span class="s">{8}</span><span class="p">,</span>
   <span class="na">number</span> <span class="p">=</span> <span class="s">{42}</span><span class="p">,</span>
   <span class="na">pages</span> <span class="p">=</span> <span class="s">{eabo7676}</span>
-<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> <li> <div class="row"> <div id="sapoval2022current" class="col-sm-10"> <div class="title">Current progress and open challenges for applying deep learning across the biosciences</div> <div class="author"> Nicolae Sapoval, Amirali Aghazadeh, Michael G Nute, and <span class="more-authors" title="click to view 8 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '8 more authors' ? 'Dinler A Antunes, Advait Balaji, Richard Baraniuk, CJ Barberan, Ruth Dannenfelser, Chen Dun, Mohammadamin Edrisi, others' : '8 more authors'; var cursorPosition=0; var textAdder=setInterval(function(){ element.html(more_authors_text.substring(0, cursorPosition + 1)); if (++cursorPosition == more_authors_text.length){ clearInterval(textAdder); } }, '10'); ">8 more authors</span> </div> <div class="periodical"> <em>Nature Communications</em>, 2022 </div> <div class="periodical"> </div> <div class="links"> <a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a> </div> <div class="badges"> <span class="altmetric-embed" data-badge-type="2" data-badge-popover="right" data-altmetric-id="125736934"></span> <a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;user=N5irv88AAAAJ&amp;citation_for_view=N5irv88AAAAJ:1qzjygNMrQYC" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-210-4285F4?logo=googlescholar&amp;labelColor=beige" alt="210 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">sapoval2022current</span><span class="p">,</span>
+<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> <li> <div class="row"> <div id="sapoval2022current" class="col-sm-10"> <div class="title">Current progress and open challenges for applying deep learning across the biosciences</div> <div class="author"> Nicolae Sapoval, Amirali Aghazadeh, Michael G Nute, and <span class="more-authors" title="click to view 8 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '8 more authors' ? 'Dinler A Antunes, Advait Balaji, Richard Baraniuk, CJ Barberan, Ruth Dannenfelser, Chen Dun, Mohammadamin Edrisi, others' : '8 more authors'; var cursorPosition=0; var textAdder=setInterval(function(){ element.html(more_authors_text.substring(0, cursorPosition + 1)); if (++cursorPosition == more_authors_text.length){ clearInterval(textAdder); } }, '10'); ">8 more authors</span> </div> <div class="periodical"> <em>Nature Communications</em>, 2022 </div> <div class="periodical"> </div> <div class="links"> <a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a> </div> <div class="badges"> <span class="altmetric-embed" data-badge-type="2" data-badge-popover="right" data-altmetric-id="125736934"></span> <a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;user=N5irv88AAAAJ&amp;citation_for_view=N5irv88AAAAJ:1qzjygNMrQYC" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-220-4285F4?logo=googlescholar&amp;labelColor=beige" alt="220 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">sapoval2022current</span><span class="p">,</span>
   <span class="na">title</span> <span class="p">=</span> <span class="s">{Current progress and open challenges for applying deep learning across the biosciences}</span><span class="p">,</span>
   <span class="na">author</span> <span class="p">=</span> <span class="s">{Sapoval, Nicolae and Aghazadeh, Amirali and Nute, Michael G and Antunes, Dinler A and Balaji, Advait and Baraniuk, Richard and Barberan, CJ and Dannenfelser, Ruth and Dun, Chen and Edrisi, Mohammadamin and others}</span><span class="p">,</span>
   <span class="na">year</span> <span class="p">=</span> <span class="s">{2022}</span><span class="p">,</span>
@@ -548,7 +548,7 @@
   <span class="na">journal</span> <span class="p">=</span> <span class="s">{bioRxiv}</span><span class="p">,</span>
   <span class="na">publisher</span> <span class="p">=</span> <span class="s">{Cold Spring Harbor Laboratory}</span><span class="p">,</span>
   <span class="na">pages</span> <span class="p">=</span> <span class="s">{2021--11}</span>
-<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> <li> <div class="row"> <div id="zhang2021deep" class="col-sm-10"> <div class="title">A deep learning model for predicting next-generation sequencing depth from DNA sequence</div> <div class="author"> Jinny X Zhang, Boyan Yordanov, Alexander Gaunt, and <span class="more-authors" title="click to view 8 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '8 more authors' ? 'Michael X Wang, Peng Dai, Yuan-Jyue Chen, Kerou Zhang, John Z Fang, Neil Dalchau, Jiaming Li, others' : '8 more authors'; var cursorPosition=0; var textAdder=setInterval(function(){ element.html(more_authors_text.substring(0, cursorPosition + 1)); if (++cursorPosition == more_authors_text.length){ clearInterval(textAdder); } }, '10'); ">8 more authors</span> </div> <div class="periodical"> <em>Nature communications</em>, 2021 </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=C1dcx88AAAAJ&amp;citation_for_view=C1dcx88AAAAJ:UeHWp8X0CEIC" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-64-4285F4?logo=googlescholar&amp;labelColor=beige" alt="64 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">zhang2021deep</span><span class="p">,</span>
+<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> <li> <div class="row"> <div id="zhang2021deep" class="col-sm-10"> <div class="title">A deep learning model for predicting next-generation sequencing depth from DNA sequence</div> <div class="author"> Jinny X Zhang, Boyan Yordanov, Alexander Gaunt, and <span class="more-authors" title="click to view 8 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '8 more authors' ? 'Michael X Wang, Peng Dai, Yuan-Jyue Chen, Kerou Zhang, John Z Fang, Neil Dalchau, Jiaming Li, others' : '8 more authors'; var cursorPosition=0; var textAdder=setInterval(function(){ element.html(more_authors_text.substring(0, cursorPosition + 1)); if (++cursorPosition == more_authors_text.length){ clearInterval(textAdder); } }, '10'); ">8 more authors</span> </div> <div class="periodical"> <em>Nature communications</em>, 2021 </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=C1dcx88AAAAJ&amp;citation_for_view=C1dcx88AAAAJ:UeHWp8X0CEIC" aria-label="Google Scholar link" role="button" rel="external nofollow noopener" target="_blank"> <img src="https://img.shields.io/badge/scholar-66-4285F4?logo=googlescholar&amp;labelColor=beige" alt="66 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">zhang2021deep</span><span class="p">,</span>
   <span class="na">title</span> <span class="p">=</span> <span class="s">{A deep learning model for predicting next-generation sequencing depth from DNA sequence}</span><span class="p">,</span>
   <span class="na">author</span> <span class="p">=</span> <span class="s">{Zhang, Jinny X and Yordanov, Boyan and Gaunt, Alexander and Wang, Michael X and Dai, Peng and Chen, Yuan-Jyue and Zhang, Kerou and Fang, John Z and Dalchau, Neil and Li, Jiaming and others}</span><span class="p">,</span>
   <span class="na">journal</span> <span class="p">=</span> <span class="s">{Nature communications}</span><span class="p">,</span>
@@ -996,4 +996,4 @@
   <span class="na">volume</span> <span class="p">=</span> <span class="s">{7}</span><span class="p">,</span>
   <span class="na">number</span> <span class="p">=</span> <span class="s">{1}</span><span class="p">,</span>
   <span class="na">pages</span> <span class="p">=</span> <span class="s">{433}</span>
-<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> </ol> </div> </article> </div> </div> <footer class="fixed-bottom" role="contentinfo"> <div class="container mt-0"> © Copyright 2024 Treangen J. Treangen. Powered by <a href="https://jekyllrb.com/" target="_blank" rel="external nofollow noopener">Jekyll</a> with <a href="https://github.com/alshedivat/al-folio" rel="external nofollow noopener" target="_blank">al-folio</a> theme. Hosted by <a href="https://pages.github.com/" target="_blank" rel="external nofollow noopener">GitHub Pages</a>. 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