rebuilding site Sun Dec 17 02:15:29 PM PST 2023

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author/simon-roux/index.html

@@ -849,7 +849,7 @@ <h3>Education</h3>
 
 
 
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authors/index.html

@@ -690,7 +690,7 @@ <h1>Authors</h1>
 
 
 
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categories/index.html

@@ -683,7 +683,7 @@ <h1>Categories</h1>
 
 
 
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index.html

@@ -888,20 +888,22 @@ <h1>Current Projects</h1>
 <strong>Computational prediction of virus:host interactions</strong> <br>
 To help with viromics analysis, we have now developed a tool (iPHoP) to integrate multiple signals of virus-host interactions and enable robust prediction of host genus for many uncultivated phages. <b>Now available on <a href=https://anaconda.org/bioconda/iphop>bioconda</a> </b>, and described in the following pre-print:  
 <a href="https://doi.org/10.1101/2022.07.28.501908" target="_blank" rel="noopener">https://doi.org/10.1101/2022.07.28.501908</a> .</p>
-<p><img src="pictures/TroutBogLake_sq.png" style="width: 200px; border:2px solid #021a40; border-radius: 50%; margin-left: 5px; opacity: 1; filter: drop-shadow(8px 8px 10px gray); float:right" alt="Picture of Trout Bog Lake"/> -
-<strong>Virus:host interactions in model freshwater lakes</strong> <br>
-We study virus:host interactions in Trout Bog Lake based on targeted metagenomics coupled with time-series samples spanning across a decade, to better understand long-term dynamics between key viruses and bacteria in this ecosystem. In collaboration with the 
-<a href="https://mcmahonlab.wisc.edu" target="_blank" rel="noopener">McMahon Lab</a>. <b>Now published !!</b> (<a href=https://doi.org/10.1038/s41396-020-00870-1>10.1038/s41396-020-00870-1</a>) <small>(Image courtesy of Trina McMahon)</small></p>
+<p><img src="https://d9-wret.s3.us-west-2.amazonaws.com/assets/palladium/production/s3fs-public/styles/thumbnail/public/img7977.jpg?itok=TOtl1jgc" style="width: 200px; border:2px solid #021a40; border-radius: 20px; margin-left: 5px; opacity: 1; filter: drop-shadow(8px 8px 10px gray); float:right" alt="Picture of Mushroom Spring in YNP"/> -
+<strong>Virus:host dynamics in Yellowstone National Park biofilms</strong> <br>
+We study virus:host dynamics across diel cycles in Octopus and Mushroom springs based on coupled metagenomics, metatranscriptomics, and viral metagenomics, to better understand phage infection triggers and synchronization in natural communities. In collaboration with the 
+<a href="https://carnegiescience.edu/dr-devaki-bhaya" target="_blank" rel="noopener">Bhaya Lab</a>. <small>(Picture: USGS / Thomas Brock)</small></p>
 <p><img src="pictures/Viruses_1.png" style="width: 180px; border:2px solid #021a40; border-radius: 20px; margin-left: 10px; margin-right: 10px; opacity: 1; filter: drop-shadow(8px 8px 10px gray); float:right" alt="Illustration of viral capsids"/>  -
 <strong>IMG/VR - Large-scale exploration of uncultivated viral diversity</strong>  <br>
 We routinely mine public genomes, metagenomes, and metatranscriptomes for new viral sequences to progressively build a large and comprehensive genomic catalog of the virosphere. <b> IMG/VR v4 now released ! </b> More into in the 
 <a href="#tools">tools section</a> <small>(Viral capsids drawing from Leah Pantea / 
 <a href="http://leahpantea.com" target="_blank" rel="noopener">http://leahpantea.com</a>)</small></p>
-<p><img src="pictures/ivirus.png" style="width: 200px; border:2px solid #021a40; border-radius: 50%; margin-left: 5px; opacity: 1; filter: drop-shadow(8px 8px 10px gray); float:right" alt="iVirus logo"/> -
-<strong>iVirus - Towards a user-friendly viral ecogenomics toolkit</strong>  <br> Developing tools to identify, clean, compare, and annotate uncultivated viral genomes (mostly) assembled from metagenomes. In collaboration with the 
-<a href="https://u.osu.edu/viruslab/" target="_blank" rel="noopener">Sullivan Lab</a> and 
-<a href="https://wrightonlab.com" target="_blank" rel="noopener">Wrighton Lab</a>. See also the 
+<p><img src="https://gitlab.com/ccoclet/mvp/-/raw/main/images/MVP_Logo.png" style="width: 200px; border:2px solid #021a40; border-radius: 20px; margin-left: 5px; opacity: 1; filter: drop-shadow(8px 8px 10px gray); float:right" alt="MVP pipeline logo"/> -
+<strong>Towards a user-friendly viral ecogenomics toolkit</strong>  <br> Developing tools to identify, clean, compare, and annotate uncultivated viral genomes (mostly) assembled from metagenomes. Currently gathered in the 
+<a href="https://gitlab.com/ccoclet/mvp/" target="_blank" rel="noopener">MVP pipeline</a>, developed by Clement Coclet. See also the 
 <a href="#tools">tools section</a></p>
+<p><img src="https://ars.els-cdn.com/content/image/1-s2.0-S2589004222003911-fx1.jpg" style="width: 200px; border:2px solid #021a40; border-radius: 20px; margin-left: 5px; opacity: 1; filter: drop-shadow(8px 8px 10px gray); float:right" alt="MVP pipeline logo"/> -
+<strong>Establishing the foundations of a high-throughput phage foundry</strong>  <br> Analyzing and modeling phage diversity and phage:host interactions to better understand how microbiomes can be altered and manipulated through the addition of (engineered) phages. Project led by 
+<a href="https://biosciences.lbl.gov/profiles/vivek-mutalik/" target="_blank" rel="noopener">Vivek Mutalik</a></p>
 
     </div>
 
@@ -960,6 +962,8 @@ <h1>Tools</h1>
 <a href="https://img.jgi.doe.gov/vr/" target="_blank" rel="noopener">https://img.jgi.doe.gov/vr/</a></li>
 <li><strong>iVirus / CyVerse</strong> Set of CyVerse applications to identify, cluster, and taxonomically classify viral genomes - 
 <a href="https://ivirus.readthedocs.io/en/latest/" target="_blank" rel="noopener">https://ivirus.readthedocs.io/en/latest/</a></li>
+<li><strong>MVP</strong> Integrated pipeline for viral ecogenomics, from virus contigs detection and QC to vOTU matrices and ordination - development led by Clement Coclet 
+<a href="https://gitlab.com/ccoclet/mvp/" target="_blank" rel="noopener">https://gitlab.com/ccoclet/mvp/</a></li>
 <li><strong>geNomad</strong> Updated tool for viral contig identification, also provides plasmid identification and viral taxonomy (for viral contigs) - development led by Antonio Camargo 
 <a href="https://portal.nersc.gov/genomad/" target="_blank" rel="noopener">https://portal.nersc.gov/genomad/</a></li>
 <li><strong>VirSorter2</strong> New version of the VirSorter tool for viral contig identification - development led by Jiarong Guo 
@@ -1320,7 +1324,7 @@ <h1>Recent Publications</h1>
 
 
       <div class="card experience course">
-        <div class="card-body"><a href="https://doi.org/10.1038/s41564-023-01347-5" target="_blank" rel="noopener"><h4 class="card-title exp-title text-muted my-0">Viruses interact with hosts that span distantly related microbial domains in dense hydrothermal mats</h4></a><div class="card-subtitle my-0 article-metadata">Hwang et al., Nature Microbiology, in press<span class="middot-divider"></span>
+        <div class="card-body"><a href="https://doi.org/10.1038/s41564-023-01347-5" target="_blank" rel="noopener"><h4 class="card-title exp-title text-muted my-0">Viruses interact with hosts that span distantly related microbial domains in dense hydrothermal mats</h4></a><div class="card-subtitle my-0 article-metadata">Hwang et al., Nature Microbiology, Nat Microbiol 8, 946–957<span class="middot-divider"></span>
 
             2023
 
@@ -1335,7 +1339,7 @@ <h1>Recent Publications</h1>
       </div>
 
       <div class="card experience course">
-        <div class="card-body"><a href="https://doi.org/10.1101/2023.03.05.531206" target="_blank" rel="noopener"><h4 class="card-title exp-title text-muted my-0">You can move, but you can’t hide: identification of mobile genetic elements with geNomad</h4></a><div class="card-subtitle my-0 article-metadata">Camargo et al., in review<span class="middot-divider"></span>
+        <div class="card-body"><a href="https://doi.org/10.1038/s41587-023-01953-y" target="_blank" rel="noopener"><h4 class="card-title exp-title text-muted my-0">You can move, but you can’t hide: identification of mobile genetic elements with geNomad</h4></a><div class="card-subtitle my-0 article-metadata">Camargo et al., Nat Biotechnol<span class="middot-divider"></span>
 
             2023
 
@@ -1351,7 +1355,7 @@ <h1>Recent Publications</h1>
       </div>
 
       <div class="card experience course">
-        <div class="card-body"><a href="https://doi.org/10.1101/2023.03.06.531389" target="_blank" rel="noopener"><h4 class="card-title exp-title text-muted my-0">Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem</h4></a><div class="card-subtitle my-0 article-metadata">Coclet et al., in review<span class="middot-divider"></span>
+        <div class="card-body"><a href="https://doi.org/10.1186/s40168-023-01666-z" target="_blank" rel="noopener"><h4 class="card-title exp-title text-muted my-0">Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem</h4></a><div class="card-subtitle my-0 article-metadata">Coclet et al., Microbiome 11, 237<span class="middot-divider"></span>
 
             2023
 
@@ -1398,7 +1402,7 @@ <h1>Recent Publications</h1>
       </div>
 
       <div class="card experience course">
-        <div class="card-body"><a href="https://doi.org/10.1101/2022.07.28.501908" target="_blank" rel="noopener"><h4 class="card-title exp-title text-muted my-0">iPHoP: an integrated machine-learning framework to maximize host prediction for metagenome-assembled virus genomes</h4></a><div class="card-subtitle my-0 article-metadata">Roux et al., in press<span class="middot-divider"></span>
+        <div class="card-body"><a href="https://doi.org/10.1371/journal.pbio.3002083" target="_blank" rel="noopener"><h4 class="card-title exp-title text-muted my-0">iPHoP: an integrated machine-learning framework to maximize host prediction for metagenome-assembled virus genomes</h4></a><div class="card-subtitle my-0 article-metadata">Roux et al., PLOS Biology 21(4): e3002083<span class="middot-divider"></span>
 
             2022
 
@@ -1740,7 +1744,7 @@ <h1>Contact</h1>
 
 
 
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post/index.html

@@ -685,7 +685,7 @@ <h1>Posts</h1>
 
 
 
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publication/index.html

@@ -711,7 +711,7 @@ <h1>Publications</h1>
 
 
 
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publication_types/index.html

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tags/index.html

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talk/index.html

@@ -686,7 +686,7 @@ <h1>Recent &amp; Upcoming Talks</h1>
 
 
 
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