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diff --git a/author/simon-roux/index.xml b/author/simon-roux/index.xml
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https://simroux.github.io/author/simon-roux/
+
+ Simon Roux
+ https://simroux.github.io/author/simon-roux/
+ Mon, 01 Jan 0001 00:00:00 +0000
+ https://simroux.github.io/author/simon-roux/
+ <p>At the DOE Joint Genome Institute, I lead the Viral Genomics group where we explore viruses of microbes and their impacts on ecosystems using (mostly) fancy ‘omics tools. Our current projects include the study of viral diversity and virus:host interactions in soil and freshwater environments, along with the development of new bioinformatics tools and experimental protocols to probe and characterize uncultivated viruses. We also assist users of the JGI Metagenome Program with their analysis, including identification of viral sequences, functional annotation, taxonomic classification, etc.</p>
+<p>The long-term goal of my research is to understand the ecological and evolutionary drivers of virus:host dynamics in natural microbial communities. This research involves a mix of experimental and computational approaches spanning from the molecular to the ecosystem scale, trying to address fundamental questions like “how do viruses spread and adapt across environments ?”, “how do viruses take over and reprogram microbial cells ?”, and “how do viral infections alter ecosystem processes ?”.</p>
+
+
+
diff --git a/authors/index.html b/authors/index.html
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+++ b/authors/index.html
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+
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-Computational prediction of virus:host interactions
-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. Now available on bioconda, and described in the following pre-print:
-https://doi.org/10.1101/2022.07.28.501908 .
-
Virus:host dynamics in Yellowstone National Park biofilms
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
Bhaya Lab. (Picture: USGS / Thomas Brock)
+
-
+Defining the healthy human virome
+The JGI Viral Genomics group is involved in the new NIH-funded Human Virome Program
+https://commonfund.nih.gov/humanvirome. We will help develop new tools and resources for viral taxonomy databases, host prediction, and viral genome annotation.
+
-
+Establishing the foundations of a high-throughput phage foundry 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
+Vivek Mutalik
-
IMG/VR - Large-scale exploration of uncultivated viral diversity
We routinely mine public genomes, metagenomes, and metatranscriptomes for new viral sequences to progressively build a large and comprehensive genomic catalog of the virosphere. IMG/VR v4 now released ! More into in the
tools section (Viral capsids drawing from Leah Pantea /
http://leahpantea.com)
-
-
-Towards a user-friendly viral ecogenomics toolkit Developing tools to identify, clean, compare, and annotate uncultivated viral genomes (mostly) assembled from metagenomes. Currently gathered in the
-MVP pipeline, developed by Clement Coclet. See also the
-tools section
-
-
-Establishing the foundations of a high-throughput phage foundry 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
-Vivek Mutalik
-
+
diff --git a/index.json b/index.json
index a440f30..1d4d62b 100644
--- a/index.json
+++ b/index.json
@@ -1 +1 @@
-[{"authors":["admin"],"categories":null,"content":"At the DOE Joint Genome Institute, I lead the Viral Genomics group where we explore viruses of microbes and their impacts on ecosystems using (mostly) fancy \u0026lsquo;omics tools. Our current projects include the study of viral diversity and virus:host interactions in soil and freshwater environments, along with the development of new bioinformatics tools and experimental protocols to probe and characterize uncultivated viruses. We also assist users of the JGI Metagenome Program with their analysis, including identification of viral sequences, functional annotation, taxonomic classification, etc.\nThe long-term goal of my research is to understand the ecological and evolutionary drivers of virus:host dynamics in natural microbial communities. This research involves a mix of experimental and computational approaches spanning from the molecular to the ecosystem scale, trying to address fundamental questions like \u0026ldquo;how do viruses spread and adapt across environments ?\u0026rdquo;, \u0026ldquo;how do viruses take over and reprogram microbial cells ?\u0026rdquo;, and \u0026ldquo;how do viral infections alter ecosystem processes ?\u0026rdquo;.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"2525497d367e79493fd32b198b28f040","permalink":"https://simroux.github.io/author/simon-roux/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/author/simon-roux/","section":"authors","summary":"At the DOE Joint Genome Institute, I lead the Viral Genomics group where we explore viruses of microbes and their impacts on ecosystems using (mostly) fancy \u0026lsquo;omics tools. Our current projects include the study of viral diversity and virus:host interactions in soil and freshwater environments, along with the development of new bioinformatics tools and experimental protocols to probe and characterize uncultivated viruses.","tags":null,"title":"Simon Roux","type":"authors"}]
\ No newline at end of file
+[{"authors":["admin"],"categories":null,"content":"At the DOE Joint Genome Institute, I lead the Viral Genomics group where we explore viruses of microbes and their impacts on ecosystems using (mostly) fancy \u0026lsquo;omics tools. Our current projects include the study of viral diversity and virus:host interactions in soil and freshwater environments, along with the development of new bioinformatics tools and experimental protocols to probe and characterize uncultivated viruses. We also assist users of the JGI Metagenome Program with their analysis, including identification of viral sequences, functional annotation, taxonomic classification, etc.\nThe long-term goal of my research is to understand the ecological and evolutionary drivers of virus:host dynamics in natural microbial communities. This research involves a mix of experimental and computational approaches spanning from the molecular to the ecosystem scale, trying to address fundamental questions like \u0026ldquo;how do viruses spread and adapt across environments ?\u0026rdquo;, \u0026ldquo;how do viruses take over and reprogram microbial cells ?\u0026rdquo;, and \u0026ldquo;how do viral infections alter ecosystem processes ?\u0026rdquo;.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"2525497d367e79493fd32b198b28f040","permalink":"https://simroux.github.io/author/simon-roux/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/author/simon-roux/","section":"authors","summary":"At the DOE Joint Genome Institute, I lead the Viral Genomics group where we explore viruses of microbes and their impacts on ecosystems using (mostly) fancy \u0026lsquo;omics tools. Our current projects include the study of viral diversity and virus:host interactions in soil and freshwater environments, along with the development of new bioinformatics tools and experimental protocols to probe and characterize uncultivated viruses. We also assist users of the JGI Metagenome Program with their analysis, including identification of viral sequences, functional annotation, taxonomic classification, etc.\n","tags":null,"title":"Simon Roux","type":"authors"}]
\ No newline at end of file
diff --git a/index.xml b/index.xml
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--- a/index.xml
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@@ -5,7 +5,7 @@
https://simroux.github.io/
Simon Roux
- Source Themes Academic (https://sourcethemes.com/academic/)en-us
+ Source Themes Academic (https://sourcethemes.com/academic/)en-usThu, 28 Jun 2018 00:00:00 +0100https://simroux.github.io/img/Capsid_logo.jpgSimon Roux
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diff --git a/pictures/HVP.png b/pictures/HVP.png
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