diff --git a/404.html b/404.html index b5c9ef2..fbfcca6 100644 --- a/404.html +++ b/404.html @@ -205,6 +205,44 @@ + + + + + @@ -214,8 +252,8 @@ - - + + @@ -309,7 +347,7 @@

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Education

- + diff --git a/author/simon-roux/index.xml b/author/simon-roux/index.xml index 8a013f4..d56bc0a 100644 --- a/author/simon-roux/index.xml +++ b/author/simon-roux/index.xml @@ -12,5 +12,15 @@ 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 &lsquo;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 &ldquo;how do viruses spread and adapt across environments ?&rdquo;, &ldquo;how do viruses take over and reprogram microbial cells ?&rdquo;, and &ldquo;how do viral infections alter ecosystem processes ?&rdquo;.</p> + + + diff --git a/authors/index.html b/authors/index.html index 9ebf07f..bbe7317 100644 --- a/authors/index.html +++ b/authors/index.html @@ -205,6 +205,44 @@ + + + + + @@ -216,8 +254,8 @@ - - + + @@ -311,7 +349,7 @@

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- + diff --git a/images/icon_hu14056126660657468073.png b/images/icon_hu14056126660657468073.png new file mode 100644 index 0000000..43c2dbd Binary files /dev/null and b/images/icon_hu14056126660657468073.png differ diff --git a/images/icon_hu7542497146199104341.png b/images/icon_hu7542497146199104341.png new file mode 100644 index 0000000..a499d28 Binary files /dev/null and b/images/icon_hu7542497146199104341.png differ diff --git a/images/icon_hu9414133254159730754.png b/images/icon_hu9414133254159730754.png new file mode 100644 index 0000000..03d6201 Binary files /dev/null and b/images/icon_hu9414133254159730754.png differ diff --git a/images/logo_hu13903402681714629955.png b/images/logo_hu13903402681714629955.png new file mode 100644 index 0000000..54455bf Binary files /dev/null and b/images/logo_hu13903402681714629955.png differ diff --git a/index.html b/index.html index 7d0b078..b383848 100644 --- a/index.html +++ b/index.html @@ -205,6 +205,44 @@ + + + + + @@ -218,8 +256,8 @@ - - + + @@ -244,7 +282,7 @@ - + @@ -321,7 +359,7 @@

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Current Projects

Brodie Lab and the Northen Lab. More information in our latest pre-print - https://doi.org/10.1101/2023.03.06.531389 (Pictures courtesy of Tamy Swenson & Brodie Lab)

-

Logo of the iPHoP tool - -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 .

Picture of Mushroom Spring in YNP - 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)

+

Logo of the iPHoP tool - +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.

+

MVP pipeline logo - +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

Illustration of viral capsids - 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)

-

MVP pipeline logo - -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

-

MVP pipeline logo - -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

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Tools

https://bitbucket.org/srouxjgi/iphop/ - https://bioconda.github.io/recipes/iphop/README.html +
  • – NEW – SpacerExtractor Identify, extract, and post-process CRISPR spacers from metagenome reads at scale - +https://code.jgi.doe.gov/SRoux/spacerextractor
  • @@ -1744,7 +1780,7 @@

    Contact

    - + 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 index ba8e068..f44c5a5 100644 --- a/index.xml +++ b/index.xml @@ -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 +0100 https://simroux.github.io/img/Capsid_logo.jpg Simon Roux diff --git a/manifest.webmanifest b/manifest.webmanifest index 39c8a2b..a1e0021 100644 --- a/manifest.webmanifest +++ b/manifest.webmanifest @@ -5,11 +5,11 @@ "theme_color": "#2962ff", "background_color": "#2962ff", "icons": [{ - "src": "/images/icon_hudcd504423819504d86a4be24c22d993f_62405_192x192_fill_lanczos_center_3.png", + "src": "/images/icon_hu9414133254159730754.png", "sizes": "192x192", "type": "image/png" }, { - "src": "/images/icon_hudcd504423819504d86a4be24c22d993f_62405_512x512_fill_lanczos_center_3.png", + "src": "/images/icon_hu14056126660657468073.png", "sizes": "512x512", "type": "image/png" }], diff --git a/pictures/HVP.png b/pictures/HVP.png new file mode 100644 index 0000000..e9b1204 Binary files /dev/null and b/pictures/HVP.png differ diff --git a/post/index.html b/post/index.html index 50544b2..609d69b 100644 --- a/post/index.html +++ b/post/index.html @@ -205,6 +205,44 @@ + + + + + @@ -216,8 +254,8 @@ - - + + @@ -311,7 +349,7 @@

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