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List of works by Simon Roux

A Viral Ecogenomics Framework To Uncover the Secrets of Nature's "Microbe Whisperers"

scientific article published on 14 May 2019

A high-throughput sequencing ecotoxicology study of freshwater bacterial communities and their responses to tebuconazole.

scientific article published on 15 September 2014

A viral reckoning: Viruses emerge as essential manipulators of global ecosystems

article

Analysis of metagenomic data reveals common features of halophilic viral communities across continents

scientific article

Assessment of viral community functional potential from viral metagenomes may be hampered by contamination with cellular sequences.

scientific article published on 11 December 2013

Author Correction: Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth's biomes

scientific article published on 01 March 2020

Benchmarking viromics: An in silico evaluation of metagenome-enabled estimates of viral community composition and diversity

article

Best Practices for Successfully Writing and Publishing a Genome Announcement in Microbiology Resource Announcements ⬇️

scientific article published on 03 September 2020

Characteristics of Wetting-Induced Bacteriophage Blooms in Biological Soil Crust

scientific article published on 17 December 2019

Chimeric viruses blur the borders between the major groups of eukaryotic single-stranded DNA viruses

scientific article

Comparison of 16S rRNA and protein-coding genes as molecular markers for assessing microbial diversity (Bacteria and Archaea) in ecosystems.

scientific article

Correction for Vangay et al., “Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities”

scientific article published in 2021

Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales

article published in the Proceedings of the National Academy of Sciences of the United States of America

Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth's biomes

scientific article published on 22 July 2019

Diversity and comparative genomics of Microviridae in Sphagnum- dominated peatlands

scientific article

Diversity, taxonomy, and evolution of archaeal viruses of the class Caudoviricetes

scientific article published on 09 November 2021

Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics

scientific article published on 11 October 2017

Ecological Assembly Processes Are Coordinated between Bacterial and Viral Communities in Fractured Shale Ecosystems

scientific article published on 17 March 2020

Ecology and molecular targets of hypermutation in the global microbiome

scientific article published on 24 May 2021

Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads

scientific article

Future-Proofing Your Microbiology Resource Announcements Genome Assembly for Reproducibility and Clarity

scientific article published on 05 September 2019

Genomic characteristics and environmental distributions of the uncultivated Far-T4 phages

scientific article

Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments

scientific article

Host population diversity as a driver of viral infection cycle in wild populations of green sulfur bacteria with long standing virus-host interactions

scientific article published on 15 January 2021

IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata

scientific article published in 2022

Illuminating structural proteins in viral "dark matter" with metaproteomics

scientific article

Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem

article

Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials

scientific article published on 16 October 2019

Metagenomic characterization of viral communities in corals: mining biological signal from methodological noise.

scientific article published on 24 February 2015

Metavir 2: new tools for viral metagenome comparison and assembled virome analysis

scientific article

Microbial metagenomes and metatranscriptomes during a coastal phytoplankton bloom

scientific article published on 22 July 2019

Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities

scientific article published on 22 February 2021

Microbiomes of Velloziaceae from phosphorus-impoverished soils of the campos rupestres, a biodiversity hotspot

scientific article published on 31 July 2019

Minimum Information about an Uncultivated Virus Genome (MIUViG)

scientific article published on 17 December 2018

Numerous cultivated and uncultivated viruses encode ribosomal proteins

scientific article published in Nature Communications

Perspective on taxonomic classification of uncultivated viruses

Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses

scientific article published on 21 June 2016

Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters

scientific article published on 16 November 2020

Regulation of infection efficiency in a globally abundant marine Bacteriodetes virus.

scientific article published on 17 May 2016

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

scientific article published on 06 May 2019

The International Virus Bioinformatics Meeting 2020

scientific article published on 06 December 2020

Updated Virophage Taxonomy and Distinction from Polinton-like Viruses

scientific article published in 2023

VirSorter: mining viral signal from microbial genomic data

scientific article published on 28 May 2015

Viral community analysis in a marine oxygen minimum zone indicates increased potential for viral manipulation of microbial physiological state

scientific article published on 06 November 2021

Virus-Host Interactions and Genetic Diversity of Antarctic Sea Ice Bacteriophages

scientific article published on 09 May 2022

Viruses infecting a warm water picoeukaryote shed light on spatial co-occurrence dynamics of marine viruses and their hosts

scientific article published on 11 May 2021

iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure

scientific article

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