Skip to Main Content

Author Details

Simon Roux
DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
2011
134
45
PMIDPaper TitleJournal TitlePublished Year
36382399The IMG/M data management and analysis system v.7: content updates and new features.Nucleic Acids Res2023
37596412Counting dots or counting reads? Complementary approaches to estimate virus-to-microbe ratios.ISME J2023
37620369MArVD2: a machine learning enhanced tool to discriminate between archaeal and bacterial viruses in viral datasets.ISME Commun2023
37891627Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem.Microbiome2023
38046673Astrovirology: how viruses enhance our understanding of life in the Universe.Int J Astrobiol2023
37608068Author Correction: Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification.Nat Biotechnol2023
37024618Viruses interact with hosts that span distantly related microbial domains in dense hydrothermal mats.Nat Microbiol2023
37158954Highly diverse and unknown viruses may enhance Antarctic endoliths' adaptability.Microbiome2023
37083735iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria.PLoS Biol2023
37377419A standardized quantitative analysis strategy for stable isotope probing metagenomics.mSystems2023
37402375Long-term CRISPR locus dynamics and stable host-virus co-existence in subsurface fractured shales.Curr Biol2023
37430074Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification.Nat Biotechnol2023
36696902Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs.Cell2023
36879606Dataset of 143 metagenome-assembled genomes from the Arctic and Atlantic Oceans, including 21 for eukaryotic organisms.Data Brief2023
36780432Four principles to establish a universal virus taxonomy.PLoS Biol2023
36399502IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata.Nucleic Acids Res2023
36830574Updated Virophage Taxonomy and Distinction from Polinton-like Viruses.Biomolecules2023
36794943Giant Virus Infection Signatures Are Modulated by Euphotic Zone Depth Strata and Iron Regimes of the Subantarctic Southern Ocean.mSystems2023
34743175Viral community analysis in a marine oxygen minimum zone indicates increased potential for viral manipulation of microbial physiological state.ISME J2022
37938263Protist impacts on marine cyanovirocell metabolism.ISME Commun2022
35644779Diversity in the soil virosphere: to infinity and beyond?Trends Microbiol2022
35532161Virus-Host Interactions and Genetic Diversity of Antarctic Sea Ice Bacteriophages.mBio2022
35484634Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans.Microbiome2022
36694818Reekeekee- and roodoodooviruses, two different <i>Microviridae</i> clades constituted by the smallest DNA phages.Virus Evol2022
36692279[A better understanding of Earth's viruses thanks to metagenomes].Med Sci (Paris)2022
36778052Expanding the genomic encyclopedia of <i>Actinobacteria</i> with 824 isolate reference genomes.Cell Genom2022
36533142New <i>Microviridae</i> isolated from <i>Sulfitobacter</i> reveals two cosmopolitan subfamilies of single-stranded DNA phages infecting marine and terrestrial Alphaproteobacteria.Virus Evol2022
36069554Draft Metagenome Sequences of the <i>Sphagnum</i> (Peat Moss) Microbiome from Ambient and Warmed Environments across Europe.Microbiol Resour Announc2022
36167684Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics.Microbiome2022
35920817Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems.Elife2022
36251644Multiomics in the central Arctic Ocean for benchmarking biodiversity change.PLoS Biol2022
32929206Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber.ISME J2021
36765102iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology.ISME Commun2021
33522966VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses.Microbiome2021
33622857Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities.mSystems2021
34752450Diversity, taxonomy, and evolution of archaeal viruses of the class Caudoviricetes.PLoS Biol2021
34781105Perspective on taxonomic classification of uncultivated viruses.Curr Opin Virol2021
34531387The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole.Nat Commun2021
34132786efam: an expanded, metaproteome-supported HMM profile database of viral protein families.Bioinformatics2021
34184913Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance.mSystems2021
34348151Virus-associated organosulfur metabolism in human and environmental systems.Cell Rep2021
34126465Global overview and major challenges of host prediction methods for uncultivated phages.Curr Opin Virol2021
34178438Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation.PeerJ2021
33981030Extreme dimensions - how big (or small) can tailed phages be?Nat Rev Microbiol2021
34006627DOE JGI Metagenome Workflow.mSystems2021
34031405Ecology and molecular targets of hypermutation in the global microbiome.Nat Commun2021
33947809Correction for Vangay et al., "Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities".mSystems2021
34281625Glacier ice archives nearly 15,000-year-old microbes and phages.Microbiome2021
33972727Viruses infecting a warm water picoeukaryote shed light on spatial co-occurrence dynamics of marine viruses and their hosts.ISME J2021
34108477Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages.Nat Commun2021
  • 1 - 50 of 134

Recommended Authors

University of Michigan ann arbor
Career Start Year 2016
Number of shared co-authors 1
Lawrence Livermore National Laboratory
Career Start Year 2015
Number of shared co-authors 2
Yale School of Medicine, USA Instituto Todos pela Saude
Career Start Year 2013
Number of shared co-authors 0
University of California berkeley
Career Start Year 2013
Number of shared co-authors 2
Los Alamos National Laboratory
Career Start Year 2012
Number of shared co-authors 17
Los Alamos National Laboratory
Career Start Year 2009
Number of shared co-authors 19
University of Geneva Medical School
Career Start Year 2007
Number of shared co-authors 2
Broad Institute of MIT and Harvard
Career Start Year 2004
Number of shared co-authors 8
University of Colorado Denver.
Career Start Year 2004
Number of shared co-authors 8
Computational Biology of Infection Research, Helmholtz Centre for Infection Research
Career Start Year 2003
Number of shared co-authors 10
Scripps Institution of Oceanography, University of California San Diego
Career Start Year 2003
Number of shared co-authors 21
University of California San Diego
Career Start Year 2001
Number of shared co-authors 0
University of Exeter
Career Start Year 2000
Number of shared co-authors 0
Chemistry Institute, Universidade de Sao Paulo - USP
Career Start Year 2000
Number of shared co-authors 7
Mayo Clinic
Career Start Year 2000
Number of shared co-authors 2
Institute of Infection, University of Liverpool
Career Start Year 2000
Number of shared co-authors 2
University of Birmingham
Career Start Year 1998
Number of shared co-authors 1
University of Central Florida
Career Start Year 1998
Number of shared co-authors 8
Center for Genomics and Bioinformatics, Indiana University
Career Start Year 1998
Number of shared co-authors 6
Institute of Biology, University of Neuchatel
Career Start Year 1998
Number of shared co-authors 4
New England Biolabs Inc.
Career Start Year 1998
Number of shared co-authors 5
Center for Cancer Research, National Cancer Institute, National Institutes of Health
Career Start Year 1997
Number of shared co-authors 3
National Institute of Allergy and Infectious Diseases, National Institutes of Health
Career Start Year 1996
Number of shared co-authors 3
Institute for Artificial Intelligence, University of Duisburg-Essen
Career Start Year 1996
Number of shared co-authors 24
J. Craig Venter Institute, 9605 Medical Center Drive
Career Start Year 1995
Number of shared co-authors 10
Pacific Northwest National Laboratory
Career Start Year 1993
Number of shared co-authors 11
NIOZ Royal Netherlands Institute for Sea Research
Career Start Year 1993
Number of shared co-authors 9
Sydney Institute for Infectious Diseases, The University of Sydney
Career Start Year 1991
Number of shared co-authors 3
University of California-San Francisco
Career Start Year 1991
Number of shared co-authors 2
McLean Hospital
Career Start Year 1988
Number of shared co-authors 20

Collaborators

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
Co-authored papers 40
Co-authored papers 28
DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
Co-authored papers 18
Co-authored papers 17
DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
Co-authored papers 17
Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory
Co-authored papers 17
DOE Joint Genome Institute
Co-authored papers 10
University of Wurzburg
Co-authored papers 8
National Institute of Allergy and Infectious Diseases, National Institutes of Health
Co-authored papers 6
The University of Arizona
Co-authored papers 5
Lawrence Berkeley National Laboratory
Co-authored papers 5
University of California-Riverside
Co-authored papers 4
US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory
Co-authored papers 4
Co-authored papers 4
University of Maryland School of Medicine, Institute for Genome Sciences
Co-authored papers 3
Lawrence Berkeley National Laboratory
Co-authored papers 3
Co-authored papers 3
Co-authored papers 3
Lawrence Berkeley National Laboratory
Co-authored papers 3
KU Leuven - University of Leuven
Co-authored papers 3
Lawrence Berkeley National Laboratory
Co-authored papers 3
Co-authored papers 3
US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory
Co-authored papers 3
Oak Ridge National Laboratory
Co-authored papers 2
Innovative Genomics Institute, University of California berkeley
Co-authored papers 2
Institut Francois Jacob, CNRS, Universite Paris-Saclay
Co-authored papers 2
Pacific Northwest National Laboratory
Co-authored papers 2
European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 2
University of Minnesota
Co-authored papers 2
Co-authored papers 2