World's Best Scientists 2026 revealed!

D-Index & Metrics

Biology and Biochemistry

D-Index
76
Citations
29597
World Ranking
4945
National Ranking
2375

Overview

Simon Roux is affiliated with the Lawrence Berkeley National Laboratory in the United States. Their research primarily spans the fields of Environmental Science and Biochemistry, Genetics and Molecular Biology, contributing extensively to subfields such as Ecology, Molecular Biology, Plant Science, Endocrinology, and Microbiology.

The scientist's work covers several core topics including:

  • Bacteriophages and microbial interactions
  • Genomics and Phylogenetic Studies
  • Microbial Community Ecology and Physiology
  • Plant Virus Research Studies
  • Plant and Fungal Interactions Research
  • Protist diversity and phylogeny
  • Environmental DNA in Biodiversity Studies

Simon Roux has published numerous papers in various peer-reviewed journals. Among the recent publications are:

  • CheckV assesses the quality and completeness of metagenome-assembled viral genomes, 2020, Nature Biotechnology
  • VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses, 2021, Microbiome
  • DRAM for distilling microbial metabolism to automate the curation of microbiome function, 2020, Nucleic Acids Research
  • A genomic catalog of Earth's microbiomes, 2020, Nature Biotechnology
  • Identification of mobile genetic elements with geNomad, 2023, Nature Biotechnology

The scientist frequently publishes in the following venues:

  • bioRxiv (Cold Spring Harbor Laboratory)
  • mSystems
  • Microbiology Resource Announcements
  • Microbiome
  • Nucleic Acids Research

Among their frequent coauthors are Emiley A. Eloe-Fadrosh, Nikos C. Kyrpides, Natalia Ivanova, T. B. K. Reddy, and Marcel Huntemann, reflecting collaboration within a network of researchers active in similar fields.

Best Publications

  • CheckV assesses the quality and completeness of metagenome-assembled viral genomes.

    Stephen Nayfach;Antonio Pedro Camargo;Frederik Schulz;Emiley Eloe-Fadrosh

  • Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study

    Dae Wook Kang;James B. Adams;Ann C. Gregory;Ann C. Gregory;Thomas Borody

  • VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses.

    Jiarong Guo;Ben Bolduc;Ahmed A. Zayed;Arvind Varsani;Arvind Varsani

  • Determinants of community structure in the global plankton interactome

    Gipsi Lima-Mendez;Karoline Faust;Nicolas Henry;Johan Decelle

  • VirSorter: mining viral signal from microbial genomic data

    Simon Roux;Francois Enault;Bonnie L. Hurwitz;Matthew B. Sullivan

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

    Ho Bin Jang;Benjamin Bolduc;Olivier Zablocki;Jens H. Kuhn

  • A genomic catalog of Earth’s microbiomes

    Stephen Nayfach;Simon Roux;Rekha Seshadri;Daniel Udwary

  • Plankton networks driving carbon export in the oligotrophic ocean.

    Lionel Guidi;Samuel Chaffron;Lucie Bittner;Damien Eveillard

  • Marine DNA Viral Macro- and Microdiversity from Pole to Pole.

    Ann C. Gregory;Ahmed A. Zayed;Nádia Conceição-Neto;Ben Temperton

  • Patterns and ecological drivers of ocean viral communities

    Jennifer R. Brum;J. Cesar Ignacio-Espinoza;Simon Roux;Guilhem Doulcier;Guilhem Doulcier

  • Minimum information about an uncultivated virus genome (MIUVIG)

    Simon Roux;Evelien M. Adriaenssens;Bas E. Dutilh;Eugene V. Koonin

  • DRAM for distilling microbial metabolism to automate the curation of microbiome function

    Michael Shaffer;Mikayla A. Borton;Bridget B. McGivern;Ahmed A. Zayed

  • Host-linked soil viral ecology along a permafrost thaw gradient

    Joanne B. Emerson;Joanne B. Emerson;Simon Roux;Simon Roux;Jennifer R. Brum;Jennifer R. Brum;Benjamin Bolduc

  • Viral dark matter and virus-host interactions resolved from publicly available microbial genomes

    Simon Roux;Steven J Hallam;Tanja Woyke;Matthew B Sullivan

  • Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

    Guillem Salazar;Lucas Paoli;Adriana Alberti;Jaime Huerta-Cepas

  • The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities

    I-Min A Chen;Ken Chu;Krishnaveni Palaniappan;Anna Ratner

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

    François Enault;Arnaud Briet;Léa Bouteille;Simon Roux

  • Plankton networks driving carbon export in the oligotrophic ocean

    Lionel Guidi;Samuel Chaffron;Lucie Bittner;Damien Eveillard

  • DRAM for distilling microbial metabolism to automate the curation of microbiome function

    M. Shaffer;M. A. Borton;B. B. McGivern;A. A. Zayed

  • Author response: Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

    Simon Roux;Steven J Hallam;Tanja Woyke;Matthew B Sullivan

Frequent Co-Authors

Matthew B. Sullivan
Matthew B. Sullivan The Ohio State University
Nikos C. Kyrpides
Nikos C. Kyrpides Joint Genome Institute
Natalia Ivanova
Natalia Ivanova Lawrence Berkeley National Laboratory
Mart Krupovic
Mart Krupovic Université Paris Cité
Patrick Wincker
Patrick Wincker University of Paris-Saclay
Alicia Clum
Alicia Clum Joint Genome Institute
Tanja Woyke
Tanja Woyke Joint Genome Institute
Shinichi Sunagawa
Shinichi Sunagawa Swiss Institute of Bioinformatics
Stephane Pesant
Stephane Pesant University of Bremen
Marc Picheral
Marc Picheral Université Paris Cité

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