Simon Roux

Career Trajectory

Research Cluster Map

Direct collaborators. Node size = influence, colour = community, dashed = past collaboration.

• Microbiome Science Certificate Program for workforce development and multi-omics expertise

  Journal of Microbiology and Biology Education · 2026-06-16

• Enabling the prediction of phage receptor specificity from genome data

  Figshare · 2026-04-02

• Changes to virus taxonomy, the international code of virus classification and nomenclature, and the ICTV statutes ratified by the International Committee on Taxonomy of Viruses (2025)

  Archives of Virology · 2025-12-18 · 5 citations

• Population ecology and biogeochemical implications of ssDNA and dsDNA viruses along a permafrost thaw gradient

  Nature Communications · 2025-12-11 · 2 citations

• STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies

  Nature Microbiology · 2025-12-01 · 6 citations

• A genomic atlas of the human gut virome elucidates genetic factors shaping host interactionsPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-11-02 · 13 citations

• Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes

  Nucleic Acids Research · 2025-10-29 · 9 citations

• VirJenDB: a FAIR (meta)data and bioinformatics platform for all viruses

  Nucleic Acids Research · 2025-10-23 · 2 citations

• Breaking the reproducibility barrier with standardized protocols for plant-microbiome research.

  UNC Libraries · 2025-10-09

• Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations

  NAR Genomics and Bioinformatics · 2025-10-07 · 2 citations

• Phage-mediated lysis does not determine <i>Cutibacterium acnes</i> colonization on human skinPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-09-15

• Breaking the reproducibility barrier with standardized protocols for plant–microbiome research

  PLoS Biology · 2025-09-08 · 12 citations

• A call for caution in the biological interpretation of viral auxiliary metabolic genes

  Nature Microbiology · 2025-08-27 · 27 citations

• Virus taxonomy proposal summaries: a searchable and citable resource to disseminate virus taxonomy advances

  Journal of General Virology · 2025-07-25 · 4 citations

• Viromics approaches for the study of viral diversity and ecology in microbiomes

  Nature Reviews Genetics · 2025-07-21 · 20 citations

• Tetranucleotide frequencies differentiate genomic boundaries and metabolic strategies across environmental microbiomes

  mSystems · 2025-07-08

• Gaia: An AI-enabled genomic context–aware platform for protein sequence annotation

  Science Advances · 2025-06-20 · 23 citations

• Small viruses reveal bidirectional evolution between HK97-fold viruses and encapsulins via procapsidsPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-06-19 · 2 citations

• Comparative Analysis of Phage Profiles in Environmental Samples: Metagenomic Sequencing Versus Culture-Based Isolation v2

  2025-06-19

• Planetary-scale metagenomic search reveals new patterns of CRISPR targetingPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-06-12 · 7 citations