Simon Roux

The paper analyzes CRISPR spacers from metagenomic data to reveal patterns of CRISPR targeting across Earth's biomes, identifying selection pressures and non-host phage interactions.

VHAMSTeR predicts viral host associations across five categories using genomic language models and biological features, outperforming existing methods and uncovering new RNA bacteriophages.

This study identifies host factors critical for ssRNA and ssDNA phage infection in E. coli, revealing conserved dependencies and lineage-specific requirements.

PhageTAILor uses LightGBM on 74 detector features to flag prophages and bacterial phage tail-like elements (tailocins, T6SS, eCIS), recovering 12 of 13 validated tailocins under leave-one-genus-out.

This paper constructs a phage-bacteria interaction atlas for Klebsiella pneumoniae and develops a genome-guided machine learning model to predict phage-host interactions, outperforming traditional methods.

The paper analyzes viral diversity and functional potential in polar and subarctic sea ice metagenomes, identifying common auxiliary metabolic genes and host interactions.

This paper organizes a community challenge to develop automated virus taxonomy classification tools and evaluates their performance on a combined dataset of expert-curated and metagenomic sequences.

The paper analyzes mobile genetic elements in thawing permafrost soils to assess their impact on microbial diversity and function using meta-omic data.

This study uses SIP-viromics to distinguish newly produced from persistent virions in soil, revealing that most virions persist without replication, linked to dominant bacterial groups.

The paper develops a genome-based framework to predict bacteriophage infectivity against diverse Pseudomonas aeruginosa strains using machine learning and experimental data.

The paper predicts phage receptor specificity from genome data using large-scale genetic screens and machine learning, achieving high accuracy for E. coli phages.

The paper analyzes the gut virome in mother-infant pairs to identify factors influencing its development and persistence, finding that delivery mode and breastmilk shape the infant virome and that viral diversity is linked to food allergies.

The paper analyzes genomic and metagenomic data to identify novel carbonic anhydrase clades, their diversity, and biome-specific distribution across microbial taxa.

The paper presents a global virome atlas, UHGV, and identifies genomic factors influencing phage-host interactions.

The paper investigates the role of phage-mediated selection in shaping Cutibacterium acnes populations on human skin and finds weak phage pressure due to physical barriers limiting phage exposure.

The paper establishes reproducible methods for plant-microbiome research using fabricated ecosystems across multiple laboratories.

The paper develops a tool to analyze tetranucleotide frequencies in metagenomes, revealing environmental-specific microbial community patterns and metabolic trends across 12,000 samples.

The paper investigates the evolutionary relationship between HK97-fold viruses and encapsulins, finding bidirectional transitions through procapsids.

The paper compares sequence search tools for detecting CRISPR spacer-target interactions and finds significant differences in their performance.

The paper isolates Acidobacteriota viruses from Arctic tundra soils and analyzes metagenome-assembled viral genomes to characterize their diversity and potential interactions with host bacteria.

This study investigates how plant-bacteria-phage interactions affect nitrogen acquisition and exometabolite composition by comparing phage-lysed and uninfected bacterial necromass.

The paper describes a high-resolution microbial metagenome dataset collected over 22 days during a phytoplankton bloom cycle, including gene abundances and time-matched environmental data.

Gaia enables context-aware protein sequence search in microbial genomes by integrating sequence, structure, and genomic context information, improving annotation of functionally related genes.

The paper analyzes the gut mobilome in mother-infant dyads, finding increased infant mobilome richness over time, formula feeding effects, and antibiotic resistance gene presence in plasmids.

The Open MetaGenomic (OMG) corpus combines 3.1T base pairs and 3.3B protein coding sequences in mixed amino-acid and nucleotide format to pretrain the genomic language model gLM2.

geNomad identifies and annotates mobile genetic elements in sequencing data, discovering millions of new viruses and plasmids in public metagenomes.

The paper expands the global RNA virome by five-fold, identifying new clades of RNA bacteriophages and revealing novel virus-host interactions.

The paper presents a gold-standard dataset of manually curated bacterial genomes and a framework to evaluate prophage prediction algorithms, showing their performance metrics across seven tools.

The paper describes a metagenome processing workflow that includes assembly, annotation, and binning, and provides tools for researchers to apply it to their data.

CheckV estimates completeness of metagenome-assembled viral contigs against GenBank plus 76,262 metagenome-derived complete genomes and trims host flanks; 86.9% of IMG/VR contigs were low-quality.