Evelien M. Adriaenssens

The paper introduces PHORAGER, a pipeline for identifying prophages in bacterial genomes, and reports the discovery of 23,132 putative prophages in ESKAPE pathogens.

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.

This study examines the impact of a bacteriophage cocktail on healthy gut microbiota using an in vitro human colon model, finding minimal disruption with specific effects on Escherichia coli.

The paper compares INPHARED database snapshots from 2021 to 2026, showing growth in phage genomes but reduced novel species diversity and persistent host bias.

The paper introduces vConTACT3, a machine learning tool that improves virus taxonomy classification, scalability, and accuracy, and identifies taxonomic issues across the virosphere.

This study analyzes prophages and defense systems in Bifidobacterium genomes to reveal co-evolutionary 'arms race' dynamics between bacteria and phages.

The paper examines bacteriophage diversity in COPD patients and finds it declines with disease severity, showing disrupted viral-bacterial relationships in those with frequent exacerbations.

The paper analyzes the dairy cow gut virome across life stages, finding distinct viral communities and identifying phages targeting methanogens.

GRAViTy-V2 classifies viruses using whole-genome analysis, achieving taxonomic accuracy comparable to expert-curated classifications down to the family level.

The paper classifies Lak megaphages into a new viral order, Grandevirales, based on protein and nucleotide analyses, revealing their unique genetic code and evolutionary relationships.

The paper compares Illumina and Oxford Nanopore sequencing for viral genome recovery from human gut samples, finding Illumina better for resolved genomes and hybrid approaches better for diversity.

The paper introduces MANIAC, a tool for estimating ANI and AF in viral genomes, revealing an ANI gap in bacterial dsDNA viruses and showing its predictive power for taxonomy.

The paper predicts stop codon reassignment in bacteriophage genomes to improve functional annotation, showing significant increases in gene length and coding density.

MetaPhage is a pipeline that automates the analysis, annotation, and classification of bacteriophages in metagenomics data, providing a comprehensive report and interactive visualization.

The paper uses shotgun metagenomics to analyze equine fecal samples, revealing taxonomic and functional diversity in the horse gut microbiome, including novel bacterial genera and species.

CoronaHiT is a method for high-throughput SARS-CoV-2 genome sequencing that improves coverage and throughput compared to existing protocols.

This study constructs a phylogenetic tree of 131 S. Typhimurium strains to reveal population structure and adaptation to domesticated and wild animal hosts.

This paper introduces vConTACT 2.0, a network-based tool for prokaryotic virus taxonomy that scales to large datasets and achieves high accuracy in taxonomic assignments.