Ryan Cook

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

The paper identifies genomic markers in Salmonella isolates that correlate with infection risk, showing lineage-specific associations and a conserved prophage marker in Salmonella Agona.

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.

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.

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