Breck A. Duerkop

TrIdent automates transductomics analysis by identifying DNA mobilized by virus-like particles, showing high agreement with manual classifications and revealing enriched bacterial families in murine gut transductomes.

The paper develops a bioinformatic pipeline using small serine recombinases to identify antiphage defense systems in bacterial genomes and metagenomes, finding they are genetically linked to these systems.

The paper analyzes the murine gut transductome before and after perturbations to identify bacterial families and mobile genetic elements involved in horizontal gene transfer.

This study identifies chemical inhibitors that block a bacterial immune system, enhancing phage therapy efficacy against resistant strains.

This study identifies sagA mutations in E. faecium that cause cell envelope defects, increasing antibiotic susceptibility and phage sensitivity.

The paper identifies a prophage-encoded sRNA, svsR, that reduces lytic phage infection in AIEC by repressing maltodextrin transport genes, thereby limiting phage receptor expression.

This study identifies pseudo-pac site sequences in Salmonella genomes that enable P22 phage to initiate generalized transduction, using bioinformatics analysis of sequencing data.

The paper develops a metagenomics pipeline to study insertion sequence (IS) elements in the microbiota, revealing their role in bacterial genome diversification and adaptation.

The paper investigates how Enterococcus faecalis protease GelE affects phage infection, finding that its reduction increases phage susceptibility and alters biofilm formation.