Laura K. Inglis

Prophages as a source of antimicrobial resistance genes in the human microbiome

The paper analyzes 15,000 bacterial genomes to investigate the presence of antimicrobial resistance (AMR) genes in prophages across human body sites and regions, finding diverse AMR genes associated with prophages.

Sphae: An automated toolkit for predicting phage therapy candidates from sequencing data

Sphae is a bioinformatics pipeline that rapidly assesses phage therapeutic potential by analyzing genomic markers for safety and efficacy in under ten minutes.

Phables: from fragmented assemblies to high-quality bacteriophage genomes

Phables improves phage genome recovery from fragmented viral metagenome assemblies, recovering more high-quality genomes and resolving variants with high nucleotide identity.

Prophage rates in the human microbiome vary by body site and host health.

The paper analyzes prophage DNA in human microbiome bacterial genomes, showing site- and health-related variations in prophage content and its impact on bacterial growth and microbiome structure.

The Promise and Pitfalls of Prophages

The paper quantifies the benefits and costs of prophages in bacterial genomes, showing uniform prophage density and estimating their energetic contribution.

Philympics 2021: Prophage Predictions Perplex Programs

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.