David L. Gally

Integrating bacterial and viral genomic information enhances and extends the machine learning predictions of bacteriophage activity against pathogenic Escherichia coli

This paper develops a machine learning model that integrates bacterial and viral genomic data to predict phage activity against E. coli, improving prediction accuracy by incorporating phage gene content.

Benchmarking nanopore-based strategies for antimicrobial resistance prediction

This study benchmarks in silico AMR prediction tools using nanopore data, finding that assembly strategy and data volume impact accuracy, but no tool perfectly matches lab-based AST results.

Analysis of a detoxified Escherichia coli strain for bacteriophage production

This paper evaluates the use of an endotoxin-reduced E. coli strain for phage production, showing it can generate diverse phage with low endotoxin and minimal downstream processing.

Quorum sensing and capsule expression enable subpopulation evasion of phage killing in Escherichia coli ST131: Implications for targeted therapy

This study identifies mechanisms by which E. coli ST131 evades phage killing through quorum sensing and capsule expression, and develops a phage therapy strategy to overcome these defenses in urine-based conditions.

Phage-encoded sRNA counteracts xenogenic silencing in pathogenic E. coli

The paper identifies a prophage-encoded sRNA, HnrS, that counteracts xenogenic silencing by repressing Hha, enabling virulence gene expression in E. coli.

Genome Analyses of A Worldwide Multisource Collection of Klebsiella variicola Reveal Adaptation Relevant for Human Infection

This study analyzes the genome of Klebsiella variicola from diverse sources to identify genetic adaptations linked to human infection.

Comparison of Shiga toxin-encoding bacteriophages in highly pathogenic strains of Shiga toxin-producing Escherichia coli O157:H7 in the UK.

The paper compares stx2a-encoding prophages in UK STEC O157:H7 sub-lineages, finding high diversity and independent acquisition, while stx2c-encoding prophages show vertical inheritance.