Claire Chewapreecha

This study tracks the 28-year evolution of a Burkholderia pseudomallei strain in sterile water, identifying genetic changes and metabolic adaptations to nutrient-depletion.

This study uses deep sequencing to analyze pneumococcal genetic diversity in infants and mothers, revealing transmission patterns and treatment impacts on resistant strains.

The paper evaluates GWAS methods for detecting antibiotic resistance in Staphylococcus aureus genomes, finding they identify novel resistance mutations but are less accurate than literature-based approaches.

This paper introduces SpydrPick, a model-free method to detect co-selection and epistasis in bacterial genomes, revealing both known and novel targets in human pathogens.

This paper introduces genomeDCA, a statistical method to identify epistatic interactions in Streptococcus pneumoniae genomes, revealing networks of resistance, virulence, and core genes.

The paper analyzes genetic data to show that pneumococcal capsule recombination generates novel serotypes, highlighting risks for vaccine efficacy.

This paper introduces SEER, a statistical method to identify sequence elements associated with bacterial phenotypes, demonstrating its application in discovering antibiotic resistance and invasiveness factors in Streptococcus species.