Rachel J. Whitaker

This study analyzes 450 Pseudomonas aeruginosa isolates from CF patients to show structured population dynamics, migration, and parallel adaptive evolution within lung infections.

This study compares the genomic adaptations of Acinetobacter baumannii strains in Mexico before and during the COVID-19 period using whole-genome sequencing, revealing increased resistance genes, virulence factors, and mobilome elements.

This study shows that inducing lysogen populations of Pseudomonas aeruginosa increases adaptive mutation diversity compared to non-lysogens under antibiotic stress.

The paper examines how ecological and evolutionary processes interact to cause mutualism breakdown between legumes and rhizobia over 33 years of nitrogen fertilization.

The paper analyzes recombination patterns in Sulfolobus islandicus by sequencing recombinant strains and using a new tool to identify breakpoints, revealing uniform recombination rates and short tract preferences.

This study shows how mobile genetic elements synergistically drive the stepwise accumulation of antibiotic resistance genes in plasmids, proposing a framework to predict and surveil multidrug resistance.

The paper analyzes plasmid transmission dynamics in Rhizobium leguminosarum, finding variation in plasmid types and their association with partner quality decline due to nitrogen fertilization.

The paper analyzes CRISPR-Cas system variation in Bombella apis strains and identifies spacer interactions with mobile elements across honey bee microbiome members.

The paper examines how host competitive asymmetries affect viral evolution in a co-evolutionary system, finding that they extend viral extinction times and accelerate adaptation.

This study identifies and characterizes chromosomal integration sites in Sulfolobus islandicus using CRISPR-COPIES and validates their utility for genetic manipulation.

The paper introduces CCTK, a toolkit for analyzing CRISPR array diversity, including tools for identifying arrays, visualizing similarities, and inferring phylogenetic trees.

This study investigates the role of S-layer genes in Sulfolobus islandicus, revealing that slaA is critical for cell morphology, division, and chromosome stability.