Johanna L. Rhodes

The paper analyzes genome variation in Sporothrix species to understand their evolutionary strategies and drug resistance mechanisms.

This paper quantifies gene gain and loss dynamics in Aspergillus fumigatus over a century using a global pangenome, revealing slow genome evolution and lineage-specific resistance mechanisms.

The paper isolates Candida auris from Antarctica, identifies cold-adapted traits, and links mutator phenotypes to rapid evolution and drug resistance in global C. auris clades.

This study analyzes 12,644 whole genome sequences of Candida auris from 1997-2024 to reveal global epidemiology, drug resistance patterns, and genomic variation across income levels.

This study profiles gene expression in Candida auris infections using a fish model, identifying clade-specific filamentation and upregulation of xenosiderophore transporter genes.

The paper curates AMR mutations in fungi to create FungAMR, identifies universal resistance mutations, and provides a tool to screen genomes for AMR mutations.

The paper characterizes a persistent, azole-resistant C. parapsilosis strain responsible for a hospital outbreak, identifying genetic mutations linked to antifungal resistance.

The paper identifies terbinafine-resistant Trichophyton indotineae isolates globally, finds high genetic similarity and resistance linked to SQLE mutations, and suggests alternative resistance mechanisms.

This study identifies genetic and metabolic adaptations in pan-drug resistant Candida auris strains that enable resistance without fitness costs.

This study uses genomic data to trace the introduction and transmission of Candida auris in the UK between 2014 and 2019, identifying at least three introductions and multiple transmission events.

HMMploidy infers ploidy levels from short-read sequencing data, outperforming existing methods at low-depth with large sample sizes and revealing aneuploidy in Cryptococcus neoformans.

The paper uses population genomics to trace the evolution and environmental acquisition of drug-resistant Aspergillus fumigatus, finding evidence of resistant isolates transmitted from the environment to patients.

This study compares the transcriptional responses of four C. gattii lineages to macrophages, identifying lineage-specific gene expression patterns and pathogenicity-related processes.

This study analyzes the population genomics of Cryptococcus neoformans var. grubii, revealing hybridization, biogeographic relationships, and genetic structure across global isolates.

The paper uses whole-genome sequencing to determine whether recurrent cryptococcal meningitis in HIV patients results from relapse or reinfection, finding clonal relationships in most cases and novel hypermutator mechanisms in others.