Rhys A. Farrer

This study identifies three hybrid groups in Cryptococcus neoformans with genomic features indicative of parasexual reproduction, including LOH, aneuploidy, and haploid recombinants.

The paper analyzes the genomic distribution of genes encoding secretion signals across eukaryotic genomes and finds they are enriched in regions with long flanking intergenic regions and specific repeat patterns.

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 identifies FKS1/2-variant independent mechanisms of echinocandin resistance in Candida auris through genomic and phenotypic analysis of clinical isolates.

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 shows how lineage-specific trait variation in an amphibian parasite leads to different coexistence and competitive exclusion dynamics in Europe and Africa.

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

The paper presents a near-complete telomere-to-telomere genome assembly for B. dendrobatidis JEL423, revealing gene family expansions and contractions.

This study introduces the thermotolerant Arabian killifish as a new model to assess C. albicans virulence at human-relevant temperatures, showing temperature-dependent virulence and drug response.

DIAMOND2GO rapidly assigns Gene Ontology terms to genes or proteins using sequence similarity searches and enables enrichment analysis for over-represented terms in novel sequence sets.

The paper identifies two-speed genome evolution in fungal pathogens, where virulence-related genes are enriched in repeat-rich regions while core genes are in repeat-poor regions.

The paper analyzes genome assemblies and RNA-Seq data from Candida auris and related species to identify genomic features associated with drug resistance, mating potential, and virulence.

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 mutations in Candida albicans during microevolution, finding that de novo substitutions and LOH events drive short-term evolution, while purifying selection is strong during host infection.

The paper develops and evaluates non-lethal protocols for isolating chytrid fungi from amphibians, showing their global application and effectiveness in recovering fungal isolates.