Dana A. Opulente

The paper uses machine learning to identify genomic signatures of antifungal drug resistance in Saccharomycotina yeasts, finding that natural resistance patterns differ from clinical isolates.

MAESTRO identifies tandem paralog copy number variation as a key mechanism for stress adaptation in Pichia kudriavzevii, linking it to drug resistance and environmental tolerance.

The paper identifies genomic factors limiting Saccharomycotina fungi's ability to infect plants, finding they lack metabolic enzymes used by other phytopathogens.

The paper investigates the relationship between gene family expansions and metabolic traits in yeasts, finding that keystone gene families drive multiple metabolic innovations.

The paper analyzes gene family evolution across nearly all known Saccharomycotina yeast species, finding distinct evolutionary patterns with gene loss linked to metabolic and genomic changes.

The paper identifies three yeast lineages with reduced DNA repair genes and high evolutionary rates, showing how gene loss can lead to persistent hypermutator phenotypes.

The paper analyzes codon usage patterns across 1,154 Saccharomycotina strains, identifying biases, correlations with GC content and tRNA-ome size, and order-specific classification using machine learning.

The paper expands mitochondrial genome sampling across Saccharomycotina yeasts by extracting sequences from nuclear genome datasets, revealing trends in size, GC content, and gene presence.

The paper shows that the fungal gene ENB1, acquired from a bacterial operon, enables iron uptake in W/S clade yeasts and evolved through horizontal transfer and gene loss.

The paper shows that galactose metabolism genes can be horizontally transferred between yeast species, allowing for the reacquisition of a lost trait after millions of years.

The paper analyzes the genomic diversity and global distribution of Saccharomyces eubayanus, identifying population structure and climatically suitable regions.

The paper shows that fructophilic yeasts in the W/S clade lost and reacquired alcoholic fermentation genes via horizontal gene transfer, adapting to high sugar environments.