John F. Wolters

Functional diversification across yeast lineages of the nucleus-vacuole junction forming protein Nvj1

The paper identifies Nvj1 orthologs across diverse yeast lineages and shows functional divergence in NVJ formation and sequence motifs.

Machine learning identifies novel signatures of antifungal drug resistance in Saccharomycotina yeasts

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.

Genomic factors limiting the diversity of Saccharomycotina plant pathogens

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

Convergent expansions of keystone gene families drive metabolic innovation in a major eukaryotic clade

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

Unique trajectory of gene family evolution from genomic analysis of nearly all known species in an ancient yeast lineage

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.

Stable hypermutators revealed by the genomic landscape of DNA repair genes among yeast species

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.

Comparative modeling reveals the molecular determinants of aneuploidy fitness cost in a wild yeast model

The paper quantifies the fitness cost of aneuploidy in yeast by analyzing chromosome duplications and identifies gene length as a key determinant of toxicity.

Genomic factors shaping codon usage across the Saccharomycotina subphylum

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.

Mitochondrial Genome Diversity across the Subphylum Saccharomycotina

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.