Chris Todd Hittinger

The paper investigates the evolutionary origins of protein novelty in Saccharomycotina yeasts, identifying two distinct modes of de novo and divergent gene evolution and their structural implications.

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

The paper expands a previous finding of a correlation between glucose uptake rates and cell surface area-to-volume ratio across 11 yeast species to 282 species, finding additional correlations with genome size and growth rate.

The paper identifies convergent evolution of aerobic fermentation in yeasts through divergent genetic mechanisms affecting shared glycolytic genes.

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.

The paper identifies proto-point centromeres in Saccharomycodales yeast, showing they evolved from retrotransposon LTRs, supporting the hypothesis that point centromeres originated from ancestral retrotransposons.

The paper discovers three novel ancient whole genome duplications in Saccharomycotina yeasts, suggesting WGD may be more common in fungi than previously thought.

This study shows that host-shift adaptation in S. eubayanus leads to genomic changes, particularly structural variants, linked to sugar metabolism and host-specific traits.

The paper examines filamentation morphology evolution in Saccharomycotina yeasts using integrated genomic, metabolic, and environmental data from 1,154 strains, finding that filamentation is common and linked to phylogeny and environmental factors.

This study evolved Spathaspora passalidarum to produce ethanol from lignocellulosic hydrolysates by improving tolerance to inhibitors like acetic acid.

The paper identifies allelic variation in MAL33 as a driver of ecological adaptation in maltose metabolism among Saccharomyces eubayanus strains.

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.

This study uses machine learning to identify gene families associated with oxidative stress resistance in yeasts and validates their roles experimentally.

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.

This study shows that adjusting pH and using SAA pretreatment improves biofuel production from drought-switchgrass hydrolysates.

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 investigates how specialization in yeast sugar transporters restricts evolutionary paths by analyzing sequence-function relationships and evolutionary history.

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

This study identifies convergent evolution in cacti-associated yeasts using genomic and phenotypic data, finding thermotolerance and horizontal gene transfer as key adaptive traits.

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 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 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 ploidy reduction in yeast populations evolved for maltose utilization is driven by an interaction between cell type and metabolism, with haploid-like transcriptional programs conferring fitness advantages.

This study uses whole genome sequencing and phenotyping to analyze 77 C. tropicalis isolates, identifying hybrid lineages and a genomic variant affecting nitrogen utilization.

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.

CRISpy-pop designs and predicts CRISPR/Cas9 guide RNA activity across diverse yeast and bacterial strains, including human genome cross-referencing for biosafety.

The paper constructs six-species synthetic yeast hybrids and shows they are chromosomally unstable but can rapidly adapt to novel environments.

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