Joseph Schacherer

The paper analyzes allopolyploidization events in Brettanomyces bruxellensis using graph pangenomes to identify structural variants and their functional impacts.

The paper investigates nitrate assimilation in B. bruxellensis lineages using genomic and phenotypic data, finding it is widespread but unevenly distributed and influenced by gene copy number and functionality.

The paper develops a barcoded yeast collection to map genotype-phenotype relationships across genetic diversity, revealing genetic variants linked to chemical responses.

This study shows that high initial fitness is necessary but not sufficient for long-term success in yeast, as adaptive mutations can override small fitness differences.

This study uses whole-genome sequencing to analyze 145 Lachancea thermotolerans strains, revealing genetic and phenotypic adaptations to the winemaking environment.

The paper analyzes 3,034 Saccharomyces cerevisiae genomes to characterize population structure, revealing 93% species diversity and ecological clustering patterns.

The paper identifies yeast strains with enhanced recombinant laccase production and characterizes genetic factors contributing to this trait.

The paper analyzes the pan-transcriptome of yeast isolates to show that accessory genes significantly contribute to gene expression variation across populations.

The paper quantifies proteomic effects of aneuploidy in natural yeast isolates, finding chromosome-wide dosage compensation in the proteome but not transcriptome.

The paper quantifies transcriptomes and proteomes across 942 yeast isolates, showing weak correlation between mRNA and protein levels and distinct genetic control mechanisms.

The paper uses a diallel panel of yeast hybrids to show low-frequency SNPs have a larger impact on gene expression than common SNPs or SVs.

The paper analyzes meiotic recombination landscapes across five yeast species, finding species-specific differences in recombination rates, crossover interference, and hotspot conservation.

The paper examines translation variation across yeast genetic backgrounds and identifies a post-transcriptional buffering signature that affects essential genes and low-transcribed genes.

The paper estimates heritability of gene expression traits in yeast hybrids and finds non-additive components account for 36% of phenotypic variance.

The paper shows that absence of Red1 and Hop1 recruitment prevents meiotic recombination on a chromosome arm containing the sex locus in Lachancea kluyveri, affecting genome evolution and fitness.

The paper investigates how copy number variants (CNVs) in yeast affect mutational tolerance and fitness, finding both increased tolerance in translation-related genes and decreased tolerance in mitochondrial function genes.

This paper presents 142 high-quality yeast genomes to improve pangenome understanding, identifying structural variants and complex genomic regions.

This study compares genomic evolution between domesticated and wild Kluyveromyces lactis yeast populations, finding reduced diversity and gene introgression in domesticated strains.

The paper analyzes meiotic recombination in Lachancea waltii, identifying differences in crossover distribution, LOH events, and recombination hotspots compared to related species.

The paper identifies background-dependent fitness genes in yeast by analyzing loss-of-function mutations across natural isolates, finding most show continuous variation while some are specific to genetic backgrounds.

This study examines LOH event frequency and spectrum across different ploidy levels in yeast isolates, finding higher LOH rates and specific tract biases in polyploids.

The paper analyzes polyploidization events in Brettanomyces bruxellensis yeast using long-read sequencing to reveal distinct genomic trajectories and donor origins.

The paper shows that Saccharomycodes ludwigii undergoes meiosis without recombination, relying on frequent fertilization within tetrads instead.

This study identifies genetic factors underlying metabolic differences between flor and wine yeasts during fermentation, revealing adaptive divergence and potential for improving oenological traits.

The paper analyzes Ty LTR-retrotransposon content across 1,011 Saccharomyces cerevisiae isolates to trace evolutionary history and identify factors shaping TE repertoires.

nPhase is a polyploidy-agnostic phasing method that achieves high accuracy and contiguity in haplotype prediction for polyploid genomes.

The paper identifies QTL hotspots in Lachancea waltii for growth fitness and shows they are not conserved in a closely related species.

The paper presents a high-throughput assay to measure the fitness of natural alleles in yeast, identifying functional and nonfunctional variants and their effects on phenotype.

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 analyzes mitochondrial and nuclear genomes of Saccharomyces cerevisiae to show discordant evolutionary patterns between the two genomes.