Audrey P. Gasch

The paper identifies RNA-binding domains of Ssd1 essential for yeast tolerance to extra chromosomes, showing their role in fitness and target binding.

This study investigates how Pde2 regulates the yeast Environmental Stress Response by affecting Msn2/4 activation and target gene expression, with minimal impact on Dot6 repression.

The paper infers fungal cis-regulatory networks from genome sequences using unsupervised and interpretable representation learning, identifying conserved motif signals that predict gene expression and regulation.

This study shows that stress-defense factors in yeast regulate the repression of growth-promoting genes, coordinating resource reallocation needed for stress response.

The paper identifies RBPs interacting with Ssd1 in yeast aneuploidy tolerance through network analysis and genetic experiments, revealing roles in translational repression and p-body formation.

The paper investigates the response to single-gene duplication in yeast, finding that translation-related genes are particularly deleterious in aneuploid cells lacking the RNA-binding protein Ssd1.

This paper measures aneuploidy reversion rates in yeast using a fluctuation assay, showing fitness effects influence estimates and chromosome-specific loss rates.

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

The paper introduces a method using the Orbitrap Astral mass spectrometer with DIA to rapidly analyze phosphoproteomes, detecting over 80,000 phosphorylation sites in mice.

This study shows that aneuploidy in yeast causes premature aging by disrupting ribosome quality control, leading to protein aggregates and cyclin dysregulation.

The paper investigates how PKA signaling coordinates growth and metabolism in yeast during anaerobic xylose fermentation by analyzing transcriptomic, lipidomic, and phosphoproteomic data.

The paper models single-cell phenotypes in yeast to show that transcriptional repression during stress improves post-stress growth recovery.

The paper measures fitness costs of overexpressed genes in yeast strains to show natural variation in tolerance to gene overexpression and its evolutionary implications.

The paper investigates how genetic background influences aneuploidy prevalence and tolerance in Saccharomyces cerevisiae across different clades.

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

This study investigates the roles of PKA and HOG signaling in anaerobic xylose fermentation and stress tolerance in yeast engineered for biofuel production, finding that HOG1 mutations specifically enhance xylose usage while PKA activity affects growth but not xylose fermentation.

The paper examines how Saccharomyces cerevisiae responds to different alcohols under aerobic and anaerobic conditions, revealing strain-specific and interaction-based transcriptomic responses.

The paper infers a signaling network regulating phosphorylation changes in yeast during salt stress, revealing novel interactions between stress and growth pathways.

The paper uses genome-wide association analysis in yeast strains to identify genetic factors affecting toxin tolerance, finding significant strain-specific variation in gene importance.

The paper uses single-cell RNA-seq to study stress response heterogeneity in yeast, finding regulatory variation and decoupled transcription-factor activation.

SCnorm provides a quantile-regression based normalization method for scRNA-seq data to reduce artifacts and improve downstream analysis accuracy.