yeast

The paper uses deep mutational scanning to analyze resistance mutations in Fks1, revealing distinct resistance landscapes for echinocandins and triterpenoids, including a novel triterpenoid-specific hotspot.

This study identifies extensive horizontal gene transfer in the fungus gnat Bradysia coprophila, showing these genes contribute to stress tolerance and ecological adaptation.

The paper identifies widespread Saccharomyces hybridization in agave fermentations, showing multiple independent origins and asymmetric parental genetic diversity.

This paper introduces two methods, SLED and GTD, to infer modular structure in genotype-phenotype maps by combining epistasis and pleiotropy, showing they yield similar modular architectures in yeast data.

The paper uses computational methods to analyze antioxidant effects on stress response mechanisms in Candida albicans, identifying naringenin and quercetin as potential modulators of Sir2/SIRT3 pathways.

tWhEEL quantifies CRISPR knockout feasibility by integrating transcriptome data with guide RNA design and functional annotations to prioritize tractable biological functions and organisms.

This study identifies Ktd1 as a phospho-regulated member of the Dup240 family essential for defense against the K28 killer toxin in yeast.

The paper uses joint QTL mapping to analyze pleiotropy patterns across structured environments in budding yeast, revealing genetic interactions influenced by environmental relationships.

This study shows that polyploidy leads to reduced mitochondrial scaling and impaired metabolic function, with conserved effects across yeast and human cells.

This study identifies Ume6 as a transcriptional repressor that regulates vacuolar protein composition and autophagy in yeast by interacting with Rph1 and being modulated by protein kinases.

This paper introduces multivariate mutual information (MMI) for selecting histone PTM features to predict epigenetic data, showing improved accuracy over traditional methods.

This paper introduces a maximum-likelihood framework to estimate gene expression noise from scRNA-seq data, accounting for technical noise and cell type heterogeneity, and demonstrates its reproducibility using yeast data.

The paper investigates multicellular traits in Saccharomyces cerevisiae, finding significant variation and genetic architecture, with some genes linked to virulence in larvae.

The paper identifies two regulatory elements in Lte1 that coordinate kinase activity to compartmentalize Lte1 at the bud cortex in S. cerevisiae, ensuring proper mitotic exit.

This study identifies Kcs1-dependent inositol pyrophosphates as regulators of DNA repair via Pho80-Pho85 in budding yeast, independent of homologous recombination.

This paper introduces TRAEV, a computational framework to predict the evolutionary robustness of metabolic traits in microbial cells, validated using yeast strains in controlled environments.

This study compares multi-omics data from yeast-derived extracellular vesicles to show conserved membrane architecture and strain-specific metabolic cargo enrichment.

This study co-cultures yeast and plant cells to generate consortia factors with a distinct metabolome enriched in antioxidants, showing stronger antioxidant activity than individual cultures.

Auto-AVS simulates autophagic vacuoles in yeast to test stereological assumptions, finding no effect of body deformation on section statistics but discrepancies in body-number estimates.

BUDDY is a web platform that streamlines the functional modeling of human missense variants using yeast orthologs, reducing bioinformatic preparation time and enabling non-experts to design experiments.

The paper quantifies mating strategies in yeast gametes, revealing a reproductive hierarchy where sibling gametes have divergent mating trajectories and temporal heterogeneity shapes compatibility.

The paper shows a domesticated totivirus-like gene array in yeasts evolves faster than its exogenous relatives and undergoes interspecific transfer and asymmetric evolution.

The paper investigates the role of RES complex subunits Snu17p and Bud13p in splicing efficiency in budding yeast, finding they buffer against weak splicing signals and are critical for inefficient intron splicing.

The paper shows that multiple mechanisms suppress meiotic recombination near chromosome ends in yeast, involving both axis protein downregulation and DNA break suppression.

The paper develops a mathematical model to infer telomere dynamics parameters from telomere length distributions in yeast using long-read sequencing data.

This study investigates the evolutionary transition of fungi from land to sea using Kluyveromyces yeasts, finding genome size reduction, phenotypic changes, and positive selection in marine species.

This study shows Rad53/Chk2 links mitochondrial function and ROS levels to G2/M cell cycle progression in yeast.