Kerry L. Bubb

This paper introduces Fiber-seq, a method for detecting chromatin accessibility on individual DNA fibers, and provides guidelines for its proper use and analysis.

This study shows duckweeds respond to combinatorial stress similarly to terrestrial plants and can serve as high-throughput models for studying abiotic stress responses.

The paper characterizes plant enhancer activity across multiple species and develops a deep learning model to predict enhancer strength and identify functional motifs.

Dosa covalently bars proteins for high-throughput biochemical analysis by linking variants to RNA barcodes via a methyltransferase, enabling assessment of protein function through direct biochemical assays.

The paper identifies FT-expressing companion cells in leaves, reveals their unique gene expression profile, and shows that NIGT1 represses FT under nitrogen-rich conditions.

This study uses Fiber-seq to analyze TE regulatory potential in maize, revealing epigenetic patterns and gene interaction mechanisms.

The paper investigates how rDNA copy number variation affects yeast fitness under different environmental conditions and finds that higher copy numbers improve fitness in stress conditions.

This study uses single-cell RNA-seq to analyze gene expression in A. thaliana root cells, identifying cell-type-specific genes and developmental trajectories, and shows cell-type differences in heat stress responses.

This study shows that HSP90 reduces the penetrance of newly introduced mutations in plants, leading to fewer embryonic lethality and phenotypic abnormalities compared to HSP90-reduced plants.

The paper examines regulatory DNA variation in Arabidopsis thaliana, finding that chromatin accessibility differences often correlate with gene expression changes despite limited sequence variation.

This paper introduces a two-state epistasis model to address missing heritability in complex traits by considering variant penetrance, improving fit with heritability observations.