Josh T. Cuperus

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.

The paper investigates the phenotypic effects of rDNA copy number variation in C. elegans using recombinant inbred lines and finds no significant correlation with key phenotypes.

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

The paper identifies small DNA elements in plants that function as both insulators and silencers depending on regulatory context, validated in multiple plant species.

The paper assesses photoperiod sensitivity in Camelina sativa accessions, finding wide variation and complex genetic underpinnings.

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.

The paper identifies FLP1 as a gene expressed in FT-producing cells in Arabidopsis that promotes flowering and stem growth under long-day conditions.

This study investigates how plant enhancers integrate transcription factor activity, finding both cooperative and additive interactions in light-responsive enhancers.

The paper inserts random 50-base sequences into yeast introns and finds that most reduce splicing efficiency, likely due to RNA secondary structures, but existing models poorly predict these effects.

The paper assesses the functional impact of sequence motifs in yeast 3' UTRs using random sequence libraries, revealing context-dependent regulatory effects.

This study uses single-cell ATAC-seq to analyze chromatin accessibility in Arabidopsis thaliana roots, revealing cell type-specific regulatory landscapes and integrating them with transcriptomes to infer gene regulatory networks.

The paper shows that reducing rDNA copy number in S. cerevisiae changes its replication timing, delays genome replication, and links rDNA to cell cycle control via Cdc14p sequestration.

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.

The paper identifies DNA-binding preferences of Ste12 in yeast and shows how mutations shift its preference toward mating or invasion.

The paper trains a CNN to predict translational efficiency of yeast 5' UTRs using synthetic sequences and validates it on native sequences and evolved designs.

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