Josh T. Cuperus

Unpacking Chromatin Accessibility with Fiber-seq

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

Duckweeds as Multiplexable Plant Models for Exploring Abiotic Stress Responses

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

Massively parallel characterization and deep learning of enhancers in plant genomes

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

Dosa: A method to covalently barcode proteinsfor high throughput biochemistry

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.

Companion cells with high florigen production express other small proteins and reveal a nitrogen-sensitive FT repressor

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.

Phenotypic tolerance for rDNA copy number variation within the natural range of C. elegans

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.

The regulatory potential of transposable elements in maize

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

Small DNA elements that act as both insulators and silencers in plants

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

Sensitivity to photoperiod is a complex trait in Camelina sativa

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

rDNA copy number variation in yeast alters response to environmental conditions

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.

Florigen-producing cells express FPF1-LIKE PROTEIN 1 that accelerates flowering and stem growth in long days with sunlight red/far-red ratio in Arabidopsis

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

Impact of random 50-base sequences inserted into an intron on splicing in Saccharomyces cerevisiae

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.

Effects of sequence motifs in the yeast 3' untranslated region determined from massively-parallel assays of random sequences

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

The regulatory landscape of Arabidopsis thaliana roots at single-cell resolution

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.

Coordination of genome replication and anaphase entry by rDNA copy number in S. cerevisiae

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.

Dynamics of gene expression in single root cells of A. thaliana

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.

Balance between mutually exclusive traits shifted by variants of a yeast transcription factor

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

Deep learning of the regulatory grammar of yeast 5’ untranslated regions from 500,000 random sequences

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.

Regulatory DNA in A. thaliana can tolerate high levels of sequence divergence

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