Polly Yingshan Hsu

The paper identifies translated overlapping upstream ORFs (ouORFs) in Arabidopsis, showing they repress translation more than non-overlapping uORFs and generate protein diversity.

The paper identifies GC3 codons as a universal factor enhancing protein production across diverse plant species by improving translation efficiency and mRNA abundance.

ggRibo is an R package that visualizes single-gene omics data, including Ribo-seq and RNA-seq, with nucleotide resolution to study gene expression and regulation.

The paper shows that transcription start site (TSS) selection influences uORF inclusion and repressive effects, highlighting the need to account for TSS heterogeneity in uORF analysis.

The paper improves super-resolution Ribo-seq in Arabidopsis to identify prevalent translation of upstream and small ORFs, revealing new translation events and regulatory mechanisms.

The paper describes an updated Ribo-seq protocol for Arabidopsis using custom library construction methods and provides a bioinformatic pipeline for quality control.

The paper identifies and functionally annotates ~130,000 lincRNAs in four Brassicaceae species using RNA-seq and epigenomic data, highlighting conserved motifs and stress-responsive features.

The paper identifies actively translated uORFs in Arabidopsis and shows they reduce mRNA stability and translation differently from NMD targets.

RiboPlotR visualizes Ribo-seq reads and RNA-seq coverage for gene isoforms, highlighting 3-nucleotide periodicity and translation features.