Runxuan Zhang

ProteoBench provides a centralized platform for comparing proteomics data analysis workflows, enabling benchmarking and community collaboration.

This study investigates the role of GERMIN3 in potato development, showing it enhances tuber yield and affects meristem activation through plasmodesmatal gating.

This study presents a barley pangenome revealing structural variation linked to traits like disease resistance and plant architecture, highlighting its role in adaptive evolution.

ProtView evaluates in silico protease digest schemes by mapping peptides to protein and genome references, enabling optimization of proteomic and proteogenomic experiments.

This study evaluates the benefits of using genotype-specific references for transcriptome analysis in barley, showing improved transcript diversity and accuracy compared to a common reference.

3D RNA-seq provides a user-friendly tool for differential expression, alternative splicing, and transcript usage analysis of RNA-seq data without requiring programming skills.

TranSuite improves transcript translation accuracy by identifying correct ORFs and distinguishing between protein-coding and NMD substrates in Arabidopsis transcriptomes.

The paper uses TAMA to analyze long-read RNA sequencing data and identifies thousands of potential novel genes while highlighting challenges in RNA preparation and data processing.

This study shows that UPF1 is essential for post-transcriptional and translational regulation in Arabidopsis, affecting alternative splicing, translation, and immune receptor activation.

The paper develops BaRTv1.0, a high-quality barley reference transcript dataset, enabling accurate RNA-seq analysis of gene expression and alternative splicing.

The paper identifies rapid and dynamic alternative splicing events in Arabidopsis during cold response, showing their distinct regulatory roles from transcription.

The paper develops AtRTD2, a comprehensive transcript dataset for Arabidopsis thaliana RNA-seq analysis, and introduces AtRTD2-QUASI to improve alternative splicing quantification.