Description: Plants have uniquely adapted to manage endoplasmic reticulum stress triggered by protein misfolding. We review the dynamics of gene expression regulation underlying the unfolded protein response in plants, highlighting recent insights provided by systems-level approaches and omics data.

Description: In this study, we performed a forward genetic screening and discovered a new regulator that helps cells determine life or death under unresolved ER stress. Using an interdisciplinary approach of omics, biochemistry, and genetics, we identified its working mechanism and functional relationship with existing regulators.

Description: Defining plant defense machinery against pathogens is significant in cell biology and crop yield. This paper shows that TGNap1, a TGN and microtubule-binding protein, is required for defense and efficient anti-microbial protein secretion, linking secretion and cytoskeleton. I performed the RNA-seq analysis as a co-author.

Description: The paper provides a step-by-step workflow for coexpression network analyses using WGCNA and discusses its potential applications.

Description: We discovered a new UPR regulator and characterized its functional role in the UPR at the mechanistic level through a multi-omics approach.

Description: In this white paper, the GLBRC colleagues and I discussed the significance and challenges of root biology in bioenergy research.

Description: To better understand the transcriptional activities of the UPR master regulators, bZIP28 and bZIP60, I generated time-series transcriptome datasets and performed coexpression analyses, which allowed me to pinpoint downstream genes for functional characterization.

Description: Plant Cell Atlas (PCA) colleagues and I reported the activities that we initiated for the plant research community.

Description: This study focused on investigating transcriptome changes affected by UPR regulators in space. Plants were germinated, grown, and harvested in spaceflight. As a co-author, I performed RNA-seq analyses.

Description: How the UPR is controlled is largely unknown in non-model plant species including maize. To better understand the regulatory landscape of the UPR, I performed TF network analyses based on enhanced Y1H screens for selected UPR marker genes in maize.

Description: In this white, Plant Cell Atlas (PCA) colleagues and I report the very first workshop that was successfully held online

Description: Understanding gene function is a critical requirement to advance knowledge of the principles underpinning fundamental and applied plant biology. In this review, we describe predictive analyses, their strengths and pitfalls that are fast-forwarding our understanding of gene regulation and function in plants.

Description: In recent years, the field of plant UPR has substantially advanced, revealing new regulators and mechanisms. My colleagues and I provide recent updates on the new development in the plant UPR to the research community.

Description: We compare three existing methods for detection of gene editing activity in potato protoplasts. In this collaborative project, I performed amplicon-seq analyses as a co-author.

Description: We describe the impact of Agrobacterium-mediated transformation of a mutated acetolactate synthase gene on the transcriptome of potato, highlight the extent of positional effect of transgene insertion and that one component of somaclonal variation is due to altered expression of transcription factors and their downstream targets.

Description: Heterosis, or hybrid vigor, has been widely used in agriculture for more than a century. Despite extensive investigation and various models proposed, the molecular basis for heterosis remains largely elusive. I led this collaborative project to identify and characterize the molecular link of growth heterosis and the circadian clock. We report that higher carbon fixation and starch accumulation in maize hybrids than in the parents are associated with differences in the diurnal regulation of gene expression.

Description: We investigate allelic expression novelties using a series of newly synthesized Arabidopsis tetraploids that contain one, two, three, and four genomes of A. thaliana or A. arenosa, as well as reciprocal crosses containing the same nuclear genomes but different cytoplasms.

Description: In my MS research, I identified and characterized a flooding stress-responsive transcription factor gene of which expression was not only responsive to flooding stress but also under the circadian clock regulation in Nicotiana. It demonstrated potential crosstalk between the clock and abiotic stress responses.