Microbiome analysis, Food microbiome database construction

• Point-of-contact for NGS data analysis at the company. Performed NGS data analysis projects including bulk/single-cell RNA-seq, and smRNA-seq, which contributed to multiple drug discovery programs at the company.• Developed an RNA-seq data analysis pipeline using open-source software covering data processing and QC, differential gene expression analysis, GO/pathway enrichment analysis, etc. Successfully applied this pipeline in various RNA-seq projects.• Developed data visualization… Show more • Point-of-contact for NGS data analysis at the company. Performed NGS data analysis projects including bulk/single-cell RNA-seq, and smRNA-seq, which contributed to multiple drug discovery programs at the company.• Developed an RNA-seq data analysis pipeline using open-source software covering data processing and QC, differential gene expression analysis, GO/pathway enrichment analysis, etc. Successfully applied this pipeline in various RNA-seq projects.• Developed data visualization programs using R Shiny and R markdown to support wet-lab scientists. • Performed maintenance on NGS core’s computing server and NextSeq/ MiSeq sequencer computers. Show less

Co-edited a chapter “Transcriptomics” in eBook “Bioinformatics Recipes for Plant Genomics: Data, Code, and Workflows”; worked with another two editors to set chapter scope, invite authors and perform review work.

• Contributed to a transcriptomics data analysis project for a seed dormancy study in rice, resulting in a co-author poster presentation at the PAG conference.

• Purified RNA-protein complexes from nuclear extract, and prepared RNA-seq libraries to dissect the RNA-protein interaction sites.• Optimized assays including protein purifications, RIP assay and cell fractionation experiments.

• Investigated the molecular-level interactions between the RNA-binding protein HuR and microRNA machinery using CLIP-seq and bioinformatics analysis. Screened HuR-miRNA interaction sites which were further tested in vitro using reporter assays; resulted in a first-author publication in the Journal of Molecular Biology.• Studied the methodology of CLIP-seq with bioinformatics analysis.• Collaborated with colleagues and performed NGS libraries preparation, yielding in a co-author… Show more • Investigated the molecular-level interactions between the RNA-binding protein HuR and microRNA machinery using CLIP-seq and bioinformatics analysis. Screened HuR-miRNA interaction sites which were further tested in vitro using reporter assays; resulted in a first-author publication in the Journal of Molecular Biology.• Studied the methodology of CLIP-seq with bioinformatics analysis.• Collaborated with colleagues and performed NGS libraries preparation, yielding in a co-author publication. Show less

• Led discussion or lab sessions for six different undergraduate courses, including Molecular Biology, Microbiology Lab, Introductory Genetics