Chao Di Email & Phone Number

Philadelphia, PA, US

United States

• Designed and developed an internal AAV vector integration analysis platform that enabled the evaluation of insertion risks in gene therapy programs, significantly reducing costs and processing time compared to.
• Optimized single-nucleus RNA-seq data analysis process for rare cell type profiling and target discovery, significantly increased the retinal ganglion cell (RGC) detection rate from 1% to 6%.
• Managed CRO for spatial profiling of NHP liver samples transfected with gene therapy products using Nanostring CosMx™, ensuring data transfer, quality assurance, and timely delivery. Provided guidance on data analysis.
• Developed a PacBio long-read sequencing data analysis pipeline using Snakemake and Nextflow for AAV vector characterization, enabling the characterization of AAV vectors for preclinical and clinical research.

Philadelphia, Pennsylvania, United States

• Studied T cell exhaustion mechanisms in primary immunodeficiency diseases using CyTOF, Olink, and scRNA-seq, providing insights into immune dysregulation.
• Investigated nutrient and metabolite deprivation effects on CD8 T cell function through Polysome Profiling, advancing understanding of metabolic influences on immune responses.
• Examined the impact of NSAIDs on gut microbiota and C. difficile infection severity using 16S rRNA sequencing and metagenomics analysis, identifying potential therapeutic targets.

• Developed bioinformatics pipelines for nascent RNA 4sU-seq and EU-seq, ChIP-seq and XLIP-seq to investigate novel RNA processing mechanisms and their impact on genome-wide gene expression regulation.
• Created methods to identify abnormal transcriptional events (alternative polyadenylation, trans-splicing, and 3' UTR shortening), uncovering potential therapeutic targets in cancers and neurodegenerative diseases.
• Mapped RNA-protein complexes genome-wide using cross-linking IP with RNA-seq (XLIP-seq) and mass spectrometry, providing insights into post-transcriptional regulation and protein interactions.

• Integrated >600 genomic and epigenomic NGS datasets (RNA-seq, miRNA-seq, DNase-seq, CHIP-seq, BS-seq) with evolutionary and biophysical scores to train a Random Forest ML model. Identified 10 features that classify.
• Identified and characterized stress-responsive long non-coding RNAs (lncRNAs) by integrating expression, epigenetic, and structural data (164 datasets), uncovering novel regulatory mechanisms and targets for stress.
• Built 'CLIPdb' by analyzing and integrating >400 RNA-binding protein CLIP-seq datasets, creating a comprehensive resource for RNA-protein interaction research.
• Characterized cancer, testis-specific, and neuronal lncRNAs using expression, clustering, conservation, and pathway analyses, elucidating lncRNA roles in health and disease.

Doctor Of Philosophy (Phd), Bioinformatics

• Conducted cDNA microarray analyses to discover and characterize the JAZ gene family, providing insights into plant adaptation to.

Visiting Student

Analyzed the evolutionary and expression profiles of the PHB gene family across species, revealing insights into their functional.