Zhicheng Ji

I am an Assistant Professor in Department of Biostatistics and Bioinformatics at Duke University.

My primary research interest is developing novel statistical and computational methods for integrating and analyzing big and complex genomic data, especially data from single-cell sequencing. Some examples include the differential analysis of single-cell RNA-sequencing (scRNA-seq) data with multiple samples, joint analysis of paired single-cell RNA and T cell receptor (TCR) sequencing data, pseudotime trajectory inference, and signal recovery for single-cell ATAC-sequencing (scATAC-seq) data. I have been actively applying these methods to various biological and clinical studies, such as immunology and cancer.

I am looking for students and postdocs to work together on exciting research projects. Please contact me if your are interested. Email: zhicheng.ji@duke.edu


1. Methods for analyzing single-cell genomic data

Single-cell ATAC-seq signal extraction and enhancement with SCATE [Paper][Software]

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis [Paper][Software]

Single-cell regulome data analysis by SCRAT [Paper][Software]

Global prediction of chromatin accessibility using small-cell-number and single-cell RNA-seq [Paper][Software]

2. Methods for integrating large-scale genomic data

Turning publicly available gene expression data into discoveries using gene set context analysis [Paper][Software]

Genome-wide prediction of DNase I hypersensitivity using gene expression [Paper][Software]

Global prediction of chromatin accessibility using small-cell-number and single-cell RNA-seq [Paper][Software]

3. Collaborations in immunology, cancer, and developmental biology

TCF-1-Centered Transcriptional Network Drives an Effector versus Exhausted CD8 T Cell-Fate Decision [Paper]

Compartmental analysis of T cell clonal dynamics as a function of pathologic response to neoadjuvant PD-1 blockade in resectable NSCLC [Paper]

GLI transcriptional repression regulates tissue-specific enhancer activity in response to Hedgehog signaling [Paper]


All Publications on Google Scholar
Name Type Author Availability
SCATE: Single-cell ATAC-seq signal extraction and enhancement R Software Package Zhicheng Ji, Hongkai Ji [Github]
TSCAN: Tools for Single-Cell ANalysis R Software Package Zhicheng Ji, Hongkai Ji [Github] [Bioconductor] [Online GUI]
BIRD: Big data regression for predicting DNase I hypersensitivity R Software Package Zhicheng Ji, Hongkai Ji [Github]
SCRAT: Single-Cell Regulome Analysis Tool R Software Package Zhicheng Ji, Weiqiang Zhou, Hongkai Ji [Github] [Online GUI]
STIP: State transition inference prediction R Software Package Zhicheng Ji, Hongkai Ji [Github]
GSCA: Gene Set Context Analysis R Software Package Zhicheng Ji, Hongkai Ji [Github] [Bioconductor] [Online GUI]
RMRCE: Regularized Maximum Rank Correlation Estimator R Software Package Fang Han, Hongkai Ji, Zhicheng Ji, Honglang Wang [Github]
SEPA: Single-cell Gene Expression Pattern Analysis R Software Package Zhicheng Ji, Hongkai Ji [Github] [Bioconductor] [Online GUI]
GEOsearch: Extendable Search Engine for GEO R Software Package Zhicheng Ji, Hongkai Ji [Github] [Bioconductor] [Online GUI]
Reproducible Interactive Data Exploration Tool Web Application Zhicheng Ji, Hongkai Ji [Online GUI]