Research interests

Our research focus on cancer immunology and immunotherapy, cell signaling, and gene expression regulation. We are developing a number of algorithms and tools to analyze high throughput genomics data, including RNA-seq, WES, CRISPR Screen, single cell, spatial transcriptomics, ATAC-seq data, etc. When data lead us to unexpected but interesting results, we also design experiments on the bench hoping to understand the underlying mechanisms. In addition, we are also developing mulitple experimental paltforms to perturb both immune and cancer cells and study their effects in tumor microenvironment.  Through data integration and algorithm development and experimental designs, we try to model the specificity and function in tumor development, progression, drug response and resistance.

Genome-wide CRISPR screens


We are collecting and integrating a large volume of immune-related genome-wide CRISPR screen data. We are also designing CRISPR screen experiements to identify gene targets with immuno-modulatory effects. Leveraging the public and our in house CRISPR screen data, we are developing machine learning models to identify gene regulators involved in the cancer immunology and immunotherapy response. After deriving a list of promising targets from our models, we will validate the targets using our established high-throughput experimental validation platforms. 

Spatial transcriptomics


We have systematcially collected and processed spatial transcriptomics datasets from the public domains. Collaborating with physicians, we are generating spatial transcriptomics data using clinical samples. Leveraging the data, we are develping tools and machine learning models to evaluate the spatial variability of genes in different tissues, visualize the spatial gene expression, and assess possible cell type interactions. 

Single cell and other omics


Leveraging our assembled omics data, we are developing machine learning and statistical methods to handle the increasing data complexity in single-cell research and further explore the underappreciated biological factors in antitumor immunity. We are unraveling the regulatory network with tumor microenvironment and identifying key regulatory genes in tumor microenvironment.