Research

Research Overview

I am developing and applying computational approaches for transcriptional and epigenetics regulation studies. As a postdoctoral fellow at Dana-Farber Cancer Institute, I developed widely used open-source algorithms, including MACS (cited over 12,000 times according to Google Scholar) to analyze ChIP-seq and ATAC-seq data, and an integrative platform for comprehensive analyses on cis-regulatory elements (Cistrome platform). I was a member of the Data Analysis Center and Analysis Working Group of the ENCODE and modENCODE consortium and was involved in deciphering functional elements through analyzing high-throughput profiles of chromatin factors and in comparing chromatin features between model organisms and the human genome. I have actively participated in the development of ChIP-seq guidelines for broad scientific communities. I am the principal investigator of MACS3 project which is supported by Chan-Zuckerberg Initiative. I am currently the tech leader of the NCI IOTN Data Management and Resource-Sharing Center, the NCI ARTNet Coordinating and Data Management Center, and the NCI CAP-IT Data and Resource Coordination Center. I am a member in the Developmental Therapeutics program under Cancer Center Support Grant (CCSG). My team at Roswell Park Comprehensive Cancer Center focuses on building bioinformatics algorithms for single-cell genomics assays to study transcriptional and epigenetic regulatory mechanisms in cancer.