His research is focused on the design and application of bioinformatics algorithms to elucidate global regulatory mechanisms in development and diseases such as cancer. He has a solid track record in large-scale genomics and epigenomics data analysis, and in developing widely used open-source bioinformatics software. In collaboration with experimental biologists, he has used big data bioinformatics analysis to gain novel biological insights in development, aging, stem cell, neurologic disorders, as well as breast, prostate, brain and blood cancers. Since establishing his own bioinformatics lab in early 2008, he have published more than 60 peer-reviewed papers through solid methodology development and extensive collaboration research, including 22 in Nature, Science and Cell series.