Our team develops systems biology approaches to study the cellular mechanisms for tissue development and human diseases. To this end, we develop novel computational methods to analyze large-scale omic datasets and partner with experimental biologists to discover the underlying gene pathways and regulatory networks. Our current research is focused on the following areas.

(1) Single-cell analysis. How many distinct cell types are there in a human and, for comparison, in a model organism? The rapid development of single-cell technologies has provided a great opportunity to address this fundamental question in depth. We develop computational methods to systematically characterize the heterogeneity, interaction, and dynamics of cellular states by analyzing single-cell gene expression data. Ultimately, these studies will lead to new insights that help develop novel therapeutic methods for cancer and other diseases.

(2) Epigenetics. What are the molecular mechanisms that maintain cell identity and enable transitions between different cell states? We develop quantitative methods to reconstruct the cell-type specific gene regulatory networks by integratively analyzing the genome-wide profiles of gene expression levels, protein-DNA binding patterns, and 3D chromatin interactions.

(3) Cancer. How are cancer cells different from normal cells? What are the molecular mechanisms that allow cancer cells to survive, proliferate, evade the immune system, and metastasize to remote locations? We use single-cell analysis and epigenetic approaches to investigate the cellular heterogeneity and gene regulatory mechanisms associated with cancer progression and treatment response. Insights from these discoveries have helped developing targeted treatment methods.

(4) Development. How are cell-type and developmental-stage specific gene activities regulated? How are cell-fate decisions determined during differentiation? We analyze and integrate genomic, transcriptomic, and epigenomic data to elucidate the gene regulatory networks for blood and heart development. We are also interested to work with clinicians to develop therapeutic methods for hematological and cardiovascular diseases.

Contact information