Our lab focuses on the development of high-throughput experimental methods and deep learning-based computational methods to study the sequence determinants of cis-regulatory elements (CREs). Elucidating the cis-regulatory grammars of CREs is of great value in genome design-based breeding, by fine-mapping causal cis-regulatory DNA variants exist in natural populations and by designing synthetic CREs with novel properties. Specifically, we pioneered the development of WHG-STARR-Seq, a groundbreaking method that allows for directly measuring enhancer activity of genome-wide sequences from the human genome, alongside allele-specific analysis—marking the first-ever assessment of the effects of tens of thousands of GWAS-associated SNPs on enhancer function using STARR-Seq. These tools greatly enhanced the fine-mapping of causal DNA variants associated with complex diseases and traits. Additionally, we developed TADA-Annotation, a statistical algorithm that extends enhancer and DNA mutation integration analysis to de novo mutations for the first time, increasing the power of discovering causal genes from trio-family WES studies. Going beyond enhancers, we have established high-throughput platforms to screen the activities of various types of cis-regulatory elements (CREs), including enhancers, promoters, silencers, insulators, 5’UTRs, 3’UTRs and splicing sites. Using these platforms, we are not only studying the general regulatory mechanisms of CREs, but also identifying functional DNA variants that affect CRE activity, which provides an unique perspective, following GWAS and molecular QTL, to dissect the genetic basis of complex traits. We are also developing deep-learning based computation methods to design synthetic CREs, which are critical to design novel cis-regulatory circuits to improve the economic traits of agricultural animals.

In the realm of industrial transformation, we devised a genotyping imputation method and a genome selection platform based on ultra-low coverage whole genome sequencing data, earning recognition such as the top ten placement in the inaugural Guangdong Seed Industry Science and Technology Competition Finals in 2021, as well as the 24th China Hi-Tech Fair Excellent Product Award.

Moreover, our lab established ZhongNong Xinyue (Shenzhen) Biotechnology Co., LTD, offering efficient and cost-effective genotyping and genomic selection services. Our achievements have been highlighted in esteemed media outlets like China Science Journal and Voice of the Greater Bay Area of China National Radio in 2023.

Over the past five years, we've led numerous national-level research projects, including initiatives under the 14th Five-Year National Key Research and Development Plan, the National Natural Science Youth Science Fund, the National Natural Science Foundation, and the Science and Technology Innovation Project of the Chinese Academy of Agricultural Sciences. Additionally, we have projects supported by the Guangdong provincial government and the Shenzhen Science and Technology Innovation Commission.