1. Animal Genomics

Pig is an important agricultural animal, as it serves as the main meat source in China. In recent years, pig starts to attract interest from the medical area as it is found to be a good biomedical model and potential xenotransplantation donor. Our group has perfomed pioneering work on pig genomics, including: (1) developing a novel pipeline for SNP detection of distinct pig breeds (2) coding the pyRSD-CoEv package for selective sweep detection across different pig breeds without replicates (3) completing the first large-scale pig bodymap for pig genome annotation (4) characterizing the genomic features of the first pig stem cell line using Hi-C technique. Using single cell resolution (scRNA-seq, snATAC-seq, scHiC-seq, scTCR/BCR-seq and spatial transcriptome) techniques, we now conduct research on pig heart/kidney development and xenotransplanted pig kidney in brain-dead human body.

2. Biomedical informatics

Inspired by the Hi-C technique, we built a mathematical model for target gene prediction based on ChIP-seq and gene expression data. Application of this model to the study of ER-positive and triple negative breast cancer shed light on the underlying molecular mechanism of this disease. Using single cell resolution (scRNA-seq, snATAC-seq and spatial transcriptome) techniques, we are now collaborating with experimental scientists and physicians to study the human heart diseases, placenta development, leukemia and etc.