We created a Kmer-based haplotype caller (Khaper) for identifying redundant sequences in heterozygous genomes, addressing the time-consuming and computationally expensive problem of de-redundancy in large heterozygous genomes (Nature Genetics, 2021).

1) Innovated the AIO-seq technique for constructing resequencing libraries, streamlining experimental processes and substantially reducing overall sequencing costs. 2) Introduced a Cost-effective, High-throughput Whole-genome Genotype Detection Technology - FBI-seq: in which a single primer enables simultaneous detection of foreground genes and tens of thousands of genetic background loci without any specie specificity.

1) ULI-ssDRIP-seq has been developed to detect R-loops from ultra-micro samples, which for the first time reduced the number of cells to 1,000 and can also boosts the resolution to near-single-nucleotide level. With this tool, we profiled R-loop landscapes during early embryogenesis in sperm, muscle, and 4-cell, 256-cell, dome/sphere stage embryos of zebrafish, which fills the gap in the multi-omics study of vertebrate embryos and demonstrates the biological functions of R-loops during zygotic genome activation (ZGA). 2) We developed a high-throughput R-loop sequencing technology mDRIP-seq based on ULI-ssDRIP-seq technology, which exponentially improves the library construction throughput while completely retaining the advantages of the original technology, dramatically reduces the cost and time-consumption of experiments. Based on this method, our team completed the quantitative mapping of multi-species R-loop from E. coli  to human cell lines. The development of mDRIP-seq makes it possible to build R-loop atlas in large-scale populations.