Yeming Xie

This paper introduces DropHiChew and loop velocity to study DNA movement dynamics, enabling accurate trajectory estimation with shallow sequencing.

HiChew improves chromatin conformation capture in single cells with higher efficiency, fewer false positives, and more contacts per cell compared to Dip-C.

This study introduces SCA-seq to resolve spatial chromatin interactions at single-molecular resolution and demonstrates its application in analyzing epigenomic markers.

This study shows that the X-linked miR-506 family miRNAs enhance sperm competitiveness and male reproductive fitness by fine-tuning gene expression during spermatogenesis.

The paper improves RNA velocity analysis by incorporating long-read single-cell sequencing to better capture gene expression dynamics and cell fate transitions.

This study introduces TEAM-seq, a method for high-coverage 5mC sequencing in single cells, achieving 70% coverage at 100pg input DNA.

The paper introduces a method called BIND&MODIFY to map histone modifications at the single-molecule level using long-read sequencing, revealing long-range chromatin states and heterogeneity.

The paper introduces CCDA-seq to study ecDNA chromatin structure, revealing distinct nucleosome and regulator binding patterns.

AASRA is a small RNA annotation pipeline that improves accuracy and speed by handling sncRNA variants and distinguishing mature from precursor miRNAs.

The paper investigates the role of DNMT2 in maternal transmission of a paramutant phenotype through the male germline.

The paper identifies artificial junction sequences formed by reverse transcriptases, leading to false circular RNA identification, and proposes methods to distinguish true circular RNAs.