Chang Ye

This paper introduces RAD-seq, a method to quantify RNA accessibility by protein binding, and shows it can detect RBP footprints and RNA structure changes under stress.

The paper reveals an m6A-dependent mechanism where microRNAs bind chromatin-associated RNAs to activate transcription by recruiting chromatin remodelers and demethylases.

UMBS-seq improves 5-methylcytosine detection in low-input DNA by reducing degradation and noise, outperforming existing methods in yield and efficiency.

This study uses 5hmC-Seal technology to detect 5hmC signatures in cfDNA from plasma, identifying peritoneal metastases in CRC and AA with high sensitivity but moderate specificity.

This study shows that Pseudomonas aeruginosa inactivates its type I R-M system via proteolysis at high temperatures, leading to prolonged genomic hypomethylation and a memory effect lasting over 60 generations.

The paper introduces eTAM-seq-v2, an improved method for m6A profiling with higher fidelity and lower input requirements, and applies it to human cells and mouse tissues.

This study introduces KAS-ATAC-seq to quantitatively analyze cis-regulatory elements in transcription, showing improved identification of functional CREs compared to standard ATAC-seq.

This paper introduces DR-6mA-seq, a method to detect 6mA at single-base resolution in mammalian genomes, finding low abundance in most tissues but distinct sites in mouse testis and glioblastoma cells.

This study uses scLOESS to trace lineage commitments in zebrafish embryos, revealing development histories and ongoing lineage events through single-cell analysis.