Prof. Ye Chang
Assistant Professor (Presidential Young Scholar)
- Y820-C
- +852 3400 2640
- chang.ye@polyu.edu.hk
Research Interests
Research Overview
Our research decodes the dynamic information of biological systems, including epigenetic marks, RNA structures, and cell lineages. We develop innovative sequencing technologies that use chemical biology to read these signals with high precision. Moving forward, we combine these tools with Artificial Intelligence to guide protein engineering and design functional RNA therapeutics.
Achievements
- Presidential Young Scholar, The Hong Kong Polytechnic University (2025)
- He, C.; Dai, Q.; Irkliyenko, I.; Ye, C. Methods and compositions for rapid detection and analysis of RNA and DNA cytosine methylation. US Patent US20250066837A1 (2025).
- He, X.; Liu, L.; Ye, C.; Liu, K.; Deng, S. Preparation and use of induced muteins based on activation-induced cytidine deaminase. CN Patent CN202010285948.1 (2023).
- Wang, P.; Ye, C.; Zhao, M.; Jiang, B.; He, C. Small-molecule-catalysed deamination enables transcriptome-wide profiling of N6-methyladenosine in RNA. Nature Chemistry 2025, 17, 1042-1052.
- Li, H.; Wang, G.; Ye, C.; Zou, Z.; Jiang, B.; Yang, F.; He, K.; Ju, C.; Zhang, L.; Gao, B.; Liu, S.; Chen, Y.; Zhang, J.; He, C. Quantitative RNA pseudouridine maps reveal multilayered translation control through plant rRNA, tRNA and mRNA pseudouridylation. Nature Plants 2025, 11, 234–247.
- Dai, Q.; Ye, C.; Irkliyenko, I.; Wang, Y.; Sun, H. L.; Gao, Y.; Liu, Y.; Beadell, A. P.; Perea, J.; Goel, A.; He, C. Ultrafast bisulfite sequencing detection of 5-methylcytosine in DNA and RNA. Nature Biotechnology 2024, 42, 1559–1570.
- Wang, G.; Li, H.; Ye, C.; He, K.; Liu, S.; Jiang, B.; Ge, R.; Gao, B.; Wei, J.; Zhao, Y.; He, C. Quantitative profiling of m6A at single base resolution across the life cycle of rice and Arabidopsis. Nature Communications 2024, 15, 4881.
- Zhang, L. S.; Ye, C.; Ju, C. W.; Gao, B.; Feng, X.; Sun, H. L.; Wei, J.; Yang, F.; Dai, Q.; He, C. BID-seq for transcriptome-wide quantitative sequencing of mRNA pseudouridine at base resolution. Nature Protocols 2024, 19, 517-538.
- Xiao, Y.; Chen, Y. M.; Zou, Z.; Ye, C.; Dou, X.; Wu, J.; Liu, C.; Liu, S.; Yan, H.; Wang, P.; He, C. Profiling of RNA-binding protein binding sites by in situ reverse transcription-based sequencing. Nature Methods 2024, 21, 247-258.
- Ge, R.; Ye, C.; Peng, Y.; Dai, Q.; Zhao, Y.; Liu, S.; Wang, P.; Hu, L.; He, C. m6A-SAC-seq for quantitative whole transcriptome m6A profiling. Nature Protocols 2023, 18, 626-657.
- Chen, L.; Zhang, L. S.; Ye, C.; Zhou, H.; Liu, B.; Gao, B.; Deng, Z.; Zhao, C.; He, C.; Dickinson, B. C. Nm-Mut-seq: a base-resolution quantitative method for mapping transcriptome wide 2'-O-methylation. Cell Research 2023, 33, 727-730.
- Liu, K.; Deng, S.; Ye, C.; Yao, Z.; Wang, J.; Gong, H.; Liu, L.; He, X. Mapping single-cell-resolution cell phylogeny reveals cell population dynamics during organ development. Nature Methods 2021, 18, 1506–1514.
- Ye, C.; Chen, Z.; Liu, Z.; Wang, F.; He, X. Defining endogenous barcoding sites for CRISPR/Cas9-based cell lineage tracing in zebrafish. Journal of Genetics and Genomics 2020, 47, 85-91.
