研究介绍
多组学自动化分析体系，智能分子设计与 AI 建模，细胞谱系追踪方法
团队成员
叶畅
Principal Investigator
董鑫
副研究员
陈宗贵
副研究员
发表论文
2025
Ultra-mild bisulfite outperforms existing methods for 5-methylcytosine detection with low input DNA
Qing Dai, Tanner Baldwin, Ruitu Lyu, Bryan Daniels, Chang Ye, Chen Cao, Chenyou Zhu, Diwen Fan, Liane Lin, Yushuai Liu, Yiding Wang, Chuan He
Nature Communications
DOI
2025
Pseudouridylation of 7SK by PUS7 regulates Pol II transcription elongation
Yutao Zhao; Hui-Lung Sun; Wenlong Li; Chang Ye; Xiaoyang Dou; Yong Peng; Tong Wu; Pingluan Wang; Cheng-Wei Ju; Shun Liu; Yuhao Zhong; Qing Dai; Kinga Pajdzik; Chuan He
Nature Communications
DOI
2025
Ultra-mild bisulfite outperforms existing methods for 5-methylcytosine detection with low input DNA
Qing Dai; Tanner Baldwin; Ruitu Lyu; Bryan Daniels; Chang Ye; Chen Cao; Chenyou Zhu; Diwen Fan; Liane Lin; Yushuai Liu; Yiding Wang; Chuan He
Journal Article
DOI
2025
Quantitative CRACI reveals transcriptome-wide distribution of RNA dihydrouridine at base resolution
Cheng-Wei Ju, Han Li, Bochen Jiang, Xuanhao Zhu, Liang Cui, Zhanghui Han, Junxi Zou, Yunzheng Liu, Shenghai Shen, Hardik Shah, Chang Ye, Yuhao Zhong, Ruiqi Ge, Peng Xia, Yiyi Ji, Shun Liu, Fan Yang, Bei Liu, Yuzhi Xu, Jiangbo Wei, Li-Sheng Zhang, Chuan He
Nature Communications
DOI
2025
Discovery of circulating cell-free DNA 5hmC biomarkers for peritoneal metastasis in colorectal and appendiceal cancer
Yuri F. M. Malina; Lu Gao; Ankit Dhiman; Diana C. West-Szymanski; Yaniv Berger; Xiao-Long Cui; Zhou Zhang; Marco Rivas; Urszula Dougherty; Chang Ye; Akushika Kwesi; Zifeng Deng; Biren Reddy; Hunter D.D. Witmer; Phillip J. Hsu; Chuan He; Wei Zhang; Marc Bissonnette; Kiran Turaga
Journal Article
DOI
2025
Multigenerational proteolytic inactivation of restriction upon subtle genomic hypomethylation in Pseudomonas aeruginosa
Esther Shmidov; Alexis Villani; Senén D. Mendoza; Ellay Avihu; Ilana Lebenthal-Loinger; Sarit Karako-Lampert; Sivan Shoshani; Chang Ye; Yiding Wang; Hao Yan; Weixin Tang; Joseph Bondy-Denomy; Ehud Banin
Nature Microbiology
DOI
2025
Modifications of microbiome-derived cell-free RNA in plasma discriminates colorectal cancer samples
Cheng-Wei Ju, Ruitu Lyu, Han Li, Jiangbo Wei, Alberto J. Parra Vitela, Urszula Dougherty, Akushika Kwesi, Alexander Luna, Xuanhao Zhu, Shenghai Shen, Yunzheng Liu, Liangliang Wang, Xiaolong Cui, Yuzhi Xu, Bochen Jiang, Yiyi Ji, Peng Xia, Diana C. West-Szymanski, Chenxi Sun, Yuhao Zhong, Chang Ye, Angelica Moran, Christopher Lehmann, Eric Pamer, Wei Zhang, Marc Bissonnette, Li-Sheng Zhang, Chuan He
Nature Biotechnology
DOI
2025
Small-molecule-catalysed deamination enables transcriptome-wide profiling of N6-methyladenosine in RNA
Pingluan Wang; Chang Ye; Michelle Zhao; Bochen Jiang; Chuan He
Nature Chemistry
DOI
2025
Advanced eTAM-seq enables high-fidelity, low-input N6-methyladenosine profiling in human cells and embryonic mouse tissues
He, E.M.; Wu, Y.; Ye, C.; Zeng, T.-B.; He, C.; Tang, W.
Biorxiv
DOI
2025
Author Correction: Quantitative RNA pseudouridine maps reveal multilayered translation control through plant rRNA, tRNA and mRNA pseudouridylation
Haoxuan Li; Guanqun Wang; Chang Ye; Zhongyu Zou; Bochen Jiang; Fan Yang; Kayla He; Chengwei Ju; Lisheng Zhang; Boyang Gao; Shun Liu; Yanming Chen; Jianhua Zhang; Chuan He
Nature Plants
DOI
2025
Quantitative RNA pseudouridine maps reveal multilayered translation control through plant rRNA, tRNA and mRNA pseudouridylation
Haoxuan Li; Guanqun Wang; Chang Ye; Zhongyu Zou; Bochen Jiang; Fan Yang; Kayla He; Chengwei Ju; Lisheng Zhang; Boyang Gao; Shun Liu; Yanming Chen; Jianhua Zhang; Chuan He
Nature Plants
DOI
2025
ScRAPdb: an integrated pan-omics database for the Saccharomyces cerevisiae reference assembly panel
Zepu Miao; Yifan Ren; Andrea Tarabini; Ludong Yang; Huihui Li; Chang Ye; Gianni Liti; Gilles Fischer; Jing Li; Jia-Xing Yue
Nucleic Acids Research
DOI
2024
Ultrafast bisulfite sequencing detection of 5-methylcytosine in DNA and RNA
Qing Dai, Chang Ye, Iryna Irkliyenko, Yiding Wang, Hui-Lung Sun, Yun Gao, Yushuai Liu, Alana Beadell, José Perea, Ajay Goel, Chuan He
Nature Biotechnology
DOI
2024
Pseudouridine Detection and Quantification Using Bisulfite Incorporation Hindered Ligation
Yutao Zhao; Xinyuan Ma; Chang Ye; Wenlong Li; Kinga Pajdzik; Qing Dai; Hui-Lung Sun; Chuan He
ACS Chemical Biology
DOI
2024
PTPN2 copper-sensing relays copper level fluctuations into EGFR/CREB activation and associated CTR1 transcriptional repression
Matthew O. Ross; Yuan Xie; Ryan C. Owyang; Chang Ye; Olivia N. P. Zbihley; Ruitu Lyu; Tong Wu; Pingluan Wang; Olga Karginova; Olufunmilayo I. Olopade; Minglei Zhao; Chuan He
Nature Communications
DOI
2024
Quantitative analysis of cis-regulatory elements in transcription with KAS-ATAC-seq
Ruitu Lyu; Yun Gao; Tong Wu; Chang Ye; Pingluan Wang; Chuan He
Nature Communications
DOI
2024
Quantitative profiling of m6A at single base resolution across the life cycle of rice and Arabidopsis
Wang, G.; Li, H.; Ye, C.; He, K.; Liu, S.; Jiang, B.; Ge, R.; Gao, B.; Wei, J.; Zhao, Y.; Li, A.; Zhang, D.; Zhang, J.; He, C.
Nature Communications
DOI
2024
Chemical manipulation of m1A mediates its detection in human tRNA
Kinga Pajdzik; Ruitu Lyu; Xiaoyang Dou; Chang Ye; Li-Sheng Zhang; Qing Dai; Chuan He
RNA
DOI
2024
Small-molecule inhibition of the METTL3/METTL14 complex suppresses neuroblastoma tumor growth and promotes differentiation
Pomaville, M.; Chennakesavalu, M.; Wang, P.; Jiang, Z.; Sun, H.-L.; Ren, P.; Borchert, R.; Gupta, V.; Ye, C.; Ge, R.; Zhu, Z.; Brodnik, M.; Zhong, Y.; Moore, K.; Salwen, H.; George, R.E.; Krajewska, M.; Chlenski, A.; Applebaum, M.A.; He, C.; Cohn, S.L.
Cell Reports
DOI
2024
Quantitative analysis of cis-regulatory elements in transcription with KAS-ATAC-seq
Ruitu Lyu; Yun Gao; Tong Wu; Chang Ye; Pingluan Wang; Chuan He
Journal Article
DOI
2024
BID-seq for transcriptome-wide quantitative sequencing of mRNA pseudouridine at base resolution
Zhang, L.-S.; Ye, C.; Ju, C.-W.; Gao, B.; Feng, X.; Sun, H.-L.; Wei, J.; Yang, F.; Dai, Q.; He, C.
Nature Protocols
DOI
2024
Profiling of RNA-binding protein binding sites by in situ reverse transcription-based sequencing
Yu Xiao, Yan-Ming Chen, Zhongyu Zou, Chang Ye, Xiaoyang Dou, Jinjun Wu, Chang Liu, Shun Liu, Hao Yan, Pingluan Wang, Tie-Bo Zeng, Qinzhe Liu, Jingyi Fei, Weixin Tang, Chuan He
Nature Methods
DOI
2024
Sequencing of N6-methyl-deoxyadenosine at single-base resolution across the mammalian genome
Xinran Feng, Xiaolong Cui, Li-Sheng Zhang, Chang Ye, Pingluan Wang, Yuhao Zhong, Tong Wu, Zhong Zheng, Chuan He
Molecular Cell
DOI
2024
Small-Molecule Inhibition of Mettl3 Suppresses Neuroblastoma Tumor Growth and Promotes Differentiation
Pomaville, Monica; Jiang, Zhiwei; Wang, Pingluan; Chennakesavalu, Mohansrinivas; Ye, Chang; Ge, Ruiqi; Zou, Zhongyu; Brodnik, Mallory; Zhong, Yuhao; Moore, Kelley; others
Journal Article
DOI
2023
Analysis of genome-wide 5-hydroxymethylation of blood samples stored in different anticoagulants: opportunities for the expansion of clinical resources for epigenetic research
Gao, L.; Zhang, Z.; Cui, X.-L.; West-Szymanski, D.; Ye, C.; He, C.; Zhang, W.; Bissonnette, M.
Epigenetics
DOI
2024
Author Correction: Light-induced LLPS of the CRY2/SPA1/FIO1 complex regulating mRNA methylation and chlorophyll homeostasis in Arabidopsis (Nature Plants, (2023), 9, 12, (2042-2058), 10.1038/s41477-023-01580-0)
Jiang, B.; Zhong, Z.; Gu, L.; Zhang, X.; Wei, J.; Ye, C.; Lin, G.; Qu, G.; Xiang, X.; Wen, C.; Hummel, M.; Bailey-Serres, J.; Wang, Q.; He, C.; Wang, X.; Lin, C.
Nature Plants
DOI
2023
Chemical Proteomic Discovery of Isotype‐Selective Covalent Inhibitors of the RNA Methyltransferase NSUN2
Yongfeng Tao, Jan G. Felber, Zhongyu Zou, Evert Njomen, Jarrett R. Remsberg, Daisuke Ogasawara, Chang Ye, Bruno Melillo, Stuart L. Schreiber, Chuan He, David Remillard, Benjamin F. Cravatt
Angewandte Chemie International Edition
DOI
2023
Light-induced LLPS of the CRY2/SPA1/FIO1 complex regulating mRNA methylation and chlorophyll homeostasis in Arabidopsis
Jiang, B.; Zhong, Z.; Gu, L.; Zhang, X.; Wei, J.; Ye, C.; Lin, G.; Qu, G.; Xiang, X.; Wen, C.; Gateas, M.; Bailey-Serres, J.; Wang, Q.; He, C.; Wang, X.; Lin, C.
Nature Plants
DOI
2023
Author Correction: m6A-SAC-seq for quantitative whole transcriptome m6A profiling
Ruiqi Ge, Chang Ye, Yong Peng, Qing Dai, Yutao Zhao, Shun Liu, Pingluan Wang, Lulu Hu, Chuan He
Nature Protocols
DOI
2023
RBFOX2 recognizes N 6-methyladenosine to suppress transcription and block myeloid leukaemia differentiation
Dou, X.; Xiao, Y.; Shen, C.; Wang, K.; Wu, T.; Liu, C.; Li, Y.; Yu, X.; Liu, J.; Dai, Q.; Pajdzik, K.; Ye, C.; Ge, R.; Gao, B.; Yu, J.; Sun, S.; Chen, M.; Chen, J.; He, C.
Nature Cell Biology
DOI
2023
PTPN2 copper-sensing rapidly relays copper level fluctuations into EGFR/CREB activation and associated CTR1 transcriptional repression
Ross, M.O.; Xie, Y.; Owyang, R.C.; Ye, C.; Zbihley, O.N.P.; Lyu, R.; Wu, T.; Wang, P.; Karginova, O.; Olopade, O.I.; Zhao, M.; He, C.
Biorxiv
DOI
2023
Small-Molecule Inhibition of Mettl3 Suppresses Neuroblastoma Tumor Growth and Promotes Differentiation
Pomaville, M.M.; Jiang, Z.; Wang, P.; Chennakesavalu, M.; Ye, C.; Ge, R.; Zhu, Z.; Brodnik, M.; Zhong, Y.; Moore, K.; Salwen, H.; Chlenski, A.; George, R.E.; Krajewska, M.; Applebaum, M.A.; He, C.; Cohn, S.L.
Ssrn
DOI
2023
YTHDF2/m6A/NF-κB axis controls anti-tumor immunity by regulating intratumoral Tregs
Zhang, L.; Dou, X.; Zheng, Z.; Ye, C.; Lu, T.X.; Liang, H.L.; Wang, L.; Weichselbaum, R.R.; He, C.
EMBO Journal
DOI
2023
Enzyme-mediated alkynylation enables transcriptome-wide identification of pseudouridine modifications
Wang, Y.; Zhang, L.; Zhang, W.; Gao, B.; Ye, C.; Dai, Q.; Wang, K.; Luo, M.; Pan, T.; He, C.
Biorxiv
DOI
2023
Nm-Mut-seq: a base-resolution quantitative method for mapping transcriptome-wide 2′-O-methylation
Chen, L.; Zhang, L.-S.; Ye, C.; Zhou, H.; Liu, B.; Gao, B.; Deng, Z.; Zhao, C.; He, C.; Dickinson, B.C.
Cell Research
DOI
2023
Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution
Dai, Qing; Zhang, Li-Sheng; Sun, Hui-Lung; Pajdzik, Kinga; Yang, Lei; Ye, Chang; Ju, Cheng-Wei; Liu, Shun; Wang, Yuru; Zheng, Zhong; others
Nature Biotechnology
DOI
2023
m6A-SAC-seq for quantitative whole transcriptome m6A profiling
Ge, R.; Ye, C.; Peng, Y.; Dai, Q.; Zhao, Y.; Liu, S.; Wang, P.; Hu, L.; He, C.
Nature Protocols
DOI
2023
Sequencing of N6-methyl-deoxyadenosine at single-base resolution across the mammalian genome
Feng, X.; Cui, X.; Zhang, L.-S.; Ye, C.; Wang, P.; Zhong, Y.; Zheng, Z.; He, C.
Biorxiv
DOI
2023
Sequencing of N6-methyl-deoxyadenosine at single-base resolution across the mammalian genome
Feng, Xinran; Cui, Xiaolong; Zhang, Li-Sheng; Ye, Chang; Wang, Pingluan; Zhong, Yuhao; Zheng, Zhong; He, Chuan
bioRxiv
DOI
2023
RBFOX2 recognizes N 6-methyladenosine to suppress transcription and block myeloid leukaemia differentiation
Dou, Xiaoyang; Xiao, Yu; Shen, Chao; Wang, Kitty; Wu, Tong; Liu, Chang; Li, Yini; Yu, Xianbin; Liu, Jun; Dai, Qing; others
Nature Cell Biology
DOI
2023
Enzyme-mediated alkynylation enables transcriptome-wide identification of pseudouridine modifications
Wang, Yuru; Zhang, Lisheng; Zhang, Wen; Gao, Boyang; Ye, Chang; Dai, Qing; Wang, Ke; Luo, Minkui; Pan, Tao; He, Chuan
bioRxiv
DOI
2022
m7G-quant-seq: Quantitative Detection of RNA Internal N7-Methylguanosine
Zhang, L.-S.; Ju, C.-W.; Liu, C.; Wei, J.; Dai, Q.; Chen, L.; Ye, C.; He, C.
ACS Chemical Biology
DOI
2022
Metabolomic analyses reveal new stage-specific features of COVID-19
Jia, Hongling; Liu, Chaowu; Li, Dantong; Huang, Qingsheng; Liu, Dong; Zhang, Ying; Ye, Chang; Zhou, Di; Wang, Yang; Tan, Yanlian; Li, Kuibiao; Lin, Fangqin; Zhang, Haiqing; Lin, Jingchao; Xu, Yang; Liu, Jingwen; Zeng, Qing; Hong, Jian; Chen, Guobing; Zhang, Hao; Zheng, Lingling; Deng, Xilong; Ke, Changwen; Gao, Yunfei; Fan, Jun; Di, Biao; Liang, Huiying
European Respiratory Journal
DOI
2021
Mapping single-cell-resolution cell phylogeny reveals cell population dynamics during organ development
Liu, K.; Deng, S.; Ye, C.; Yao, Z.; Wang, J.; Gong, H.; Liu, L.; He, X.
Nature Methods
DOI
2020
Lineage recording of zebrafish embryogenesis reveals historical and ongoing lineage commitments
Chen, Z.; Ye, C.; Liu, Z.; Deng, S.; He, X.; Xu, J.
Biorxiv
DOI
2020
Defining endogenous barcoding sites for CRISPR/Cas9-based cell lineage tracing in zebrafish
Chang Ye, Zhuoxin Chen, Zhan Liu, Feng Wang, Xionglei He
Journal of Genetics and Genomics
DOI
2019
Assessing the Influence of Dietary History on Gut Microbiota
Bo Yang, Chang Ye, Bingyu Yan, Xionglei He, Ke Xing
Current Microbiology
DOI
联系方式
叶畅 Lab
Sycamore Research Institute of Life Sciences
上海市浦东新区张江路88号
上海梧桐岛生命科学研究院