ZHANG Group @ HKUST

(Peer-reviewed journals; ​† First Author; * Corresponding Author.)

Google Scholar https://scholar.google.com/citations?user=YMZv4UAAAAAJ&hl=en

2025

[44] Yiyi Ji†, Cheng-Wei Ju†, Lei Chen†, Kai Shen, Ruopeng Su, Ang Li, Xinyu Liu, Bo Liu, Xinran Zhang, Ruitu Lyu, Peng Xia, Han Li, Yiqian Pan, Yunzheng Liu, Man Hin Tse, Yizheng Xue, Hongyang Qian, Na Jing, Helen He Zhu, Liangliang Wang, Li-Sheng Zhang, Shu-Heng Jiang, Weiwei Zhang, Liang Dong, Zejun Yan, Jiahua Pan, Yinjie Zhu*, Jiangbo Wei*, Qi Wang*, Wei Xue*

Serotonin modulates lineage plasticity in neuroendocrine prostate cancer via epigenetic reprogramming.

Cancer Discovery (2025)

[43] Jingfang Zhao, Liu Liu, Yunpeng Song, Yuang Wang, Jingwen Deng, Li-Sheng Zhang, Yibin Liu, Shuoxing Jiang, Limin Xiang*

Single-Cell Super-Resolution Quantification of Oxidative DNA Damage via Aptamer-Assisted DNA-PAINT.

Analytical Chemistry (2025)

[42] Li-Sheng Zhang, Yuexiu Zhang, Amit Sharma, Chuan He, Jianrong Li*

Bisulfite Sequencing to Map 5-Methylcytosine Sites in Human Respiratory Syncytial Virus RNA.

Human Respiratory Syncytial Virus: Methods and Protocols 233–247 (2025)

[41] Jiakai Hou†, Cheng‐Wei Ju†, Nicholas A Egan, Yanjun Wei, Yunfei Wang, Minghao Dang, Tianyi Zhou, Leilei Shi, Ningbo Zheng, Si Chen, Ashley M Guerrero, Xiaofang Liang, Wanfu Wu, Areej Akhtar, Chitra Dhiman, Debanwita Roy Burman, Andro E Gerges, Mason D Flores, Han Li, Li‐Sheng Zhang, Marleen Kok, Xiaobo Mao, Linghua Wang, Qin Feng, Yiwen Chen, Sanghoon Lee, Daniel J McGrail, Nidhi Sahni, Chuan He, Amir A Jazaeri, Weiyi Peng*

Tumor Intrinsic METTL5 Modulates ATF4 Translation to Prevent T Cell‐Induced Ferroptosis in Ovarian Cancer.

Advanced Science e07718 (2025)

[40] Boyang Gao, Bochen Jiang, Zhongyu Zou, Bei Liu, Weijin Liu, Li Chen, Lisheng Zhang, Chuan He*.

Nuclear 2′-O-methylation regulates RNA splicing through its binding protein FUBP1.

Science Advances 11, eady3894 (2025)

[39] Letong Xu†, Shenghai Shen†, Yizhou Zhang, Zhihao Guo, Beifang Lu, Jiadai Huang, Runsheng Li, Yitong Shen, Li-Sheng Zhang*, Xin Deng*.

Quantitative RNA pseudouridine landscape reveals dynamic modification pattern and evolutionary conservation across bacterial species. 

eLife (2025) DOI: 10.7554/eLife.107545.1.

[38] Cheng-Wei Ju†, Han Li†, Bochen Jiang, Jiangbo Wei, 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, Li-Sheng Zhang*, Chuan He*.

Quantitative CRACI reveals transcriptome-wide distribution of RNA dihydrouridine at base resolution. Nature Communications 16, 8863 (2025)

[37] 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*

Modifications of microbiome-derived cell-free RNA in plasma discriminates colorectal cancer samples.

Nature Biotechnology (2025). DOI: 10.1038/s41587-025-02731-8

[36] Chuan He, Qing Dai, Li-Sheng Zhang, Chang Ye

Compositions and methods related to modification and detection of pseudouridine and 5-hydroxymethylcytosine.

US Patent App. 18/556,842 (2025)

[35] Haoxuan Li†, Guanqun Wang†, Chang Ye†, Zhongyu Zou, Bochen Jiang, Fan Yang, Kayla He, Chengwei Ju, Li-Sheng Zhang, Boyang Gao, Shun Liu, Yanming Chen, Jianhua Zhang, Chuan He* 

Quantitative RNA pseudouridine maps reveal multilayered translation control through plant rRNA, tRNA and mRNA pseudouridylation. 

Nature Plants 11, 234–247 (2025).

2024

[34] Chang Liu†, Xiaoyang Dou†, Yutao Zhao†, Linda Zhang, Li-Sheng Zhang, Qing Dai, Jun Liu, Tong Wu, Yu Xiao, Chuan He* 

IGF2BP3 promotes mRNA degradation through internal m⁷G modification. 

Nature Communications 15, 7421 (2024).

[33] Yanqiang Li†, Yang Yi†, Xinlei Gao, Xin Wang, Dongyu Zhao, Rui Wang, Li-Sheng Zhang, Boyang Gao, Yadong Zhang, Lili Zhang, Qi Cao*, Kaifu Chen*

Sequencing of N6-methyl-deoxyadenosine at single-base resolution across the mammalian genome. 

Molecular Cell 84, 2320–2336 (2024)

[32] Kinga Pajdzik†, Ruitu Lyu†, Xiaoyang Dou†, Chang Ye, Li-Sheng Zhang, Qing Dai, Chuan He*

Chemical manipulation of m¹A mediates its detection in human tRNA.

RNA 30, 548–559 (2024)

[31] Xinran Feng†, Xiao-Long Cui†, Li-Sheng Zhang†, Chang Ye, Pingluan Wang, Zhong Zheng, Chuan He*

Sequencing of N6-methyl-deoxyadenosine at single-base resolution across the mammalian genome. 

Molecular Cell 84, 596–610 (2024)

[30] Li-Sheng Zhang†, Qing Dai†, Chuan He*

Base-resolution sequencing methods for whole-transcriptome quantification of messenger RNA modifications

Accounts of Chemical Research 57, 47–58 (2024)

[29] Li-Sheng Zhang†, Chang Ye†, Cheng-Wei Ju†, Boyang Gao, Xinran Feng, Hui-Lung Sun, Jiangbo Wei, Fan Yang, Qing Dai, Chuan He*

BID-seq for transcriptome-wide quantitative sequencing of mRNA pseudouridine at base resolution

Nature Protocols 19, 517–538 (2024)

2023

[28] Ruitu Lyu†, Kinga Pajdzik†, Hui-Lung Sun, Linda Zhang, Li-Sheng Zhang, Tong Wu, Lei Yang, Tao Pan*, Chuan He*, Qing Dai*.

A Quantitative Sequencing Method for 5-Formylcytosine in RNA.

Israel Journal of Chemistry (2023) DOI: 10.1002/ijch.202300111

[27] Shenghai Shen, Li-Sheng Zhang*.

The Regulation of Antiviral Innate Immunity through Non-m6A RNA Modifications.

Frontiers in Immunology (2023) DOI: 10.3389/fimmu.2023.1286820.

[26] Li-Sheng Zhang*, Cheng-Wei Ju, Bochen Jiang, Chuan He.

Base-resolution quantitative DAMM-seq for mapping RNA methylations in tRNA and mitochondrial polycistronic RNA.

Methods in Enzymology 692, 39–54 (2023)

[25] Li-Sheng Zhang*, Qing Dai, Chuan He.

Quantitative base-resolution sequencing technology for mapping pseudouridines in mammalian mRNA.

Methods in Enzymology 692, 23–38 (2023)

[24] Li Chen†, Li-Sheng Zhang†, Chang Ye†, Huiqing Zhou, Bei Liu, Boyang Gao, Zixin Deng, Changming Zhao*, Chuan He*, Bryan Dickinson*.

Nm-Mut-seq: The base-resolution quantitative method for mapping transcriptome-wide 2’-O-methylations.

Cell Research 33, 727–730 (2023).

[23] Yuexiu Zhang, Li-Sheng Zhang, Dai Qing, Jiayu Xu, Phylip Chen, Mark Peeples, Amit Sharma, Chuan He, Jianrong Li*.

Abstract 2659: 5-methylcytosine (m⁵C) RNA modification controls the innate immune response to virus infection by regulating type I interferons.

Journal of Biological Chemistry 299 (3), 104261(2023).

[22] P. Cody He, Jiagnbo Wei, Xiaoyang Dou, Bryan T. Harada, Zijie Zhang, Ruiqi Ge, Chang Liu, Li-Sheng Zhang, Xianbin Yu, Shuai Wang, Ruitu Lyu, Zhongyu Zou, Mengjie Chen, Chuan He*

Exon architecture controls mRNA m⁶A suppression and gene expression.

Science 379, 677–682 (2023).

[21] Li-Sheng Zhang, Qing Dai, Chuan He*

BID-seq: The Quantitative and Base-Resolution Sequencing Method for RNA Pseudouridine.

ACS Chemical Biology 18, 4–6 (2023).

[20] Qing Dai†^,*, Li-Sheng Zhang†^,*, Hui-Lung Sun†, Kinga Pajdzik†, Lei Yang, Chang Ye, Cheng-Wei Ju, Shun Liu, Yuru Wang, Zhong Zheng, Linda Zhang, Bryan T. Harada, Xiaoyang Dou, Iryna Irkliyenko, Xinran Feng, Tao Pan, Chuan He*.

Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution.

Nature Biotechnology 41, 344–354 (2023).

Before joining HKUST

[19] Li-Sheng Zhang†^,*, Cheng-Wei Ju†, Chang Liu†, Jiangbo Wei, Qing Dai, Li Chen, Chang Ye, Chuan He*

m⁷G-quant-seq: Quantitative Detection of RNA Internal N⁷-Methylguanosine.

ACS Chemical Biology 17, 3306–3312 (2022).

[18] Yuexiu Zhang†, Li-Sheng Zhang†, Qing Dai, Phylip Chen, Mijia Lu, Elizabeth Kairis, Valarmathy Murugaiah, Jiayu Xu, Rajni Shukla, Xueya Liang, Zhongyu Zou, Estelle Cormet-Boyaka, Jianming Qiu, Mark E. Peeples, Amit Sharma, Chuan He*, Jianrong Li*.

5-methylcytosine (m⁵C) RNA modification controls the innate immune response to virus infection by regulating type I interferons.

Proc. Natl. Acad. Sci. U.S.A. 119, e2123338119 (2022).

[17] Jiangbo Wei†, Xianbin Yu†, Lei Yang†, Xuelian Liu†, Boyang Gao, Boxian Huang, Xiaoyang Dou, Jun Liu, Zhongyu Zou, Xiao-Long Cui, Li-Sheng Zhang, Xingsen Zhao, Qinzhe Liu, P Cody He, Caraline Sepich-Poore, Nicole Zhong, Wenqiang Liu, Yanhe Li, Xiaochen Kou, Yanhong Zhao, You Wu, Xuejun Cheng, Chuan Chen, Yiming An, Xueyang Dong, Huanyu Wang, Qiang Shu, Ziyang Hao, Tao Duan, Yu-Ying He, Xuekun Li, Shaorong Gao*, Yawei Gao*, Chuan He*.  

FTO mediates LINE1 m⁶A demethylation and chromatin regulation in mESCs and mouse development.

Science 376, 968–973 (2022).

[16] Lulu Hu†^,*, Shun Liu†, Yong Peng†, Ruiqi Ge†, Rui Su†, Chamara Senevirathne, Bryan T. Harada, Qing Dai, Jiangbo Wei, Li-Sheng Zhang, Ziyang Hao, Liangzhi Luo, Huanyu Wang, Yuru Wang, Mingkui Luo, Mengjie Chen*, Jianjun Chen*, Chuan He*.

m⁶A RNA modifications are measured at single-base resolution across the mammalian transcriptome.

Nature Biotechnology 40, 1210–1219 (2022).

[15] Ning Tsao†, Joshua R. Brickner†, Rebecca Rodell, Adit Ganguly, Matthew Wood, Clement Oyeniran, Tanveer Ahmad, Hua Sun, Albino Bacolla, Li-Sheng Zhang, Valentina Lukinović, Jennifer M. Soll, Brittany A. Townley, Alexandre G. Casanova, John A. Tainer, Chuan He, Alessandro Vindigni, Nicolas Reynoird, Nima Mosammaparast*.

Aberrant RNA methylation triggers recruitment of an alkylation repair complex.

Molecular Cell 81, 4228–4242 (2021).

[14] Li-Sheng Zhang, Qing-Ping Xiong, Sonia Peña Perez, Chang Liu, Jiangbo Wei, Cassy Le, Linda Zhang, Bryan T. Harada, Qing Dai, Xinran Feng, Ziyang Hao, Yuru Wang, Xueyang Dong, Lulu Hu, En-Duo Wang, Tao Pan, Arne Klungland, Ru-Juan Liu*, Chuan He*.

ALKBH7-mediated demethylation regulates mitochondrial polycistronic RNA processing.

Nature Cell Biology 23, 684–691 (2021).

[13] Yuru Wang, Zijie Zhang, Caraline Sepich Poore, Li-Sheng Zhang, Yu Xiao, Chuan He*.

LEAD-m⁶A-seq for locus-specific detection of N⁶-Methyladenosine and quantification of differential methylation.

Angew. Chem. Int. Ed. 60, 873–880 (2021).

[12] Li-Sheng Zhang, Chang Liu, Chuan He*.

Transcriptome-wide detection of internal N⁷-methylguanosine.

Methods in Molecular Biology 2298, 97-104 (2021).
[11] Ziyang Hao, Tong Wu, Xiaolong Cui, Pingping Zhu, Caiping Tan, Xiaoyang Dou, Kai-Wen Hsu, Yueh-Te Lin, Pei-Hua Peng, Li-Sheng Zhang, Yawei Gao, Lulu Hu, Hui-Lung Sun, Allen Zhu, Jianzhao Liu, Kou-Juey Wu, Chuan He*.

N⁶-deoxyadenosine methylation in mammalian mitochondrial DNA.

Molecular Cell 78, 382-395 (2020).

[10] Chang Liu†, Xiaolong Cui†, Boxuan Simen Zhao†, Pradnya Narkhede, Yawei Gao, Jun Liu, Xiaoyang Dou, Qing Dai, Li-Sheng Zhang, Chuan He*.

DNA 5-methylcytosine specific amplification and sequencing.

J. Am. Chem. Soc. 142, 4539–4543 (2020).

[9] Li-Sheng Zhang†, Chang Liu†, Honghui Ma, Hui-Lung Sun, Qing Dai, Guanzheng Luo, Zijie Scott Zhang, Linda Zhang, Lulu Hu, Xueyang Dong, Chuan He*.

Transcriptome-wide mapping of internal N⁷-methylguanosine methylome in mammalian mRNA.

Molecular Cell 74, 1304–1316 (2019).

[8] Isao Masuda, Ryuma Matsubara, Thomas Christian, Enrique R. Rojas, Srujana S. Yadavalli, Li-Sheng Zhang, Mark Goulian, Leonard Foster, Kerwyn Casey Huang, Ya-Ming Hou*.

tRNA methylation is a global determinant of bacterial multi-drug resistance.

Cell Systems 8, 302–314 (2019).
[7] Xin Li, Xing Che, Gui-Hua Chen, Jun Zhang, Jia-Lei Yan, Yun-Fei Zhang, Li-Sheng Zhang, Chao-Ping Hsu, Yi Qin Gao, Zhang-Jie Shi*.

Site-selective oxidation of targeted aliphatic C–H bonds using a removable electron shuttle tag.

Org. Lett. 18, 1234–1237 (2016).

[6] Wen-Juan Shi, Hong-Wei Zhao, Yang Wang, Zhi-Chao Cao, Li-Sheng Zhang, Da-Gang Yu, Zhang-Jie Shi*.

Nickel- or iron- catalyzed cross-coupling of aryl carbamates with arylsilanes.

Adv. Synth. Catal. 358, 2410–2416 (2016).

[5] Xingyu Lu†, Dali Han†, Boxuan Simen Zhao†, Chun-Xiao Song, Li-Sheng Zhang, Louis C Doré, Chuan He*.

Base-resolution maps of 5-formylcytosine and 5-carboxylcytosine reveal genome-wide DNA demethylation dynamics.

Cell Research 25, 386–389 (2015).

[4] Li-Sheng Zhang, Guihua Chen, Xin Wang, Qing-Yun Guo, Xi-Sha Zhang, Fei Pan, Kang Chen, Zhang-Jie Shi*.

Direct borylation of primary C–H bonds in functionalized molecules by palladium catalysis.

Angew. Chem. Int. Ed. 53, 3899–3903 (2014).

[3] Fei Pan, Peng-Xiang Shen, Li-Sheng Zhang, Zhang-Jie Shi*.

Direct arylation of primary and secondary sp³ C–H bonds with diarylhyperiodonium salts via Pd catalysis.

Org. Lett. 15, 4758–4761 (2013).

[2] Li-Sheng Zhang, Kang Chen, Guihua Chen, Bi-Jie Li, Shuang Luo, Zhang-Jie Shi*.

Palladium-catalyzed trifluoromethylation of aromatic C–H bond directed by an acetamino group.

Org. Lett. 15, 10–13 (2013).

[1] Kang Chen, Hu Li, Zhi-Quan Lei, Yang Li, Wen-He Ye, Li-Sheng Zhang, Jian Sun, Zhang-Jie Shi*.

Reductive cleavage of the C_sp2–C_sp3 bond of secondary benzyl alcohols: Rhodium catalysis directed by N-containing groups.

Angew. Chem. Int. Ed. 51, 9851–9855 (2012).