Publications
# First author
* Correspondence author
Detailed publications on Google scholar page
2026
Yining Liu, Yichen Ma, Panfeng Li, Yongjie Li, Guixian Liang, Xiaoting Zhang, Baofeng Huang, Jinying Peng, Dongyuan Ma, Lu Wang, Ang Li, Chengqi Yi, Feng Liu. tRNA-m1A Modification Safeguards Fetal Liver HSPCs from DNA Damage via Maintaining Iron Homeostasis. Blood. 2026 Apr 13. ONLINE
Wenqing Liu, Yichen Ma, Liping Wang, Bo Lu, Yuyang Dong, Yuan Zhuang, Bo He, Meiling Zhang*, Chengqi Yi*. Quantitative analysis of small RNA pseudouridylation reveals interplay of PUS enzymes in tRNA anticodon stem-loop. Nat Commun. 2026 Feb 16;17(1):2811. ONLINE
Yuan Zhuang#, Qingguo Zhu#, Hao Wu#, Xiangyue Lin#, Yongchang Yan, Puze Geng, Rong Yang, Ruoyu Shen, Yuhao Zhang, Zhixin Lei, Haowei Meng, Aidan Wang, Mingyao Cui, Huifen Xiang, Chengqi Yi*. Single-strand deaminase-assisted editing for functional RNA manipulation. Nat Biotechnol. 2026 Jan 02. ONLINE
2025
Hanxiao Sun#, Qi Teng#, Wenqing Liu#, Rui Guo#, Menghua Li#, Wei Xiong, Qiang Huang, Qianru Yu, Nan Luo, Yang Li, Jinghui Song, Shusheng Gong, Xi Shi, Chengqi Yi, Ke Liu. CRISPR-free RNA base editing mediated PTC-readthrough restores hearing in mice with Otof nonsense mutation. Nat Commun. 2025 Dec 06;17(1):413. ONLINE
Bo He, Yu Fan, Jizhou Liu, Yuting Chen, Jinmin Yang, Huifen Xiang*, Jinying Peng*, Chengqi Yi*. Advancing DNA and RNA Modification Detection via Nanopore Sequencing. ACS Nano. 2025 Nov 04;19(43):37468-37483. ONLINE
Chuyun Shao, Mingyang Li, Liuyi Liu, Dongsheng Bai, Jinmin Yang, Cong Liu, Linxiang Cai, Xiaoyong Wang, Jinying Peng, Zijian Guo, Chengqi Yi*. Pt-seq unveils the genomic binding pattern of platinum-based drugs. Sci Adv. 2025 Oct 31;11(44):eadx6809. ONLINE
Jiaming Li, Mengmeng Jiang, Qiaoran Wang, Zikai Zheng, Jianghua Shen, Jingyi Li, Muzhao Xiong, Yandong Zheng, Xiaoyong Lu, Yusheng Cai, …, Chengqi Yi, …, Guang-Hui Liu*. The X-Age Project to construct a Chinese aging clock. Nat Aging. 2025 Sep;5(9):1669-1685. ONLINE
Nan Luo#, Qiang Huang#, Meiling Zhang#, Chengqi Yi*. Functions and therapeutic applications of pseudouridylation. Nat Rev Mol Cell Biol. 2025 Sep;26(9):691-705. ONLINE
Jiangle Liu#, Xueqing Yan#, Hao Wu#, Ziqin Ji, Ye Shan, Xinyan Wang, Yunfan Ran, Yichen Ma, Caitao Li, Yuchao Zhu, Ruichu Gu, Han Wen, Chengqi Yi*, Peng R. Chen*. RNA codon expansion via programmable pseudouridine editing and decoding. Nature. 2025 Jul;643(8074):1410-1420. ONLINE
Hanxiao Sun, Bo Lu, Zeyu Zhang, Ye Xiao, Zhe Zhou, Xi Lin, Zhichao Li, Zhe Jiang, Jiayi Zhang, Meng Wang, Cong Liu, Yichen Ma, Jinying Peng, Xiujie Wang, Chengqi Yi*. Mild and ultrafast GLORI enables absolute quantification of m6A methylome from low-input samples. Nat Methods. 2025 Jun;22(6):1226-1236. ONLINE
Dongsheng Bai#, Jinmin Yang#, Xiaohui Xue#, Yun Gao#, Yan Wang, Mengge Cui, Bo He, Hu Zeng, Huifen Xiang, Zijian Guo, Lan Zhu, Juan Gao, Chenxu Zhu, Fuchou Tang, Chengqi Yi*. Single-cell 5-hydroxymethylcytosine landscapes of mouse early embryos at single-base resolution. Cell Rep. 2025 Apr 22;44(4):115520. ONLINE
Xiaoting Zhang, Liang Lu, Chengqi Yi, Xiaoyu Li*. Protocol for profiling RNA m5C methylation at base resolution using m5C-TAC-seq. STAR Protoc. 2025 Mar 21;6(1):103599. ONLINE
Bolin Xiang#, Meiling Zhang#, Kai Li#, Zijian Zhang#, Yutong Liu#, Minling Gao, Xiyong Wang, Xiangling Xiao, Yishuang Sun, Chuan He, Jie Shi, Hongzeng Fan, Xixin Xing, Gaoshan Xu, Yingmeng Yao, Gang Chen, Haichuan Zhu, Chengqi Yi*, Jinfang Zhang*. The epitranscriptional factor PCIF1 orchestrates CD8+ T cell ferroptosis and activation to control antitumor immunity. Nat Immunol. 2025 Feb;26(2):252-264. ONLINE
2024
Yujie Wang#, Chen Yang#, Hanxiao Sun, Hui Jiang, Pin Zhang, Yue Huang, Zhenran Liu, Yaru Yu, Zuying Xu, Huifen Xiang*, Chengqi Yi*. The Role of N6-methyladenosine Modification in Gametogenesis and Embryogenesis: Impact on Fertility. Genomics Proteomics Bioinformatics. 2024 Oct 15;22(4):qzae050. ONLINE
Lei Yang#, Yanan Huo#, Man Wang#, Dan Zhang#, Tianai Zhang, Hao Wu, Xichen Rao, Haowei Meng, Shuming Yin, Jiale Mei, Dexin Zhang, Xi Chen, Jia Lv, Meizhen Liu, Yiyun Cheng, Yuting Guan, Bo Feng, Gaojie Song, Chengqi Yi, Mingyao Liu*, Fanyi Zeng*, Liren Wang*, Dali Li*. Engineering APOBEC3A deaminase for highly accurate and efficient base editing. Nat Chem Biol. 2024 Sep;20(9):1176-1187. ONLINE
Zhang, M., Zhang, X., Ma, Y., Yi, C.*. New directions for Ψ and m1A decoding in mRNA: deciphering the stoichiometry and function. RNA. 2024 Apr 16;30(5):537-547. ONLINE
Bo He, Haojun Yao, Chengqi Yi*. Advances in the joint profiling technologies of 5mC and 5hmC. RSC Chem Biol. 2024 Apr 05;5:500-507. ONLINE
Jinghui Song, Nan Luo, Liting Dong, Jinying Peng*, Chengqi Yi*. RNA base editors: The emerging approach of RNA therapeutics. Wiley Interdiscip Rev RNA. 2024 Mar-Apr;15(2):e1844. ONLINE
Nan Luo#, Qiang Huang#, Liting Dong#, Wenqing Liu, Jinghui Song, Hanxiao Sun, Hao Wu, Yuan Gao, Chengqi Yi*. Near-cognate tRNAs increase the efficiency and precision of pseudouridine-mediated readthrough of premature termination codons. Nat Biotechnol. 2024 Mar 06. ONLINE
Song, J #, Zhuang, Y #, Yi, C.* Programmable RNA base editing via targeted modifications. Nat Chem Biol 2024 Feb 28. ONLINE
Bai, D.#, Zhang, X., Xiang, H., Guo Z., Zhu C.*, Yi C.*. Simultaneous single-cell analysis of 5mC and 5hmC with SIMPLE-seq. Nat Biotechnol. 2024, Feb 09. ONLINE
W Shen#, H Sun#, C Liu#, Y Yi#, Y Hou, Y Xiao, Y Hu, B Lu, J Peng, J Wang, …, Yi C.*. GLORI for absolute quantification of transcriptome-wide m6A at single-base resolution. Nat Protoc 2024 Jan 22. ONLINE
He H#, Wang Y#, Zhang X#, Li X#, Liu C, Yan D, Deng H, Sun W, Yi C*, Wang J*. Age-related noncanonical TRMT6-TRMT61A signaling impairs hematopoietic stem cells. Nat Aging. 2024 Feb;4(2):213-230. ONLINE
2023
Zhang, M.#, Xiao, Y.#, Jiang, Z.#, Yi, C.*. Quantifying m6A and Ψ Modifications in the Transcriptome via Chemical-Assisted Approaches. Acc Chem Res. 2023, Oct 18. ONLINE
[82] Lei Z#, Meng H#, Zhuang Y#, Zhu Q, Yi C.*. Chemical and Biological Approaches to Interrogate off-Target Effects of Genome Editing Tools. ACS Chem. Biol. 2023, Feb 18. ONLINE
[81]Sun, H#, Li, K#, Liu, C#, Yi C.*. Regulation and functions of non-m6A mRNA modifications. Nat Rev Mol Cell Biol 2023 Jun 27. ONLINE
[80] Lei Z#, Meng H#, Rao X, Zhao H, Yi C.*. Detect-seq, a chemical labeling and biotin pull-down approach for the unbiased and genome-wide off-target evaluation of programmable cytosine base editors. Nat Protoc 2023 Jun 5. ONLINE
[79] Rao, Xi#; Zhao, Hua#; Shao, Chu; Yi, C.*. Characterizing off-target effects of genome editors. Current Opinion in Biomedical Engineering 2023 100480. ONLINE
[78] Zhang, M.#, Jiang, Z.#, Ma, Y., Liu, W., Zhuang, Y., Lu, B., Li, K., Peng, J., Yi, C.*. Quantitative profiling of pseudouridylation landscape in the human transcriptome. Nat Chem Biol 2023 Mar 30. ONLINE
2022
[77] Song, J.#, Dong, L.#, Sun, H.#, Luo, N.#, Huang, Q.#, Li, K., Shen, X., Jiang, Z., Lv, Z., Peng, L., Zhang, M., Wang, K., Liu, K., Hong, J., Yi, C.*. CRISPR-free, programmable RNA pseudouridylation to suppress premature termination codons. Mol Cell 2022 Dec 3:S1097-2765(22)01100-5. ONLINE
[76] Chen, L.#, Zhu, B.#, Ru, G.#, Meng, H.#, Yan, Y.#, Hong, M., Zhang, D., Luan, C., Zhang, S., Wu, H., Gao, H., Bai, S., Li, C., Ding, R., Xue, N., Lei, Z., Chen, Y., Guan, Y., Siwko, S., Cheng, Y., Song, G., Wang, L., Yi, C.*, Liu, M.*, Li, D*. Re-engineering the adenine deaminase TadA-8e for efficient and specific CRISPR-based cytosine base editing. Nat Biotechnol 2022 Nov 10. ONLINE
[75] Liu, C.#, Sun, H.#, Yi, Y.#, Shen, W.#, Li, K.#, Xiao, Y., Li, F., Li, Y., Hou, Y., Lu, B., Liu, W., Meng, H., Peng, J., Yi, C.*, Wang, J*. Absolute quantification of single-base m6A methylation in the mammalian transcriptome using GLORI. Nat Biotechnol 2022 Oct 27. ONLINE
[74] Shen, Y.#, Ou, J.#, He, B.#, Yang, J., Liu, H., Wang, L., Wang, B., Gao, L., Yi, C., Peng, J.*, Cen, X.*. 5-Hydroxymethylation alterations in cell-free DNA refect molecular distinctions of difuse large B cell lymphoma at diferent primary sites. Clin Epigenetics 2022 Oct 11;14(1):126. ONLINE
[73] Liu, Y.#, Zhou, J.#, Li, X.#, Zhang, X.#, Shi, J.#, Wang, X., Li, H., Miao, S., Chen, H., He, X., Dong, L., Lee, GR., Zheng, J., Liu, RJ., Su, B., Ye, Y., Flavell, RA.*, Yi, C.*, Wu, Y.*, Li, HB.*. tRNA-m1A modification promotes T cell expansion via efficient MYC protein synthesis. Nat Immunol 2022 Oct;23(10):1433-1444. ONLINE
[72] Liu, Y.#, Li, K.#, Xu, YP.#*, Zhu, Z., Zhao, H., Li, XF., Ye, Q., Yi, C.*, Qin, CF.*. Characterization of m6A modifications in the contemporary Zika virus genome and host cellular transcripts. J Med Virol 2022 Sep;94(9):4309-4318. ONLINE
[71] Xiao, M.#, Lu, B.#, Ding, R., Liu, X., Wu, X., Li, Y., Liu, X., Qiu, L., Zhang, Z., Xie, J., Chen, Y., Zhang, D., Dong, L., Zhang, M., Peng, J., Yang, H., Kudihna, T., Xu, Y., Li, T., Yi, C.*, Zhu, L.*. Metatranscriptomic analysis of host response and vaginal microbiome of patients with severe COVID-19. Sci China Life Sci 2022 Jul;65(7):1473-1476. ONLINE
[70] Zhang, M.#, Sun, H.#, Li, K., Xiao, Y., Yi, C.*. m6Am RNA modification detection by m6Am-seq. Methods 2022 Jul;203:242-248. ONLINE
[69] Zhuo, W.#*, Sun, M.#, Wang, K.#, Zhang, L.#, Li, K., Yi, D., Li, M., Sun, Q., Ma, X., Liu, W., Teng, L., Yi, C.*, Zhou, T.*. m6Am methyltransferase PCIF1 is essential for aggressiveness of gastric cancer cells by inhibiting TM9SF1 mRNA translation. Cell Discov 2022 May 21;8(1):48. ONLINE
[68] Lei, Z.#, Meng, H.#, Liu, L.#, Zhao, H.#, Rao, X., Yan, Y., Wu, H., Liu, M., He, A. & Yi, C.*. Mitochondrial base editor induces substantial nuclear off-target mutations. Nature 2022 606(7915), 804-811. ONLINE
2021
[67] Wang, Y.#*, Wang, J.#, Li, X.#, Xiong, X.#, Wang, J., Zhou, Z., Zhu, X., Gu, Y., Dominissini, D., He, L., Tian, Y.*, Yi, C.* & Fan, Z.* N1-methyladenosine methylation in tRNA drives liver tumourigenesis by regulating cholesterol metabolism. Nature Communications 2021 12(1), 1-19. ONLINE
[66] Zhuang, Y.#, Liu, J.#, Wu, H.#, Zhu, Q., Yan, Y., Meng, H., Chen, P., and Yi, C.* Increasing the efficiency and precision of prime editing with guide RNA pairs. Nat Chem Biol 2021 doi.org/10.1038/s41589-021-0088 PDF ONLINE
[65] Zhang M#, Sun H#, Li K, Xiao Y, Yi C.* m6Am RNA modification detection by m6Am-seq. Methods 2021 Oct 5:S1046-2023(21)00226-7. doi: 10.1016/j.ymeth.2021.10.001. Epub ahead of print. PMID: 34624505. PDF ONLINE
[64] Bai D#, Peng J, Yi C.* Advances in single-cell multi-omics profiling. RSC Chem Biol 2021 Jan 20;2(2):441-449. doi: 10.1039/d0cb00163e. PMID: 34458793; PMCID: PMC8341011. PDF ONLINE
[63] Cui, Q.#, Yin, K.#, Zhang, X.#, Ye, P., Chen, X., Chao, J., Meng, H., Wei, J., Roeth, D., Li, L., Qin, Y., Sun, G.H., Zhang, M.Z., Klein, J., Huynhle, M., Wang, C., Zhang, L.Y., Badie, B., Kalkum, M. He, C., Yi, C.* and Shi, Y.H.* Targeting PUS7 suppresses tRNA pseudouridylation and glioblastoma tumorigenesis. Nature Cancer 2021 PDF ONLINE
[62] Sun, H.#, Li, K.#, Zhang, X., Liu, J.E., Zhang, M., Meng, H. and Yi, C.* m6Am-seq reveals the dynamic m6Am methylation in the human transcriptome. Nature Communications 2021 PDF ONLINE
[61] He, B.#, Zhang, C.#, Zhang, X.#, Fan, Y.#, Zeng, H., Meng, H., Bai, D., Peng, J., Zhang, Q.*, Tao, W*. and Yi, C.* Tissue-specific 5-hydroxymethylcytosine landscape of the human genome. Nature Communications 2021 PDF ONLINE
[60] Liu, M.#, Zhang, J.#, Zhu, C.#, Zhang, X.#, Xiao, W., Yan, Y., Liu, L., Zeng, H., Gao, Y.Q.* and Yi, C.* DNA repair glycosylase hNEIL1 triages damaged bases via competing interaction modes. Nature Communications 2021 PDF ONLINE
[59] Lei, Z.#, Meng, H.#, Lv, Z.#, Liu, M., Zhao, H., Wu, H., Zhang, X., Liu, L., Zhuang, Y., Yin, K., Yan, Y. And Yi, C.* Detect-seq reveals out-of-protospacer editing and target-strand editing by cytosine base editors. Nature Methods 2021 PDF ONLINE Cover article
[58]Wang, K.#, Peng, J. and Yi, C.* The m6A Consensus Motif Provides a Paradigm of Epitranscriptomic Studies. Biochemistry 2021 PDF ONLINE
[57] Lu, B.#, Yan, Y., Dong, L., Han, L., Liu, Y., Yu, J., Chen, J., Yi, D., Zhang, M., Deng, X. Wang, C., Wang, R., Wang, D. And Yi C* Integrated characterization of SARS-CoV-2 genome, microbiome, antibiotic resistance and host response from single throat swabs. Cell discovery 2021 PDF ONLINE
[56]Liu, J.E.#, Xu, Y.P.#, Li, K.#, Ye, Q.#, Zhou, H.Y.|#, Sun, H., Li, X., Yu, L., Deng, Y.Q., Li, R.T., Cheng, M.L., He, B., Zhou, J., Li, X.F., Wu, A.P. and Yi C* The m6A methylome of SARS-CoV-2 in host cells. Cell research 2021 PDF ONLINE
2020
[55] Lu B#, Dong L#, Yi D#, Zhang M#, Zhu C, Li X, Yi C.* Transposase-assisted tagmentation of RNA/DNA hybrid duplexes. Elife. 2020 Jul 23;9:e54919. doi: 10.7554/eLife.54919. PMID: 32701057; PMCID: PMC7402673. PDF ONLINE
[54] Li X#, Liang QX, Lin JR, Peng J, Yang JH, Yi C*, Yu Y*, Zhang QF*, Zhou KR*. Epitranscriptomic technologies and analyses. Sci China Life Sci. 2020 Apr;63(4):501-515. doi: 10.1007/s11427-019-1658-x. Epub 2020 Mar 11. PMID: 32170629. PDF ONLINE
[53] Zhao, L.Y.#, Song, J., Liu, Y., Song, C.X. and Yi, C.* Mapping the epigenetic modifications of DNA and RNA. Protein & Cell 2020 PDF ONLINE
2019
[52] Liu L#, Zhang Y, Liu M, Wei W, Yi C, Peng J*. Structural Insights into the Specific Recognition of 5-methylcytosine and 5-hydroxymethylcytosine by TAL Effectors. J Mol Biol. 2020 Feb 14;432(4):1035-1047. doi: 10.1016/j.jmb.2019.11.023. Epub 2019 Dec 19. PMID: 31863750. PDF ONLINE
[51] Song, J.#; Zhuang, Y.#; Zhu, C.#; Meng, H.; Lu, B.; Xie, B.; Peng, J; Li, M.*; Yi, C.* Differential roles of human PUS10 in miRNA processing and tRNA pseudouridylation. Nature Chemical Biology 2020 PDF ONLINE
[50] Liu, J.#; Li, K.#; Cai, J.#; Zhang, M.#; Zhang, X.; Xiong, X.; Meng, H.; Xu, X.; Huang, Z.; Peng, J.; Fan, J.*; Yi, C.* Landscape and Regulation of m6A and m6Am Methylome across Human and Mouse Tissues. Molecular cell 2019 PDF ONLINE
[49] Song J#, Yi C.* Reading Chemical Modifications in the Transcriptome. J Mol Biol. 2019 Oct 16:S0022-2836(19)30598-4. doi: 10.1016/j.jmb.2019.10.006. Epub ahead of print. PMID: 31628951. PDF ONLINE
[48]Li X#, Yi C.* A Novel Epigenetic Mark Derived from Vitamin C. Biochemistry. 2020 Jan 14;59(1):8-9. doi: 10.1021/acs.biochem.9b00779. Epub 2019 Sep 20. PMID: 31538774. PDF ONLINE
[47] Zhu C#, Gao Y, Peng J, Tang F, Yi C.* Single-Cell 5fC Sequencing. Methods Mol Biol. 2019;1979:251-267. doi: 10.1007/978-1-4939-9240-9_16. PMID: 31028643. PDF ONLINE
[46] Li X#, Peng J, Yi C.* Acetylation Enhances mRNA Stability and Translation. Biochemistry. 2019 Mar 26;58(12):1553-1554. doi: 10.1021/acs.biochem.9b00061. Epub 2019 Mar 15. PMID: 30875197. PDF ONLINE
[45] Zeng, H.#; He, B.#; Yi, C.* Compilation of modern technologies to map genome-wide cytosine modifications in DNA. ChemBioChem 2019 PDF ONLINE
2018
[44] Sun, H.#; Zhang, M.#; Li, K.; Bai, D.; Yi, C.* Cap-specific, terminal N(6)-methylation by a mammalian m(6)Am methyltransferase. Cell Res. 2019 PDF ONLINE
[43] Zeng, H.#; Mondal, M.#; Song, R. Y.#; Zhang, J.; Xia, B.; Liu, M. H.; Zhu, C. X.; He, B.; Gao, Y. Q.*; Yi, C. Q.* Unnatural Cytosine Bases Recognized as Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry. Angew Chem Int Edit 2019 PDF ONLINE
[42] Zeng, H.#; He, B.#; Xia, B.; Bai, D. S.; Lu, X. Y.; Cai, J. B.; Chen, L.; Zhou, A. K.; Zhu, C. X.; Meng, H. W.; Gao, Y.; Guo, H. S.; He, C.*; Dai, Q.*; Yi, C. Q.* Bisulfite-Free, Nanoscale Analysis of 5-Hydroxymethylcytosine at Single Base Resolution. J. Am. Chem. Soc. 2018, 140, 13190-13194. PDF ONLINE
[41] Wang, K.#; Yi, C.* Coupling Transcription and Translation via the Epitranscriptomic m(6)A Mark. Biochemistry 2019 PDF ONLINE
[40] Xiong, X.#; Li, X.#; Wang, K.; Yi, C.* Perspectives on topology of the human m(1)A methylome at single nucleotide resolution. RNA 2018, 24, 1437-1442. PDF ONLINE
[39] Xiong, X.#; Li, X.#; Yi, C.* N(1)-methyladenosine methylome in messenger RNA and non-coding RNA. Curr. Opin. Chem. Biol. 2018, 45, 179-186. PDF ONLINE
[38] Shu, X.#; Liu, M.#; Lu, Z.#; Zhu, C.; Meng, H.; Huang, S.; Zhang, X.; Yi, C.* Genome-wide mapping reveals that deoxyuridine is enriched in the human centromeric DNA. Nat. Chem. Biol. 2018, 14, 680-687. PDF ONLINE
[37] Zeng, H.#; He, B.#; Yi, C.*; Peng, J.* Liquid biopsies: DNA methylation analyses in circulating cell-free DNA. J Genet Genomics 2018, 45, 185-192. PDF ONLINE
2017
[36] Zhu, R.#; Song, Y.#; Liu, H.#; Yang, Y.; Wang, S.; Yi, C.; Chen, P. R.* Allosteric histidine switch for regulation of intracellular zinc(II) fluctuation. Proc Natl Acad Sci U S A 2017, 114, 13661-13666. PDF ONLINE
[35] Li, X.#; Xiong, X.#; Zhang, M.#; Wang, K.#; Chen, Y.#; Zhou, J.; Mao, Y.; Lv, J.; Yi, D.; Chen, X. W.; Wang, C.; Qian, S. B.; Yi, C.* Base-Resolution Mapping Reveals Distinct m(1)A Methylome in Nuclear- and Mitochondrial-Encoded Transcripts. Mol. Cell 2017, 68, 1-13. PDF ONLINE
[34] Zhang, Y.#; Liu, L.#; Guo, S.#; Song, J.#; Zhu, C.; Yue, Z.; Wei, W.*; Yi, C.* Deciphering TAL effectors for 5-methylcytosine and 5-hydroxymethylcytosine recognition. Nat Commun 2017, 8, 901. PDF ONLINE
[33] Lei, Z.#; Yi, C.* A Radiolabeling-Free, qPCR-Based Method for Locus-Specific Pseudouridine Detection. Angewandte Chemie 2017, 56, 14878-14882. PDF ONLINE
[32] Zhu, C.#; Gao, Y.#; Guo, H.#; Xia, B.#; Song, J.; Wu, X.; Zeng, H.; Kee, K.; Tang, F.*; Yi, C.* Single-Cell 5-Formylcytosine Landscapes of Mammalian Early Embryos and ESCs at Single-Base Resolution. Cell Stem Cell 2017, 20, 1-12. PDF ONLINE
[31] Xiong, X.; Yi, C.; Peng, J.* Epitranscriptomics: Toward A Better Understanding of RNA Modifications. Genomics Proteomics Bioinformatics 2017, 15, 147-153. PDF ONLINE
[30] Li, X.#; Peng, J.#; Yi, C.* Transcriptome-Wide Mapping of N1-Methyladenosine Methylome. Methods Mol Biol 2017, 1562, 245-255. PDF ONLINE
[29] Song, J#.; Yi, C.* Chemical Modifications to RNA: A New Layer of Gene Expression Regulation. ACS Chem Biol 2017, 12, 316-325. PDF ONLINE
2016
[28] Zhu, C.#; Lu, L.#; Zhang, J.#; Yue, Z.; Song, J.; Zong, S.; Liu, M.; Stovicek, O.; Gao, Y. Q.; Yi, C.* Tautomerization-dependent recognition and excision of oxidation damage in base-excision DNA repair. Proc Natl Acad Sci U S A 2016, 113, 7792-7797. PDF ONLINE
[27] Shu, X.#; Xiong, X.#; Song, J.; He, C.*; Yi, C.* Base-Resolution Analysis of Cisplatin-DNA Adducts at the Genome Scale. Angew. Chem. Int. Ed. Engl. 2016, 55, 14246-14249. PDF ONLINE
[26] Peng, J.#; Xia, B.; Yi, C.* Single-base resolution analysis of DNA epigenome via high-throughput sequencing. Sci China Life Sci 2016, 59, 219-226. PDF ONLINE
[25] Li, X.#; Xiong, X.; Yi, C.* Epitranscriptome sequencing technologies: decoding RNA modifications. Nat Methods 2016, 14, 23-31. PDF ONLINE
[24] Li, X.#; Xiong, X.#; Wang, K.; Wang, L.; Shu, X.; Ma, S.; Yi, C.* Transcriptome-wide mapping reveals reversible and dynamic N(1)-methyladenosine methylome. Nat. Chem. Biol. 2016, 12, 311-316. PDF ONLINE
[23] Li, X.#; Ma, S.#; Yi, C.* Pseudouridine: the fifth RNA nucleotide with renewed interests. Curr. Opin. Chem. Biol. 2016, 33, 108-116. PDF ONLINE
2015
[22] Xia, B.#; Han, D.#; Lu, X.#; Sun, Z.; Zhou, A.; Yin, Q.; Zeng, H.; Liu, M.; Jiang, X.; Xie, W.; He, C.*; Yi, C.* Bisulfite-free, base-resolution analysis of 5-formylcytosine at the genome scale. Nat. Methods 2015, 12, 1047-1050. PDF ONLINE
[21] Song, J.#; Zhu, C.; Zhang, X.; Wen, X.; Liu, L.; Peng, J.; Guo, H.; Yi, C.* Biochemical and Structural Insights into the Mechanism of DNA Recognition by Arabidopsis ETHYLENE INSENSITIVE3. Plos One 2015, 10, e0137439. PDF ONLINE
[20] Li, X.#; Zhu, P.#; Ma, S.#; Song, J.; Bai, J.; Sun, F.; Yi, C.* Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome. Nat. Chem. Biol. 2015, 11, 592-597. PDF ONLINE
[19] Karijolich, J.; Yi, C.; Yu, Y. T. Transcriptome-wide dynamics of RNA pseudouridylation. Nat. Rev. Mol. Cell Biol. 2015, 16, 581-585. PDF ONLINE
2014
[18] Zhu, C.#; Yi, C.* Switching demethylation activities between AlkB family RNA/DNA demethylases through exchange of active-site residues. Angew. Chem. Int. Ed. Engl. 2014, 53, 3659-3662. PDF ONLINE
[17] Zhang, X.#; Zhu, Z.#; An, F.; Hao, D.; Li, P.; Song, J.; Yi, C.*; Guo, H.* Jasmonate-activated MYC2 represses ETHYLENE INSENSITIVE3 activity to antagonize ethylene-promoted apical hook formation in Arabidopsis. Plant Cell 2014, 26, 1105-1117. PDF ONLINE
[16] Yin, Y.#; Yang, L.#; Zheng, G.; Gu, C.; Yi, C.; He, C.; Gao, Y. Q.; Zhao, X. S.* Dynamics of spontaneous flipping of a mismatched base in DNA duplex. Proc Natl Acad Sci U S A 2014, 111, 8043-8048. PDF ONLINE
[15] Lu, L.#; Zhu, C.; Xia, B.; Yi, C.* Oxidative demethylation of DNA and RNA mediated by non-heme iron-dependent dioxygenases. Chem Asian J 2014, 9, 2018-2029. PDF ONLINE
[14] Li, X.#; Song, J.#; Yi, C.* Genome-wide mapping of cellular protein-RNA interactions enabled by chemical crosslinking. Genomics Proteomics Bioinformatics 2014, 12, 72-78. PDF ONLINE
2013
[13] **Yi, C.**#; He, C.* DNA repair by reversal of DNA damage. Cold Spring Harb Perspect Biol 2013, 5, a012575. PDF ONLINE
2012
[12] **Yi, C.**#; Chen, B.; Qi, B.; Zhang, W.; Jia, G.; Zhang, L.; Li, C. J.; Dinner, A. R.; Yang, C. G.; He, C.* Duplex interrogation by a direct DNA repair protein in search of base damage. Nat. Struct. Mol. Biol. 2012, 19, 671-676. PDF ONLINE
[11] Song, C. X.#; Yi, C.; He, C.* Mapping recently identified nucleotide variants in the genome and transcriptome. Nat. Biotechnol. 2012, 30, 1107-1116. PDF ONLINE
[10] Parisien, M.#; **Yi, C.**#; Pan, T.* Rationalization and prediction of selective decoding of pseudouridine-modified nonsense and sense codons. RNA 2012, 18, 355-367. PDF ONLINE
2011
[9] **Yi, C.**#; Pan, T.* Cellular dynamics of RNA modification. Acc. Chem. Res. 2011, 44, 1380-1388. PDF ONLINE
[8] Song, C. X.#; Szulwach, K. E.; Fu, Y.; Dai, Q.; Yi, C.; Li, X.; Li, Y.; Chen, C. H.; Zhang, W.; Jian, X.; Wang, J.; Zhang, L.; Looney, T. J.; Zhang, B.; Godley, L. A.; Hicks, L. M.; Lahn, B. T.; Jin, P.; He, C.* Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat. Biotechnol. 2011, 29, 68-72. PDF ONLINE
[7] Jia, G.#; Fu, Y.#; Zhao, X.#; Dai, Q.; Zheng, G.; Yang, Y.; Yi, C.; Lindahl, T.; Pan, T.; Yang, Y. G.; He, C.* N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat. Chem. Biol. 2011, 7, 885-887. PDF ONLINE
2010
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