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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]
31. Xiong, X.; Yi, C.; Peng, J.* Epitranscriptomics: Toward A Better Understanding of RNA Modifications. Genomics Proteomics Bioinformatics 2017, 15, 147-153.  [PDF]
30. Li, X.#; Peng, J.#; Yi, C.* Transcriptome-Wide Mapping of N1-Methyladenosine Methylome. Methods Mol Biol 2017, 1562, 245-255.  [PDF]
29. Song, J.; Yi, C.* Chemical Modifications to RNA: A New Layer of Gene Expression Regulation. ACS Chem Biol 2017, 12, 316-325.  [PDF]



28. Li, X.; Xiong, X.; Yi, C.* Epitranscriptome sequencing technologies: decoding RNA modifications. Nat Methods 2016, 14, 23-31.  [PDF]
27. Shu, X.#; Xiong, X.#; Song, J.; He, C.*; Yi, C.* Base-Resolution Analysis of Cisplatin-DNA Adducts at the Genome Scale. Angewandte Chemie 2016, 55, 14246-14249.  [PDF]
26. 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]
25. Li, X.#; Ma, S.#; Yi, C.* Pseudouridine: the fifth RNA nucleotide with renewed interests. Curr Opin Chem Biol 2016, 33, 108-116.  [PDF]
24. 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]
23. 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]



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]
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]
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]
19.  Karijolich, J.; Yi, C.; Yu, Y. T.* Transcriptome-wide dynamics of RNA pseudouridylation. Nature reviews. Molecular cell biology 2015, 16, 581-585.  [PDF]



18. Zhu, C.; Yi, C.* Switching demethylation activities between AlkB family RNA/DNA demethylases through exchange of active-site residues. Angewandte Chemie 2014, 53, 3659-3662.   [PDF]
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] 
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]
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]
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]



13. Yi, C.*; He, C.* DNA repair by reversal of DNA damage. Cold Spring Harb Perspect Biol 2013, 5, a012575.  [PDF] 



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]
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]
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] 


Before 2012

9. Yi, C.; Pan, T*. Cellular dynamics of RNA modification. Acc Chem Res 2011, 44, 1380-1388.  [PDF]
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]
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]
6. Yi, C.; Jia, G.; Hou, G.; Dai, Q.; Zhang, W.; Zheng, G.; Jian, X.; Yang, C. G.; Cui, Q.; He, C*. Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase. Nature 2010, 468, 330-333.  [PDF]
5. Lu, L.; Yi, C.; Jian, X.; Zheng, G.; He, C*. Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked protein-DNA system. Nucleic Acids Res 2010, 38, 4415-4425.  [PDF]
4. Chen, H.*; Yi, C.; Zhang, J.; Zhang, W.; Ge, Z.; Yang, C. G.*; He, C.* Structural insight into the oxidation-sensing mechanism of the antibiotic resistance of regulator MexR. Embo Rep 2010, 11, 685-690.  [PDF]
3. Yi, C.; Yang, C. G.; He, C.* A non-heme iron-mediated chemical demethylation in DNA and RNA. Acc Chem Res 2009, 42, 519-529.  [PDF]
2. Yang, C. G.#; Yi, C.#; Duguid, E. M.; Sullivan, C. T.; Jian, X.; Rice, P. A.; He, C.* Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA. Nature 2008, 452, 961-965.  [PDF]
1. Jia, G.#; Yang, C. G.#; Yang, S.; Jian, X.; Yi, C.; Zhou, Z.; He, C.* Oxidative demethylation of 3-methylthymine and 3-methyluracil in single-stranded DNA and RNA by mouse and human FTO. Febs Lett 2008, 582, 3313-3319.  [PDF]


Li, X.; Xiong, X.; Yi, C. Epitranscriptome sequencing technologies: decoding RNA modifications. Nat Methods 2016, 14, 23-31.
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