Ding, C.; Wang, Z.; Li, B.-W.; Shao, J.; Tang, Y.; Yang, W.; Weng, X.; Yu, Z.-X.*; Zhou, X.*; Liu, Y.* Mechanistic Insights into the Borane-Mediated Conversion of 5-Carboxylcytosine to Dihydrouracil in DNA Enable an Efficient Labeling Method Using Alkoxyamines. J Am Chem Soc 2025. DOI: 10.1021/jacs.5c13154.

Lin, B.; Jiao, Z.; Dong, S.; Yan, W.; Jiang, J.; Du, Y.; Weng, X.*; Wang, H.*; Hu, Z.*; Liu, Y.*; Zhou, X.* Whole-genome methylation profiling of extracellular vesicle DNA in gastric cancer identifies intercellular communication features. Nat Commun 2025, 16 (1). DOI: 10.1038/s41467-025-63435-w

Chen, X.; Cheng, J.; Kong, L.; Shu, X.; Xu, H.; Inoue, M.; Fernandez-Berrocal, M. S.; Doskeland, D. S.; Bjoras, M.; Sivakumar, S.; Liu, Y.*; Ye, J.*; Song, C. X.* Direct and bisulfite-free 5-methylcytosine and 5-hydroxymethylcytosine sequencing at single-cell resolution with scTAPS and scCAPS +. Genome Biol 2025, 26 (1), 244. DOI: 10.1186/s13059-025-03708-1.

Zhang, S.; Liang, Y.; Feng, T.; Guo, X.; Wang, M.; Ji, T. T.; Xiong, J.; Xiao, X.; Liu, Y.; Liu, Y. B.; Ci, W. M.; Xie, N. B.; Yuan, B. F. Whole-Genome Mapping of DNA Hydroxymethylation at Single-Base Resolution by Double-Stranded DNA Deamination Sequencing. Ccs Chemistry 2025, 1-18, rapid-communications. DOI: 10.31635/ccschem.025.202405023.

Vavoulis, D. V.; Cutts, A.; Thota, N.; Brown, J.; Sugar, R.; Rueda, A.; Ardalan, A.; Howard, K.; Matos Santo, F.; Sannasiddappa, T.; Miller, B.; Ash, S.; Liu, Y.; Song, C. X.; Nicholson, B. D.; Dreau, H.; Tregidgo, C.; Schuh, A. Multimodal cell-free DNA whole-genome TAPS is sensitive and reveals specific cancer signals. Nat Commun 2025, 16 (1), 430. DOI: 10.1038/s41467-024-55428-y.

Geisenberger, C.; van den Berg, J.; van Batenburg, V.; de Barbanson, B.; Lyubimova, A.; Verity-Legg, J.; Chen, X.; Liu, Y.; Song, C.-X.; de Ridder, J.; et al. Single-cell multi-omic detection of DNA methylation and histone modifications reconstructs the dynamics of epigenomic maintenance. Nat. Methods 2025. DOI: 10.1038/s41592-025-02847-4.

Xu, H.; Chen, J.; Cheng, J.; Kong, L.; Chen, X.; Inoue, M.; Liu, Y.; Kriaucionis, S.; Zhao, M.; Song, C. X. Modular Oxidation of Cytosine Modifications and Their Application in Direct and Quantitative Sequencing of 5-Hydroxymethylcytosine. J Am Chem Soc 2023, 145 (13), 7095-7100. DOI: 10.1021/jacs.3c01663

Du, Y.; Tang, Y.; Lin, B.; Xue, X.; Wang, Y.*; Liu, Y.* Bisulfite-free mapping of DNA cytosine modifications: challenges and perspectives. Sci. China Chem. 2023, 66 (11), 3044-3053. DOI: 10.1007/s11426-023-1729-2.

独立前工作

Liu, Y.; Xie, H.; Li, X.; Sun, Y.; Zhu, Z.; Zhao, M. On-line monitoring of the dopamine-based molecular imprinting processes for protein templates with the assistance of a fluorescent indicator. Mikrochim Acta 2022, 189 (4), 138. DOI: 10.1007/s00604-022-05221-9.

Liu, Y.; Hu, Z.; Cheng, J.; Siejka-Zielinska, P.; Chen, J.; Inoue, M.; Ahmed, A. A.; Song, C. X. Subtraction-free and bisulfite-free specific sequencing of 5-methylcytosine and its oxidized derivatives at base resolution. Nat Commun 2021, 12 (1), 618. DOI: 10.1038/s41467-021-20920-2.

Liu, Y.; Cheng, J.; Siejka-Zielinska, P.; Weldon, C.; Roberts, H.; Lopopolo, M.; Magri, A.; D'Arienzo, V.; Harris, J. M.; McKeating, J. A.; et al. Accurate targeted long-read DNA methylation and hydroxymethylation sequencing with TAPS. Genome Biol 2020, 21 (1), 54. DOI: 10.1186/s13059-020-01969-6.

Liu, Y.; Siejka-Zielinska, P.; Velikova, G.; Bi, Y.; Yuan, F.; Tomkova, M.; Bai, C.; Chen, L.; Schuster-Bockler, B.; Song, C. X. Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution. Nat Biotechnol 2019, 37 (4), 424-429. DOI: 10.1038/s41587-019-0041-2.

Liu, Y.; Song, C.; Ladas, I.; Fitarelli-Kiehl, M.; Makrigiorgos, G. M. Methylation-sensitive enrichment of minor DNA alleles using a double-strand DNA-specific nuclease. Nucleic Acids Res 2017, 45 (6), e39. DOI: 10.1093/nar/gkw1166.

Liu, Y.; Fang, S.; Zhai, J.; Zhao, M. Construction of antibody-like nanoparticles for selective protein sequestration in living cells. Nanoscale 2015, 7 (16), 7162-7167. DOI: 10.1039/c4nr07615j.

Liu, Y.; Wang, S.; Zhang, C.; Su, X.; Huang, S.; Zhao, M. Enhancing the selectivity of enzyme detection by using tailor-made nanoparticles. Anal Chem 2013, 85 (10), 4853-4857. DOI: 10.1021/ac4007914.