First/Co-first Author Publications:

1. Bai, D.^#, Cao, Z.^#, Attada, N., Song, J., Zhu, C.*. Single-cell parallel analysis of DNA damage and transcriptome reveals selective genome vulnerability. Nature Methods. (2025), 22, 962-972. (Highlighted in Nature Methods)
2. Bai, D., Zhang, X., Xiang, H., Guo, Z., Zhu, C.* & Yi, C.*. Simultaneous single-cell analysis of 5mC and 5hmC with SIMPLE-seq. Nature Biotechnology (2025), 43(1), 85-96. (Highlighted in Nature Reviews Genetics)
3. Bai, D.^#, Yang, J.^#, Xue, X.^#, Gao, Y.^#, Wang, Y., Cui, M., He, B., Zeng, H., Xiang, H., Guo, Z., Zhu, L., Gao, J., Zhu, C.*, Tang, F.*, Yi, C.*. Single-Cell 5-hydroxymethylcytosine landscapes of mouse early embryos at single-base resolution. Cell Reports. (2025), 44(4), 115520.
4. Bai, D.^#, Cao, Z., Zhu, C.*.The ‘vulnerability code’: Is cell identity the architect of its own decay?. Clinical and Translational Medicine. (2025), e70555.
5. Bai, D.*, Zhu, C.*. SIMPLE-seq to decode DNA methylation dynamics in single cells. Nature Reviews Genetics (2024), 25, 377.
6. Bai, D., Peng, J.* & Yi, C.*. Chemical-assisted epigenome sequencing. Handbook of Chemical Biology of Nucleic Acids. Springer Nature Singapore (2023), 1265-1289.
7. Bai, D., Zhu, C.*. Single-cell technologies for multimodal omics measurements. Frontiers in Systems Biology (2023), 3:1155990.
8. Bai, D., Peng, J., & Yi, C.*. Advances in single-cell multi-omics profiling. RSC Chemical Biology (2021), 2(2), 441-449.
9. Bai, D., & Yi, C.*. Advances in the profiling of single-cell DNA modifications. Small Methods (2019), 3(10), 1900137.

Co-author Publications:

1. Shao, C.^#, Li, M.^#, Liu, L.^#, Bai, D., Liu, C., Cai, L., Wang, X., Guo, Z.*, Yi, C.*. Pt-seq unveils the genomic binding pattern of platinum-based drugs. Science Advances (2025), 11(44), eadx6809
2. He, B.^#, Zhang, C.^#, Zhang, X.^#, Fan, Y., Zeng, H., Liu, J., Meng, H., Bai, D., Peng, J., Zhang, Q.*, Tao, W.*, Yi, C.*. Tissue-specific 5-hydroxymethylcytosine landscape of the human genome. Nature Communications (2021), 12(1), 1-12.
3. Sun, H., Zhang, M., Li, K., Bai, D., & Yi, C.*. Cap-specific, terminal N6-methylation by a mammalian m6Am methyltransferase. Cell Research (2019), 29(1), 80-82.
4. Zeng, H.^#, He, B.^#, Xia, B., Bai, D., Lu, X., Cai, J., Chen, L., Zhou, A., Zhu, C., Meng, H., Gao, Y., Guo, H., He, C.*, Dai, Q.*, Yi, C.*. Bisulfite-free, nanoscale analysis of 5-hydroxymethylcytosine at single base resolution. Journal of the American Chemical Society (2018), 140(41), 13190-13194.
5. Wu, J.^#, Xiao, H.^#, Wang, T., Hong, T., Fu, B., Bai, D., He, Z., Peng, S., Xing, X., Hu, J., Guo, P., Zhou, X.*. N⁶-Hydroperoxy-methyladenosine: A new intermediate of chemical oxidation of N⁶-methyladenosine mediated by bicarbonate-activated hydrogen peroxide. Chemical Science (2015), 6(5), 3013-3017.
6. Fu, B., Huang, J., Bai, D., Xie, Y., Wang, Y., Wang, S.*, & Zhou, X.*. Label-free detection of pH based on the i-motif using an aggregation-caused quenching strategy. Chemical Communications (2015), 51(95), 16960-16963.