Skip to content

Publications

2025

  • Wang, P., Ye, C., Zhao, M., Jiang, B., and He, C. (2025-4). Small-molecule-catalysed deamination enables transcriptome-wide profiling of N6-methyladenosine in RNA. Nat Chem. 17, 1042-1052.
  • Li, H., Wang, G., Ye, C., Zou, Z., Jiang, B., Yang, F., He, K., Ju, C., Zhang, L., Gao, B., Liu, S., Chen, Y., Zhang, J., and He, C. (2025-2). Quantitative RNA pseudouridine maps reveal multilayered translation control through plant rRNA, tRNA and mRNA pseudouridylation. Nat Plants. 11, 234-247.

2024

  • Miao, Z., et al. (2024-10). ScRAPdb: an integrated pan-omics database for the Saccharomyces cerevisiae reference assembly panel. Nucleic Acids Research gkae955.
  • Lyu, R., et al. (2024-8). Quantitative analysis of cis-regulatory elements in transcription with KAS-ATAC-seq. Nature Communications 15, 6852.
  • Ross, M. O., et al. (2024-8). PTPN2 copper-sensing relays copper level fluctuations into EGFR/CREB activation and associated CTR1 transcriptional repression. Nature Communications 15, 6947.
  • Zhao, Y., et al. (2024-7). Pseudouridine Detection and Quantification Using Bisulfite Incorporation Hindered Ligation. ACS Chemical Biology 19, 1813-1819.
  • Wang, G.‡, Li, H.‡, Ye, C.‡, He, K., Liu, S., Jiang, B., Ge, R., Gao, B., Wei, J., Zhao, Y., and He, C.* (2024-6). Quantitative profiling of m6A at single base resolution across the life cycle of rice and Arabidopsis. Nature Communications 15, 4881.
  • Pomaville, M., et al. (2024-5). Small-molecule inhibition of the METTL3/METTL14 complex suppresses neuroblastoma tumor growth and promotes differentiation. Cell Reports 43.
  • Sepich-Poore, C., et al. (2024-3). Detection of N3-methylcytidine in RNA at single base resolution using Protoscript II to read through and generate high mutation rates. Bioorganic and Medicinal Chemistry.
  • Pajdzik, K., et al. (2024-3). Chemical manipulation of m1A mediates its detection in human tRNA. RNA 30, 548-559.
  • Zhang, L.-S.‡, Ye, C.‡, Ju, C.-W.‡, Gao, B., Feng, X., Sun, H.-L., Wei, J., Yang, F., Dai, Q., and He, C. (2024-2). BID-seq for transcriptome-wide quantitative sequencing of mRNA pseudouridine at base resolution. Nature Protocols 19, 517-538.
  • Feng, X., et al. (2024-2). Sequencing of N6-methyl-deoxyadenosine at single-base resolution across the mammalian genome. Molecular Cell 84, 596-610.
  • Dai, Q.‡, Ye, C.‡, Irkliyenko, I.‡, Wang, Y.‡, Sun, H.-L., Gao, Y., Liu, Y., Beadell, A., Perea, J., Goel, A., and He, C.* (2024-1). Ultrafast bisulfite sequencing detection of 5-methylcytosine in DNA and RNA. Nature Biotechnology 1-12.
  • Xiao, Y., et al. (2024-1). Profiling of RNA-binding protein binding sites by in situ reverse transcription-based sequencing. Nature Methods 21, 247-258.

2023

  • Jiang, B., et al. (2023-12). Light-induced LLPS of the CRY2/SPA1/FIO1 complex regulating mRNA methylation and chlorophyll homeostasis in Arabidopsis. Nature Plants 9, 2042-2058.
  • Tao, Y., et al. (2023-11). Chemical Proteomic Discovery of Isotype-Selective Covalent Inhibitors of the RNA Methyltransferase NSUN2. Angewandte Chemie International Edition 62, e202311924.
  • Gao, L., et al. (2023-10). Analysis of genome-wide 5-hydroxymethylation of blood samples stored in different anticoagulants. Epigenetics 18, 2271692.
  • Dai, Q., et al. (2023-10). Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution. Nature Biotechnology 41, 344-354.
  • Dou, X., et al. (2023-8). RBFOX2 recognizes N6-methyladenosine to suppress transcription and block myeloid leukaemia differentiation. Nature Cell Biology 25, 1359-1368.
  • Ge, R.‡, Ye, C.‡, Peng, Y., Dai, Q., Zhao, Y., Liu, S., Wang, P., Hu, L., and He, C. (2023-6). m6A-SAC-seq for quantitative whole transcriptome m6A profiling. Nature Protocols 18, 626-657.
  • Chen, L.‡, Zhang, L.-S.‡, Ye, C.‡, Zhou, H., Liu, B., Gao, B., Deng, Z., Zhao, C., He, C., and Dickinson, B. C. (2023-6). Nm-Mut-seq: a base-resolution quantitative method for mapping transcriptome-wide 2'-O-methylation. Cell Research 33, 727-730.
  • Zhang, L., et al. (2023-6). YTHDF2/m6A/NF-kappaB axis controls anti-tumor immunity by regulating intratumoral Tregs. The EMBO Journal 42, e113126.
  • Wang, Y., et al. (2023-6). Enzyme-mediated alkynylation enables transcriptome-wide identification of pseudouridine modifications. bioRxiv.

2022

  • Zhang, L.-S., et al. (2022-11). m7G-quant-seq: Quantitative Detection of RNA Internal N7-Methylguanosine. ACS Chemical Biology 17, 3306-3312.
  • Jia, H., et al. (2022-7). Metabolomic analyses reveal new stage-specific features of COVID-19. European Respiratory Journal 59, 2.

2021

  • Liu, K.‡, Deng, S.‡, Ye, C.‡, Yao, Z., Wang, J., Gong, H., Liu, L., and He, X.* (2021-12). Mapping single-cell-resolution cell phylogeny reveals cell population dynamics during organ development. Nature Methods 18, 1506-1514.

Before 2021

  • Chen, Z.‡, Ye, C.‡, Liu, Z., Deng, S., He, X., and Xu, J. (2020-7). Lineage recording of zebrafish embryogenesis reveals historical and ongoing lineage commitments. bioRxiv.
  • Ye, C., Chen, Z., Liu, Z., Wang, F., and He, X.* (2020-2). Defining endogenous barcoding sites for CRISPR/Cas9-based cell lineage tracing in zebrafish. Journal of Genetics and Genomics 47, 85-91.
  • Yang, B., et al. (2019-12). Assessing the influence of dietary history on gut microbiota. Current Microbiology 76, 237-247.