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Publications

2025

  • Wang P, Ye C, Zhao M, Jiang B, He C. Small-molecule-catalysed deamination enables transcriptome-wide profiling of N6-methyladenosine in RNA. Nat Chem. 2025 Jul;17(7):1042-1052. doi: 10.1038/s41557-025-01801-3. Epub 2025 Apr 17. PMID: 40247118; PMCID: PMC12345379.
  • 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, He C. Quantitative RNA pseudouridine maps reveal multilayered translation control through plant rRNA, tRNA and mRNA pseudouridylation. Nat Plants. 2025 Feb;11(2):234-247. doi: 10.1038/s41477-024-01894-7. Epub 2025 Jan 9. Erratum in: Nat Plants. 2025 Feb;11(2):376. doi: 10.1038/s41477-025-01913-1. PMID: 39789092; PMCID: PMC12273003.

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 m6 A 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 & Medicinal Chemistry.
  • Pajdzik, K., et al. (2024‑3). Chemical manipulation of m1 A 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). m6 A‑SAC‑seq for quantitative whole transcriptome m6 A 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/m6 A/NF‑𝜅B 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.