Publications

Sorted according to publication date in descending order.

  1. Li, R., Chen, X., Yang, X.*, Navigating the landscapes of spatial transcriptomics: How computational methods guide the way. WIREs RNA, 2024. 🔗
  2. Xiang, X., He, Y., Zhang, Z.*, Yang, X.*, Interrogations of single-cell RNA splicing landscapes with SCASL define new cell identities with physiological relevance. Nat Commun, 2024. 🔗
  3. Zhuang, Y., Li, Z., Xiong, S., Sun, C., Li, B., Wu, S., Lyu, J., Shi, X., Yang, L., Chen, Y., Bao, Z., Li, X., Sun, C., Chen, Y., Deng, H., Li, T., Wu, Q., Qi, L.,Huang, Y., Yang, X.*, Lin, Y.*, Circadian clocks are modulated by compartmentalized oscillating translation. Cell, 2023. 🔗
  4. Li, R., Yang, X.*, De novo reconstruction of cell interaction landscapes from single-cell spatial transcriptome data with DeepLinc. Genome Biol, 2022. 🔗
  5. Hu, X., Zou, Q., Yao, L., Yang, X.*, Survey of the binding preferences of RNA-binding proteins to RNA editing events. Genome Biol, 2022. 🔗
  6. Wang, Y., Zou, Q., Li, F., Zhao W., Xu, H., Zhang, W., Deng, H., Yang, X.*, Identification of the cross-strand chimeric RNAs generated by fusions of bi-directional transcripts. Nat Commun, 2021. 🔗
  7. Wang, X., Hu, X., Song, W., Xu, H., Xiao, Z., Huang, R., Bai, Q., Zhang, F., Chen, Y., Liu, Y., Fang, J., Li, X., Shen, Q., Zhao, H., Yang, X.*, Mutual dependency between lncRNA LETN and protein NPM1 in controlling the nucleolar structure and functions sustaining cell proliferation. Cell Res, 2021. 🔗
  8. Wang, X., Yang, X.*, A Simple Blocking PCR-Based Method for the Synthesis of High-Copy dsDNA Tandem Repeats. Small, 2020. e2003671. 🔗
  9. Zhu, M., Zou, Q., Huang, R., Li, Y., Xing, X., Fang, J., Ma, L., Li, L., Yang, X.*, Yu, L.*, Lateral transfer of mRNA and protein by migrasomes modifies the recipient cells. Cell Res, 2020. 🔗
  10. Xu, F., Du, W., Zou, Q., Wang, Y., Zhang, X., Xing, X., Li, Y., Zhang, D., Wang, H., Zhang, W., Hu, X., Liu, X., Liu, X., Zhang, S., Yu, J., Fang, J., Li, F., Zhou, Y., Yue, T., Mi, N., Deng, H., Zou, P., Chen, X., Yang, X.*, Yu, L.*, COPII mitigates ER stress by promoting formation of ER whorls. Cell Res, 2020. 🔗
  11. Li, F., Xing, X., Xiao, Z., Xu, G., and Yang, X.*, RiboMiner: a toolset for mining multi-dimensional features of the translatome with ribosome profiling data. BMC Bioinformatics, 2020. 21: p. 340.🔗
  12. Lin, Y., Li, F., Huang, L., Polte, C., Duan, H., Fang, J., Sun, L., Xing, X., Tian, G., Cheng, Y., Ignatova, Z., Yang, X.*, and Wolf, D.*, eIF3 Associates with 80S Ribosomes to Promote Translation Elongation, Mitochondrial Homeostasis, and Muscle Health. Mol Cell, 2020. 79(4): p. 575-587.🔗
  13. Wang, Y., Song, W., Wang, J., Wang, T., Xiong, X., Qi, Z., Fu, W.*, Yang, X.*, and Chen, Y.*, Single-cell transcriptome analysis reveals differential nutrient absorption functions in human intestine. J Exp Med, 2020. 217(2): p. e20191130.🔗
  14. Zou, Q., Xiao, Z., Huang, R., Wang, X., Wang, X., Zhao, H., Yang, X.*, Survey of the translation shifts in hepatocellular carcinoma with ribosome profiling. Theranostics, 2019. 9(14): p. 4141-4155.🔗
  15. Liu, Y., Liu, Y., Huang, R., Song, W., Wang, J., Xiao,Z., Dong, S., Yang,Y. and Yang, X.*,Dependency of the Cancer-Specific Transcriptional Regulation Circuitry on the Promoter DNA Methylome. Cell Reports, 2019. 3: p. 3461-3474.🔗
  16. Liu, Y., Huang, R., Liu, Y., Song, W., Wang, Y., Yang, Y., Dong, S. and Yang, X.*, Insights from multidimensional analyses of the pan‐cancer DNA methylome heterogeneity and the uncanonical CpG–gene associations. Int J Cancer, 2018. 143: p. 2814-2827.🔗
  17. Wu, Y., Zhao W., Liu Y., Tan X., Li X., Zou Q., Xiao Z., Xu H., Wang Y., Yang X.*, Function of HNRNPC in breast cancer cells by controlling the dsRNA-induced interferon response. EMBO J, 2018. 37: p. e99017🔗
  18. Li, X., Wang, X., Song, W., Xu, H., Huang, R., Wang, Y., Zhao, W., Xiao, Z., and Yang, X.*, Oncogenic properties of NEAT1 in prostate cancer cells depend on the CDC5L-AGRN transcriptional regulation circuit. Cancer Research, 2018.6. DOI: 10.1158/0008-5472.CAN-18-0688. 🔗
  19. Xiao, Z., Huang, R., Xing, X., Chen, Y., Deng, H., and Yang, X.*, De novo annotation and characterization of the translatome with ribosome profiling data. Nucleic Acids Res, 2018. 46(10): p. e61.🔗
  20. Chiu, H.S., Martinez, M.R., Komissarova, E.V., Llobet-Navas, D., Bansal, M., Paull, E.O., Silva, J., Yang, X.*, Sumazin, P.*, and Califano, A.*, The number of titrated microRNA species dictates ceRNA regulation. Nucleic Acids Res, 2018. 46(9): p. 4354-4369.🔗
  21. Lin, Z., Hsu, P.J., Xing, X., Fang, J., Lu, Z., Zou, Q., Zhang, K.J., Zhang, X., Zhou, Y., Zhang, T., Zhang, Y., Song, W., Jia, G., Yang, X.*, He, C.*, and Tong, M.H.*, Mettl3-/Mettl14-mediated mRNA N(6)-methyladenosine modulates murine spermatogenesis. Cell Res, 2017. 27(10): p. 1216-1230.🔗
  22. Zhang, Y., Xiao, Z., Zou, Q., Fang, J., Wang, Q., Yang, X.*, and Gao, N.*, Ribosome Profiling Reveals Genome-wide Cellular Translational Regulation upon Heat Stress in Escherichia coli. Genomics Proteomics Bioinformatics, 2017. 15(5): p. 324-330.🔗
  23. Xu, W., Xu, H., Li, K., Fan, Y., Liu, Y., Yang, X.*, and Sun, Q.*, The R-loop is a common chromatin feature of the Arabidopsis genome. Nat Plants, 2017. 3(9): p. 704-714.🔗
  24. Wang, Y., Shi, J., Yan, J., Xiao, Z., Hou, X., Lu, P., Hou, S., Mao, T., Liu, W., Ma, Y., Zhang, L., Yang, X., and Qi, H.*, Germinal-center development of memory B cells driven by IL-9 from follicular helper T cells. Nat Immunol, 2017. 18(8): p. 921-930.🔗
  25. Chiu, H.S., Martinez, M.R., Bansal, M., Subramanian, A., Golub, T.R., Yang, X.*, Sumazin, P.*, and Califano, A.*, High-throughput validation of ceRNA regulatory networks. BMC Genomics, 2017. 18(1): p. 418.🔗
  26. Wu, J., Huang, B., Chen, H., Yin, Q., Liu, Y., Xiang, Y., Zhang, B., Liu, B., Wang, Q., Xia, W., Li, W., Li, Y., Ma, J., Peng, X., Zheng, H., Ming, J., Zhang, W., Zhang, J., Tian, G., Xu, F., Chang, Z., Na, J., Yang, X., and Xie, W.*, The landscape of accessible chromatin in mammalian preimplantation embryos. Nature, 2016. 534(7609): p. 652-7.🔗
  27. Xiao, Z., Zou, Q., Liu, Y., and Yang, X.*, Genome-wide assessment of differential translations with ribosome profiling data. Nat Commun, 2016. 7: p. 11194.🔗