Xuerui YANG Ph. D.
Associate Professor
1999-2003 B.S., Chemical Engineering, Tsinghua University
2003-2009 Dual Major Ph.D., Chemical Engineering & Biochemistry and Molecular Biology, Michigan State University
2009-2012 Post-Doc Research Scientist, Joint Centers for Systems Biology, Irving Cancer Research Center, Columbia University
2012-present Assistant Professor, Associate Professor, School of Life Sciences, Tsinghua University
Research interest
Cancer systems biology and functional multi-omics. Our group has been dedicated to developing question-oriented data-mining tools for dissection of the multi-level gene regulatory programs with complex, multi-modal data. We have been particularly interested in the landscapes of translatomes and translation regulation, modulation of the transcriptional and post-transcriptional regulation circuits under the context of cancer. Emerging from our research investigations are bioinformatics algorithms and deep-learning tools for multi-omics data-mining, resources of biological insights and testable hypotheses that eventually led to novel biological discoveries, mostly in the field of cancer research.
Lab website: labyang.com
Selected publications
1. Wang, Y., Zou, Q., Li, F., Zhao, W., Xu, H., Zhang, W., Deng, H., and Yang, X.*, Identification of the cross-strand chimeric RNAs generated by fusions of bi-directional transcripts. Nat Commun, 2021. 12(1): p. 4645.
2. 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., and Yang, X.*, Mutual dependency between lncRNA LETN and protein NPM1 in controlling the nucleolar structure and functions sustaining cell proliferation. Cell Res, 2021. 31(6): p. 664-683.
3. Wang, X. and Yang, X.*, A Simple Blocking PCR-Based Method for the Synthesis of High-Copy dsDNA Tandem Repeats. Small, 2020: p. e2003671.
4.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.*, and Yu, L.*, COPII mitigates ER stress by promoting formation of ER whorls. Cell Res, 2021. 31(2): p. 141-156.
5.Zhu, M., Zou, Q., Huang, R., Li, Y., Xing, X., Fang, J., Ma, L., Li, L., Yang, X.*, and Yu, L.*, Lateral transfer of mRNA and protein by migrasomes modifies the recipient cells. Cell Res, 2021. 31(2): p. 237-240.
7.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.A.*, eIF3 Associates with 80S Ribosomes to Promote Translation Elongation, Mitochondrial Homeostasis, and Muscle Health. Mol Cell, 2020. 79(4): p. 575-587 e7.
8.Wang, Y., Song, W., Wang, J., Wang, T., Xiong, X., Qi, Z., Fu, W.*, Yang, X.*, and Chen, Y.G.*, Single-cell transcriptome analysis reveals differential nutrient absorption functions in human intestine. J Exp Med, 2020. 217(2).
9.Zou, Q., Xiao, Z., Huang, R., Wang, X., Wang, X., Zhao, H., and Yang, X.*, Survey of the translation shifts in hepatocellular carcinoma with ribosome profiling. Theranostics, 2019. 9(14): p. 4141-4155.
10.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 Rep, 2019. 26(12): p. 3461-3474 e5.
11.Wu, Y., Zhao, W., Liu, Y., Tan, X., Li, X., Zou, Q., Xiao, Z., Xu, H., Wang, Y., and Yang, X.*, Function of HNRNPC in breast cancer cells by controlling the dsRNA-induced interferon response. EMBO J, 2018. 37(23).
12. 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(11): p. 2814-2827.
13. 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 Res, 2018. 78(15): p. 4138-4149.
14. 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.
15. 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.
17. 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.
18. 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.
19. 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.
20. 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.
Contact information
Tel: +86-10-62783943
E-mail: yangxuerui@tsinghua.edu.cn
