Xuerui YANG, Ph. D.

Principal Investigator, 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, Principle Investigator, 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 multi-omics data. We have been particularly interested in the landscapes of translatomes and translation regulation, modulation of the transcriptional and post-transcriptional regulation circuits in the context of cancer. Emerging from our research investigations are bioinformatics algorithms and data-mining pipelines, resources of biological insights from multi-omics data-mining, and testable hypotheses that eventually led to novel biological discoveries, mostly in the field of cancer research.

Lab website: labyang.com

Selected publications

1.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.

2.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.

3.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).

4.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.

5. 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.

6. 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.

7. 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.

8. 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.

9. 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.

10. 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.

11. 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.

12. 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.

13. 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.

14. 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.

15. Sumazin, P.#, Yang, X.#, Chiu, H.S.#, Chung, W.J., Iyer, A., Llobet-Navas, D., Rajbhandari, P., Bansal, M., Guarnieri, P., Silva, J., and Califano, A.*, An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. Cell, 2011. 147(2): p. 370-81.

Contact information

Tel: +86-10-62783943
E-mail: yangxuerui@tsinghua.edu.cn