杨雪瑞 博士

研究员(PI),博导


1999-2003  清华大学,化学工程系,学士
2003-2009  美国密歇根州立大学,化学工程系/生物化学及分子生物学系,双学科博士
2009-2012  美国哥伦比亚大学,Irving癌症研究中心,系统生物学联合中心,博士后
2012-至今  清华大学生命科学学院,研究员(PI)、博导

●  研究兴趣、领域:


基因组学与癌症系统生物学:发挥交叉学科的优势,利用统计学、数学、信息科学、计算机科学的概念与工具,针对复杂疾病及相关重要生物学问题开发多组学大数据的生物信息分析方法,并结合实验生物学手段研究肿瘤中基因转录、转录后及翻译组的调控过程,为理解肿瘤致病通路、鉴定干预靶点提供方法学支持、新的科学假说及分子机理信息。实验室有机地结合计算与实验的优势,并开展广泛的合作研究。主要研究方向:

1.肿瘤中跨尺度、多组学大数据的整合分析及基因多级调控网络的构建;

2.翻译组学的系统、定量分析及翻译调控在肿瘤中的参与机制;

3.非编码转录组的系统分析与非编码RNA生物学功能的系统鉴定。

实验室网站:labyang.com

●  代表性论文:


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.

●  联系方式:


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