个人简历

1999-2003 清华大学，化学工程系，学士\r
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\r
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\r
2012-至今 清华大学生命科学学院，助理教授、副教授

研究领域

"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：\r
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1. 多模态、跨尺度、多组学大数据的整合分析及多级调控网络与机制解析；\r
2. 大规模复杂生物数据的深度学习工具开发；\r
3. 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；\r
4. 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。"

近期论文

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.\r
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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.\r
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Wang, X. and Yang, X.*, A Simple Blocking PCR-Based Method for the Synthesis of High-Copy dsDNA Tandem Repeats. Small, 2020: p. e2003671.\r
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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.\r
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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.\r
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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.\r
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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).\r
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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.\r
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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.\r
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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).\r
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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.\r
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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.\r
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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.\r
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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.\r
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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.\r
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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.\r
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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.\r
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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.