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

RNA bioinformatics and cancer systems biology. 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. Li, F., Fang, J., Yu, Y., Hao, S., Zou, Q., Zeng, Q., and Yang, X.*, Reanalysis of ribosome profiling datasets reveals a function of rocaglamide A in perturbing the dynamics of translation elongation via eIF4A. Nat Commun, 2023. 14(1): p. 553.

2. Hu, X., Zou, Q., Yao, L., and Yang, X.*, Survey of the binding preferences of RNA-binding proteins to RNA editing events. Genome Biol, 2022. 23(1): p. 169.

3. Li, R. and Yang, X.*, De novo reconstruction of cell interaction landscapes from single-cell spatial transcriptome data with DeepLinc. Genome Biol, 2022. 23(1): p. 124.

4. 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.

5. 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.

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

7. 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.

8. 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.

9. 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.

10. 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.

11. 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.

12. 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).

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. 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.

Contact information

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