Xuerui YANG     Ph.D.

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, Professor, School of Life Sciences, Tsinghua University

Research interest

Bioinformatics and RNA Biology: Developing novel bioinformatics and artificial intelligence algorithms to study post-transcriptional RNA processing, translation, and non-coding RNA regulation. Through in-depth mining of complex omics data and studies of molecular and cellular mechanisms, we aim to decipher the multi-level processing and regulation of genetic information under physiological and pathological conditions, identify RNA intervention targets, and design artificial RNA molecules and processes. Main research topics include:

1. Development of new AI tools for deep mining of multimodal, cross-scale, and complex omics data;

2. Cell-specific regulation of RNA post-transcriptional processing, localization, and translation processes under spatiotemporal resolution;

3. Systematic identification of physiological functions and molecular mechanisms of the non-coding transcriptome;

4. Identification of RNA intervention targets for complex diseases such as cancer and design of artificial functional RNA molecules.

Lab website: labyang.com

Selected publications

1. Kang, Z., Li, R., Liu, C., Dong, X., Hu, Y., Xu, L., Liu, X., Xiang, Y., Gao, L., Si, W., Wang, L., Li, Q., Zhang, L., Wang, H., Yang, X.*, and Liu, J.*, m6A-modified cenRNA stabilizes CENPA to ensure centromere integrity in cancer cells. Cell, 2024. 187(21).

2. Li, R., Chen, X., and Yang, X.*, Navigating the Landscapes of Spatial Transcriptomics: How Computational Methods Guide the Way. Invited Review. WIREs RNA, 2024. 15(2):e1839.

3. Xiang, X., He, Y., Zhang, Z., and Yang, X.*, Interrogations of single-cell RNA splicing landscapes with SCASL define new cell identities with physiological relevance. Nat Commun, 2024. 15(1): p. 2164.

4. Zhuang, Y., Li, Z., Xiong, S., Sun, C., Li, B., Wu, S.A., Lyu, J., Shi, X., Yang, L., Chen, Y., Bao, Z., Li, X., Sun, C., Chen, Y., Deng, H., Li, T., Wu, Q., Qi, L., Huang, Y., Yang, X.*, and Lin, Y.*, Circadian clocks are modulated by compartmentalized oscillating translation. Cell, 2023. 186(15): p. 3245-3260.

5. 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.

6. 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.

7. 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.

8. 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.

9. 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.

10. 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.

11. 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.

12. 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.

13. 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).

14. 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.

15. 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.

Contact information

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