Full time faculty

Adjunct professor

Chair professor


Xuerui Yang

Xuerui Yang, Ph. D.

Principal Investigator, Assistant Professor

Young 1000-Talent Plan


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 Interests:

    Cancer systems biology and functional “-omics”. We apply multidisciplinary approaches to systematically study gene regulatory networks and pathways that play important roles in pathogenesis of major diseases such as cancers.

    Both computational and experimental principles from systems biology, bioinformatics, genetics and molecular biology are being used. Current research is focused on post-transcriptional and translational regulatory networks and their detailed functional mechanisms in cancers. Our long-term goal is to provide molecular basis of novel therapeutic approaches.

Representative Publications:

1. Sumazin P*, Yang X*, Chiu HS*, Chung W, Iyer A, Llobet-Navas D, Silva J & Califano A. An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma, Cell, 147(2), 2011: 370-81. (*: co-first author. Featured cover article)

2. Wang X, Nath A, Yang X, Portis A, Walton SP, and Chan C. Synergy analysis reveals association between insulin signaling and desmoplakin expression in palmitate treated HepG2 cells. PLoS ONE, 6(11), 2011: e28138.

3. Yang X, Nath A, Opperman MJ and Chan C. The double-stranded RNA-dependent protein kinase differentially regulates insulin receptor substrates 1 and 2 in HepG2 cells, Molecular Biology of the Cell, 21(19), 2010: 3449-58.

4. Yang X, Zhou Y, Jin R and Chan C. Reconstruct modular phenotype-specific gene networks by knowledge-driven matrix factorization, Bioinformatics, 25(17), 2009: 2236-43.

5. Yang X and Chan C. Repression of PKR mediates palmitate-induced apoptosis in HepG2 cells through Bcl-2, Cell Research, 19(4), 2009: 469-86.

6. Wu M*, Yang X*, and Chan C. A dynamic analysis of IRS-PKR signaling in liver cells: a discrete modeling approach, PLoS ONE, 4(12), 2009: e8040. (*: co-first author)

7. Yang X, Wang X, Wu M, Dalkic E, and Chan C. Construction of gene networks by synergy analysis of the genes related to palmitate-induced cytotoxicity, Methods in Bioengineering: Systems Analysis of Biological Networks, chapter 5, 2009: 75-93.

8. Zhou Y, Li Z, Yang X, Zhang L, Srivastava S, Jin R and Chan C. Using knowledge driven matrix factorization to reconstruct modular gene regulatory network. Assn for the Adv. of Artificial Intelligence proceedings, 2008: 811-6.

9. Li Z, Srivastava S, Yang X, and Chan C. A hierarchical approach employing metabolic and gene expression profiles to identify the pathways that confer cytotoxicity in HepG2 cells, BMC Systems Biology, 1, 2007: 21-35.

10. Srivastava S, Li Z, Yang X, Yedwabnick M, Shaw S, and Chan C. Identification of genes that regulate multiple cellular processes/responses in the context of lipotoxicity in hepatoma cells, BMC Genomics, 8(1), 2007: 364-75.

11. Li Z, Srivastava S, Mittal S, Yang X, Sheng L, and Chan C. A Three Stage Integrative Pathway Search (TIPS©) framework to identify toxicity relevant genes and pathways, BMC Bioinformatics, 8, 2007: 202-18.

12. 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 Research, 2018. In press.

13. Xiao, Z., Zou, Q., Liu, Y., and Yang, X.*, Genome-wide assessment of differential translations with ribosome profiling data. Nature Communications, 2016. 7: p. 11194.
14. 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 Research, 2017. 27(10): p. 1216-1230.

15. 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. Nature Plants, 2017. 3(9): p. 704-714.

16. 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.


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

Tsinghua University,Beijing,China,100084
Tel:+86-10-62788604  Fax:+86-10-62788604  Email:admin-life@biomed.tsinghua.edu.cn