xuerui yang-凯发k8

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