2019 年03 月－至今：研究员，博导，中国科学院上海巴斯德研究所，病原生物信息学研究组组长

1. Tang X, Wu C, Li X, Song Y, Yao X, Wu X, Duan Y, Zhang H, Wang Y, Qian Z, Cui J^*, Lu J^*. (2020) On the origin and continuing evolution of SARS-CoV-2. Natl Sci Rev. 7:1012-1023.

2. Wei X, Li X, Cui J^*. (2020) Evolutionary perspectives on novel coronaviruses identified in pneumonia cases in China. Natl Sci Rev. 7:239-242.

3. Li X, Song Y, Wong G, Cui J^*. (2020) Bat origin of a new human coronavirus: there and back again. Sci China Life Sci. 63:461-462.

4. Chen Y, Wei X, Zhang G, Holmes EC, Cui J^*. (2019) Identification and evolution of avian endogenous foamy viruses. Virus Evol. 5:vez049.

5. Wei X, Chen Y, Duan G, Holmes EC, Cui J^*. (2019) A reptilian endogenous foamy virus sheds light on the early evolution of retroviruses. Virus Evol. 5:vez001.

6. Yu P, Hu B, Shi ZL, Cui J^*. (2019) Geographical structure of bat SARS-related coronaviruses. Infect Genet Evol. 69:224-229.

7. Cui J, Li F, Shi ZL^*. (2019) Origin and evolution of pathogenic coronaviruses. Nature Rev Microbiol. 17:181-192.

8. Wei X, Chen M, Cui J^*. (2017) Bayesian evolutionary analysis for emerging infectious disease: an exemplified application for H7N9 avian influenza viruses. Sci China Life Sci. 60:1392-1395.

9. Hu B, Zeng LP, Yang XL, Ge XY, Zhang W, Li B, Xie JZ, Shen XR, Zhang YZ, Wang N,Luo DS, Zheng XS, Wang MN, Daszak P, Wang LF, Cui J^*, Shi ZL^*. (2017) Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus. PLoS Pathog. 13:e1006698.

10. Wang H, Zhao Y, Chen M^*, Cui J^*. (2017) Identification of Novel Long Non-coding and Circular RNAs in Human Papillomavirus-Mediated Cervical Cancer. Front Microbiol. 8:1720.

11. Du Y, Chen M, Yang J, Jia Y, Han S, Holmes EC, Cui J^*. (2017) Molecular evolution and emergence of H5N6 avian influenza virus in central China. J Virol. 91:e00143-17.

12. Cui J^*, Zhao W, Huang Z, Jarvis ED, Gilbert M, Walker PJ, Holmes EC, Zhang G^*. (2014) Low frequency of paleoviral infiltration across the avian phylogeny. Genome Biol.15:539.

13. Cui J, Schlub TE, Holmes EC. (2014). An allometric relationship between the genomelength and virion volume of viruses. J Virol. 88:6403-6410. 

（1）内源逆转录病毒（ERV）与宿主互作（Chen et al., Virus Evol., 2019；Wei et al., Virus Evol., 2019；Hayward et al., Mol Biol Evol., 2018; Cui et al., Genome Biol., 2014）。

（2）冠状病毒起源与进化（Tang et al., Natl Sci Rev., 2020; Wei et al., Natl Sci Rev., 2020; Li et al., Sci China Life Sci., 2020; Cui et al., Nature Rev Microbiol., 2019; Yu et al., Infect Genet Evol., 2019），2项成果受到F1000推荐。

研究组长期从事病原进化、开发病毒组学新方法等研究，特别关注：1) 病毒生态学和病毒组（virome）, 研究组基于基因组测序技术研究病毒在大时间尺度下的进化多态性。同时也利用宏基因组或宏转录组技术来发现未知的新病毒；2）癌症进化，结合高通量及单细胞测序技术，阐述癌症早期发生原因和影响因素，分析肿瘤细胞种群的动态，并从分子数据中推断肿瘤的进化历史；3）基于生物信息学的病原大数据，对新发及再发传染病通过大数据分析，结合系统发生、群体遗传及流行病学进行病原溯源和传播建模。

实验室成员(Lab member)

科研助理：韩紫轩，陈毅聪，任梦

硕士研究生：张誉译，余俊单

硕博连读研究生：樊天娇，李逸岸，李祥，王晓静

联培生：魏小曼，宋雨荷

毕业研究生(Graduate student)

招生信息(admission information)

欢迎具有生物学、病毒学、生物信息学等学科背景的优秀学生加入本团队攻读硕士和博士研究生。