人体内的病毒组复杂、多样，且与多种人类疾病紧密相关。病毒组学一直是领域内研究的重点。一方面，流感病毒的感染导致了季节性的流行性感染且在个体间存在显著差异，而致癌病毒的感染则是多种癌症发生的直接原因，且它们中的绝大多数都能将其遗传物质整合到人基因组中；另一方面，人基因组中来自祖先病毒感染的内源性逆转录病毒等转座子重复序列元件，则通过其扩散且富集的转录因子结合位点，参与并在进化过程中重塑了免疫相关转录调控网络。因此内源性逆转录病毒等转座子元件在癌症、感染和免疫相关疾病中发挥重要的作用。课题组致力于开发新型多组学测序技术、机器学习与生物信息学算法，研究感染和免疫相关疾病的发病机理和个体差异，指导开发预防和个性化、精准治疗相关疾病的疫苗和药物。

目前招收相关研究方向的本科科研实习生、硕士研究生和博士研究生，欢迎勇于创新、敢于挑战、热爱科研的学生报考并加入该团队，一起勇攀科研高峰。 

2008-09--2014-06   华中农业大学   博士
2004-09--2008-06   华中农业大学   学士

2024年4月至今：研究组组长，中国科学院上海免疫与感染研究所

2021年6月-2024年3月：特任助理教授，京都大学

2020年2月-2021年5月：特任研究员，京都大学

2014年10月-2019年5月：博士后，佛蒙特大学

1. Chen X*#, Zhang JC, Guillaume B#, Fumitaka Inoue#: Cryptic endogenous retrovirus subfamilies in the primate lineage. Under revision with Nature Communications. BioRxiv: https://doi.org/10.1101/2023.12.07.570592

2. Liu G, Chen X, Luan Y, and Li D: VirusPredictor: XGBoost-based software to predict virus-related sequences in human data. Bioinformatics. 2024 Mar 29;40(4):btae192

3. Aracena K, Lin YL, Luo K, Pacis A, Gona S, Mu ZP, Yotova V, Sindeaux R, Pramatarova A, Simon MM, Chen X, Groza C, Lougheed D, Gregoire R, Brownlee D, Li Y, He X, Bujold D, Pastinen T, Bourque G, Barreiro L: Epigenetic variation impacts ancestry-associated differences in the transcriptional response to influenza infection. Nature Genetics. 2024 Mar; 56(3):408-419

4. Ren H*#, Chen X*#, Wang J*, Chen Y, Gandhi S, Bueker A, Tu L, Xiao Q, Fu S, Madireddy A, Li WW, Cao J#: Temporal and structural patterns of hepatitis B virus insertions in hepatocellular carcinoma. Journal of Medical Virology. 2023 Oct;95:e29187

5. Chen X*, Pacis A, Aracena A, Gona S, Kwan T, Groza C, Lin YL, Sindeaux R, Yotova V, Pramatarova A, Simon MM, Pastinen T, Barreiro L, Bourque G: Transposable elements are associated with the variable response to influenza infection. Cell Genomics. 2023 May;3(5):100292

6. Groza C, Chen X, Pacis A, Simon MM, Pramatarova A, Aracena K, Pastinen T, Barreiro L, Bourque G: Genome graphs detect human polymorphisms in active epigenomic states during influenza infection. Cell Genomics. 2023 May;3(5):100294

7. Chen X*#, Guillaume B, Clement G#: Genotyping of transposable element insertions segregating in human populations using short-read re-alignments. Methods Mol Biol. 2023 Jan;2607:63-83

8. Mathkar PP*, Chen X#, Sulovari A, and Li D#: Characterization of hepatitis B virus integrations identified in hepatocellular carcinoma genomes. Viruses. 2021 Jan;13(2):245

9. Chen X*, Li D: Sequencing facility and DNA source associated patterns of virus-mappable reads in whole-genome sequencing data. Genomics. 2021 Jan;113:1189-1198

10. Chen X*, Kost J, Li D: Comprehensive comparative analysis of methods and software for identifying viral integrations. Briefings in Bioinformatics. 2019 Nov 27; 20(6):2088-2097

11. Chen X*, Li D: ERVcaller: Identifying polymorphic endogenous retrovirus and other transposable element insertions using whole-genome sequencing data. Bioinformatics. 2019 Oct;35(20):3913-3922

12. Chen X*, Kost J, Sulovari A, Wong N, Liang WS, Cao J, and Li D: A virome-wide clonal integration analysis platform for discovering cancer viral etiologies. Genome Research. 2019 May;29(5):819-830

日本学術振興会（JSPS）青年科学家基金（主持） 2021-2024，468万日元 

ASHBi 融合研究基金（主持） 2020-2022，440万日元 

ASHBi 融合研究基金（共同主持） 2022-2024，440万日元

（1）Transposable elements are associated with the variable response to influenza infection   2022-12-01
（2）Transposable elements reveal inter-individual variability in the human response to influenza infection   2021-01-15
（3）Identifying and characterizing novel virus integrations in hepatocellular carcinoma genomes by virome-wide analysis of whole-genome sequencing data   2017-10-17