Human virome is complex and diverse, and associated with many human diseases. Influenza virus infection causes seasonal epidemics and results in a wide range of disease severity between individuals. Oncovirus infection is responsible for a large proportion of cancer in humans, while most of which could be integrated in the human genome. On the other hand, endogenous retrovirus, a subclass of transposable elements, are derived from ancient retroviruses. Through their distributed and enriched transcriptional factor bindings sites, they co-opt and re-shape the immune-related regulatory networks. Thus, endogenous retroviruses and other TEs play important roles in cancer, infection- and immune-related diseases. 

Our lab focuses on developing innovative multi-omics sequencing technology, machine learning and bioinformatics algorithms to study the pathogenesis and individual variability of infection- and immune-related diseases, and to guide the development of vaccines and drugs for the prevention and precision medicine of these human diseases.

2008-2014: Ph.D., Huazhong Agricultural University, China 

2004-2008: B.S., Huazhong Agricultural University, China

2024-present: Principal Investigator, Shanghai Institute of Immunity and Infection, CAS

2021-2024: Program-specific Assistant Professor, Kyoto University, Japan

2020-2021: Program-specific Researcher, Kyoto University, Japan

2014-2019: Postdoctoral researcher, University of Vermont, USA

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