Selected publications

*:corresponding author

#:co-first author

1. Jinying Shen#, Jing Li#, Quan Shen#, Jihuan Hou#, Chunhe Zhang#, Haiqing Bai#, Xiaoni Ai#, Yinlei Su, Zihao Wang, Yunfei Zhang, Beibei Xu, Jiawei Hao, Ping Wang, Qisi Zhang, Adam Yongxin Ye, Zhen Li, Tang Feng, Le Li, Fei Qi, Qikai Wang, Yacong Sun, Chengyao Liu, Xuetong Xi, Lei Yan, Hanhui Hong, Yuting Chen, Xin Xie, Jing Xie, Xiaoheng Liu, Ruikun Du, Roberto Plebani, Lihe Zhang, Demin Zhou, George Church, Longlong Si*. Proteolysis-targeting influenza vaccine strains induce broad-spectrum immunity and in vivo protection. Nature Microbiology 2025, doi: 10.1038/s41564-024-01908-2.
2. Chunhe Zhang#, Jihuan Hou#, Zhen Li#, Quan Shen#, Haiqing Bai#, Li Chen#, Jinying Shen#, Ping Wang#, Yinlei Su, Jing Li, Qisi Zhang, Chengyao Liu, Xuetong Xi, Fei Qi, Yuting Chen, Xin Xie, Adam Yongxin Ye, Xiaoheng Liu, Roberto Plebani, George Church, Longlong Si*. PROTAR Vaccine 2.0 generates influenza vaccines by degrading multiple viral proteins. Nature Chemical Biology 2025, doi: 10.1038/s41589-024-01813-z.

3. Le Tong#,*, Weiyingqi Cui, Boya Zhang, Pedro Fonseca, Qian Zhao, Ping Zhang, Beibei Xu, Qisi Zhang, Zhen Li, Brinton Seashore-Ludlow1, Ying Yang, Longlong Si*, Andreas Lundqvist*. Patient-derived organoids in precision cancer medicine. Med 2024, 5 (11), 1351-1377.

4. Longlong Si#,*, Quan Shen#, Jing Li#, Li Chen, Jinying Shen, Xue Xiao, Haiqing Bai, Tang Feng, Adam Yongxin Ye, Le Li, Chunhe Zhang, Zhen Li, Ping Wang, Crystal Yuri Oh, Atiq Nurani, Siwen Niu, Chengxin Zhang, Xiaoqiong Wei, Wanqiong Yuan, Hao Liao, Xiaojie Huang, Ning Wang, Wen-xia Tian, Hongwei Tian, Li Li, Xiaoheng Liu, Roberto Plebani. Generation of a live attenuated influenza A vaccine by proteolysis targeting. Nature Biotechnology 2022, doi: 10. 1038/s41587-022-01381-4.

5. Haiqing Bai#, Longlong Si#,Amanda Jiang, Chaitra Belgur, Yunhao Zhai, Roberto Plebani, Crystal Yuri Oh, Melissa Rodas, Aditya Patil, Atiq Nurani, Sarah E Gilpin, Rani K Powers, Girija Goyal, Rachelle Prantil-Baun, Donald E Ingber*. Mechanical control of innate immune responses against viral infection revealed in a human lung alveolus chip. Nature Communications 2022, 13 (1): 1928.

6. Longlong Si#, Haiqing Bai#, Crystal Yuri Oh, Amanda Jiang, Fan Hong, Tian Zhang, Yongxin Ye, Tristan X. Jordan, James Logue, Marisa McGrath, Chaitra Belgur, Karina Calderon, Atiq Nurani, Wuji Cao, Kenneth E. Carlson, Rachelle Prantil-Baun, Steven P. Gygi, Dong Yang, Colleen B. Jonsson, Benjamin R. tenOever, Matthew Frieman, Donald E. Ingber*. Self-assembling short immunostimulatory duplex RNAs with broad spectrum antiviral activity. Molecular Therapy-Nucleic Acids 2022, doi: 10. 1016/j.omtn.2022.08.031.

7. Longlong Si#, Haiqing Bai#, Melissa Rodas, Wuji Cao, Crystal Yuri Oh, Amanda Jiang, Rasmus Moller, Daisy Hoagland, Kohei Oishi, Shu Horiuchi, Skyler Uhl, Daniel Blanco-Melo, Randy A Albrecht, Wen-Chun Liu,Tristan Jordan, Benjamin E Nilsson-Payant, Ilona Golynker, Justin Frere, James Logue, Robert Haupt, Marisa McGrath, Stuart Weston, Tian Zhang, Roberto Plebani, Mercy Soong, Atiq Nurani, Seong Min Kim, Danni Y Zhu, Kambez H Benam, Girija Goyal, Sarah E Gilpin, Rachelle Prantil-Baun, Steven P Gygi, Rani K Powers, Kenneth E Carlson, Matthew Frieman, Benjamin R TenOever, Donald E. Ingber*. A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics. Nature Biomedical Engineering 2021, 5 (8), 815-829.

8. Longlong Si#, Haiqing Bai#, Crystal Yuri Oh, Lei Jin, Rachelle Prantil-Baun, Donald E Ingber*. Clinically Relevant Influenza Virus Evolution Reconstituted in a Human Lung Airway-on-a-Chip. Microbiology Spectrum 2021, 9 (2), e00257-21. 6.
9. Longlong Si, Kun Meng, Zhenyu Tian, Jiaqi Sun, Huiqiang Li, Ziwei Zhang, Veronica Soloveva, Haiwei Li, Ge Fu, Qing Xia, Sulong Xiao, Lihe Zhang, Demin Zhou*. Triterpenoids manipulate a broad range of virus-host fusion via wrapping the HR2 domain prevent in viral envelopes. Science Advances 2018, 4, eaau8408. DOI: 10. 1126/sciadv.aau8408.
10. Longlong Si#, Huan Xu#, Xueying Zhou, Ziwei Zhang, Zhenyu Tian, Yiming Wu, Bo Zhang, Yan Wang,Zhenglan Niu, Chuanling Zhang, Ge Fu, Sulong Xiao, Qing Xia, Lihe Zhang, Demin Zhou*. Generation of influenza A viruses as live but replication-incompetent virus vaccines. Science 2016, 354, 1170- 1173.