About me

I’m currently a postdoctoral researcher at the Ragon Institute at MGH, MIT, and Harvard, supervised by Prof. Alex Shalek. Prior to that, I obtained my PhD degree in Microbiology and Immunology from Stanford University, under the supervision of Prof. Garry Nolan. I received my bachelor’s degree in Biology from Cornell University and Zhejiang University.

Research Interest

My doctoral research focused on:

  • Experimental assay development for multiplex imaging platforms
  • Computational algorithm development for single-cell multi-omic integrations
  • Application of the above tools in various biological systems

Selected Publications

Single-cell and Spatial-omics integration
integration spatial-omics single-cell genomics
Shuxiao Chen*, Bokai Zhu*, Sijia Huang, John W. Hickey, Kevin Z. Lin, Michael Snyder, William J. Greenleaf, Garry P. Nolan#, Nancy R. Zhang#, Zongming Ma#
Nature Biotechnology (2023)
Bokai Zhu*, Shuxiao Chen*, Yunhao Bai, Han Chen, Guanrui Liao, Nilanjan Mukherjee, Gustavo Vazquez, David R. McIlwain, Alexandar Tzankov, Ivan T. Lee, Matthias S. Matter, Yury Goltsev, Zongming Ma#, Garry P. Nolan#, Sizun Jiang#
Nature Methods (2023)
Quantitative tissue biology
graph neural network spatial statistics ecology
Bokai Zhu*, Sheng Gao*, Shuxiao Chen*, Yuchen Wang, Jason Yeung, Yunhao Bai, Amy Y. Huang, Yao Yu Yeo, Guanrui Liao, Shulin Mao, Zhenghui G. Jiang, Scott J. Rodig, Ka-Chun Wong, Alex K. Shalek, Garry P. Nolan#, Sizun Jiang#, Zongming Ma#
Nature Immunology (2025)
Daisy Yi Ding*, Zeyu Tang*, Bokai Zhu*, Hongyu Ren, Alex K. Shalek, Robert Tibshirani#, Garry P. Nolan#
Nature Genetics (2025)
Assay development and applications
mucosal immunity tech dev
Bokai Zhu, Yunhao Bai, Yao Yu Yeo, Xiaowei Lu, Xavier Rovira-Clavé, Han Chen, Jason Yeung, Dingani Nkosi, Jonathan Glickman, Antonio Delgado-Gonzalez, Georg K. Gerber, Mike Angelo, Alex K. Shalek, Garry P. Nolan#, Sizun Jiang#
Nature Communications (2025)
Guanrui Liao*, Tsuguhisa Nakayama*, Bokai Zhu*, Ivan T. Lee*, Jason Yeung, Yao Yu Yeo, Yuzhou Chang, Cankun Wang, Steven Chun-Kang Liao, ...., Dan H. Barouch, Qin Ma, Jayakar V. Nayak#, Sizun Jiang#
Immunity (2025)