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*: Co-first author
§: Co-senior author
Gabriella Quinn, Gianna Maggiore & Bo Li§. Genomic investigation of innate sensing pathways in the tumor microenvironment. BMC Cancer, 2024.
Jing Hu, Mingyao Pan, Brett Reid, Shelley Tworoger & Bo Li§. Quantifiable blood TCR repertoire components associate with immune aging. Nature Communications, 2024.
Xuexin Yu, Mingyao Pan, Jianfeng Ye, Cassandra A. Hathaway, Shelley S. Tworoger, Jayanthi Lea§, Bo Li§. Quantifiable TCR repertoire changes in prediagnostic blood specimens among patients with high-grade ovarian cancer. Cell Reports Medicine, 2024.
Hongyi Zhang, Bo Li. A novel computational tool for tracking cancer energy hijacking from immune cells. Clinical and Translational Medicine, 2024.
Hongyi Zhang*, Xuexin Yu*, Jianfeng Ye*, Huiyu Li, Jing Hu, Yuhao Tan, Yan Fang, Esra Akbay, Fulong Yu, Chen Weng, Vijay G. Sankaran, Robert M. Bachoo, Elizabeth Maher, John Minna, Anli Zhang§, Bo Li§. Systematic investigation of mitochondrial transfer between cancer cells and T cells at single-cell resolution. Cancer Cell, 2023. PDF file of the paper can be downloaded here.
Mingyao Pan, Bo Li. T cell receptor convergence is an indicator of antigen-specific T cell response in cancer immunotherapies. eLife, 2022.
Galen F Gao, Dajiang Liu, Xiaowei Zhan, Bo Li§. Analysis of KIR gene variants in The Cancer Genome Atlas and UK Biobank using KIRCLE. BMC biology, 2022.
Xuexin Yu*, Wanrun Lin*, Alexandra Spirtos*, Yan Wang, Hao Chen, Jianfeng Ye, Jessica Parker, Ci Ci Liu, Yiying Wang, Gabriella Quinn, Feng Zhou, Setsuko K. Chambers, Cheryl Lewis, Jayanthi Lea§, Bo Li§, Wenxin Zheng§. Dissection of transcriptome dysregulation and immune characterization in women with germline BRCA1 mutation at single-cell resolution. BMC Medicine, 2022.
Daria Beshnova, Yan Fang, Mingjian Du, Yehui Sun, Fenghe Du , Jianfeng Ye, Zhijian James Chen§, Bo Li§. Computational approach for binding prediction of SARS-CoV-2 with neutralizing antibodies. Computational and Structural Biotechnology Journal, 2022.
Longchao Liu*, Jiahui Chen*, Hongyi Zhang*, Jianfeng Ye, Casey Moore, Changzheng Lu, Yan Fang, Yang-xin Fu§, Bo Li§. Concurrent delivery of immune checkpoint blockade modulates T cell dynamics to enhance neoantigen vaccine-generated antitumor immunity. Nature Cancer, 2022.
Xuexin Yu, Bo Li. Seed or soil: Tracing the immune subsets in metastatic tumors. Cancer Cell, 2022.
Christina Wong, Bo Li. AutoCAT: Automated cancer-associated TCRs discovery from TCR-seq data. Bioinformatics, 2021.
Hongyi Zhang, Xiaowei Zhan, Bo Li. GIANA allows computationally-efficient TCR clustering and multi-disease repertoire classification by isometric transformation. Nature Communications, 2021.
Yinghua Li*, Bo Li*, Wei Li*, Yuan Wang, Seçkin Akgül, Daniel Treisman, Kevin Heist, Brianna Pierce, Benjamin Hoff, Cheng-Ying Ho, David Ferguson, Alnawaz Rehemtulla, SiyuanZheng, Brian Ross, Jun Li, and Yuan Zhu. Murine models of IDH-wild-type glioblastoma exhibit spatial segregation of tumor initiation and manifestation during evolution. Nature Communications. 11: 3669 (2020)
Daria Beshnova, Jianfeng Ye, Oreoluwa Onabolu, Benjamin Moon , Wenxin Zheng, Yang-Xin Fu, James Brugarolas, Jayanthi Lea, Bo Li. De novo prediction of cancer-associated TCRs for non-invasive cancer detection. Science Translational Medicine, 2020.
Fathima Zumla Cader, Xihao Hu, Walter L. Goh, Kirsty Wienand, Jing Ouyang, Elisa Mandato, Robert Redd, Lee N. Lawton, Pei-Hsuan Chen, Jason L. Weirather, Ron C.J. Schackmann, Bo Li, Wenjiang Ma, Phillppe Armand, Scott J. Rodig, Donna Neuberg, X. Shirley Liu§ and Margaret A. Shipp§. A peripheral immune signature of responsiveness to PD-1 blockade in patients with classical Hodgkin lymphoma. Nature Medicine, 2020.
Hongyi Zhang*, Longchao Liu*, Jian Zhang, Jiahui Chen, Jianfeng Ye, Sachet Shukla, Jian Qiao, Xiaowei Zhan, Hao Chen, Catherine Wu, Yang-Xin Fu§, & Bo Li§. Investigation of antigen-specific T cell receptor clusters in human cancers. Clin Cancer Res, 2019.
Jian Zhang, Xihao Hu, Jin Wang, Avinash Das Sahu, David Cohen, Li Song, Zhangyi Ouyang, Jingyu Fan, Binbin Wang, Jingxin Fu, Shengqing Gu, Moshe Sade-Feldman, Nir Hacohen, Wuju Li, Xiaomin Ying§, Bo Li§, X Shirley Liu§. Immune receptor repertoires in pediatric and adult acute myeloid leukemia. Genome Medicine 11(1): 1-11, 2019.
Xihao Hu*, Jian Zhang*, Jin Wang, Jingxin Fu, Taiwen Li, Xiaoqi Zheng, Binbin Wang, Shengqing Gu, Peng Jiang, Jingyu Fan, Xiaomin Ying, Jing Zhang,Michael C. Carroll, Kai Wucherpfennig, Nir Hacohen, Fan Zhang, Peng Zhang, Jun S. Liu§, Bo Li§, & X. Shirley Liu§. Landscape of B cell immunity and related immune evasion in human cancers. Nat Genetics, 2019
Xihao Hu*, Jian Zhang*, Jun S. Liu§, Bo Li§, & X. Shirley Liu§, Evaluation of immune repertoire inference methods from RNA-seq data. Nat Biotech, 2018, 36(11):1034-1034
Peng Jiang, Shengqing Gu, Deng Pan, Jingxin Fu, Avinash Sahu, Xihao Hu, Ziyi Li, Nicole Traugh, Xia Bu, Bo Li, Jun Liu, Gordon J Freeman, Myles A Brown, Kai W Wucherpfennig, X Shirley Liu. Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response. Nat Medicine, 2018, 24:1550-1558
Taiwen Li, Jingyu Fan, Binbin Wang, Qianming Chen, Jun S Liu, Bo Li§ and X. Shirley Liu§. TIMER: A web-interface for comprehensive analysis of tumor-infiltrating lymphocytes. (accepted to Cancer Research) (2017).
Bo Li, Jun S Liu and X. Shirley Liu. Revisit linear regression-based deconvolution methods for tumor gene expression data. Genome Biology, 18:127 (2017).
Bo Li§, Taiwen Li, Binbin Wang, Ruoxu Dou, Jun S Liu and X. Shirley Liu§. Ultrasensitive detection of TCR hypervariable region in solid-tissue RNA-seq data. Nature Genetics, 49(4):482-483 (2017).
Bo Li*, Taiwen Li*, Jean-Christophe Pignon, Binbin Wang, Jinzeng Wang, Sachet Shukla, Ruoxu Dou, Qianming Chen, F. Stephen Hodi, Toni K. Choueiri, Catherine Wu, Nir Hacohen, Sabina Signoretti, Jun S. Liu and X. Shirley Liu. Landscape of tumor-infiltrating T cell repertoire of human cancers. Nature Genetics, 48:725–732 (2016).
Bo Li, Eric Severson, Jean-Christophe Pignon, Taiwen Li, Haoquan Zhao, Jesse Novak, Peng Jiang, Hui Shen, Jon C. Aster, Scott Rodig, Sabina Signoretti, Jun S. Liu and X. Shirley Liu, Comprehensive analyses of tumor immunity: implications for cancer immunotherapy. Genome Biology, 17:174 (2016).
Bo Li, J. Z. Li, A general framework for analyzing tumor heterogeneity using DNA sequencing and SNP array data, Genome Biology, 15(9):473 (2014).
Bo Li, Yasin Senbabaoglu, Weiping Peng, Min-Lee Yang, Jishu Xu, and Jun Z. Li, Genomic Estimates of Aneuploid Content in Glioblastoma Multiforme and Improved Classification, Clinical Cancer Research, 18:5595 (2012).
Bo Li*, Bin Shao*, Chenlu Yu*, Qi Ouyang and Hongli Wang, A mathematical model for cell size control in fission yeast, Journal of Theoretical Biology, 264(3): 771-781 (2010).
Chongzhi Zang*, Tao Wang*, Ke Deng, Bo Li, Sheng’en Hu, Qian Qin, Tengfei Xiao, Shihua Zhang, Clifford A. Meyer, Housheng Hansen He, Myles Brown, Jun S. Liu, Yang Xie, X. Shirley Liu. High-dimensional genomic data bias correction and data integration using MANCIE. Nature Communications 7:11305 (2016).
Peng Jiang, Hongfang Wang, Wei Li, Chongzhi Zang, Bo Li, Yinling J Wong, Cliff Meyer, Jun S Liu, Jon C Aster, X Shirley Liu. Network analysis of gene essentiality in functional genomics experiments. Genome Biology 16:239 (2015).
Casey M. Theriot, Mark J. Koenigsknecht, Paul E. Carlson Jr, Gabrielle E. Hatton, Adam M. Nelson, Bo Li, Gary B. Huffnagle, Jun Z. Li & Vincent B. Young, Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection, Nature Communications, 5: 3114 (2014).
Mark Kiel, T. Velusamy, D. Rolland, A. Sahasrabuddhe, F. Chung, N. Bailey, A. Schrader, B. Li, J. Li, A. Ozel, D. Bahler, B. Betz, D. Huebner-Chan, R. Miranda, L. Medeiros, M. Herling, M. Lim and K. Elenitoba-Johnson, Integrated genomic sequencing reveals mutational landscape of T-cell prolymphocytic leukemia, Blood, 124(9): 1460–1472 (2013).