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Bo Li, Ph.D.
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Associate Professor of Pathology and Laboratory Medicine
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Department: Pathology and Laboratory Medicine
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Contact information
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3501 Civic Center Blvd.
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Philadelphia, PA 19104
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Philadelphia, PA 19104
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Office: 734-546-7574
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Email:
libo2@pennmedicine.upenn.edu
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libo2@pennmedicine.upenn.edu
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Education:
21 9 B.S. 28 (Physics; Advisor: Ouyang Qi) c
2b Peking University , 2009.
21 a Ph.D. 2f (Bioinformatics; Advisor: Jun Z. Li) c
30 University of Michigan , 2014.
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Permanent link21 9 B.S. 28 (Physics; Advisor: Ouyang Qi) c
2b Peking University , 2009.
21 a Ph.D. 2f (Bioinformatics; Advisor: Jun Z. Li) c
30 University of Michigan , 2014.
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Description of Research Expertise
59d My research focuses on decoding the functional impacts of adaptive immune receptors using computational, genomic and experimental approaches. We are a hybrid lab with both wet and dry components. We have three major ongoing directions: First, the adaptive immune system is sensitive to early disease cues, such as cancer, providing a unique opportunity for detection of early-stage cancers. My lab is dedicated to developing novel computational tools to extract useful information from the TCR or BCR repertoires to achieve immune-based early cancer detection. Second, we investigate the complicated interactions between tumor and the immune system through novel methodology development. In a recent work, we observed that cancer cells can 'hijack' mitochondria from nearby T cells, thus causing T cell metabolic dysfunction. We have introduced a novel computational tool to investigate this process in the human cancers, and we are actively investigating potential targets to block this process. Third, autologous antibodies produced by tumor-infiltrating B/plasma cells provide valuable information in the spontaneous anti-tumor immune response. We develop novel deep neural network methods to infer the antibody-antigen interactions by using the BCR sequences identified in the tumor microenvironment, aiming to find novel tumor antigen targets as well as high-affinity antibodies for effective cancer immunotherapies.e 29
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148 Xuexin Yu, Mingyao Pan, Jianfeng Ye, Cassandra A Hathaway, Shelley Tworoger, Jayanthi Lea§, Bo Li§: Quantifiable TCR repertoire changes in pre-diagnostic blood specimens among high-grade ovarian cancer patients. Cell Reports Medicine 5(7): 101612, 2024.
1a7 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 and Bo Li: Systematic investigation of mitochondrial transfer between cancer cells and T cells at single-cell resolution. Cancer Cell 41: 1788-1802, Oct 2023.
148 Longchao Liu*, Jiahui Chen*, Hongyi Zhang*, Jianfeng Ye, Changzheng Lu, Yang-Xin Fu§ and Bo Li§: Concurrent delivery of immune checkpoint blockade improves tumor microenvironment for vaccine-generated immunity. Nature Cancer 3(4): 437-452, October 2022.
109 Pan Mingyao, Li Bo : T cell receptor convergence is an indicator of antigen-specific T cell response in cancer immunotherapies. eLife 11(e81952), November 2022 Notes: DOI: 10.7554/eLife.81952.
119 Hongyi Zhang, Xiaowei Zhan, Bo Li§: GIANA allows computationally-efficient TCR clustering and multi-disease repertoire classification by isometric transformation. Nature Communications 12(4699), August 2021.
159 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 12(557): eaaz3738, August 2020.
155 Hongyi Zhang*, Longchao Liu*, Jian Zhang, Jiahui Chen, Jianfeng Ye, Sachet Shukla, Jian Qiao, Xiaowei Zhan, Catherine Wu, Yang-Xin Fu§, Bo Li§: Investigation of antigen-specific T cell clusters in human cancers. Clinical Cancer Research 26(6): 1359-1371, March 2020.
1c8 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 W. 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 51: 560-567, February 2019.
113 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, March 2017.
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Selected Publications
f7 Jing Hu, Mingyao Pan, Brett Reid, Shelley Tworoger, Bo Li: Quantifiable blood TCR repertoire components associated with immune aging. Nature Communications 15(1): 8171, 2024.148 Xuexin Yu, Mingyao Pan, Jianfeng Ye, Cassandra A Hathaway, Shelley Tworoger, Jayanthi Lea§, Bo Li§: Quantifiable TCR repertoire changes in pre-diagnostic blood specimens among high-grade ovarian cancer patients. Cell Reports Medicine 5(7): 101612, 2024.
1a7 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 and Bo Li: Systematic investigation of mitochondrial transfer between cancer cells and T cells at single-cell resolution. Cancer Cell 41: 1788-1802, Oct 2023.
148 Longchao Liu*, Jiahui Chen*, Hongyi Zhang*, Jianfeng Ye, Changzheng Lu, Yang-Xin Fu§ and Bo Li§: Concurrent delivery of immune checkpoint blockade improves tumor microenvironment for vaccine-generated immunity. Nature Cancer 3(4): 437-452, October 2022.
109 Pan Mingyao, Li Bo : T cell receptor convergence is an indicator of antigen-specific T cell response in cancer immunotherapies. eLife 11(e81952), November 2022 Notes: DOI: 10.7554/eLife.81952.
119 Hongyi Zhang, Xiaowei Zhan, Bo Li§: GIANA allows computationally-efficient TCR clustering and multi-disease repertoire classification by isometric transformation. Nature Communications 12(4699), August 2021.
159 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 12(557): eaaz3738, August 2020.
155 Hongyi Zhang*, Longchao Liu*, Jian Zhang, Jiahui Chen, Jianfeng Ye, Sachet Shukla, Jian Qiao, Xiaowei Zhan, Catherine Wu, Yang-Xin Fu§, Bo Li§: Investigation of antigen-specific T cell clusters in human cancers. Clinical Cancer Research 26(6): 1359-1371, March 2020.
1c8 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 W. 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 51: 560-567, February 2019.
113 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, March 2017.
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