Zhicheng Ji
Assistant Professor of Biostatistics & Bioinformatics
Current Appointments & Affiliations
- Assistant Professor of Biostatistics & Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2020
Contact Information
- Background
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Education, Training, & Certifications
- Expertise
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Subject Headings
- Research
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Selected Grants
- NSF Engineering Research Center for Precision Microbiome Engineering (PreMiEr) awarded by National Science Foundation 2022 - 2027
- Neuro-immune modulation of pain in health and disease awarded by National Institutes of Health 2022 - 2027
- Targeting Ferroptosis in Lethal RB1 Deficient Prostate Cancer awarded by National Institutes of Health 2022 - 2027
- Sexually dimorphic pain signaling mechanisms awarded by National Institutes of Health 2022 - 2026
- Neural Architecture of the Murine and Human Temporomandibular Joint awarded by National Institutes of Health 2022 - 2025
- Training Program in Bioinformatics at the Intersection of Cancer Immunology and Microbiome awarded by National Institutes of Health 2020 - 2025
- Identification of TMD pain drivers through patient stratification and multi-omic analyses awarded by National Institutes of Health 2022 - 2023
- Publications & Artistic Works
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Selected Publications
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Academic Articles
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Hou, Wenpin, and Zhicheng Ji. “Palo: spatially aware color palette optimization for single-cell and spatial data.” Bioinformatics 38, no. 14 (July 11, 2022): 3654–56. https://doi.org/10.1093/bioinformatics/btac368.Full Text Link to Item
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Stephens, Kimberly E., Weiqiang Zhou, Zachary Renfro, Zhicheng Ji, Hongkai Ji, Yun Guan, and Sean D. Taverna. “Global gene expression and chromatin accessibility of the peripheral nervous system in animal models of persistent pain.” J Neuroinflammation 18, no. 1 (August 26, 2021): 185. https://doi.org/10.1186/s12974-021-02228-6.Full Text Link to Item
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Caushi, Justina X., Jiajia Zhang, Zhicheng Ji, Ajay Vaghasia, Boyang Zhang, Emily Han-Chung Hsiue, Brian J. Mog, et al. “Transcriptional programs of neoantigen-specific TIL in anti-PD-1-treated lung cancers.” Nature 596, no. 7870 (August 2021): 126–32. https://doi.org/10.1038/s41586-021-03752-4.Full Text Link to Item
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Ji, Zhicheng, and Hongkai Ji. “Discussion of "Exponential-family Embedding with Application to Cell Developmental Trajectories for Single-cell RNA-seq Data".” J Am Stat Assoc 116, no. 534 (2021): 471–74. https://doi.org/10.1080/01621459.2021.1880920.Full Text Link to Item
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Dangi, Anil, Naveen R. Natesh, Irma Husain, Zhicheng Ji, Laura Barisoni, Jean Kwun, Xiling Shen, Edward B. Thorp, and Xunrong Luo. “Single cell transcriptomics of mouse kidney transplants reveals a myeloid cell pathway for transplant rejection.” Jci Insight 5, no. 20 (October 15, 2020). https://doi.org/10.1172/jci.insight.141321.Full Text Open Access Copy Link to Item
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Chen, Zeyu, Zhicheng Ji, Shin Foong Ngiow, Sasikanth Manne, Zhangying Cai, Alexander C. Huang, John Johnson, et al. “TCF-1-Centered Transcriptional Network Drives an Effector versus Exhausted CD8 T Cell-Fate Decision.” Immunity 51, no. 5 (November 2019): 840-855.e5. https://doi.org/10.1016/j.immuni.2019.09.013.Full Text
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Guinney, Justin, Tao Wang, Teemu D. Laajala, Kimberly Kanigel Winner, J Christopher Bare, Elias Chaibub Neto, Suleiman A. Khan, et al. “Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data.” Lancet Oncol 18, no. 1 (January 2017): 132–42. https://doi.org/10.1016/S1470-2045(16)30560-5.Full Text Link to Item
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Ji, Zhicheng, and Hongkai Ji. “TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis.” Nucleic Acids Research 44, no. 13 (July 27, 2016): e117–e117. https://doi.org/10.1093/nar/gkw430.Full Text
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Hou, Wenpin, and Zhicheng Ji. “Single-Cell Unbiased Visualization With SCUBI,” n.d.
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Stephens, Kimberly E., Weiqiang Zhou, Zachary Renfro, Zhicheng Ji, Hongkai Ji, Yun Guan, and Sean D. Taverna. “Dynamics of Global Gene Expression and Chromatin Accessibility of the Peripheral Nervous System in Animal Models of Persistent Pain,” n.d.
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