Scholars@Duke

• Background
• 

  Education, Training, & Certifications

  • Ph.D., Johns Hopkins Unversity, Bloomberg School of Public Health 2020
• Expertise
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  Subject Headings

  • Big data
  • Biostatistics
  • Computational Biology
  • Genomics
  • Single-Cell Analysis
• 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

  • Academic Articles

    • 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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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    • Hou, Wenpin, and Zhicheng Ji. “Single-Cell Unbiased Visualization With SCUBI,” n.d.
    • 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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