Zhicheng Ji

Education

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

Positions

• Assistant Professor of Biostatistics & Bioinformatics
• Assistant Professor in the Department of Pierre R. Lamond Department of Electrical and Computer Engineering

Courses Taught

• BIOSTAT 824: Case Studies in Biomedical Data Science

Publications

• Zhuang H, Ji Z. PreTSA: computationally efficient modeling of temporal and spatial gene expression patterns. Genome Biol. 2026 Feb 12;27(1).
• Qu Y, Ji B, Dong R, Gu L, Chan C, Xie J, et al. Single-cell and spatial detection of senescent cells using DeepScence. Cell Genom. 2025 Dec 10;5(12):101035.
• Zhuang H, Shang X, Hou W, Ji Z. Identifying cell-type-specific spatially variable genes with ctSVG. Genome Biol. 2025 Dec 8;26(1):416.
• Ma H, Zhang X, Qu Y, Zhang AR, Ji Z. Vispro improves imaging analysis for Visium spatial transcriptomics. Genome Biol. 2025 Jun 18;26(1):173.
• Wan C, Qu Y, Ye Z, Zhang T, Ma H, Chen M, et al. Comparative analysis of gene regulation in single cells using Compass. Cell Rep Methods. 2025 May 19;5(5):101035.
• Hou W, Ji Z. Assessing GPT-4 for cell type annotation in single-cell RNA-seq analysis. Nat Methods. 2024 Aug;21(8):1462u20135.
• Wang Y, Wang W, Liu D, Hou W, Zhou T, Ji Z. GeneSegNet: a deep learning framework for cell segmentation by integrating gene expression and imaging. Genome Biol. 2023 Oct 19;24(1):235.
• Ji Z, Ma L. Controlling taxa abundance improves metatranscriptomics differential analysis. BMC Microbiol. 2023 Mar 7;23(1):60.
• Hou W, Ji Z. Palo: spatially aware color palette optimization for single-cell and spatial data. Bioinformatics. 2022 Jul 11;38(14):3654u20136.
• Stephens KE, Zhou W, Renfro Z, Ji Z, Ji H, Guan Y, et al. Global gene expression and chromatin accessibility of the peripheral nervous system in animal models of persistent pain. J Neuroinflammation. 2021 Aug 26;18(1):185.
• Caushi JX, Zhang J, Ji Z, Vaghasia A, Zhang B, Hsiue EH-C, et al. Transcriptional programs of neoantigen-specific TIL in anti-PD-1-treated lung cancers. Nature. 2021 Aug;596(7870):126u201332.
• Ji Z, Ji H. Discussion of "Exponential-family Embedding with Application to Cell Developmental Trajectories for Single-cell RNA-seq Data". J Am Stat Assoc. 2021;116(534):471u20134.
• Dangi A, Natesh NR, Husain I, Ji Z, Barisoni L, Kwun J, et al. Single cell transcriptomics of mouse kidney transplants reveals a myeloid cell pathway for transplant rejection. JCI Insight. 2020 Oct 15;5(20).
• Chen Z, Ji Z, Ngiow SF, Manne S, Cai Z, Huang AC, et al. TCF-1-Centered Transcriptional Network Drives an Effector versus Exhausted CD8u00a0T Cell-Fate Decision. Immunity. 2019 Nov;51(5):840-855.e5.
• Guinney J, Wang T, Laajala TD, Winner KK, Bare JC, Neto EC, 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. 2017 Jan;18(1):132u201342.
• Ji Z, Ji H. TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis. Nucleic Acids Research. 2016 Jul 27;44(13):e117u2013e117.
• Stephens KE, Zhou W, Renfro Z, Ji Z, Ji H, Guan Y, et al. Dynamics of Global Gene Expression and Chromatin Accessibility of the Peripheral Nervous System in Animal Models of Persistent Pain.
• Hou W, Ji Z. Single-Cell Unbiased Visualization With SCUBI.