I am a tenure-track Assistant Professor in the Department of Biostatistics and Bioinformatics at Duke University, where I develop AI-driven methods for biomedical data science. My research focuses on building intelligent, generalizable systems that integrate machine learning, large language models, and multimodal biological data to advance scientific discovery.
A major direction of my work is the use of large language models in biomedical research. I study how models such as GPT-4 can perform tasks including cell-type annotation, code generation, and automated data analysis, and how they compare to human experts. My goal is to transform biomedical data analysis from manual, fragmented pipelines into adaptive, AI-guided systems that improve accessibility, efficiency, and reproducibility.
In parallel, I develop AI and deep learning methods for spatial transcriptomics and biomedical imaging, enabling the integration of molecular and spatial information to better understand tissue organization. I also apply these approaches to study cellular senescence and aging at single-cell resolution.
Overall, my research aims to build next-generation AI systems that not only analyze complex biomedical data but also guide how science is conducted.
Hou W*, Ji Z*. Assessing GPT-4 for cell type annotation in single-cell RNA-seq analysis. 2024.
Nature Methods
Hou W*, Ji Z*. Comparing large language models and human programmers for generating programming code. 2025.
Advanced Science
Ma H, BIOSTAT 824 Student Consortium, Ji Z*. Evaluating large language models in biomedical data science challenges through a classroom experiment. 2025.
PNAS
Zhuang H, Ji Z*. PreTSA: computationally efficient modeling of temporal and spatial gene expression patterns. 2026.
Genome Biology
Zhuang H, Shang X, Hou W*, Ji Z*. Identifying cell-type-specific spatially variable genes with ctSVG. 2025.
Genome Biology
Ma H, Zhang X, Qu Y, Zhang AR, Ji Z*. Vispro improves imaging analysis for Visium spatial transcriptomics. 2025.
Genome Biology
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. 2023. Genome Biology
Qu Y, Ji B, Dong R, Gu L, Chan C, Xie J, Glass C, Wang X, Nixon A, Ji Z*. Single-cell and spatial detection of senescent cells using DeepScence. 2025. Cell Genomics
BIOSTAT 824, Case Studies in Biomedical Data Science (2025). Course Link