Jing Zhang, Ph.D.

Our lab develops AI and computational genomics methods to understand gene regulation, cellular states, and tissue organization in human disease. We build models for single-cell and spatial omics, integrate functional and regulatory genomics, and connect disease-associated molecular programs to perturbation and therapeutic discovery. We apply these approaches across complex disease, including psychiatric, neurodegenerative, substance-use, HIV-associated, and other human disease settings.

1. 01AI & Machine Learning for Single-Cell and Spatial Genomics
2. 02Gene Regulation & Functional Genomics
3. 03Human Disease Genomics
4. 04AI-Guided Perturbation & Therapeutic Discovery

• TargetSage: Identifying Therapeutic Target Genes with Interpretable and Robust LLM Reasoning

  Ziheng Duan, Tong Wu, Xi Li, Simon Dongbo Sun, Chaoyang Wang, Junhao Liu, Martin Renqiang Min, Jing Zhang

  NeurIPS · 2026 · Accepted

  • AI/ML
  • Perturbation / Therapeutic Discovery

• sMMC-22M: A Context-Aware Dataset and Benchmark for Single-Cell Spatial Transcriptomics

  Xi Li, Yaqi Hu, Ziheng Duan, Xinyi Wang, Simon Dongbo Sun, Diptanshu Sikdar, Yang Liu, Jing Zhang

  NeurIPS · 2026 · Accepted

  • AI/ML for Single-Cell & Spatial

• Single-cell transcriptomic and chromatin dynamics of the human brain in PTSD

  Ahyeon Hwang, Mario Skarica, Siwei Xu, et al.

  Nature · 2025

  • Human Disease Genomics
  • Gene Regulation

  • Paper: Single-cell transcriptomic and chromatin dynamics of the human brain in PTSD

• Single-cell genomics and regulatory networks for 388 human brains

  Prashant S. Emani, Jason J. Liu, Declan Clarke, et al.

  Science · 2024

  • Gene Regulation
  • Human Disease Genomics

  • Paper: Single-cell genomics and regulatory networks for 388 human brains

• MUGO: Differentiable Combinatorial Optimization for Causal Variant Discovery in the Non-coding Genome

  Simon Dongbo Sun, Junhao Liu, Pengcheng Xu, Yaqi Hu, Martin Jinye Zhang, Jing Zhang

  KDD · 2026 · Accepted

  • Gene Regulation
  • Perturbation / Therapeutic Discovery

• Identifying Combinatorial Regulatory Genes for Cell Fate Decision via Reparameterizable Subset Explanations

  Junhao Liu, Pengpeng Zhang, Martin Renqiang Min, Jing Zhang

  KDD · 2025

  • AI/ML for Single-Cell & Spatial
  • Perturbation / Therapeutic Discovery

  • Paper: Identifying Combinatorial Regulatory Genes for Cell Fate Decision via Reparameterizable Subset Explanations