Gene regulation
Learning regulatory networks and chromatin organization from single-cell transcriptomic and epigenetic data.
scENCOREiHerdArtificial Intelligence & Computational Biology
Ziheng Duan
Postdoctoral researcher · Yale University
I develop trustworthy computational methods to understand single-cell gene regulation, particularly in spatial contexts, and translate these insights into disease understanding and drug discovery.
I earned my Ph.D. in Computer Science at UC Irvine, advised by Prof. Jing Zhang. My research connects single-cell genomics and spatial transcriptomics with therapeutic target discovery. I also work with Genesis Molecular AI in computational biology.
Education
Ph.D. in Computer Science
UC Irvine · 2025
B.S. in Automation and Computer Science
Zhejiang University · 2020
Latest updates
News
Joining Prof. Mark Gerstein’s lab at Yale University as a postdoctoral researcher in November 2026.
Upcoming talk: AI-Driven Therapeutic Target Discovery and Cell-State Reprogramming, SCORCH 2026 Fall Meeting, San Diego. Talk details ↗
Earned my Ph.D. in Computer Science from UC Irvine.
Our collaborative study of single-cell transcriptomic and chromatin dynamics in PTSD was published in Nature. Read the paper ↗
01 / Research
From genes to
cellular landscapes.
Learning how cells regulate, communicate,
and change in disease.
Spatial Transcriptomics
Joint analysis across tissue slices and modeling intercellular gene regulation from spatial transcriptomics.
MUSEiMIRACLEDisease & discovery
Identifying disease-associated network changes and prioritizing genes for therapeutic investigation.
PTSD atlas02 / Publications
Selected work
2025
2025
2024
2024
2024
2024
Briefings in Bioinformatics
scENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding
2023
03 / Experience
Industry experience
Apr 2026 – present
Consultant
Genesis Molecular AI Computational Biology
Jun – Sep 2025
Machine Learning Research Intern
Genesis Molecular AI Computational Biology
04 / Talks
Talks & presentations
2026
Upcoming
AI-Driven Therapeutic Target Discovery and Cell-State Reprogramming
Talk · SCORCH 2026 Fall Meeting · September 15, 2026 · San Diego, California
2024
scENCORE: reconstructing chromatin compartments from single-cell epigenetic data
Invited talk · 13th Annual Symposium, Southern California Systems Biology · May 2024
2023
iHerd: identifying key driver genes through changes in gene networks
Invited talk · SCORCH Consortium Meeting · December 2023
05 / Service
Academic community
Google Summer of Code
Mentor
- 2026 · StaR — A Stability-Aware Representation Learning Framework for Spatial Domain Identification
- 2025 · RAG-ST — Retrieval-Augmented Generation for Spatial Transcriptomics
- 2024 · BenchmarkST — Spatial Transcriptomics Gene Imputation Benchmarking
Teaching
Reader · UC Irvine
- ICS 178 · Machine Learning and Data Mining
Winter & Fall 2021 - ICS 6D · Discrete Mathematics for Computer Science
Spring 2022
Reviewing (selected)
Conferences
ISMB · Learning on Graphs (LoG) · IEEE BIBM
Journals
Nature Communications · Genome Medicine · BMC Medicine · IEEE TPAMI · IEEE TKDE · Pattern Recognition · Neural Networks