Pengzhi Zhang
Zhejiang University
We study how disease micro-environments shape human health by integrating multimodal omics with digital pathology. By linking spatial transcriptomics and single-cell genomics to tissue architecture in clinical imaging, we capture how cells interact within complex tissues.
We develop robust, interpretable machine learning methods to analyze large-scale patient data. Our goal is to identify spatial and molecular patterns that inform prognosis, treatment response, and disease risk. By connecting molecular activity with tissue organization, we aim to discover clinically actionable biomarkers and therapeutic targets that advance precision medicine and improve public health.
We are an interdisciplinary group and welcome trainees from biomedical and quantitative fields.
Research
We develop computational methods for multimodal biology, linking cell-state dynamics, tissue morphology, and spatial molecular measurements.
cellDancer
A deep-learning framework for RNA velocity with cell-specific kinetics. By estimating local velocities and relaying them across neighboring cells, cellDancer improves inference of multi-lineage cell-state transitions.
Nature Biotechnology, 2023Loki
A visual-omics platform built from OmiCLIP to align H&E histology with spatial transcriptomics. It turns paired image-omics data into a shared representation for annotation, retrieval, decomposition, and expression prediction.
Nature Methods, 2025Thor
A platform for cell-level spatial transcriptomics and histology. Thor uses anti-shrinking Markov diffusion to refine spot-level measurements toward cell-level tissue maps, paired with interactive whole-slide visualization through Mjolnir.
Nature Communications, 2025CV
Education
-
2016
PhD
University of Houston, Houston, TX, USA
-
Theoretical and Computational Biohysics
- advised by Margaret S. Cheung, Pacific Northwest National Laboratory
-
Research topics
- Biological physics of protein association and regulation on synaptic plasticity
- Induced polarization on light-harvesting macromolecules
-
Theoretical and Computational Biohysics
-
2010
Bachelor of Science
University of Science and Technology of China, Hefei, Anhui Province, China
- Atomic and Molecular Physics
Experience
-
2026 - present
Research Scientist
Zhejiang University
- Digital pathology
- multi-omics
-
2022 - 2026
Research Associate
Houston Methodist Research Institute
- Algorithm development for single-cell RNA-seq analysis
- Spatial transcriptomics analysis using deep learning
-
2017 - 2021
Research Scientist
University of Houston, Houston, TX, USA
- Organic photovoltaic compounds
- Calcium atomic charges in protein environment