Research

28 papers, grouped by theme · Google Scholar

Agentic systems for scientific discovery

Multi-agent frameworks that plan, run, and reason over scientific analyses.

PantheonOS: An Evolvable Multi-Agent Framework for Automatic Genomics Discovery
Weize Xu , Erwin Poussi , Quan Zhong , Zehua Zeng , Christopher Zou , Xuehai Wang , Yifan Lu , Miao Cui , Daiji Okamura , Cinlong Huang , Jiayuan Ding , Zhe Zhao , et al.
First author · bioRxiv · 2026
Universal agentic probe design for imaging-based spatial-omics
Qian Zhang , Huaiyuan Cai , Jiahao Zhang , Lingkai Zhang , Xiaoyu Wu , Yuting Wei , Yu Chen , Xiaofeng Wu , Wenru Su , Wenbao Qi , Xiaojie Qiu , Gang Cao , Weize Xu
Corresponding author · bioRxiv · 2026

Imaging-based spatial transcriptomics

Methods and deep-learning tools that read gene expression in situ from microscopy.

U-FISH: a fluorescent spot detector for imaging-based spatial-omics analysis and AI-assisted FISH diagnosis
Weize Xu , Huaiyuan Cai , Qian Zhang , Zhengze Wang , Jiajun Yang , Xiaofeng Wu , Chengwen Li , Chenghua Cui , Changzhi Liu , Jing He , Florian Mueller , Jinxia Dai , et al.
First author · Genome Biology · 2025
Spatial multi-omics at subcellular resolution via high-throughput in situ pairwise sequencing
Xiaofeng Wu , Weize Xu , Lulu Deng , Yue Li , Zhongchao Wang , Leqiang Sun , Anran Gao , Haoqi Wang , Xiaodan Yang , Chengchao Wu , Yan Zou , Keji Yan , et al.
Co-first author · Nature Biomedical Engineering · 2024
A Guide for Spatial Omics Technologies: Innovation, Evaluation, and Application
Xiaofeng Wu , Weize Xu , Da Lin , Leqiang Sun , Jinxia Dai , Gang Cao
Advancement of science · 2026
The application and prospects of spatial omics technologies in clinical medical research and molecular diagnostics
Xiaofeng Wu , Weize Xu , Da Lin , Leqiang Sun , L. Loo , Jinxia Dai , Gang Cao
Journal of genetics and genomics = Yi chuan xue bao · 2025

3D genomics

Mapping and visualizing chromosome conformation and the spatial organization of the genome.

Decoding the spatial chromatin organization and dynamic epigenetic landscapes of macrophage cells during differentiation and immune activation
Da Lin , Weize Xu , Ping Hong , Chengchao Wu , Zhihui Zhang , Siheng Zhang , Lingyu Xing , Bing Yang , Wei Zhou , Qin Xiao , Jinyue Wang , Cong Wang , et al.
Co-first author · Nature Communications · 2022
CoolBox: a flexible toolkit for visual analysis of genomics data
Weize Xu , Quan Zhong , Da Lin , Guoliang Li , Gang Cao
First author · BMC Bioinformatics · 2021
Identification of multiple genomic alterations and prediction of neoantigens from circulating tumor cells at the single-cell level
Xiaochen Gao , Xinyu Li , Weize Xu , Ming Jiao , Yu Guo , Jiajia Wang , Weihao Wang , Jiling Feng , Qianqian Guo , Chengchao Wu , Taiyu Zhang , Yuqin Yang , Da Lin
Nature Communications · 2025
MGA-seq: robust identification of extrachromosomal DNA and genetic variants using multiple genetic abnormality sequencing
Da Lin , Yan Zou , Xinyu Li , Jinyue Wang , Qin Xiao , Xiaochen Gao , Fei Lin , Ningyuan Zhang , Ming Jiao , Yu Guo , Zhaowei Teng , Shiyi Li , et al.
Genome Biology · 2023
3D genome architecture coordinates trans and cis regulation of differentially expressed ear and tassel genes in maize
Yonghao Sun , Liang Dong , Ying Zhang , Da Lin , Weize Xu , Changxiong Ke , Linqian Han , Lulu Deng , Guoliang Li , D. Jackson , Xingwang Li , Fang Yang
Genome Biology · 2020
+ 4 more on Google Scholar →

Microbiology

Host–pathogen biology and functional genomics of bacterial and viral infection.

Rapid bacteria identification using structured illumination microscopy and machine learning
Ying He , Weize Xu , Yao Zhi , R. Tyagi , Zhe Hu , Gang Cao
Co-first author · 2018
Heterogeneous viral-host response at single-cell resolution and viral adaptive mutational atlas in birds and mammals upon H5 influenza virus infection
Jiahao Zhang , Huaiyuan Cai , Tingting Man , Lihong Huang , Letian Li , Yu Chen , Haixing Yang , Shiping Ding , Yiqun Chen , Ruixuan Zhu , Zhengze Wang , Qian Zhang , et al.
National Science Review · 2026
Interactome between ASFV and host immune pathway proteins
Qijun Wu , Yingying Lei , Ya-Gang Zuo , Ji Zhang , Fenglin Guo , Weize Xu , Tanghui Xie , Dang Wang , Guiqing Peng , Xiangru Wang , Huanchun Chen , Zhenfang Fu , Gang Cao , Jinxia Dai
mSystems · 2023
Reprogramming Mycobacterium tuberculosis CRISPR System for Gene Editing and Genome-wide RNA Interference Screening
K. Rahman , M. Jamal , X. Chen , Wei Zhou , Bin Yang , Yan Zou , Weize Xu , Yingying Lei , Chengchao Wu , Xiaojian Cao , R. Tyagi , Muhammad Ahsan Naeem , et al.
Genomics, Proteomics & Bioinformatics · 2021
Distinct Persistence Fate of Mycobacterium tuberculosis in Various Types of Cells
Xi Chen , Xiaojian Cao , Yingying Lei , Aikebaier Reheman , Wei Zhou , Bing Yang , Weipan Zhang , Weize Xu , S. Dong , R. Tyagi , Zhenfang Fu , Gang Cao
mSystems · 2021
+ 2 more on Google Scholar →

Other contributions

Selected collaborative work across single-cell biology, immunology, and gene delivery.

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Neuron-derived neuropeptide Y fine-tunes the splenic immune responses
Jinsong Yu , Ke Xiao , Xiaohua Chen , Lulu Deng , Lu Zhang , Yue Li , Anran Gao , J. Gao , Chengchao Wu , Xinmei Yang , Qiudi Zhou , Jian Yang , et al.
Neuron · 2022
Strategies to package recombinant Adeno-Associated Virus expressing the N-terminal gasdermin domain for tumor treatment
Yuan Lu , Wenbo He , Xin Huang , Yu He , Xiaojuan Gou , Xiaoke Liu , Zhe Hu , Weize Xu , K. Rahman , Shan Li , Sheng Hu , Jie Luo , Gang Cao
Nature Communications · 2021
Remodels the Immunosuppressive Tumor Microenvironment by Combination of Bacillus Calmette–Guérin and Anti-PD-L1 in an Orthotopic Triple-Negative Breast Cancer Mouse Model
Yuan Lu , Xin Huang , Xiaoke Liu , Yu He , Zhe Hu , Weize Xu , Gang Cao , Wenbo He
OncoTargets and Therapy · 2021
Differences in neurotropism and neurotoxicity among retrograde viral tracers
Leqiang Sun , Yajie Tang , Keji Yan , Jinsong Yu , Yan Zou , Weize Xu , Ke Xiao , Zhihui Zhang , Weiming Li , Beili Wu , Zhe Hu , Kening Chen , et al.
Molecular Neurodegeneration · 2019
Development and application of a recombination-based library versus library high- throughput yeast two-hybrid (RLL-Y2H) screening system
Fang Yang , Yingying Lei , Meiling Zhou , Qili Yao , Yichao Han , Xiang Wu , W. Zhong , Cheng-Shu Zhu , Weize Xu , R. Tao , Xi Chen , Da Lin , et al.
Nucleic Acids Research · 2017
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