Author

Chihao Zhang

Chinese Academy of SciencesORCID 0000-0002-2135-5690Unclaimed ORCID profile · follow to get notified of new preprints

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Chihao Zhang1 paper · Yale University

Biology Disciplines

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Bioinformatics· 3

Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 2 Approach:deep learning· 2 Assay:spatial transcriptomics· 2 Assay:bulk RNA-seq· 1 Research Focus:database / resource· 1 Research Focus:differential expression· 1 Approach:machine learning (classical)· 1 Organism:mouse· 1

Frequent Co-Authors

Shihua ZhangiD· 3 shared Kangning DongiD· 1 shared Kazuyuki AiharaiD· 1 shared Linting Wang· 1 shared Luonan CheniD· 1 shared

Activity by Year

2023-2026 · peak 1/yr

Co-Author Collaboration Network

5 top collaborators · 7 mutual co-author links

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3 shared papersBioinformatics

Shihua ZhangORCID

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3 papers

Recent·Most cited

STADiffuser: high-fidelity simulation and full-view 3D modeling of spatial transcriptomics

Chihao Zhang, Shihua Zhang

STADiffuser simulates spatial transcriptomic data with high fidelity and enables 3D modeling of large-scale spatial datasets.

Nature Communications · Aug 19, 2026Peer-reviewedBioinformatics

Batch Effects Remain a Fundamental Barrier to Universal Embeddings in Single-Cell Foundation Models

Linting Wang, Chihao Zhang, Shihua Zhang

This paper evaluates single-cell foundation models and finds they struggle to remove batch effects, limiting their ability to create universal cellular embeddings.

bioRxiv · Dec 22, 2025 · PreprintBioinformatics

STAMarker: Determining spatial domain-specific variable genes with saliency maps in deep learning

Chihao Zhang, Kangning Dong, Kazuyuki Aihara, Luonan Chen, Shihua Zhang

STAMarker identifies spatial domain-specific variable genes using saliency maps in deep learning, outperforming existing methods on sparse spatial transcriptomic data.

Nucleic Acids Research · Sep 19, 2023Peer-reviewedBioinformatics