Author

Jianhuan Qi

Harvard University

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioengineering· 1 Bioinformatics· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:cell type annotation· 2 Approach:deep learning· 2 Organism:human· 2 Assay:imaging· 2 Organism:mouse· 2 Assay:spatial transcriptomics· 2 Research Focus:clustering· 1 Research Focus:differential expression· 1

Frequent Co-Authors

Jian ShuiD· 3 shared Ke ZhangiD· 3 shared Xingjian CheniD· 3 shared Francesco Monticolo· 2 shared Koseki J. Kobayashi-KirschvinkiD· 2 shared Thai Nam Son Dang· 2 shared Yinghan Wu· 2 shared Alvaro Quintanal Villalonga· 1 shared

Activity by Year

2023-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 39 mutual co-author links

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3 shared papersBioengineering

Jian ShuORCID

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

VIP-OT: Dissecting Single-Cell Biochemical State Dynamics under Perturbation via Vibrational Painting and Optimal Transport

Xuemeng Li, Stefan G. Stark, Xinwen Liu, Mian Wei, Zhilun Zhao, Jianhuan Qi, Xingjian Chen, Thai Nam Son Dang, Yinghan Wu, Ke Zhang, Wei Min, Jian Shu

VIP-OT traces drug response heterogeneity in single cells using vibrational imaging and optimal transport to predict post-treatment metabolic states from pre-treatment spectra.

bioRxiv · Dec 12, 2025 · PreprintBioengineering

RamanOmics Decodes Spatial Vibrational-Molecular Architecture and Rewiring in Aging and Repair

Ke Zhang, Xingjian Chen, Francesco Monticolo, Salvatore Sorrentino, Haochun Huang, Claire Callahan, Yueqing Qiao, Judy Zhou, Sonia Brodowska, Styliani Sapantzi, Jianhuan Qi, Yinghan Wu, Thai Nam Son Dang, Francesca Viggiani, Chia-Kang Ho, , Jian Shu

RamanOmics integrates snRNA-seq, spatial transcriptomics, and Raman imaging to map spatial biochemical and molecular changes in aging and repair, identifying senescent cell signatures and their functional roles.

bioRxiv · Dec 8, 2025 · PreprintSystems Biology

Inference of single cell profiles from histology stains with the Single-Cell omics from Histology Analysis Framework (SCHAF)

Charles S. Comiter, Xingjian Chen, Eeshit Dhaval Vaishnav, Koseki J. Kobayashi-Kirschvink, Metamia Ciampricotti, Ke Zhang, Jason Murray, Francesco Monticolo, Jianhuan Qi, Ryota Tanaka, Sonia E. Brodowska, Bo Li, Yiming Yang, Scott J. Rodig, Angeliki Karatza, , Aviv Regev

SCHAF generates spatially resolved single-cell transcriptomes from H&E histology images using vision transformers and adversarial learning, showing good agreement with ground-truth data.

bioRxiv · Mar 21, 2023 · PreprintBioinformatics