Author

Francesca Viggiani

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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Bioinformatics· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:cell type annotation· 2 Research Focus:clustering· 2 Assay:spatial transcriptomics· 2 Approach:deep learning· 1 Approach:machine learning (classical)· 1 Organism:mouse· 1 Assay:snRNA-seq· 1

Frequent Co-Authors

Claire CallahaniD· 2 shared Jian ShuiD· 2 shared Ke ZhangiD· 2 shared Bruce J. AronowiD· 1 shared Chia-Kang Ho· 1 shared Francesco Monticolo· 1 shared Haochun Huang· 1 shared Hemali Phatnani· 1 shared

Activity by Year

2025-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 35 mutual co-author links

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2 shared papersSystems Biology

Claire CallahanORCID

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Author profile →

2 papers

Recent·Most cited

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

Bering: joint cell segmentation and annotation for spatial transcriptomics with transferred graph embeddings

Kang Jin, Zuobai Zhang, Ke Zhang, Francesca Viggiani, Claire Callahan, Jian Tang, Bruce J. Aronow, Jian Shu

Bering improves cell segmentation and annotation in spatial transcriptomics by using graph embeddings and transfer learning, achieving better accuracy across different technologies and tissues.

Nature Communications · Jul 18, 2025Peer-reviewedBioinformatics