Author

Francesco Monticolo

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 Developmental Biology· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:cell type annotation· 3 Organism:mouse· 3 Organism:human· 2 Assay:spatial transcriptomics· 2 Assay:bulk RNA-seq· 1 Research Focus:cell-cell communication· 1 Research Focus:clustering· 1 Approach:deep learning· 1

Frequent Co-Authors

Jian ShuiD· 3 shared Jianhuan Qi· 2 shared Ke ZhangiD· 2 shared Koseki J. Kobayashi-KirschvinkiD· 2 shared Xingjian CheniD· 2 shared Alvaro Quintanal Villalonga· 1 shared Amanda M. MackieiD· 1 shared Amander T. ClarkiD· 1 shared

Activity by Year

2023-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 31 mutual co-author links

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3 shared papersSystems Biology

Jian ShuORCID

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3 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

Defining the cell and molecular origins of the primate ovarian reserve

Sissy E. Wamaitha, Ernesto J. Rojas, Francesco Monticolo, Fei‐Man Hsu, Enrique Sosa, Amanda M. Mackie, Kiana Oyama, Maggie Custer, Melinda Murphy, Diana J. Laird, Jian Shu, Jon D. Hennebold, Amander T. Clark

The paper investigates the cell and molecular origins of the primate ovarian reserve using rhesus macaques, identifying PG2 cells as the primary source of primordial follicles and describing the recruitment of fetal theca cells for hormone production.

Nature Communications · Aug 26, 2025Peer-reviewedDevelopmental 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