Author

Cristina Almagro-Pérez

Broad InstituteORCID 0000-0002-1409-3880Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Pathology· 3 Cancer Biology· 1

Signature Assays, Organisms & Methods

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Organism:human· 4 Assay:imaging· 3 Research Focus:cell type annotation· 2 Research Focus:cell-cell communication· 2 Approach:deep learning· 2 Assay:spatial transcriptomics· 2 Research Focus:differential expression· 1 Research Focus:drug response / drug discovery· 1

Frequent Co-Authors

Andrew H. SongiD· 3 shared David BrenesiD· 2 shared Faisal MahmoodiD· 2 shared Jonathan T.C. LiuiD· 2 shared Lawrence D. TrueiD· 2 shared Priti LaliD· 2 shared Renao YaniD· 2 shared Sarah S. L. ChowiD· 2 shared

Activity by Year

2024-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 36 mutual co-author links

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3 shared papersPathology

Andrew H. SongORCID

Mutual co-authors in cluster

Author profile →

4 papers

Recent·Most cited

Prototype-based AI triage for 3D pathology

Renao Yan, Gan Gao, Andrew H. Song, Huai-Ching Hsieh, Yujie Zhao, Cristina Almagro-Pérez, David Brenes, Sarah S. L. Chow, Jeanne Shen, Deepti Reddi, Lawrence D. True, Priti Lal, Anant Madabhushi, Faisal Mahmood, Jonathan T.C. Liu

SCOPE improves AI triage in 3D pathology by using morphology-aware prototypes to identify high-risk 2D slices for pathologist review.

bioRxiv · Jul 15, 2026 · PreprintPathology

Scalable 3D cell-interaction analysis via supercell graphs for prostate cancer risk stratification

Yujie Zhao, Sarah S. L. Chow, Renao Yan, David Brenes, Robert Serafin, Cristina Almagro-Pérez, Andrew H. Song, Priti Lal, Emily Chan, Michelle R. Downes, Elena Baraznenok, Jennifer Salguero López, Anant Madabhush, Faisal Mahmood, Lawrence D. True, Jonathan T.C. Liu

SCALE3D improves prostate cancer risk prediction by analyzing 3D cell interactions through supercell graphs, outperforming traditional features and reducing computational demands.

bioRxiv · Jul 11, 2026 · PreprintPathology

Histology-guided 3D virtual staining of microCT-imaged lung tissue via deep learning

Cristina Almagro-Pérez, Niccolò Peruzzi, Csaba Galambos, Andrew H. Song, Hans Brunnström, Kinga I. Gawlik, Marco Stampanoni, Karin Tran‐Lundmark, Goran Lovrić

This paper develops a deep learning method to virtually stain 3D microCT lung tissue, mimicking histological stains and enabling 3D pathology analysis.

Journal of The Royal Society Interface · Jun 17, 2026Peer-reviewedPathology

3D histology reveals that immune response to pancreatic precancers is heterogeneous and depends on global pancreas structure

Ashley L. Kiemen, Cristina Almagro-Pérez, Valentina Matos, André Forjaz, Alicia M. Braxton, Lucie Dequiedt, Jeeun Parksong, Courtney D. Cannon, Xuan Yuan, Sarah M. Shin, Jaanvi Mahesh Babu, Elizabeth D. Thompson, Toby C. Cornish, Won Jin Ho, Laura DeLong Wood, , Denis Wirtz

The paper profiles the immune microenvironment of PanINs in 3D at single-cell resolution to understand inflammation's role in cancer progression and finds immune heterogeneity and correlations with PanIN grade.

bioRxiv · Aug 3, 2024 · PreprintCancer Biology