Author

Carlo Leonardi

Wellcome Sanger InstituteORCID 0000-0001-5348-8300Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Research Focus:cell type annotation· 2 Approach:deep learning· 2 Research Focus:gene regulatory network inference· 2 Organism:human· 2 Assay:spatial transcriptomics· 2 Approach:transformer / foundation model· 2 Research Focus:cell-cell communication· 1 Research Focus:differential expression· 1

Frequent Co-Authors

Amirhossein VahidiiD· 2 shared April Rose FosteriD· 2 shared Arpit MerchantiD· 2 shared Benjamin M. RumneyiD· 2 shared Ciro Ramírez-SuásteguiiD· 2 shared Daniyal J. JafreeiD· 2 shared Hon Man Chan· 2 shared Kenny RobertsiD· 2 shared

Activity by Year

2026-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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2 shared papersGenomics

Amirhossein VahidiORCID

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Author profile →

2 papers

Recent·Most cited

Multi-scale modeling of human tissues from spatial transcriptomics with TERRA

Sebastian Birk, Mohammad Vali Sanian, Amirhossein Vahidi, Samuel Ogden, Daniyal J. Jafree, Adib Miraki Feriz, Carlo Leonardi, Arpit Merchant, Zichen He, Lloyd Steele, Adam R. Boxall, Marta Rosa Sallese, Jonas Maaskola, Ciro Ramírez-Suástegui, Sevda Öğüt, , Mohammad Lotfollahi

TERRA is a foundation model for spatial transcriptomics that predicts tissue behavior under perturbation and identifies multi-scale biological insights across tissues.

bioRxiv · Aug 4, 2026 · PreprintGenomics

Self-supervised learning for a gene program-centric view of cell states

Marie Moullet, Tomoya Isobe, Amirhossein Vahidi, Carlo Leonardi, Licyel Paulas-Condori, Christopher J. Soelistyo, Lloyd Steele, Kevin Chi Hao Ly, Mariana Quiroga Londoño, Nicole Mende, Emily Stephenson, Deena Iskander, Simone Webb, Issac Goh, M. S. Vijayabaskar, , Mohammad Lotfollahi

Tripso, a self-supervised transformer model, identifies gene program-specific embeddings and discovers novel gene programs, revealing biological insights in hematopoietic development and disease.

bioRxiv · Mar 26, 2026 · PreprintBioinformatics