The Human Cell Atlas from a cell census to a unified foundation model

Jennifer E. Rood, Samantha Wynne, Lucia Robson, Anna Hupalowska, John Randell, Sarah A. Teichmann () and Aviv Regev ()
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Jennifer E. Rood: Human Cell Atlas
Samantha Wynne: Human Cell Atlas
Lucia Robson: Human Cell Atlas
Anna Hupalowska: Human Cell Atlas
John Randell: Human Cell Atlas
Sarah A. Teichmann: Human Cell Atlas
Aviv Regev: Human Cell Atlas

Nature, 2025, vol. 637, issue 8048, 1065-1071

Abstract: Abstract With the convergence of notable advances in molecular and spatial profiling methods and new computational approaches taking advantage of artificial intelligence and machine learning, the construction of cell atlases is progressing from data collection to atlas integration and beyond. Here, we explore five ways in which cell atlases, including the Human Cell Atlas, are already revealing valuable biological insights, and how they are poised to provide even greater benefits in the coming years. In particular, we discuss cell atlases as censuses of cells; as 3D maps of cells in the body, across modalities and scales; as maps connecting genotype causes to phenotype effects; as 4D maps of development; and, ultimately, as foundation models of biology unifying all of these aspects and helping to transform medicine.

Date: 2025
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DOI: 10.1038/s41586-024-08338-4

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