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. 2025 Jan;637(8048):1065-1071.
doi: 10.1038/s41586-024-08338-4. Epub 2024 Nov 20.

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

Jennifer E Rood  1   2 , Samantha Wynne  1 , Lucia Robson  1 , Anna Hupalowska  1   2 , John Randell  1 , Sarah A Teichmann  3   4 , Aviv Regev  5   6
Affiliations

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

Jennifer E Rood et al. Nature. 2025 Jan.

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.

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Conflict of interest statement

Competing interests: J.E.R., A.H. and A.R. are employees of Genentech, a member of the Roche Group and have equity in Roche. A.R. is a co-founder and equity holder of Celsius Therapeutics, an equity holder in Immunitas and, until 31 July 2020, was an scientific advisory board member of Thermo Fisher Scientific, Syros Pharmaceuticals, Neogene Therapeutics and Asimov. A.R. is a named inventor on multiple filed patents related to single-cell and spatial genomics. In the past three years, S.A.T. has consulted for or been a member of scientific advisory boards at Qiagen, Sanofi, GlaxoSmithKline and ForeSite Labs. S.A.T. is a consultant and equity holder for TransitionBio and EnsoCell. From 8 January 2024, S.A.T. is a part-time employee of GlaxoSmithKline.

References

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    1. Regev, A. et al. The Human Cell Atlas White Paper. Preprint at https://doi.org/10.48550/arXiv.1810.05192 (2018). This article provided a detailed plan for the Human Cell Atlas community to build a comprehensive cell atlas of the human body.
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