Developing Brain

Published in Nature, November 5, 2025

A cell census of the developing human and mammalian brain

How does the brain build itself? What sparks the transformation from a handful of cells into a complex organ that powers thought, emotion, and behavior?

This ground-breaking publication from the BRAIN Initiative Cell Census Network (BICCN) and BRAIN Initiative Cell Atlas Network (BICAN) brings us closer to answering those questions. It’s the result of a massive scientific collaboration, spanning multiple institutions and disciplines, mapping brain development in extraordinary detail.

Nature Collection

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About

A collection of papers in Nature journals and 2 companion papers
Supported by the National Institutes of Health BRAIN Initiative with funding from BICCN and BICAN awards.
Includes spatial and single cell omics datasets from multiple species, a 3D developmental mouse Common Coordinate Framework, and perturbation and lineage tracing.

Findings

Mapping the developing human brain: Single-cell multiomics data chart how genes and regulatory programs shape region-specific cell types during early development.
Origins and trajectories of brain cells: Studies reveal multipurpose progenitors, developmental “switches” in neurogenesis, and links between specific developing neurons and autism risk.
Sex-specific development: Work in the hypothalamus uncovers sex-specific developmental programs and signals that guide the timing of cell maturation.
Evolutionary insights: Cross-species comparisons showed both conserved and primate-specific neuronal programs, revealing how brain evolution refines existing cell classes.
New community resources: The consortium released 3D developmental brain models, multi-omic datasets, spatial maps, and benchmarking tools for organoid models.

Scientific Publications

Nowakowski et al., Nature

The new frontier in understanding human and mammalian brain development

Nowakowski, T., et al. The new frontier of human and mammalian brain development. Nature (2025). https://doi.org/10.1038/s41586-025-09652-1

perspective

Wang et al., Nature

Molecular and cellular dynamics of the developing human neocortex

Wang, L., Wang, C., Moriano, J.A. et al. Molecular and cellular dynamics of the developing human neocortex. Nature (2025). https://doi.org/10.1038/s41586-024-08351-7

core

Keefe et al., Nature

Lineage-resolved atlas of the developing human cortex

Keefe, M.G., Steyert, M.R., et al. Developmental lineage relationships of radial glial cells. Nature (2025) https://doi.org/10.1038/s41586-025-09033-8

core

Kaplan et al., Nature

Sensory input, sex and function shape hypothalamic cell type development

Kaplan, H.S., Logeman, B.L., Zhang, K. et al. Sensory input, sex and function shape hypothalamic cell type development. Nature (2025). https://doi.org/10.1038/s41586-025-08603-0

core

Gao et al., Nature

Continuous cell-type diversification in mouse visual cortex development

Gao, Y., et al. Continuous cell-type diversification in mouse visual cortex development. Nature (2025). https://doi.org/10.1038/s41586-025-09644-1

core

Corrigan et al., Nature

Conservation and alteration of mammalian striatal interneurons

Corrigan, E., et al. Conservation and alteration of mammalian striatal interneurons. Nature (2025). https://doi.org/10.1038/s41586-025-09592-w

core

Mannens et al., Nature

Chromatin accessibility during human first-trimester neurodevelopment

Mannens, C.A., et al. Chromatin accessibility during human first-trimester neurodevelopment. Nature (2024). https://doi.org/10.1038/s41586-024-07234-1

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Zhang et al., Nature

Spatial dynamics of brain development and neuroinflammation

Zhang, D., et al. Spatial dynamics of brain development and neuroinflammation. Nature (2025). https://doi.org/10.1038/s41586-025-09663-y

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van Velthoven et al., Nature

Transcriptomic and spatial organization of telencephalic GABAergic neurons

van Velthoven, C.T.J., et al. The transcriptomic and spatial organization of telencephalic GABAergic neuronal types. Nature (2025). https://doi.org/10.1038/s41586-025-09296-1

core

Kronman et al., Nature Communications

Developmental mouse brain common coordinate framework

Kronman, F.N., Liwang, J.K., Betty, R. et al. Developmental mouse brain common coordinate framework. Nat Commun 15, 9072 (2024). https://doi.org/10.1038/s41467-024-53254-w

core

Nano et al., Nature Neuroscience

Integrated analysis of molecular atlases unveils modules driving developmental cell subtype specification in the human cortex

Nano, P.R., Fazzari, E., Azizad, D. et al. Integrated analysis of molecular atlases unveils modules driving developmental cell subtype specification in the human cortex. Nat Neurosci 28, 949–963 (2025). https://doi.org/10.1038/s41593-025-01933-2

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Sonthalia et al., BioRxiv

A Curated Compendium of Transcriptomic Data for the Exploration of Neocortical Development

Sonthalia, S., et al. A curated compedium of transcriptomic data for the exploration of neocortical development. bioRxiv (2024).

companion

Chen et al., Nature

Whole-cortex in situ sequencing reveals input-dependent area identity

Chen, X., Fischer, S., Rue, M.C.P. et al. Whole-cortex in situ sequencing reveals input-dependent area identity. Nature (2024). https://doi.org/10.1038/s41586-024-07221-6

core

Werner et al., PLoS Biology

Meta-analysis of single-cell RNA sequencing co-expression in human neural organoids reveals their high variability in recapitulating primary tissue

Werner, J.M. and Gillis, J. Meta-analysis of single-cell RNA sequencing co-expression in human neural organoids reveals their high variability in recapitulating primary tissue. PLoS Biology (2024). https://doi.org/10.1371/journal.pbio.3002912