Scientists complete first drafts of developing mammalian brain cell atlases
New research reveals how early brains form and the critical periods that could help diagnose and treat brain disease.
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Mapping the whole human brain: Allen Institute to lead global collaboration
NIH BRAIN Initiative to fund primate brain atlases, maps of developing mouse brain, coordination and knowledge sharing, and brain function research
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Reflections on the beginnings of the Allen Institute
The Allen Institute houses some impressive statistics behind its glassy facade: more than 2.7 million high-resolution science images and nearly 1,400 hours of movies of brain activity shared with the global scientific community.
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publication / 2025
Data-driven fine-grained region discovery in the mouse brain with transformers
Nature Communications
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A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types
Cell
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Enhancer AAV toolbox for accessing and perturbing striatal cell types and circuits
Neuron
publication / 2025
Integrating multimodal data to understand cortical circuit architecture and function
Nature Neuroscience
publication / 2025
Bridging the Scientific Knowledge Gap and Reproducibility: A Survey of Provenance, Assertion and Evidence Ontologies
Proceedings of the ... International World-Wide Web Conference. International WWW Conference
publication / 2024
Developmental mouse brain common coordinate framework
Nature Communications
publication / 2024
Integrated multimodal cell atlas of Alzheimer's disease
Nature Neuroscience
publication / 2024
SEA-AD is a multimodal cellular atlas and resource for Alzheimer's disease
Nature Aging
publication / 2024
Cross-modality mapping using image varifolds to align tissue-scale atlases to molecular-scale measures with application to 2D brain sections
Nature Communications
publication / 2023
A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain
Nature
publication / 2023
Online conversion of reconstructed neural morphologies into standardized SWC format
Nature Communications
publication / 2023
A guide to the BRAIN Initiative Cell Census Network data ecosystem
PLoS biology
preprint / 2023
Stimulus novelty uncovers coding diversity in visual cortical circuits
publication / 2023
A whole-brain monosynaptic input connectome to neuron classes in mouse visual cortex
Nature Neuroscience
publication / 2022
The Neurodata Without Borders ecosystem for neurophysiological data science
eLife
publication / 2022
Cellular resolution anatomical and molecular atlases for prenatal human brains
The Journal of Comparative Neurology
publication / 2021
A multimodal cell census and atlas of the mammalian primary motor cortex
Nature
publication / 2021
Human neocortical expansion involves glutamatergic neuron diversification
Nature
publication / 2021
Morphological diversity of single neurons in molecularly defined cell types
Nature
publication / 2021
Cellular anatomy of the mouse primary motor cortex
Nature
publication / 2021
Survey of spiking in the mouse visual system reveals functional hierarchy
Nature
publication / 2021
Regional, Layer, and Cell-Type-Specific Connectivity of the Mouse Default Mode Network
Neuron
publication / 2021
Highlights from the Era of Open Source Web-Based Tools
The Journal of Neuroscience: The Official Journal of the Society for Neuroscience
publication / 2020
Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells
Cell
publication / 2020
The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas
Cell
publication / 2020
A large-scale standardized physiological survey reveals functional organization of the mouse visual cortex
Nature Neuroscience
publication / 2019
Hierarchical organization of cortical and thalamic connectivity
Nature
publication / 2019
Conserved cell types with divergent features in human versus mouse cortex
Nature
publication / 2019
Automatic navigation system for the mouse brain
The Journal of Comparative Neurology
publication / 2019
Classification of electrophysiological and morphological neuron types in the mouse visual cortex
Nature Neuroscience
publication / 2018
An anatomic transcriptional atlas of human glioblastoma
Science (New York, N.Y.)
publication / 2017
Neuropathological and transcriptomic characteristics of the aged brain
eLife
publication / 2017
Organization of the connections between claustrum and cortex in the mouse
The Journal of Comparative Neurology
publication / 2017
Diverse Central Projection Patterns of Retinal Ganglion Cells
Cell Reports
publication / 2017
An extended retinotopic map of mouse cortex
eLife
publication / 2016
Comprehensive cellular-resolution atlas of the adult human brain
The Journal of Comparative Neurology
publication / 2016
A comprehensive transcriptional map of primate brain development
Nature
publication / 2016
Effects of Chronic Sleep Restriction during Early Adolescence on the Adult Pattern of Connectivity of Mouse Secondary Motor Cortex
eNeuro
publication / 2015
Canonical genetic signatures of the adult human brain
Nature Neuroscience
publication / 2015
Exploration and visualization of connectivity in the adult mouse brain
Methods (San Diego, Calif.)
publication / 2015
Neuroinformatics of the Allen Mouse Brain Connectivity Atlas
Methods (San Diego, Calif.)
publication / 2015
Mapping social behavior-induced brain activation at cellular resolution in the mouse
Cell Reports
publication / 2014
A high-resolution spatiotemporal atlas of gene expression of the developing mouse brain
Neuron
publication / 2014
Transcriptional landscape of the prenatal human brain
Nature
publication / 2014
A mesoscale connectome of the mouse brain
Nature
publication / 2014
Cell-type-based model explaining coexpression patterns of genes in the brain
Proceedings of the National Academy of Sciences of the United States of America
publication / 2013
Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system
Nucleic Acids Research
publication / 2012
An anatomically comprehensive atlas of the adult human brain transcriptome
Nature
publication / 2011
Multi-scale correlation structure of gene expression in the brain
Neural Networks: The Official Journal of the International Neural Network Society
publication / 2011
Cell-type-specific consequences of Reelin deficiency in the mouse neocortex, hippocampus, and amygdala
The Journal of Comparative Neurology
publication / 2010
Areal and laminar differentiation in the mouse neocortex using large scale gene expression data
Methods (San Diego, Calif.)
publication / 2010
Surface-based mapping of gene expression and probabilistic expression maps in the mouse cortex
Methods (San Diego, Calif.)
publication / 2010
Clustering of spatial gene expression patterns in the mouse brain and comparison with classical neuroanatomy
Methods (San Diego, Calif.)
publication / 2009
An anatomic gene expression atlas of the adult mouse brain
Nature Neuroscience
publication / 2008
Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain
BMC bioinformatics
publication / 2008
Quantitative methods for genome-scale analysis of in situ hybridization and correlation with microarray data
Genome Biology
publication / 2007
Neuroinformatics for genome-wide 3D gene expression mapping in the mouse brain
IEEE/ACM transactions on computational biology and bioinformatics
