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news
Allen Institute President and Chief Executive Officer, Allan Jones, Ph.D., announces plan to step down in 2021
Today the Allen Institute’s founding CEO, Allan Jones, Ph.D., announced he will step down after nearly 18 years with the organization.
news
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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featured publications

publication / 2008
Genomic anatomy of the hippocampus
Neuron
publication / 2009
A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale
PLoS computational biology
publication / 2009
The Allen Brain Atlas: 5 years and beyond
Nature Reviews. Neuroscience
publication / 2009
An anatomic gene expression atlas of the adult mouse brain
Nature Neuroscience
publication / 2010
A robust and high-throughput Cre reporting and characterization system for the whole mouse brain
Nature Neuroscience
publication / 2010
Surface-based mapping of gene expression and probabilistic expression maps in the mouse cortex
Methods (San Diego, Calif.)
publication / 2010
Areal and laminar differentiation in the mouse neocortex using large scale gene expression data
Methods (San Diego, Calif.)
publication / 2010
Molecular and anatomical signatures of sleep deprivation in the mouse brain
Frontiers in Neuroscience
publication / 2010
Divergent and nonuniform gene expression patterns in mouse brain
Proceedings of the National Academy of Sciences of the United States of America
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 / 2011
Visual tuning properties of genetically identified layer 2/3 neuronal types in the primary visual cortex of cre-transgenic mice
Frontiers in Systems Neuroscience
publication / 2012
Transcriptional architecture of the primate neocortex
Neuron
publication / 2012
A toolbox of Cre-dependent optogenetic transgenic mice for light-induced activation and silencing
Nature Neuroscience
publication / 2012
Large-scale cellular-resolution gene profiling in human neocortex reveals species-specific molecular signatures
Cell
publication / 2012
An anatomically comprehensive atlas of the adult human brain transcriptome
Nature
publication / 2012
The Allen Human Brain Atlas: comprehensive gene expression mapping of the human brain
Trends in Neurosciences
publication / 2013
Conserved molecular signatures of neurogenesis in the hippocampal subgranular zone of rodents and primates
Development (Cambridge, England)
publication / 2014
Altered gene expression in the dorsolateral prefrontal cortex of individuals with schizophrenia
Molecular Psychiatry
publication / 2014
A mesoscale connectome of the mouse brain
Nature
publication / 2014
Transcriptional landscape of the prenatal human brain
Nature
publication / 2014
Systematic comparison of adeno-associated virus and biotinylated dextran amine reveals equivalent sensitivity between tracers and novel projection targets in the mouse brain
The Journal of Comparative Neurology
publication / 2014
A high-resolution spatiotemporal atlas of gene expression of the developing mouse brain
Neuron
publication / 2015
Correlated gene expression and target specificity demonstrate excitatory projection neuron diversity
Cerebral Cortex (New York, N.Y.: 1991)
publication / 2015
Canonical genetic signatures of the adult human brain
Nature Neuroscience
publication / 2016
A comprehensive transcriptional map of primate brain development
Nature
publication / 2016
Comprehensive cellular-resolution atlas of the adult human brain
The Journal of Comparative Neurology
publication / 2016
Big Science, Team Science, and Open Science for Neuroscience
Neuron
publication / 2018
An anatomic transcriptional atlas of human glioblastoma
Science (New York, N.Y.)
publication / 2018
Shared and distinct transcriptomic cell types across neocortical areas
Nature
publication / 2019
Conserved cell types with divergent features in human versus mouse cortex
Nature
publication / 2019
Hierarchical organization of cortical and thalamic connectivity
Nature
publication / 2021
Human neocortical expansion involves glutamatergic neuron diversification
Nature
publication / 2022
Cellular resolution anatomical and molecular atlases for prenatal human brains
The Journal of Comparative Neurology
publication / 2007
Neuroinformatics for genome-wide 3D gene expression mapping in the mouse brain
IEEE/ACM transactions on computational biology and bioinformatics
publication / 2007
Genome-wide atlas of gene expression in the adult mouse brain
Nature
publication / 2008
Quantitative methods for genome-scale analysis of in situ hybridization and correlation with microarray data
Genome Biology
publication / 2008
Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain
BMC bioinformatics
publication / 2011
Adult spinal cord radial glia display a unique progenitor phenotype
PloS One
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