The Allen Brain Atlas: 5 years and beyond

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The Allen Brain Atlas, a Web-based, genome-wide atlas of gene expression in the adult mouse brain, was an experiment on a massive scale. The development of the atlas faced a combination of great technical challenges and a non-traditional open research model, and it encountered many hurdles on the path to completion and community adoption. Having overcome these challenges, it is now a fundamental tool for neuroscientists worldwide and has set the stage for the creation of other similar open resources. Nevertheless, there are many untapped opportunities for exploration.

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Figure 1: The Allen Institute technology platform.


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This work was sponsored by the Allen Institute for Brain Science. The authors wish to thank the Allen Institute founders, Paul G. Allen and Jody Allen, for their vision, encouragement and support.

Author information

Correspondence to Allan R. Jones.

Supplementary information

Supplementary information S1 (box)

Top 1,000 genes analysis (PDF 745 kb)

Supplementary information S2 (figure)

Genes viewed in the Allen Brain Atlas. (PDF 172 kb)

Related links

Related links


Allen Brain Atlas portal

Allen Developing Mouse Brain Atlas

Allen Institute for Brain Science

Allen Institute Human Cortex Study

Allen Institute Mouse Diversity Study

Allen Institute Sleep Study

Allen Institute Transgenic Mouse Study


Allen Mouse Brain Atlas (original ABA)

Allen Spinal Cord Atlas

Brain Explorer self-guided tutorial for education



International Neuroinformatics Coordinating Facility

Mouse BIRN Atlasing Toolkit

Mutant Mouse Regional Resource Centers (MMRRC)

Neurocommons project

Neuroscience Information Framework


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