Below is a list of scientific publications by Allen Institute scientists, as well as publications by Allen Brain Atlas users outside of the Institute.  If you are aware of other publications citing the Atlas or using Atlas data, please submit a comment on this site with the citation information so that it can be added to the list.  Thank you.

For information about Allen Institute presentations at scientific conferences, go to the Events section of these pages.

Primary Publication Describing the Allen Brain Atlas-Mouse Brain

Genome-wide atlas of gene expression in the adult mouse brain Lein, E.S., Hawrylycz, M.J. et. al. (2007) Nature 445:168-176, doi:10.1038/nature05453.

Supplementary Materials

• Detailed methodologies for tissue processing, probe design and generation, data generation, and image acquisition used for the Allen Brain Atlas project
• Detailed methodologies for informatics-based image quantification and mapping of ISH data to a common 3D coordinate system for genome-wide analysis
• Detailed methodologies used to generate the Allen Reference Atlas
• Description of methods used for voxel-based correlation analysis
• Comparison of non-isotopic in situ hybridization (ISH) data generated for the Allen Brain Atlas project to comparable radioactive ISH data from other sources
• Side-by-side image comparison of non-isotopic in situ hybridization (ISH) data generated for the Allen Brain Atlas project to comparable radioactive ISH data. Accompanies Supplemental Data 1
• Control data demonstrating the reproducibility of the ABA ISH platform across conditions and across the duration of the ABA project
• Comparison of expression patterns of the ligand-gated ion channel family to available literature and other data sources, as well as methodology for fine-detailed expert annotation of the ligand-gated ion channel family in the neocortex
• Detailed expert annotation of the complete ligand-gated ion channel family in layers of the neocortex. Accompanies Supplemental Data 4
• Genome-wide analysis of expression level vs. percentage of expressing cells in 12 major brain regions
• Genes enriched in major cell populations in the brain (neurons, oligodendrocytes, astrocytes, and choroid plexus cells) identified through correlation-based searches seeded with cell-type specific gene expression patterns. Also included are genes with apparent ubiquity as well as genes that do not have detectable expression in the brain
• Gene Ontology (GO) categories over-represented in genes enriched in major neural cell types and in genes that are either apparently ubiquitous or not expressed. Accompanies Supplemental Table 1
• Genes identified as the most specific for each of 12 different major brain regions
• Genes displaying mRNA targeting to dendrites (neurons) or processes (non-neuronal cells)

Allen Institute & Collaborative Publications

2008 Publications

• Ablation of neurons expressing agouti-related protein activates fos and gliosis in postsynaptic target regions  Wu, Q., Howell, M.P., and Palmiter, R.D.  (2008) Journal of Neuroscience  28(37): 9218-9226, doi:10.1523/JNEUROSCI.2449-08.2008
• Sleep deprivation effects on circadian clock gene expression in the cerebral cortex parallel electroencephalographic differences among mouse strains  Wisor, J.P., Pasumarthi, R.K., Gerashchenko, D., Thompson, C.L., Pathak, S., Sancar, A., Franken, P., Lein, E.S., and Kilduff, T.S. (2008)  Journal of Neuroscience  28(28): 7193-7201, doi:10.1523/JNEUROSCI.1150-08.2008
• Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain  Lau, C. et al. (2008) BMC Bioinformatics  9:153, doi:10.1186/1471-2105-9-153
• Starvation after AgRP neuron ablation is independent of melanocortin signaling  Wu, Q., Howell, M.P., Cowley, M.A., and Palmiter, R.D. (2008)  PNAS  105(7):2687-2692, doi:10.1073/pnas.0712062105
• Quantitative methods for genome-scale analysis of in situ hybridization and correlation with microarray data  Lee, C-K. et al. (2008)  Genome Biology  9(1):R23, doi:10.1186/gb-2008-9-1-r23
• Specific expression of long noncoding RNAs in the mouse brain  Mercer, T.R., Dinger, M.E., Sunkin, S.M., Mehler, M.F. and Mattick, J.S. (2008) PNAS  105(2):716-721, doi:10.1073/pnas.0706729105
• Allen Reference Atlas: A digital color brain atlas of the C57Bl/6J male mouse  Dong, H.W. (2008) John Wiley & Sons, Inc., Hoboken, New Jersey.

2007 Publications

• High-throughput automated microscopy platform for the Allen Brain Atlas  Slaughterbeck, C.R. et al. (2007) Journal of the Association of Laboratory Automation (JALA)  12(6):377-383, doi:10.1016/j.jala.2007.07.003
• Insights from spatially mapped gene expression in the mouse brain  Sunkin, S.M. and Hohmann, J.G. (2007) Human Molecular Genetics  16(Review Issue 2):R209-R219, doi:10.1093/hmg/ddm183
• Non-negative matrix factorization framework for dimensionality reduction and unsupervised clustering  Pathak, S. et al. (2007) Insight Journal  January-June, http://hdl.handle.net/1926/502
• The Allen Brain Atlas: Delivering neuroscience to the Web on a genome wide scale  Dang, C. et al. (2007) Data Integration in the Life Sciences in Lecture Notes in Computer Science  4544:17-26, doi:10.1007/978-3-540-73255-6_4
• Neuroinformatics for genome-wide 3-D gene expression mapping in the mouse brain  Ng, L. et al. (2007) IEEE/ACM Transactions on Computational Biology and Bioinformatics  4(3):382-393, doi:10.1109/tcbb.2007.1035
• Genome-wide atlas of gene expression in the adult mouse brain  Lein, E.S., Hawrylycz, M.J. et al. (2007) Nature 445:168-176, doi:10.1038/nature05453.

2006 Publications

• Toward the integration of spatially and temporally resolved murine gene expression databases  Sunkin, S.M. (2006) Trends in Genetics 22:211-217. 

Other Atlas User Publications 

Publications citing the Allen Brain Atlas-Mouse Brain primary publication

• See Google Scholar search returns

2007 Publications

• Spatial mapping of protein abundances in the mouse brain by voxelation integrated with high-throughput liquid chromatography-mass spectrometry.  Petuyk, V.A. et al. (2007) Genome Research, doi:10.1101/gr.5799207. 
• Genetic and structural analysis of the basolateral amygdala complex in BXD recombinant inbred mice.  Mozhui, K. et al. (2007) Behavioral Genetics 37:223-243, doi:10.1007/s10519-006-9122-3.
• Zooming in: a new high-resolution gene expression atlas of the brain.  Jessberger, S. and Gage, F.H. (2007) Molecular Systems Biology 3:75, doi:10.1038/msb4100122.

2006 Publications

• Transcriptional signatures of cellular plasticity in mice lacking the alpha1 subunit of GABAa receptors.  Ponomarev, I. et al. (2006) Journal of Neuroscience 26:5673-5683, doi:10.1523/JNEUROSCI.0860-06.2006.
• Common Kibra Alleles Are Associated with Human Memory Performance.  Papassotiropoulos, A. et al. (2006) Science 314:475-478, doi:10.1126/science.1129837.
• Functional genomic analysis of oligodendrocyte differentiation.  Dugas,  J.C. et. al. (2006) Journal of Neuroscience 26:10967-10983, doi:10.1523/JNEUROSCI.2572-06.2006.
• Virtues and woes of AChE alternative splicing in stress-related neuropathologies.  Meshorer, E. and Soreq, H. (2006) Trends in Neurosciences 29(4): 216-224, doi:10.1016/j.tins.2006.02.005.