The DOI matches its Crossref record; 57 of the 58 references it cites were found in a registry or an index.
Genome-wide atlas of gene expression in the adult mouse brain
Abstract
Molecular approaches to understanding the functional circuitry of the nervous system promise new insights into the relationship between genes, brain and behaviour. The cellular diversity of the brain necessitates a cellular resolution approach towards understanding the functional genomics of the nervous system. We describe here an anatomically comprehensive digital atlas containing the expression patterns of approximately 20,000 genes in the adult mouse brain. Data were generated using automated high-throughput procedures for in situ hybridization and data acquisition, and are publicly accessible online. Newly developed image-based informatics tools allow global genome-scale structural analysis and cross-correlation, as well as identification of regionally enriched genes. Unbiased fine-resolution analysis has identified highly specific cellular markers as well as extensive evidence of cellular heterogeneity not evident in classical neuroanatomical atlases. This highly standardized atlas provides an open, primary data resource for a wide variety of further studies concerning brain organization and function.
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“In order to independently validate our findings about the spatial distribution of astrocytes (Figure S5C), we analyzed in situ hybridization images of marker genes obtained from the Allen Mouse Brain Atlas”
From Molecular Architecture of the Mouse Nervous System (2018) · cites this paper as Lein et al., 2007
In the citing paper
“Allen Brain Atlas in situ hybridization data [24] show ATF3 expression only in granular neurons of the olfactory bulb and dentate gyrus”
From Tamoxifen induces cellular stress in the nervous system by inhibiting cholesterol synthesis (2015) · cites this paper as [24]
In the citing paper
“Further in situ hybridization reveals that cerebellar Purkinje cells and neurons of the deep cerebellar nuclei express high levels of Clec16a (Allen Mouse Brain Atlas, http://mouse.brain-map.org/gene/show/50215)242526.”
From Clec16a is Critical for Autolysosome Function and Purkinje Cell Survival (2016) · cites this paper as [24]
In the citing paper
“we analyzed Nlk expression by LacZ staining and found that LacZ staining was strongest in the Purkinje cell layer (Fig.4D)”
From Polyglutamine Disease Toxicity Is Regulated by Nemo-like Kinase in Spinocerebellar Ataxia Type 1 (2013) · cites this paper as Lein et al., 2007
In the citing paper
“In animal studies (rodents and non-human primates), this is feasible through the use of comprehensive, histologically and functionally defined whole-brain areal parcellations (Bezgin et al., 2012; Lein et al., 2007; Paxinos et al., 2000; Saleem and Logothetis, 2007; Swanson, 2015; Van Essen et al., 2012).”
From Development of large-scale functional networks from birth to adulthood: A guide to the neuroimaging literature (2017) · cites this paper as Lein et al., 2007
In the citing paper
“ApoE expression, in both mice and humans, begins relatively late in development [46, 47].”
From ApoE, ApoE Receptors, and the Synapse in Alzheimer's Disease (2017) · cites this paper as [47]
In the citing paper
“To complement and validate the microarray data, several targeted, large-scale in situ hybridization (ISH) data sets were generated using a high-throughput ISH platform1, 8.”
From An anatomically comprehensive atlas of the adult human brain transcriptome (2012) · cites this paper as [1]
In the citing paper
“In rodents, brain- and transcriptome-wide, cellular-resolution maps of transcript distributions are widely useful resources to complement genomic sequence data1, 2, 3.”
From An anatomically comprehensive atlas of the adult human brain transcriptome (2012) · cites this paper as [1]
In the citing paper
“consistent with the percentage of genes expressed in mouse brain by ISH (80%; ref. 1) and fetal human brain by microarrays (76%; ref. 11).”
From An anatomically comprehensive atlas of the adult human brain transcriptome (2012) · cites this paper as [1]
In the citing paper
“expression in human differs from that in mouse (Fig. 5d) and rhesus monkey (Fig. 5e), where CALB1 is robustly expressed in CA1 and CA2 in addition to dentate gyrus.”
From An anatomically comprehensive atlas of the adult human brain transcriptome (2012) · cites this paper as [1]
In the citing paper
“The atlas of the mid-gestational human brain described here, part of the BrainSpan Atlas of the Developing Human Brain, builds on digital molecular brain atlasing efforts in mouse20,22,24 and adult human23 by providing transcriptome resources on prenatal specimens typically inaccessible for research.”
From Transcriptional landscape of the prenatal human brain (2014) · cites this paper as [24]
In the citing paper
“These cell-type-specific expression patterns exhibited specific anatomical localization in the developing cerebellum (Fig. 1c) 26 .”
From Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells (2018) · cites this paper as [26]
In the citing paper
“The distribution of specific markers ( Pcp4 and Slc17a7 ) captured by Stereo-seq exhibited the expected similarity to in situ hybridization (ISH) data taken from Allen Brain Atlas (ABA) (Lein et al., 2007) and clearer patterns than HDST (Vickovic et al., 2019) or Slide-seqV2-resolved (Stickels et al., 2021) expression data (Figure S1E).”
From Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays (2022) · cites this paper as Lein et al., 2007
In the citing paper
“The expression patterns of Hes1 and Hes5 are consistent with ISH images taken from ABA (Figure S7H) (Lein et al., 2007).”
From Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays (2022) · cites this paper as Lein et al., 2007
In the citing paper
“These results are in line with ISH images of the Rspo1 and Fgf15 taken from ABA (Lein et al., 2007) (Figure S7F).”
From Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays (2022) · cites this paper as Lein et al., 2007
In the citing paper
“The expression patterns of Erbb4 and Gad2 are consistent with ISH images taken from ABA (Lein et al., 2007) (Figure S6F).”
From Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays (2022) · cites this paper as Lein et al., 2007
In the citing paper
“Finally, we compared all marker genes that we highlight in this paper (those in Table 1 and all figures) to their patterns in a recent spatial transcriptomics analysis of the spinal cord28 and to the Allen29 and Gensat30 expression databases and found general concordance between these resources (Supplementary Table 4).”
From A harmonized atlas of mouse spinal cord cell types and their spatial organization (2021) · cites this paper as [29]
In the citing paper
“Initial clustering identified 106,728 neurons, of which 70.2% were localized to BNST by examination of marker expression in the Allen Brain Atlas (ABA) (Lein et al., 2007) (Figure S3B).”
From Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity (2019) · cites this paper as Lein et al., 2007
In the citing paper
“In situ hybridization and microarray data, for example the Allen Brain Atlases (Hawrylycz et al., 2012; Lein et al., 2007), have also established that mRNA transcripts encoding these five NPPs and that many other NPPs and NP-GPCR genes are expressed differentially in many brain regions.”
From Single-cell transcriptomic evidence for dense intracortical neuropeptide networks (2019) · cites this paper as Lein et al., 2007
In the citing paper
“Inspection of ISHs from the Allen Brain Atlas (Lein et al., 2007) indicated that these neurons were located in the Edinger-Westphal nucleus, which is adjacent to the DRN, confirming that our dissection region spanned most of the DRN along the anterior-posterior axis.”
From Molecular and anatomical organization of the dorsal raphe nucleus (2019) · cites this paper as Lein et al., 2007
In the citing paper
“We leveraged the inclusion of adjacent brain tissue in our atlas to map the boundary between the 3V ChP and developing pineal gland using published ISH (Lein et al., 2007; Visel et al., 2004) of marker genes from our data (Figure S2C).”
From A cellular and spatial map of the choroid plexus across brain ventricles and ages (2021) · cites this paper as Lein et al., 2007
In the citing paper
“Signature scores were distinctly elevated in areas corresponding to the anatomical structures annotated in the Allen brain reference atlas (Figure S3A) (Lein et al., 2007).”
From Atlas of the aging mouse brain reveals white matter as vulnerable foci (2023) · cites this paper as Lein et al., 2007
In the citing paper
“We compared the expression of marker genes to insitu hybridization (ISH) data from the Allen Mouse Brain Atlas(Lein et al., 2007) and visual landmarks from the H&E microscopy images”
From Atlas of the aging mouse brain reveals white matter as vulnerable foci (2023) · cites this paper as Lein et al., 2007
Citations
Cites
DAVID: Database for Annotation, Visualization, and Integrated Discovery
Dennis, G., Sherman, B. T., Hosack, D. A., Yang, J., Gao, W., Lane, H. C., & Lempicki, R. A. (2003) · Genome Biology · doi:10.1186/gb-2003-4-5-p3 · Cited by 9,327
The Transcriptional Landscape of the Mammalian Genome
Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M. C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C. A., et al. (2005) · Science · doi:10.1126/science.1112014 · Cited by 3,492
Interneurons of the neocortical inhibitory system
Markram, H., Toledo-Rodriguez, M., Wang, Y., Gupta, A., Silberberg, G., & Wu, C. (2004) · Nature Reviews Neuroscience · doi:10.1038/nrn1519 · Cited by 2,954
Alignment by Maximization of Mutual Information
Viola, P. A., & Wells, W. M. (1997) · International Journal of Computer Vision · doi:10.1023/a:1007958904918 · Cited by 2,610
Coordinated Transcription of Key Pathways in the Mouse by the Circadian Clock
Panda, S., Antoch, M. P., Miller, B. H., Su, A. I., Schook, A. C., Straume, M., Schultz, P. G., Kay, S. A., Takahashi, J. S., & Hogenesch, J. B. (2002) · Cell · doi:10.1016/s0092-8674(02)00722-5 · Cited by 2,310
The three-dimensional organization of the hippocampal formation: A review of anatomical data
Amaral, D. G., & Witter, M. P. (1989) · Neuroscience · doi:10.1016/0306-4522(89)90424-7 · Cited by 2,180
A gene expression atlas of the central nervous system based on bacterial artificial chromosomes
Gong, S., Zheng, C., Doughty, M. L., Losos, K., Didkovsky, N., Schambra, U. B., Nowak, N. J., Joyner, A., Leblanc, G., Hatten, M. E., et al. (2003) · Nature · doi:10.1038/nature02033 · Cited by 2,108
Zola-Morgan, S., Squire, L., & Amaral, D. (1986) · The Journal of Neuroscience · doi:10.1523/jneurosci.06-10-02950.1986 · Cited by 1,997
de Nó, R. L. (1934) · Cited by 1,974
Brain Maps: Structure of the Rat Brain
Swanson, L. W. (1992) · Medical Entomology and Zoology · Cited by 1,878
Flagged first, then by citations
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- Voogd, J., Hess, D. & Marani, E. The Parasagittal Zonation of the Cerebellar Cortex in Cat and Monkey: Topography, Distribution of Acetylcholinesterase, and Development (ed. King, E. S.) (Liss, New York, 1987)
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Sorted by citations
Items 401–500 of 1,058
L’Episcopo, F., Serapide, M. F., Tirolo, C., Testa, N., Caniglia, S., Morale, M. C., Pluchino, S., & Marchetti, B. (2011) · Molecular Neurodegeneration · doi:10.1186/1750-1326-6-49 · Cited by 198
Sodium glucose cotransporter SGLT1 as a therapeutic target in diabetes mellitus
Song, P., Ōnishi, A., Koepsell, H., & Vallon, V. (2016) · Expert Opinion on Therapeutic Targets · doi:10.1517/14728222.2016.1168808 · Cited by 196
Dissociable Structural and Functional Hippocampal Outputs via Distinct Subiculum Cell Classes
Cembrowski, M. S., Phillips, M. G., DiLisio, S. F., Shields, B. C., Winnubst, J., Chandrashekar, J. V., Bas, E., & Spruston, N. (2018) · Cell · doi:10.1016/j.cell.2018.03.031 · Cited by 195
Single cell molecular alterations reveal target cells and pathways of concussive brain injury
Arneson, D., Zhang, G., Ying, Z., Zhuang, Y., Byun, H. R., Ahn, I. S., Gomez-Pinilla, F., & Yang, X. (2018) · Nature Communications · doi:10.1038/s41467-018-06222-0 · Cited by 193
Wirth, E. K., Roth, S., Blechschmidt, C., Hölter, S. M., Becker, L., Rácz, I., Zimmer, A., Klopstock, T., Gailus‐Durner, V., Fuchs, H., et al. (2009) · Journal of Neuroscience · doi:10.1523/jneurosci.6055-08.2009 · Cited by 196
Sovio, U., Mook-Kanamori, D. O., Warrington, N. M., Lawrence, R., Briollais, L., Palmer, C. N. A., Cecil, J. E., Sandling, J. K., Syvänen, A., Kaakinen, M., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1001307 · Cited by 196
Thalamic subnetworks as units of function
Roy, D. S., Zhang, Y., Halassa, M. M., & Feng, G. (2022) · Nature Neuroscience · doi:10.1038/s41593-021-00996-1 · Cited by 177
Krienen, F. M., Yeo, B. T. T., Ge, T., Buckner, R. L., & Sherwood, C. C. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1510903113 · Cited by 190
Chandrasekaran, S., Ament, S. A., Eddy, J. A., Rodriguez‐Zas, S. L., Schatz, B. R., Price, N. D., & Robinson, G. E. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1114093108 · Cited by 195
Chemical neuroanatomy of the dorsal raphe nucleus and adjacent structures of the mouse brain
Fu, W.-Y., Maître, E. L., Fabre, V., Bernard, J., Xu, Q., & Hökfelt, T. G. M. (2010) · The Journal of Comparative Neurology · doi:10.1002/cne.22407 · Cited by 186
NO/cGMP-Dependent Modulation of Synaptic Transmission
Feil, R., & Kleppisch, T. (2007) · Handbook of experimental pharmacology · doi:10.1007/978-3-540-74805-2_16 · Cited by 192
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Kahvejian, A., Quackenbush, J., & Thompson, J. F. (2008) · Nature Biotechnology · doi:10.1038/nbt1494 · Cited by 189
Zalocusky, K. A., Najm, R., Taubes, A. L., Hao, Y., Yoon, S. Y., Koutsodendris, N., Nelson, M. R., Rao, A., Bennett, D. A., Bant, J., et al. (2021) · Nature Neuroscience · doi:10.1038/s41593-021-00851-3 · Cited by 189
Jelescu, I. O., Zurek, M., Winters, K. V., Veraart, J., Rajaratnam, A., Kim, N. S., Babb, J. S., Shepherd, T. M., Novikov, D. S., Kim, S. G., et al. (2016) · NeuroImage · doi:10.1016/j.neuroimage.2016.02.004 · Cited by 188
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Bayés, À., & Grant, S. G. N. (2009) · Nature reviews. Neuroscience · doi:10.1038/nrn2701 · Cited by 192
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Inestrosa, N. C., Montecinos-Oliva, C., & Fuenzalida, M. (2012) · Journal of Neuroimmune Pharmacology · doi:10.1007/s11481-012-9417-5 · Cited by 192
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Singh, N., Vrontakis, M. E., Parkinson, F. E., & Chelikani, P. (2011) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2011.02.016 · Cited by 195
Shanks, N. F., Savas, J. N., Maruo, T., Cais, O., Hirao, A., Oe, S., Ghosh, A., Noda, Y., Greger, I. H., Yates, J. R., et al. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.05.004 · Cited by 194
A genetic map of the mouse dorsal vagal complex and its role in obesity
Ludwig, M. Q., Cheng, W., Gordian, D., Lee, J., Paulsen, S. J., Hansen, S. N., Egerod, K. L., Barkholt, P., Rhodes, C. J., Secher, A., et al. (2021) · Nature Metabolism · doi:10.1038/s42255-021-00363-1 · Cited by 186
Chang, E. H., Argyelan, M., Aggarwal, M., Chandon, T.-S. S., Karlsgodt, K. H., Mori, S., & Malhotra, A. K. (2017) · NeuroImage · doi:10.1016/j.neuroimage.2016.11.068 · Cited by 186
Calcium Signaling in Dendritic SpinesPreprint
Higley, M. J., & Sabatini, B. L. (2012) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a005686 · Cited by 187
An atlas of gene regulatory elements in adult mouse cerebrum
Li, Y. E., Preissl, S., Hou, X., Zhang, Z., Zhang, K., Qiu, Y., Poirion, O. B., Li, B., Chiou, J., Liu, H., et al. (2021) · Nature · doi:10.1038/s41586-021-03604-1 · Cited by 185
Hippocampal AMPA Receptor Gating Controlled by Both TARP and Cornichon Proteins
Kato, A., Gill, M. B., Ho, M. T., Yu, H. Y., Tu, Y., Siuda, E. R., Wang, H., Qian, Y., Nisenbaum, E. S., Tomita, S., et al. (2010) · Neuron · doi:10.1016/j.neuron.2010.11.026 · Cited by 190
The unipolar brush cell: A remarkable neuron finally receiving deserved attention
Mugnaini, E., Sekerková, G., & Martina, M. (2010) · Brain Research Reviews · doi:10.1016/j.brainresrev.2010.10.001 · Cited by 177
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Siddiqui, T. J., Tari, P. K., Connor, S. A., Zhang, P., Dobie, F. A., She, K., Kawabe, H., Wang, Y. T., Brose, N., & Craig, A. M. (2013) · Neuron · doi:10.1016/j.neuron.2013.06.029 · Cited by 186
Puchades, M. A., Csucs, G., Ledergerber, D., Leergaard, T. B., & Bjaalie, J. G. (2019) · PLoS ONE · doi:10.1371/journal.pone.0216796 · Cited by 191
Fulcher, B. D., Arnatkeviciute, A., & Fornito, A. (2021) · Nature Communications · doi:10.1038/s41467-021-22862-1 · Cited by 164
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Schuman, B., Machold, R. P., Hashikawa, Y., Fuzik, J., Fishell, G. J., & Rudy, B. (2019) · The Journal of Neuroscience · doi:10.1523/jneurosci.1613-18.2018 · Cited by 184
“To find markers that could help the segregation of L1 INs, we mined data from our own studies, as well as from the Allen Institute in situ hybridization (ISH) gene expression databases (Lein et al., 2007).”
MethodFlexible, Penetrating Brain Probes Enabled by Advances in Polymer Microfabrication
Weltman, A., Yoo, J. J., & Meng, E. F. (2016) · Micromachines · doi:10.3390/mi7100180 · Cited by 192
Tepe, B., Hill, M. C., Pekarek, B. T., Hunt, P. J., Martin, T. J., Martin, J. F., & Arenkiel, B. R. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.11.034 · Cited by 183
Zywitza, V., Misios, A., Bunatyan, L., Willnow, T. E., & Rajewsky, N. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.11.003 · Cited by 183
O’Hurley, G., Sjöstedt, E., Rahman, A., Li, B., Kampf, C., Pontén, F., Gallagher, W. M., & Lindskog, C. (2014) · Molecular Oncology · doi:10.1016/j.molonc.2014.03.008 · Cited by 187
State-specific gating of salient cues by midbrain dopaminergic input to basal amygdala
Lutas, A., Kucukdereli, H., Alturkistani, O., Carty, C., Sugden, A. U., Fernando, K., Diaz, V. E., Flores-Maldonado, V., & Andermann, M. L. (2019) · Nature Neuroscience · doi:10.1038/s41593-019-0506-0 · Cited by 165
Regulation of synaptic transmission and plasticity by neuronal nicotinic acetylcholine receptors
McKay, B. E., Placzek, A. N., & Dani, J. A. (2007) · Biochemical Pharmacology · doi:10.1016/j.bcp.2007.07.001 · Cited by 181
Weak correlations between hemodynamic signals and ongoing neural activity during the resting state
Winder, A. T., Echagarruga, C., Zhang, Q., & Drew, P. J. (2017) · Nature Neuroscience · doi:10.1038/s41593-017-0007-y · Cited by 178
Arbogast, T., Ouagazzal, A.-M., Chevalier, C., Kopanitsa, M., Afinowi, N., Migliavacca, E., Cowling, B. S., Birling, M.-C., Champy, M.-F., Reymond, A., et al. (2016) · PLOS Genetics · doi:10.1371/journal.pgen.1005709 · Cited by 151
Selective Neuronal Vulnerability in Alzheimer’s Disease: A Network-Based Analysis
Roussarie, J.-P., Yao, V., Rodriguez-Rodriguez, P., Oughtred, R., Rust, J., Plautz, Z., Kasturia, S., Albornoz, C., Wang, W., Schmidt, E. F., et al. (2020) · Neuron · doi:10.1016/j.neuron.2020.06.010 · Cited by 180
Dolan, J., Walshe, K., Alsbury, S., Hokamp, K., O’Keeffe, S., Okafuji, T., Miller, S. F. C., Tear, G., & Mitchell, K. J. (2007) · BMC Genomics · doi:10.1186/1471-2164-8-320 · Cited by 180
A Milieu Molecule for TGF-β Required for Microglia Function in the Nervous System
Qin, Y., Garrison, B. S., Ma, W., Wang, R., Jiang, A., Li, J., Mistry, M., Bronson, R. T., Santoro, D., Franco, C., et al. (2018) · Cell · doi:10.1016/j.cell.2018.05.027 · Cited by 180
Kim, D. W., Washington, P. W., Wang, Z. Q., Lin, S. H., Sun, C., Ismail, B. T., Wang, H., Jiang, L., & Blackshaw, S. (2020) · Nature Communications · doi:10.1038/s41467-020-18231-z · Cited by 177
Ome sweet ome: what can the genome tell us about the connectome?
Lichtman, J. W., & Sanes, J. R. (2008) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2008.08.010 · Cited by 176
Zhang, Y., Zhou, Y., Schweizer, U., Savaskan, N. E., Hua, D., Kipnis, J., Hatfield, D. L., & Gladyshev, V. N. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m707951200 · Cited by 179
BK Channels in the Central Nervous System
Contet, C., Goulding, S. P., Kuljis, D. A., & Barth, A. L. (2016) · International review of neurobiology · doi:10.1016/bs.irn.2016.04.001 · Cited by 180
Hartmann, J., Karl, R. M., Alexander, R. P. D., Adelsberger, H., Brill, M. S., Rühlmann, C., Ansel, A., Sakimura, K., Baba, Y., Kurosaki, T., et al. (2014) · Neuron · doi:10.1016/j.neuron.2014.03.027 · Cited by 177
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Mandelbaum, G., Taranda, J., Haynes, T. M., Hochbaum, D. R., Huang, K. W., Hyun, M., Venkataraju, K. U., Straub, C., Wang, W., Robertson, K., et al. (2019) · Neuron · doi:10.1016/j.neuron.2019.02.035 · Cited by 179
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Nagarajan, R. P., & Costello, J. F. (2009) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2009.02.005 · Cited by 176
Fu, Y., Yuan, Y., Halliday, G. M., Rusznák, Z., WATSON, C. R. R., & Paxinos, G. (2011) · Brain Structure and Function · doi:10.1007/s00429-011-0349-2 · Cited by 176
Brain-Derived Neurotrophic Factor (BDNF): Novel Insights into Regulation and Genetic Variation
Notaras, M. J., & van den Buuse, M. (2018) · The Neuroscientist · doi:10.1177/1073858418810142 · Cited by 184
Li, Z., & Zhou, X. (2022) · Genome biology · doi:10.1186/s13059-022-02734-7 · Cited by 176
Bożek, K., Wei, Y., Zheng, Y., Liu, X., Xiong, J., Sugimoto, M., Tomita, M., Pääbo, S., Sherwood, C. C., Hof, P. R., et al. (2015) · Neuron · doi:10.1016/j.neuron.2015.01.003 · Cited by 166
Molecular Mechanisms of Synaptic Specificity in Developing Neural Circuits
Williams, M. E., de Wit, J., & Ghosh, A. (2010) · Neuron · doi:10.1016/j.neuron.2010.09.007 · Cited by 180
A high resolution atlas of gene expression in the domestic sheep (Ovis aries)
Clark, E. L., Bush, S. J., McCulloch, M. E. B., Farquhar, I., Young, R. A., Lefèvre, L., Pridans, C., Tsang, H., Wu, C., Afrasiabi, C., et al. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1006997 · Cited by 176
Self-citationEndogenous Wnt Signaling Maintains Neural Progenitor Cell Potency
Wexler, E. M., Paucer, A., Kornblum, H. I., Palmer, T. D., & Geschwind, D. H. (2009) · Stem Cells · doi:10.1002/stem.36 · Cited by 174
Archer, S. N., & Oster, H. (2015) · Journal of Sleep Research · doi:10.1111/jsr.12307 · Cited by 176
Kuhlman, S. J., & Huang, Z. J. (2008) · PLoS ONE · doi:10.1371/journal.pone.0002005 · Cited by 179
Transplanted embryonic neurons integrate into adult neocortical circuits
Falkner, S., Grade, S., Dimou, L., Conzelmann, K.-K., Bonhoeffer, T., Götz, M., & Hübener, M. (2016) · Nature · doi:10.1038/nature20113 · Cited by 174
Zhao, Z., Zhu, H., Li, X., Sun, L., He, F., Chung, J. E., Liu, D. F., Frank, L. M., Luan, L., & Xie, C. (2022) · Nature Biomedical Engineering · doi:10.1038/s41551-022-00941-y · Cited by 188
Accurate measurements of dynamics and reproducibility in small genetic networks
Dubuis, J., Samanta, R., & Gregor, T. (2013) · Molecular Systems Biology · doi:10.1038/msb.2012.72 · Cited by 173
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Steinert, J. R., Kopp‐Scheinpflug, C., Baker, C., Challiss, R. A. J., Mistry, R., Haustein, M. D., Griffin, S. J., Tong, H., Graham, B. P., & Forsythe, I. D. (2008) · Neuron · doi:10.1016/j.neuron.2008.08.025 · Cited by 173
Epigenetic Alterations in Alzheimer’s Disease
Sanchez-Mut, J. V., & Gräff, J. (2015) · Frontiers in Behavioral Neuroscience · doi:10.3389/fnbeh.2015.00347 · Cited by 175
Zech, M., Boesch, S., Maier, E. M., Borggraefe, I., Vill, K., Laccone, F. A., Pilshofer, V., Ceballos-Baumann, A., Alhaddad, B., Berutti, R., et al. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2016.10.010 · Cited by 178
Unique functional responses differentially map onto genetic subtypes of dopamine neurons
Azcorra, M., Gaertner, Z. A., Davidson, C., He, Q., Kim, H., Nagappan, S., Hayes, C. K., Ramakrishnan, C., Fenno, L. E., Kim, Y. S., et al. (2023) · Nature Neuroscience · doi:10.1038/s41593-023-01401-9 · Cited by 172
High-Yield Methods for Accurate Two-Alternative Visual Psychophysics in Head-Fixed Mice
Burgess, C., Lak, A., Steinmetz, N. A., Zatka-Haas, P., Reddy, C. B., Jacobs, E. A. K., Linden, J. F., Paton, J. J., Ranson, A., Schröder, S., et al. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.08.047 · Cited by 180
The mechanosensitive ion channel Piezo1 contributes to ultrasound neuromodulation
Zhu, J., Xian, Q., Hou, X., Wong, K. F., Zhu, T., Chen, Z., He, D., Kala, S., Murugappan, S., Jing, J., et al. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2300291120 · Cited by 178
Moberly, A. H., Schreck, M., Bhattarai, J. P., Zweifel, L. S., Luo, W., & Ma, M. (2018) · Nature Communications · doi:10.1038/s41467-018-03988-1 · Cited by 170
Increased catecholamine secretion contributes to hypertension in TRPM4-deficient mice
Mathar, I., Vennekens, R., Meissner, M., Kees, F., der Mieren, G. V., Londoño, J. E. C., Uhl, S., Voets, T., Hummel, B., den Bergh, A. V., et al. (2010) · Journal of Clinical Investigation · doi:10.1172/jci41348 · Cited by 170
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Colquitt, B. M., Merullo, D. P., Konopka, G., Roberts, T. F., & Brainard, M. S. (2021) · Science · doi:10.1126/science.abd9704 · Cited by 167
Transcriptional regulation of vertebrate axon guidance and synapse formation
Polleux, F., Ince-Dunn, G., & Ghosh, A. (2007) · Nature Reviews Neuroscience · doi:10.1038/nrn2118 · Cited by 168
Genetic mapping of canine fear and aggression
Zapata, I., Serpell, J. A., & Alvarez, C. E. (2016) · BMC Genomics · doi:10.1186/s12864-016-2936-3 · Cited by 168
Copper regulates rest-activity cycles through the locus coeruleus-norepinephrine system
Xiao, T., Ackerman, C. M., Carroll, E. C., Jia, S., Hoagland, A., Chan, J., Thai, B., Liu, C. S., Isacoff, E. Y., & Chang, C. J. (2018) · Nature Chemical Biology · doi:10.1038/s41589-018-0062-z · Cited by 168
Simultaneous cortex-wide fluorescence Ca2+ imaging and whole-brain fMRI
Lake, E. M. R., Ge, X., Shen, X., Hermán, P., Hyder, F., Cardin, J. A., Higley, M. J., Scheinost, D., Papademetris, X., Crair, M. C., et al. (2020) · Nature Methods · doi:10.1038/s41592-020-00984-6 · Cited by 168
Lee, H., Wang, C., Deshmukh, S. S., & Knierim, J. J. (2015) · Neuron · doi:10.1016/j.neuron.2015.07.012 · Cited by 173
Justice, N. J., Yuan, Z. F., Sawchenko, P. E., & Vale, W. (2008) · The Journal of Comparative Neurology · doi:10.1002/cne.21848 · Cited by 167
Enomoto, A., Asai, N., Namba, T., Wang, Y., Kato, T., Tanaka, M., Tatsumi, H., Taya, S., Tsuboi, D., Kuroda, K., et al. (2009) · Neuron · doi:10.1016/j.neuron.2009.08.015 · Cited by 164
LRP8-Reelin-regulated neuronal enhancer signature underlying learning and memory formation
Telese, F., Ma, Q., Perez, P. M., Notani, D., Oh, S., Li, W., Comoletti, D., Ohgi, K. A., Taylor, H., & Rosenfeld, M. G. (2015) · Neuron · doi:10.1016/j.neuron.2015.03.033 · Cited by 166
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Lewitus, É., Kelava, I., Kalinka, A. T., Tomančák, P., & Huttner, W. Β. (2014) · PLoS Biology · doi:10.1371/journal.pbio.1002000 · Cited by 169
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Widera, D., Zander, C., Heidbreder, M., Kasperek, Y., Noll, T., Seitz, O., Saldamli, B., Sudhoff, H. H., Sader, R. A., Kaltschmidt, C., et al. (2009) · Stem Cells · doi:10.1002/stem.104 · Cited by 165
Garden, D. L. F., Dodson, P. D., O’Donnell, C., White, M. D., & Nolan, M. F. (2008) · Neuron · doi:10.1016/j.neuron.2008.10.044 · Cited by 166
Kctd13 deletion reduces synaptic transmission via increased RhoA
Escamilla, C. O., Filonova, I., Walker, A. K., Xuan, Z. X., Holehonnur, R., Espinosa, F., Liu, S., Thyme, S. B., López-García, I. A., Mendoza, D. B., et al. (2017) · Nature · doi:10.1038/nature24470 · Cited by 165
Lerchner, W., Xiao, C., Nashmi, R., Slimko, E. M., van Trigt, L., Lester, H. A., & Anderson, D. J. (2007) · Neuron · doi:10.1016/j.neuron.2007.02.030 · Cited by 163
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Heymann, G., Jo, Y. S., Reichard, K. L., McFarland, N., Chavkin, C., Palmiter, R. D., Soden, M. E., & Zweifel, L. S. (2019) · Neuron · doi:10.1016/j.neuron.2019.11.024 · Cited by 165
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D'Angelo, E. U., & Jirsa, V. (2022) · Trends in Neurosciences · doi:10.1016/j.tins.2022.06.007 · Cited by 162
Gofflot, F., Chartoire, N., Vasseur, L., Heikkinen, S., Dembélé, D., Merrer, J. L., & Auwerx, J. H. (2007) · Cell · doi:10.1016/j.cell.2007.09.012 · Cited by 176
Single-cell-resolution transcriptome map of human, chimpanzee, bonobo, and macaque brains
Khrameeva, E., Kurochkin, I., Han, D., Guijarro, P., Kanton, S., Santel, M., Qian, Z., Rong, S., Mazin, P., Sabirov, M., et al. (2020) · Genome Research · doi:10.1101/gr.256958.119 · Cited by 162
Jakovcevski, M., Ruan, H., Shen, E., Dincer, A., Javidfar, B., Ma, Q., Peter, C. J., Cheung, I. K., Mitchell, A., Jiang, Y., et al. (2015) · Journal of Neuroscience · doi:10.1523/jneurosci.3004-14.2015 · Cited by 161
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Falomir‐Lockhart, L. J., Cavazzutti, G. F., Giménez, E., & Toscani, A. M. (2019) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2019.00162 · Cited by 164
Hase, T., Shishido, S., Yamamoto, S., Yamashita, R., Nukima, H., Taira, S., Toyoda, T., Abe, K., Hamaguchi, T., Ono, K., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-45168-1 · Cited by 162
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Pauli, J. L., Chen, J., Basiri, M. L., Park, S., Carter, M. E., Sanz, E., McKnight, G. S., Stuber, G. D., & Palmiter, R. D. (2022) · eLife · doi:10.7554/elife.81868 · Cited by 173
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Kleppisch, T., & Feil, R. (2009) · Handbook of Experimental Pharmacology · doi:10.1007/978-3-540-68964-5_24 · Cited by 161
Rapid β-oxidation of eicosapentaenoic acid in mouse brain: An in situ study
Chen, C. T., Liu, Z., Ouellet, M., Calon, F., & Bazinet, R. P. (2009) · Prostaglandins Leukotrienes and Essential Fatty Acids · doi:10.1016/j.plefa.2009.01.005 · Cited by 161
Spatial expression of transcription factors in Drosophilaembryonic organ development
Hammonds, A. S., Bristow, C. A., Fisher, W. W., Weiszmann, R., Wu, S., Hartenstein, V., Kellis, M., Yu, B., Frise, E., & Celniker, S. (2013) · Genome biology · doi:10.1186/gb-2013-14-12-r140 · Cited by 160
Hippocampome.org: a knowledge base of neuron types in the rodent hippocampus
Wheeler, D. W., White, C. M., Rees, C. L., Komendantov, A. O., Hamilton, D. J., & Ascoli, G. A. (2015) · eLife · doi:10.7554/elife.09960 · Cited by 161
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Goode, T. D., Tanaka, K. Z., Sahay, A., & McHugh, T. J. (2020) · Neuron · doi:10.1016/j.neuron.2020.07.011 · Cited by 170
The cell biology of Parkinson’s disease
Panicker, N., Ge, P., Dawson, V. L., & Dawson, T. M. (2021) · The Journal of Cell Biology · doi:10.1083/jcb.202012095 · Cited by 179
A functional cellular framework for sex and estrous cycle-dependent gene expression and behavior
Knoedler, J. R., Inoue, S., Bayless, D. W., Yang, T., Tantry, A., Davis, C.-H. O., Leung, N. Y., Parthasarathy, S., Wang, G., Alvarado, M., et al. (2022) · Cell · doi:10.1016/j.cell.2021.12.031 · Cited by 168
Clinical correlates in an experimental model of repetitive mild brain injury
Mannix, R., Meehan, W. P., III, Mandeville, J. B., Grant, P. E., Gray, T., Berglass, J., Zhang, J., Bryant, J., Rezaie, S., Chung, J. Y., et al. (2013) · Annals of Neurology · doi:10.1002/ana.23858 · Cited by 160
ApoE, ApoE Receptors, and the Synapse in Alzheimer's Disease
Lane-Donovan, C., & Herz, J. (2017) · Trends in Endocrinology & Metabolism · doi:10.1016/j.tem.2016.12.001 · Cited by 157
“This is partially due to the fact that ApoE expression, in both mice and humans, begins relatively late in development [46, 47].”
BackgroundComputational approaches to disease‐gene prediction: rationale, classification and successes
Piro, R. M., & Cunto, F. D. (2012) · FEBS Journal · doi:10.1111/j.1742-4658.2012.08471.x · Cited by 156
Population neuroscience: Why and how
Paus, T. (2010) · Human Brain Mapping · doi:10.1002/hbm.21069 · Cited by 157
Cornichon proteins determine the subunit composition of synaptic AMPA receptors
Herring, B. E., Shi, Y., Suh, Y. H., Zheng, C.-Y., Blankenship, S. M., Roche, K. W., & Nicoll, R. A. (2013) · Neuron · doi:10.1016/j.neuron.2013.01.017 · Cited by 155
Metadata
- Authors
- Lein, E. S., Hawrylycz, M. J., Ao, N., Ayres, M., Bensinger, A., Bernard, A., Boe, A. F., Boguski, M. S., Brockway, K. S., Byrnes, E. J., Chen, L., Chen, L., Chen, T.-M., Chi Chin, M., Chong, J., Crook, B. E., Czaplinska, A., Dang, C. N., Datta, S., Dee, N. R., Desaki, A. L., Desta, T., Diep, E., Dolbeare, T. A., Donelan, M. J., Dong, H.-W., Dougherty, J. G., Duncan, B. J., Ebbert, A. J., Eichele, G., Estin, L. K., Faber, C., Facer, B. A., Fields, R., Fischer, S. R., Fliss, T. P., Frensley, C., Gates, S. N., Glattfelder, K. J., Halverson, K. R., Hart, M. R., Hohmann, J. G., Howell, M. P., Jeung, D. P., Johnson, R. A., Karr, P. T., Kawal, R., Kidney, J. M., Knapik, R. H., Kuan, C. L., Lake, J. H., Laramee, A. R., Larsen, K. D., Lau, C., Lemon, T. A., Liang, A. J., Liu, Y., Luong, L. T., Michaels, J., Morgan, J. J., Morgan, R. J., Mortrud, M. T., Mosqueda, N. F., Ng, L. L., Ng, R., Orta, G. J., Overly, C. C., Pak, T. H., Parry, S. E., Pathak, S. D., Pearson, O. C., Puchalski, R. B., Riley, Z. L., Rockett, H. R., Rowland, S. A., Royall, J. J., Ruiz, M. J., Sarno, N. R., Schaffnit, K., Shapovalova, N. V., Sivisay, T., Slaughterbeck, C. R., Smith, S. C., Smith, K. A., Smith, B. I., Sodt, A. J., Stewart, N. N., Stumpf, K.-R., Sunkin, S. M., Sutram, M., Tam, A., Teemer, C. D., Thaller, C., Thompson, C. L., Varnam, L. R., Visel, A., Whitlock, R. M., Wohnoutka, P. E., Wolkey, C. K., Wong, V. Y., Wood, M., Yaylaoglu, M. B., Young, R. C., Youngstrom, B. L., Feng Yuan, X., Zhang, B., Zwingman, T. A., & Jones, A. R.
- Affiliations
- Allen Institute for Brain Science (US)
- Baylor College of Medicine (US)
- Novartis (Switzerland) (CH)
- Lawrence Berkeley National Laboratory (US)
- Corresponding author
- Lein, Ed S.
- Jones, Allan R.
- ORCID
- Lein, Ed S.
- Hawrylycz, Michael J.
- Bernard, Amy
- Chen, Lin
- Chong, Jimmy
- Dee, Nick R.
- Desta, Tsega
- Dolbeare, Tim A.
- Dong, Hong-Wei
- Fliss, Tim P.
- Glattfelder, Katie J.
- Hart, Matthew R.
- Hohmann, John G.
- Liu, Ying
- Ng, Lydia L.
- Puchalski, Ralph B.
- Shapovalova, Nadiya V.
- Smith, Kimberly A.
- Sunkin, Susan M.
- Thompson, Carol L.
- Visel, Axel
- Wohnoutka, Paul E.
- Wood, Matthew
- Zhang, Bin
- Zwingman, Theresa A.
- Jones, Allan R.
- Venue
- Nature
- Published
- 2006-12-06
- Volume
- 445
- Issue
- 7124
- Pages
- 168-176
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W2123491442
- Cited by
- 5,572
- References
- 58
- Citations by year
- 2026: 237 · 2025: 327 · 2024: 368 · 2023: 347 · 2022: 409 · 2021: 435 · 2020: 398 · 2019: 342 · 2018: 320 · 2017: 296 · 2016: 280 · 2015: 236 · 2014: 252 · 2013: 203 · 2012: 223
- FWCI
- 68.18
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Max Planck Institute for Plasma Physics (submittedVersion)
- Max Planck Digital Library (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Keywords
- gene expression atlas, mouse brain, Allen Brain Atlas, cellular resolution, in situ hybridization, brain region-specific gene expression, cell markers, brain organization
- MeSH terms
- Animals, Brain, Gene Expression Regulation, Hippocampus, Male, Mice, Inbred C57BL, Organ Specificity, RNA, Messenger, Genome, Computational Biology, Gene Expression Profiling, Genomics, Mice
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