-
1
-
-
0042209598
-
From gene networks to brain networks
-
PID: 12886225, COI: 1:CAS:528:DC%2BD3sXlslOis7w%3D
-
Bota, M., Dong, H.W. and Swanson, L.W. (2003) From gene networks to brain networks. Nat. Neurosci. 6, 795–799.
-
(2003)
Nat. Neurosci.
, vol.6
, pp. 795-799
-
-
Bota, M.1
Dong, H.W.2
Swanson, L.W.3
-
2
-
-
33846252240
-
Genome-wide atlas of gene expression in the adult mouse brain
-
PID: 17151600, COI: 1:CAS:528:DC%2BD2sXjtFKjtw%3D%3D
-
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., et al. (2007) Genome-wide atlas of gene expression in the adult mouse brain. Nature 445, 168–176.
-
(2007)
Nature
, vol.445
, pp. 168-176
-
-
Lein, E.S.1
Hawrylycz, M.J.2
Ao, N.3
Ayres, M.4
Bensinger, A.5
Bernard, A.6
Boe, A.F.7
Boguski, M.S.8
Brockway, K.S.9
Byrnes, E.J.10
-
3
-
-
38449118153
-
Insights from spatially mapped gene expression in the mouse brain
-
Sunkin, S. M., Hohmann, J. G. (2007) Insights from spatially mapped gene expression in the mouse brain. Hum. Mol. Genet. 16, 2.
-
(2007)
Hum. Mol. Genet.
, vol.16
, pp. 2
-
-
Sunkin, S.M.1
Hohmann, J.G.2
-
5
-
-
34547964832
-
Neuroinformatics for genome-wide 3D gene expression mapping in the mouse brain
-
PID: 17666758, COI: 1:CAS:528:DC%2BD2sXhtVOgtLzK
-
Ng, L., Pathak, S. D., Kuan, C., Lau, C., Dong, H., et al. (2007) Neuroinformatics for genome-wide 3D gene expression mapping in the mouse brain. IEEE/ACM Trans. Comput. Biol. Bioinform. Jul–Sep 4(3), 382–393.
-
(2007)
IEEE/ACM Trans. Comput. Biol. Bioinform.
, vol.4
, Issue.3
, pp. 382-393
-
-
Ng, L.1
Pathak, S.D.2
Kuan, C.3
Lau, C.4
Dong, H.5
-
6
-
-
70350228331
-
The Allen Brain Atlas: 5 years and beyond
-
PID: 19826436, COI: 1:CAS:528:DC%2BD1MXht1GlsrnN
-
Jones, A. R., Overly, C. C. and Sunkin, S. M. (2009) The Allen Brain Atlas: 5 years and beyond. Nat. Rev. Neurosci. 10, 821–828.
-
(2009)
Nat. Rev. Neurosci.
, vol.10
, pp. 821-828
-
-
Jones, A.R.1
Overly, C.C.2
Sunkin, S.M.3
-
7
-
-
80053218338
-
Multi-scale correlation structure of gene expression in the brain
-
PID: 21764550
-
Hawrylycz, M., Ng, L., Page, D., Morris, J., Lau, C., Faber, S., Faber, V., Sunkin, S., Menon, V., Lein, E., et al. (2011) Multi-scale correlation structure of gene expression in the brain. Neural Netw. 24, 933–942.
-
(2011)
Neural Netw.
, vol.24
, pp. 933-942
-
-
Hawrylycz, M.1
Ng, L.2
Page, D.3
Morris, J.4
Lau, C.5
Faber, S.6
Faber, V.7
Sunkin, S.8
Menon, V.9
Lein, E.10
-
9
-
-
84930635479
-
-
Grange, P., Bohland, J.W., Hawrylycz, M. and Mitra, P. P. (2012) Brain Gene Expression Analysis: a MATLAB toolbox for the analysis of brain-wide gene-expression data, arXiv:1211.6177 [q-bio.QM].
-
(2012)
Brain Gene Expression Analysis: a MATLAB toolbox for the analysis of brain-wide gene-expression data
-
-
Grange, P.1
Bohland, J.W.2
Hawrylycz, M.3
Mitra, P.P.4
-
10
-
-
38949164506
-
Genes and (common) pathways underlying drug addiction
-
PID: 18179280
-
Li, C. Y., Mao, X. and Wei, L. (2008) Genes and (common) pathways underlying drug addiction. PLOS Comput. Biol. 4, e2.
-
(2008)
PLOS Comput. Biol.
, vol.4
-
-
Li, C.Y.1
Mao, X.2
Wei, L.3
-
11
-
-
49549111404
-
Systematic biological prioritization after a genome-wide association study: an application to nicotine dependence
-
PID: 18565990, COI: 1:CAS:528:DC%2BD1cXpslarsr8%3D
-
Saccone, S. F., Saccone, N. L., Swan, G. E., Madden, P. A. F., Goate, A. M., Rice, J. P. and Bierut, L. J. (2008) Systematic biological prioritization after a genome-wide association study: an application to nicotine dependence. Bioinformatics 24, 1805–1811.
-
(2008)
Bioinformatics
, vol.24
, pp. 1805-1811
-
-
Saccone, S.F.1
Saccone, N.L.2
Swan, G.E.3
Madden, P.A.F.4
Goate, A.M.5
Rice, J.P.6
Bierut, L.J.7
-
12
-
-
0025183708
-
Basic local alignment search tool
-
PID: 2231712, COI: 1:CAS:528:DyaK3MXitVGmsA%3D%3D
-
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. and Lipman, D. J. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403–410.
-
(1990)
J. Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
13
-
-
70350223749
-
NeuroBlast: a 3D spatial homology search tool for gene expression
-
Ng, L., Lau, C., Young, R., Pathak, S., Kuan, L., Sodt, A., Sutram, M., Lee, C. K., Dang, C. and Hawrylycz, M. (2007) NeuroBlast: a 3D spatial homology search tool for gene expression. BMC Neurosci. 8, 11.
-
(2007)
BMC Neurosci.
, vol.8
, pp. 11
-
-
Ng, L.1
Lau, C.2
Young, R.3
Pathak, S.4
Kuan, L.5
Sodt, A.6
Sutram, M.7
Lee, C.K.8
Dang, C.9
Hawrylycz, M.10
-
14
-
-
60749125717
-
An anatomic gene expression atlas of the adult mouse brain
-
PID: 19219037, COI: 1:CAS:528:DC%2BD1MXhvFKjurg%3D
-
Ng, L., Bernard, A., Lau, C., Overly, C. C., Dong, H. W., Kuan, C., Pathak, S., Sunkin, S. M., Dang, C., Bohland, J. W., et al. (2009) An anatomic gene expression atlas of the adult mouse brain. Nat. Neurosci. 12, 356–362.
-
(2009)
Nat. Neurosci.
, vol.12
, pp. 356-362
-
-
Ng, L.1
Bernard, A.2
Lau, C.3
Overly, C.C.4
Dong, H.W.5
Kuan, C.6
Pathak, S.7
Sunkin, S.M.8
Dang, C.9
Bohland, J.W.10
-
15
-
-
23944458138
-
A general framework for weighted gene co-expression network analysis
-
Zhang, B. and Horvath, S. (2005) A general framework for weighted gene co-expression network analysis. Stat. Appl. Genet. Mol. Biol. 4, e17.
-
(2005)
Stat. Appl. Genet. Mol. Biol.
, vol.4
-
-
Zhang, B.1
Horvath, S.2
-
16
-
-
44449145053
-
Analysis of the network of feeding neuroregulators using the Allen Brain Atlas
-
PID: 18457878, COI: 1:CAS:528:DC%2BD1cXms1Whtrg%3D
-
Olszewski, P. K., Cedernaes, J., Olsson, F., Levine, A. S. and Schiöth, H. B. (2008) Analysis of the network of feeding neuroregulators using the Allen Brain Atlas. Neurosci. Biobehav. Rev. 32, 945–956.
-
(2008)
Neurosci. Biobehav. Rev.
, vol.32
, pp. 945-956
-
-
Olszewski, P.K.1
Cedernaes, J.2
Olsson, F.3
Levine, A.S.4
Schiöth, H.B.5
-
19
-
-
42549114238
-
Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain
-
PID: 18366675
-
Lau, C., Ng, L., Thompson, C., Pathak, S., Kuan, L., Jones, A. and Hawrylycz, M. (2008) Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain. BMC Bioinformatics 9, 153.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 153
-
-
Lau, C.1
Ng, L.2
Thompson, C.3
Pathak, S.4
Kuan, L.5
Jones, A.6
Hawrylycz, M.7
-
20
-
-
79952481631
-
Digital atlasing and standardization in the mouse brain
-
PID: 21304938, COI: 1:CAS:528:DC%2BC3MXitV2rsbk%3D
-
Hawrylycz, M., Baldock, R. A., Burger, A., Hashikawa, T., Johnson, G. A., Martone, M., Ng, L., Lau, C., Larson, S. D., Nissanov, J., et al. (2011) Digital atlasing and standardization in the mouse brain. PLOS Comput. Biol. 7, e1001065.
-
(2011)
PLOS Comput. Biol.
, vol.7
-
-
Hawrylycz, M.1
Baldock, R.A.2
Burger, A.3
Hashikawa, T.4
Johnson, G.A.5
Martone, M.6
Ng, L.7
Lau, C.8
Larson, S.D.9
Nissanov, J.10
-
22
-
-
0001790593
-
Depth first search and linear graph algorithms
-
Tarjan, R. E. (1972) Depth first search and linear graph algorithms. SIAM J. Comput. 1, 146–160.
-
(1972)
SIAM J. Comput.
, vol.1
, pp. 146-160
-
-
Tarjan, R.E.1
-
23
-
-
74149083446
-
Clustering of spatial gene expression patterns in the mouse brain and comparison with classical neuroanatomy
-
PID: 19733241, COI: 1:CAS:528:DC%2BC3cXotVyluw%3D%3D
-
Bohland, J. W., Bokil, H., Pathak, S. D., Lee, C. K., Ng, L., Lau, C., Kuan, C., Hawrylycz, M. and Mitra, P. P. (2010) Clustering of spatial gene expression patterns in the mouse brain and comparison with classical neuroanatomy. Methods 50, 105–112.
-
(2010)
Methods
, vol.50
, pp. 105-112
-
-
Bohland, J.W.1
Bokil, H.2
Pathak, S.D.3
Lee, C.K.4
Ng, L.5
Lau, C.6
Kuan, C.7
Hawrylycz, M.8
Mitra, P.P.9
-
25
-
-
85042792884
-
-
Menashe, I., Grange, P., Larsen, E. C., Banerjee-Basu, S. and Mitra, P. P. (2012) Co-expression profiling of autism genes in the mouse brain. SFN Abstracts, and submitted.
-
(2012)
Co-expression profiling of autism genes in the mouse brain
-
-
Menashe, I.1
Grange, P.2
Larsen, E.C.3
Banerjee-Basu, S.4
Mitra, P.P.5
-
26
-
-
84866518216
-
An anatomically comprehensive atlas of the adult human brain transcriptome
-
PID: 22996553, COI: 1:CAS:528:DC%2BC38Xhtlymu77N
-
Hawrylycz, M. J., Lein, E. S., Guillozet-Bongaarts, A. L., Shen, E. H., Ng, L., Miller, J. A., van de Lagemaat, L. N., Smith, K. A., Ebbert, A., Riley, Z. L., et al. (2012) An anatomically comprehensive atlas of the adult human brain transcriptome. Nature 489, 391–399.
-
(2012)
Nature
, vol.489
, pp. 391-399
-
-
Hawrylycz, M.J.1
Lein, E.S.2
Guillozet-Bongaarts, A.L.3
Shen, E.H.4
Ng, L.5
Miller, J.A.6
van de Lagemaat, L.N.7
Smith, K.A.8
Ebbert, A.9
Riley, Z.L.10
-
27
-
-
77950376512
-
The genome of a songbird
-
PID: 20360741, COI: 1:CAS:528:DC%2BC3cXktVyhu7c%3D
-
Warren, W. C., Clayton, D. F., Ellegren, H., Arnold, A. P., Hillier, L.W., Künstner, A., Searle, S., White, S., Vilella, A. J. and Fairley, S. (2010) The genome of a songbird. Nature 464, 757–762.
-
(2010)
Nature
, vol.464
, pp. 757-762
-
-
Warren, W.C.1
Clayton, D.F.2
Ellegren, H.3
Arnold, A.P.4
Hillier, L.W.5
Künstner, A.6
Searle, S.7
White, S.8
Vilella, A.J.9
Fairley, S.10
-
28
-
-
85042740798
-
-
(Oregon Health and Science University, Portland, OR 97239;)
-
Data can be retrieved from the ZEBrA database. (Oregon Health and Science University, Portland, OR 97239; http://www.zebrafinchatlas.org).
-
Data can be retrieved from the ZEBrA database
-
-
-
29
-
-
77955454185
-
Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways
-
PID: 20616000, COI: 1:CAS:528:DC%2BC3cXpt1Shuro%3D
-
Miller, J. A., Horvath, S. and Geschwind, D. H. (2010) Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways. Proc. Natl. Acad. Sci. USA 107, 12698–12703.
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, pp. 12698-12703
-
-
Miller, J.A.1
Horvath, S.2
Geschwind, D.H.3
-
30
-
-
33749175091
-
Global transcriptome analysis of genetically identified neurons in the adult cortex
-
PID: 17005859, COI: 1:CAS:528:DC%2BD28XhtVOmtLnF
-
Rossner, M. J., Hirrlinger, J., Wichert, S. P., Boehm, C., Newrzella, D., Hiemisch, H., Eisenhardt, G., Stuenkel, C., von Ahsen, O. and Nave, K. A. (2006) Global transcriptome analysis of genetically identified neurons in the adult cortex. J. Neurosci. 26, 9956–9966.
-
(2006)
J. Neurosci.
, vol.26
, pp. 9956-9966
-
-
Rossner, M.J.1
Hirrlinger, J.2
Wichert, S.P.3
Boehm, C.4
Newrzella, D.5
Hiemisch, H.6
Eisenhardt, G.7
Stuenkel, C.8
von Ahsen, O.9
Nave, K.A.10
-
31
-
-
38149129457
-
A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function
-
PID: 18171944, COI: 1:CAS:528:DC%2BD1cXmtV2ltw%3D%3D
-
Cahoy, J. D., Emery, B., Kaushal, A., Foo, L. C., Zamanian, J. L., Christopherson, K. S., Xing, Y., Lubischer, J. L., Krieg, P. A., Krupenko, S. A., et al. (2008) A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function. J. Neurosci. 28, 264–278.
-
(2008)
J. Neurosci.
, vol.28
, pp. 264-278
-
-
Cahoy, J.D.1
Emery, B.2
Kaushal, A.3
Foo, L.C.4
Zamanian, J.L.5
Christopherson, K.S.6
Xing, Y.7
Lubischer, J.L.8
Krieg, P.A.9
Krupenko, S.A.10
-
32
-
-
55449103144
-
Application of a translational profiling approach for the comparative analysis of CNS cell types
-
PID: 19013282, COI: 1:CAS:528:DC%2BD1cXhsVCls7vL
-
Doyle, J. P., Dougherty, J. D., Heiman, M., Schmidt, E. F., Stevens, T. R., Ma, G., Bupp, S., Shrestha, P., Shah, R. D., Doughty, M. L., et al. (2008) Application of a translational profiling approach for the comparative analysis of CNS cell types. Cell 135, 749–762.
-
(2008)
Cell
, vol.135
, pp. 749-762
-
-
Doyle, J.P.1
Dougherty, J.D.2
Heiman, M.3
Schmidt, E.F.4
Stevens, T.R.5
Ma, G.6
Bupp, S.7
Shrestha, P.8
Shah, R.D.9
Doughty, M.L.10
-
33
-
-
26444529541
-
Cell type-specific gene expression of midbrain dopaminergic neurons reveals molecules involved in their vulnerability and protection
-
PID: 15888489, COI: 1:CAS:528:DC%2BD2MXmvV2htL8%3D
-
Chung, C. Y., Seo, H., Sonntag, K. C., Brooks, A., Lin, L. and Isacson, O. (2005) Cell type-specific gene expression of midbrain dopaminergic neurons reveals molecules involved in their vulnerability and protection. Hum. Mol. Genet. 14, 1709–1725.
-
(2005)
Hum. Mol. Genet.
, vol.14
, pp. 1709-1725
-
-
Chung, C.Y.1
Seo, H.2
Sonntag, K.C.3
Brooks, A.4
Lin, L.5
Isacson, O.6
-
34
-
-
12344252023
-
Neuronal subtype-specific genes that control corticospinal motor neuron development in vivo
-
PID: 15664173, COI: 1:CAS:528:DC%2BD2MXhtFOrt7o%3D
-
Arlotta, P., Molyneaux, B. J., Chen, J., Inoue, J., Kominami, R. and Macklis, J. D. (2005) Neuronal subtype-specific genes that control corticospinal motor neuron development in vivo. Neuron 45, 207–221.
-
(2005)
Neuron
, vol.45
, pp. 207-221
-
-
Arlotta, P.1
Molyneaux, B.J.2
Chen, J.3
Inoue, J.4
Kominami, R.5
Macklis, J.D.6
-
35
-
-
55449107738
-
A translational profiling approach for the molecular characterization of CNS cell types
-
PID: 19013281, COI: 1:CAS:528:DC%2BD1cXhsVCls7vK
-
Heiman, M., Schaefer, A., Gong, S., Peterson, J. D., Day, M., Ramsey, K. E., Suárez-Fariñas M., Schwarz, C., Stephan, D. A., Surmeier, D. J., et al. (2008) A translational profiling approach for the molecular characterization of CNS cell types. Cell 135, 738–748.
-
(2008)
Cell
, vol.135
, pp. 738-748
-
-
Heiman, M.1
Schaefer, A.2
Gong, S.3
Peterson, J.D.4
Day, M.5
Ramsey, K.E.6
Suárez-Fariñas, M.7
Schwarz, C.8
Stephan, D.A.9
Surmeier, D.J.10
-
36
-
-
29444452573
-
Molecular taxonomy of major neuronal classes in the adult mouse forebrain
-
PID: 16369481, COI: 1:CAS:528:DC%2BD2MXhtlCms7jN
-
Sugino, K., Hempel, C. M., Miller, M. N., Hattox, A. M., Shapiro, P., Wu, C., Huang, Z. J. and Nelson, S. B. (2006) Molecular taxonomy of major neuronal classes in the adult mouse forebrain. Nat. Neurosci. 9, 99–107.
-
(2006)
Nat. Neurosci.
, vol.9
, pp. 99-107
-
-
Sugino, K.1
Hempel, C.M.2
Miller, M.N.3
Hattox, A.M.4
Shapiro, P.5
Wu, C.6
Huang, Z.J.7
Nelson, S.B.8
-
37
-
-
46249132930
-
Quantitative methods for genome-scale analysis of in situ hybridization and correlation with microarray data
-
PID: 18234097
-
Lee, C. K., Sunkin, S. M., Kuan, C., Thompson, C. L., Pathak, S., Ng, L., Lau, C., Fischer, S., Mortrud, M., Slaughterbeck, C., et al. (2008) Quantitative methods for genome-scale analysis of in situ hybridization and correlation with microarray data. Genome Biol. 9, R23.
-
(2008)
Genome Biol.
, vol.9
, pp. R23
-
-
Lee, C.K.1
Sunkin, S.M.2
Kuan, C.3
Thompson, C.L.4
Pathak, S.5
Ng, L.6
Lau, C.7
Fischer, S.8
Mortrud, M.9
Slaughterbeck, C.10
-
38
-
-
85042773256
-
-
Grange, P., Bohland, J.W., Bokil, H., Nelson, S., Okaty, B., Sugino, K., Ng, L., Hawrylycz, M. and Mitra, P. P. (2011) A cell-type based model explaining co-expression patterns of genes in the brain, arXiv:1111.6217 [q-bio.QM].
-
(2011)
A cell-type based model explaining co-expression patterns of genes in the brain
-
-
Grange, P.1
Bohland, J.W.2
Bokil, H.3
Nelson, S.4
Okaty, B.5
Sugino, K.6
Ng, L.7
Hawrylycz, M.8
Mitra, P.P.9
|