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1
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0035222137
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Expressing what's on your mind: DNA arrays and the brain
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A review of the major advances in the use of gene expression profiling in the brain prior to mid-2001, which also contains some practical tips.
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Lockhart D.J., Barlow C. Expressing what's on your mind: DNA arrays and the brain. Nat Rev Neurosci. 2:2001;63-68. A review of the major advances in the use of gene expression profiling in the brain prior to mid-2001, which also contains some practical tips.
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(2001)
Nat Rev Neurosci
, vol.2
, pp. 63-68
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Lockhart, D.J.1
Barlow, C.2
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2
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0034718595
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Regional and strain-specific gene expression mapping in the adult mouse brain
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This is the first publication to use gene expression profiling to identify strain-specific expression patterns in the brain, unique brain region-specific and subregion-specific patterns of gene expression. The authors also compare the pattern of gene expression between two strains in response to seizures in the hippocampus and cerebellum.
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Sandberg R., Yasuda R., Pankratz D.G., Carter T.A., Del Rio J.A., Wodicka L., Mayford M., Lockhart D.J., Barlow C. Regional and strain-specific gene expression mapping in the adult mouse brain. Proc Natl Acad Sci USA. 97:2000;11038-11043. This is the first publication to use gene expression profiling to identify strain-specific expression patterns in the brain, unique brain region-specific and subregion-specific patterns of gene expression. The authors also compare the pattern of gene expression between two strains in response to seizures in the hippocampus and cerebellum.
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(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 11038-11043
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Sandberg, R.1
Yasuda, R.2
Pankratz, D.G.3
Carter, T.A.4
Del Rio, J.A.5
Wodicka, L.6
Mayford, M.7
Lockhart, D.J.8
Barlow, C.9
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3
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0036500643
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High-density microarray analysis of hippocampal gene expression following experimental brain injury
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Matzilevich D.A., Rall J.M., Moore A.N., Grill R.J., Dash P.K. High-density microarray analysis of hippocampal gene expression following experimental brain injury. J Neurosci Res. 67:2002;646-663.
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(2002)
J Neurosci Res
, vol.67
, pp. 646-663
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Matzilevich, D.A.1
Rall, J.M.2
Moore, A.N.3
Grill, R.J.4
Dash, P.K.5
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4
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0035905027
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Transcriptional profiling reveals strict boundaries between hippocampal subregions
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Here Zhao et al. used Affymetrix arrays to identify genes expressed in the CA1, CA3 and dentate gyrus of the hippocampus. Importantly, many of the genes were followed up using in situ hybridization. The results show that there is in fact a CA2 region in the mouse with unique expression patterns.
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Zhao X., Lein E.S., He A., Smith S.C., Aston C., Gage F.H. Transcriptional profiling reveals strict boundaries between hippocampal subregions. J Comp Neurol. 441:2001;187-196. Here Zhao et al. used Affymetrix arrays to identify genes expressed in the CA1, CA3 and dentate gyrus of the hippocampus. Importantly, many of the genes were followed up using in situ hybridization. The results show that there is in fact a CA2 region in the mouse with unique expression patterns.
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(2001)
J Comp Neurol
, vol.441
, pp. 187-196
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Zhao, X.1
Lein, E.S.2
He, A.3
Smith, S.C.4
Aston, C.5
Gage, F.H.6
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5
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0034828022
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Gene expression profiling in the amygdala: An approach to examine the molecular substrates of mammalian behavior
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Dent G.W., O'Dell D.M., Eberwine J.H. Gene expression profiling in the amygdala: an approach to examine the molecular substrates of mammalian behavior. Physiol Behav. 73:2001;841-847.
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(2001)
Physiol Behav
, vol.73
, pp. 841-847
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Dent, G.W.1
O'Dell, D.M.2
Eberwine, J.H.3
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6
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0035942240
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Amygdala-enriched genes identified by microarray technology are restricted to specific amygdaloid subnuclei
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Similarly to [2•] and [4•], these authors identified genes in the amygdala using Affymetrix arrays. The genes identified as unique to subregions of the amygdala were further characterized using in situ hybridization.
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Zirlinger M., Kreiman G., Anderson D.J. Amygdala-enriched genes identified by microarray technology are restricted to specific amygdaloid subnuclei. Proc Natl Acad Sci USA. 98:2001;5270-5275. Similarly to [2•] and [4•], these authors identified genes in the amygdala using Affymetrix arrays. The genes identified as unique to subregions of the amygdala were further characterized using in situ hybridization.
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(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 5270-5275
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Zirlinger, M.1
Kreiman, G.2
Anderson, D.J.3
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7
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0000847978
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Gene-expression profile of the ageing brain in mice
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Although slightly older, this paper is important because it was one of the first to demonstrate that very subtle changes (∼30% change in gene expression levels), which occur in the rodent brain during the process of aging, can be detected using oligonucleotide arrays. The authors conclusively show this by confirming the results by QT-PCR.
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Lee C.K., Weindruch R., Prolla T.A. Gene-expression profile of the ageing brain in mice. Nat Genet. 25:2000;294-297. Although slightly older, this paper is important because it was one of the first to demonstrate that very subtle changes (∼30% change in gene expression levels), which occur in the rodent brain during the process of aging, can be detected using oligonucleotide arrays. The authors conclusively show this by confirming the results by QT-PCR.
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(2000)
Nat Genet
, vol.25
, pp. 294-297
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Lee, C.K.1
Weindruch, R.2
Prolla, T.A.3
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8
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0036138937
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Changes in gene expression linked to methamphetamine-induced dopaminergic neurotoxicity
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Xie T., Tong L., Barrett T., Yuan J., Hatzidimitriou G., McCann U.D., Becker K.G., Donovan D.M., Ricaurte G.A. Changes in gene expression linked to methamphetamine-induced dopaminergic neurotoxicity. J Neurosci. 22:2002;274-283.
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(2002)
J Neurosci
, vol.22
, pp. 274-283
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Xie, T.1
Tong, L.2
Barrett, T.3
Yuan, J.4
Hatzidimitriou, G.5
McCann, U.D.6
Becker, K.G.7
Donovan, D.M.8
Ricaurte, G.A.9
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9
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0030575911
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Laser capture microdissection
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Emmert-Buck M.R., Bonner R.F., Smith P.D., Chuaqui R.F., Zhuang Z., Goldstein S.R., Weiss R.A., Liotta L.A. Laser capture microdissection. Science. 274:1996;998-1001.
-
(1996)
Science
, vol.274
, pp. 998-1001
-
-
Emmert-Buck, M.R.1
Bonner, R.F.2
Smith, P.D.3
Chuaqui, R.F.4
Zhuang, Z.5
Goldstein, S.R.6
Weiss, R.A.7
Liotta, L.A.8
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10
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0033010885
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Gene expression profiles of laser-captured adjacent neuronal subtypes
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Luo L., Salunga R.C., Guo H., Bittner A., Joy K.C., Galindo J.E., Xiao H., Rogers K.E., Wan J.S., Jackson M.R., Erlander M.G. Gene expression profiles of laser-captured adjacent neuronal subtypes. Nat Med. 5:1999;117-122.
-
(1999)
Nat Med
, vol.5
, pp. 117-122
-
-
Luo, L.1
Salunga, R.C.2
Guo, H.3
Bittner, A.4
Joy, K.C.5
Galindo, J.E.6
Xiao, H.7
Rogers, K.E.8
Wan, J.S.9
Jackson, M.R.10
Erlander, M.G.11
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11
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0035515512
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Single-cell molecular biology
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This recent review examines the status of studies that assess mRNA in single cells.
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Eberwine J. Single-cell molecular biology. Nat Neurosci. 4:(Suppl):2001;1155-1156. This recent review examines the status of studies that assess mRNA in single cells.
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(2001)
Nat Neurosci
, vol.4
, Issue.SUPPL.
, pp. 1155-1156
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Eberwine, J.1
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12
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0026588147
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Analysis of gene expression in single live neurons
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Eberwine J., Yeh H., Miyashiro K., Cao Y., Nair S., Finnell R., Zettel M., Coleman P. Analysis of gene expression in single live neurons. Proc Natl Acad Sci USA. 89:1992;3010-3014.
-
(1992)
Proc Natl Acad Sci USA
, vol.89
, pp. 3010-3014
-
-
Eberwine, J.1
Yeh, H.2
Miyashiro, K.3
Cao, Y.4
Nair, S.5
Finnell, R.6
Zettel, M.7
Coleman, P.8
-
13
-
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0031973245
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Cloning of genes from single neurons
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Dulac C. Cloning of genes from single neurons. Curr Top Dev Biol. 36:1998;245-258.
-
(1998)
Curr Top Dev Biol
, vol.36
, pp. 245-258
-
-
Dulac, C.1
-
14
-
-
85017258406
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DNA arrays and gene expression analysis in the brain
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S. Molding, & H. Chin. Boca Raton, Florida: CRC Press
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Lockhart D.J., Barlow C. DNA arrays and gene expression analysis in the brain. Molding S., Chin H., Methods in Genomic Neuroscience. 2001;143-170 CRC Press, Boca Raton, Florida. This methods book covers topics including genetics, genomics, expression profiling techniques (multiple different platforms) and a host of other topics, including neural stem cell cloning and two-photon microscopy. The chapter cited here focuses on the use of oligonucleotide arrays for neuroscience studies.
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(2001)
Methods in Genomic Neuroscience
, pp. 143-170
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Lockhart, D.J.1
Barlow, C.2
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15
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0011156047
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D.H. Geshwind, & J.P. Gregg. Boston: MIT Press
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Geshwind D.H., Gregg J.P., Microarrays for the Neurosciences. 2002;MIT Press, Boston. Another methods based book that is focused on microarray applications for neuroscientists.
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(2002)
Microarrays for the Neurosciences
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16
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0036550998
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Gene expression profiling reveals alterations of specific metabolic pathways in schizophrenia
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This paper follows up previous work. More specific paired specimens were studied here than in the original paper.
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Middleton F.A., Mirnics K., Pierri J.N., Lewis D.A., Levitt P. Gene expression profiling reveals alterations of specific metabolic pathways in schizophrenia. J Neurosci. 22:2002;2718-2729. This paper follows up previous work. More specific paired specimens were studied here than in the original paper.
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(2002)
J Neurosci
, vol.22
, pp. 2718-2729
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Middleton, F.A.1
Mirnics, K.2
Pierri, J.N.3
Lewis, D.A.4
Levitt, P.5
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17
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0036105484
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Gene-microarray analysis of multiple sclerosis lesions yields new targets validated in autoimmune encephalomyelitis
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This excellent study uses genomics to identify targets for changes in gene expression in MS. The authors then use mouse genetics and pharmacology to further assess the biological significance of these changes. See also [18•]
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Lock C., Hermans G., Pedotti R., Brendolan A., Schadt E., Garren H., Langer-Gould A., Strober S., Cannella B., Allard J., et al. Gene-microarray analysis of multiple sclerosis lesions yields new targets validated in autoimmune encephalomyelitis. Nat Med. 8:2002;500-508. This excellent study uses genomics to identify targets for changes in gene expression in MS. The authors then use mouse genetics and pharmacology to further assess the biological significance of these changes. See also [18•] .
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(2002)
Nat Med
, vol.8
, pp. 500-508
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Lock, C.1
Hermans, G.2
Pedotti, R.3
Brendolan, A.4
Schadt, E.5
Garren, H.6
Langer-Gould, A.7
Strober, S.8
Cannella, B.9
Allard, J.10
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18
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0036113747
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An array of possibilities for multiple sclerosis
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A 'News and Views' articles accompanying [17••] that discusses the new results and the prior publications in the area. The authors point out that although there have now been three independent reports using genomics to study MS, Lock et al. [17••] were not able to adequately compare their results to those from prior studies. The authors believe this problem highlights the necessity of developing databases that serve as repositories of raw data and the need to provide the tools for data analysis directly to the bench biologist.
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Tompkins S.M., Miller S.D. An array of possibilities for multiple sclerosis. Nat Med. 8:2002;451-453. A 'News and Views' articles accompanying [17••] that discusses the new results and the prior publications in the area. The authors point out that although there have now been three independent reports using genomics to study MS, Lock et al. [17••] were not able to adequately compare their results to those from prior studies. The authors believe this problem highlights the necessity of developing databases that serve as repositories of raw data and the need to provide the tools for data analysis directly to the bench biologist.
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(2002)
Nat Med
, vol.8
, pp. 451-453
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Tompkins, S.M.1
Miller, S.D.2
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19
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0035500619
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Genome of the apes
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An excellent recent review of the field, including an analysis of the status of gene expression profiling in the brain and other tissues from non-human primates and humans.
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Hacia J.G. Genome of the apes. Trends Genet. 17:2001;637-645. An excellent recent review of the field, including an analysis of the status of gene expression profiling in the brain and other tissues from non-human primates and humans.
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(2001)
Trends Genet
, vol.17
, pp. 637-645
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Hacia, J.G.1
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20
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0037066542
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Intra- and interspecific variation in primate gene expression patterns
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Enard et al. provide the first overall index of differences in gene expression between human and chimpanzee liver. They demonstrate that the 'evolutionary distance' between primate species is greater when brains are compared than when livers are compared. No specific genes were analyzed and the trends of expression differences were not specified in any particular direction. Proteome comparison was also shown, but no specific genes or proteins were described. Importantly, these authors posted their raw data after publication.
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Enard W., Khaitovich P., Klose J., Zollner S., Heissig F., Giavalisco P., Nieselt-Struwe K., Muchmore E., Varki A., Ravid R., et al. Intra- and interspecific variation in primate gene expression patterns. Science. 296:2002;340-343. Enard et al. provide the first overall index of differences in gene expression between human and chimpanzee liver. They demonstrate that the 'evolutionary distance' between primate species is greater when brains are compared than when livers are compared. No specific genes were analyzed and the trends of expression differences were not specified in any particular direction. Proteome comparison was also shown, but no specific genes or proteins were described. Importantly, these authors posted their raw data after publication.
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(2002)
Science
, vol.296
, pp. 340-343
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Enard, W.1
Khaitovich, P.2
Klose, J.3
Zollner, S.4
Heissig, F.5
Giavalisco, P.6
Nieselt-Struwe, K.7
Muchmore, E.8
Varki, A.9
Ravid, R.10
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21
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0034820774
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Chipping away at complex behavior: Transcriptome/phenotype correlations in the mouse brain
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Carter T.A., Del Rio J.A., Greenhall J.A., Latronica M.L., Lockhart D.J., Barlow C. Chipping away at complex behavior: transcriptome/phenotype correlations in the mouse brain. Physiol Behav. 73:2001;849-857.
-
(2001)
Physiol Behav
, vol.73
, pp. 849-857
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Carter, T.A.1
Del Rio, J.A.2
Greenhall, J.A.3
Latronica, M.L.4
Lockhart, D.J.5
Barlow, C.6
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22
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0035827344
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In silico mapping of complex disease-related traits in mice
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This is the first study to show that identification of a gene can be greatly accelerated using a combination of genetic, genomic and computational approaches. In this study, the gene in question was responsible for increased sensitivity to reactive airway disease in mice.
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Grupe A., Germer S., Usuka J., Aud D., Belknap J.K., Klein R.F., Ahluwalia M.K., Higuchi R., Peltz G. In silico mapping of complex disease-related traits in mice. Science. 292:2001;1915-1918. This is the first study to show that identification of a gene can be greatly accelerated using a combination of genetic, genomic and computational approaches. In this study, the gene in question was responsible for increased sensitivity to reactive airway disease in mice.
-
(2001)
Science
, vol.292
, pp. 1915-1918
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-
Grupe, A.1
Germer, S.2
Usuka, J.3
Aud, D.4
Belknap, J.K.5
Klein, R.F.6
Ahluwalia, M.K.7
Higuchi, R.8
Peltz, G.9
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23
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0036215226
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Finding new candidate genes for learning and memory
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Leil T.A., Ossadtchi A., Cortes J.S., Leahy R.M., Smith D.J. Finding new candidate genes for learning and memory. J Neurosci Res. 68:2002;127-137.
-
(2002)
J Neurosci Res
, vol.68
, pp. 127-137
-
-
Leil, T.A.1
Ossadtchi, A.2
Cortes, J.S.3
Leahy, R.M.4
Smith, D.J.5
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24
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18544382234
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Genetic analysis of the mouse brain proteome
-
Klose J., Nock C., Herrmann M., Stuhler K., Marcus K., Bluggel M., Krause E., Schalkwyk L.C., Rastan S., Brown S.D., et al. Genetic analysis of the mouse brain proteome. Nat Genet. 30:2002;385-393.
-
(2002)
Nat Genet
, vol.30
, pp. 385-393
-
-
Klose, J.1
Nock, C.2
Herrmann, M.3
Stuhler, K.4
Marcus, K.5
Bluggel, M.6
Krause, E.7
Schalkwyk, L.C.8
Rastan, S.9
Brown, S.D.10
-
25
-
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0035375137
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Computational analysis of microarray data
-
Quackenbush J. Computational analysis of microarray data. Nat Rev Genet. 2:2001;418-427.
-
(2001)
Nat Rev Genet
, vol.2
, pp. 418-427
-
-
Quackenbush, J.1
-
26
-
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0035793042
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Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection
-
Li C., Wong W.H. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci USA. 98:2001;31-36.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 31-36
-
-
Li, C.1
Wong, W.H.2
-
27
-
-
0036289082
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A new algorithm for analysis of oligonucleotide arrays: Application to expression profiling in mouse brain regions
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Zhang L., Wang L., Ravindranathan A., Miles M.F. A new algorithm for analysis of oligonucleotide arrays: application to expression profiling in mouse brain regions. J Mol Biol. 317:2002;225-235.
-
(2002)
J Mol Biol
, vol.317
, pp. 225-235
-
-
Zhang, L.1
Wang, L.2
Ravindranathan, A.3
Miles, M.F.4
-
28
-
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0036042919
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Software and methods for oligonucleotide and cDNA array data analysis
-
software0001.1-0001.9
-
Zapala MA, Lockhart DJ, Pankratz DG, Garcia AJ, Barlow C, Lockhart DJ: Software and methods for oligonucleotide and cDNA array data analysis. Genome Biol 2002, 3:software0001.1-0001.9. Published online: http://genomebiology.com/2002/3/6/software/0001/
-
(2002)
Genome Biol
, vol.3
-
-
Zapala, M.A.1
Lockhart, D.J.2
Pankratz, D.G.3
Garcia, A.J.4
Barlow, C.5
Lockhart, D.J.6
-
29
-
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0036368805
-
Characterization of the expression ratio noise structure in high-density oligonucleotide arrays
-
preprint0001.1-0001.24
-
Naef F, Hacker CR, Patil N, Magnasco M: Characterization of the expression ratio noise structure in high-density oligonucleotide arrays. Genome Biol 2001, 3:preprint0001.1-0001.24. Published online: http://genomebiology.com/2001/3/1/preprint/0001/
-
(2001)
Genome Biol
, vol.3
-
-
Naef, F.1
Hacker, C.R.2
Patil, N.3
Magnasco, M.4
-
30
-
-
0034868258
-
The power of public access: The human genome project and the scientific process
-
Quackenbush J. The power of public access: the human genome project and the scientific process. Nat Genet. 29:2001;4-6.
-
(2001)
Nat Genet
, vol.29
, pp. 4-6
-
-
Quackenbush, J.1
-
31
-
-
0037046558
-
Creating a bioinformatics nation
-
Stein L. Creating a bioinformatics nation. Nature. 417:2002;119-120.
-
(2002)
Nature
, vol.417
, pp. 119-120
-
-
Stein, L.1
-
32
-
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0036546074
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Opinion: Sharing primary data: A threat or asset to discovery?
-
A good review of the status of the human brain map project and a discussion of data sharing issues.
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Koslow S.H. Opinion: sharing primary data: a threat or asset to discovery? Nat Rev Neurosci. 3:2002;311-313. A good review of the status of the human brain map project and a discussion of data sharing issues.
-
(2002)
Nat Rev Neurosci
, vol.3
, pp. 311-313
-
-
Koslow, S.H.1
-
33
-
-
18344396568
-
Minimum information about a microarray experiment (MIAME)-toward standards for microarray data
-
Brazma A., Hingamp P., Quackenbush J., Sherlock G., Spellman P., Stoeckert C., Aach J., Ansorge W., Ball C.A., Causton H.C., et al. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet. 29:2001;365-371.
-
(2001)
Nat Genet
, vol.29
, pp. 365-371
-
-
Brazma, A.1
Hingamp, P.2
Quackenbush, J.3
Sherlock, G.4
Spellman, P.5
Stoeckert, C.6
Aach, J.7
Ansorge, W.8
Ball, C.A.9
Causton, H.C.10
-
34
-
-
0029047723
-
NeuroNames brain hierarchy
-
Bowden D.M., Martin R.F. NeuroNames brain hierarchy. Neuroimage. 2:1995;63-83.
-
(1995)
Neuroimage
, vol.2
, pp. 63-83
-
-
Bowden, D.M.1
Martin, R.F.2
-
35
-
-
0037007639
-
Information overload
-
Dennis C. Information overload. Nature. 417:2002;14.
-
(2002)
Nature
, vol.417
, pp. 14
-
-
Dennis, C.1
|