Technology Insight: querying the genome with microarrays—progress and hope for neurological disease

Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray

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Genome sequencing in microfabricated high-density picolitre reactors

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A haplotype map of the human genome

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A General Framework for Weighted Gene Co-Expression Network Analysis

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Complement factor H polymorphism in age-related macular degeneration

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Comparative Genomic Hybridization for Molecular Cytogenetic Analysis of Solid Tumors

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Expression monitoring by hybridization to high-density oligonucleotide arrays

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Large-scale copy number polymorphism in the human genome

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Gene-microarray analysis of multiple sclerosis lesions yields new targets validated in autoimmune encephalomyelitis

Lock, C., Hermans, G., Pedotti, R., Brendolan, A., Schadt, E. E., Garren, H., Langer-Gould, A. M., Strober, S., Cannella, B., Allard, J. D., et al. (2002) · Nature Medicine · doi:10.1038/nm0502-500 · Cited by 1,659 · see citing works

Accessing Genetic Information with High-Density DNA Arrays

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Genome-wide analysis of DNA copy-number changes using cDNA microarrays

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Whole-Genome Patterns of Common DNA Variation in Three Human Populations

Hinds, D., Stuve, L., Nilsen, G. B., Halperin, E., Eskin, E., Ballinger, D., Frazer, K., & Cox, D. (2005) · Science · doi:10.1126/science.1105436 · Cited by 1,245 · see citing works

Microarray identification of FMRP-associated brain mRNAs and altered mRNA translational profiles in fragile X syndrome

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Incipient Alzheimer's disease: Microarray correlation analyses reveal major transcriptional and tumor suppressor responses

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Segmental Duplications and Copy-Number Variation in the Human Genome

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Environmental Enrichment Reduces Aβ Levels and Amyloid Deposition in Transgenic Mice

Lazarov, O., Robinson, J., Tang, Y.-P., Hairston, I. S., Korade-Mirnics, Z., Lee, V. M.-Y., Hersh, L. B., Sapolsky, R. M., Mirnics, K., & Sisodia, S. S. (2005) · Cell · doi:10.1016/j.cell.2005.01.015 · Cited by 885 · see citing works

Molecular Characterization of Schizophrenia Viewed by Microarray Analysis of Gene Expression in Prefrontal Cortex

Mirnics, K., Middleton, F. A., Marquez, A., Lewis, D. A., & Levitt, P. (2000) · Neuron · doi:10.1016/s0896-6273(00)00085-4 · Cited by 882 · see citing works

Molecular interactions on microarrays

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Gene Expression Profiling of Gliomas Strongly Predicts Survival

Freije, W. A., Castro-Vargas, F. E., Fang, Z., Horvath, S., Cloughesy, T. F., Liau, L. M., Mischel, P. S., & Nelson, S. F. (2004) · Cancer Research · doi:10.1158/0008-5472.can-04-0452 · Cited by 745 · see citing works

Histone Deacetylase Inhibition by Sodium Butyrate Chemotherapy Ameliorates the Neurodegenerative Phenotype in Huntington's Disease Mice

Ferrante, R. J., Kubilus, J. K., Lee, J.-H., Ryu, H., Beesen, A. A., Zucker, B., Smith, K., Kowall, N. W., Ratan, R. R., Luthi‐Carter, R., et al. (2003) · Journal of Neuroscience · doi:10.1523/jneurosci.23-28-09418.2003 · Cited by 694 · see citing works

A genome-wide scalable SNP genotyping assay using microarray technology

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Large-scale genotyping of complex DNA

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Array comparative genomic hybridization and its applications in cancer

Pinkel, D., & Albertson, D. G. (2005) · Nature Genetics · doi:10.1038/ng1569 · Cited by 585 · see citing works

Gene expression profiling of 12633 genes in Alzheimer hippocampal CA1: transcription and neurotrophic factor down-regulation and up-regulation of apoptotic and pro-inflammatory signaling

Colangelo, V., Schurr, J., Ball, M. J., Pelaez, R. P., Bazan, N. G., & Lukiw, W. J. (2002) · Journal of Neuroscience Research · doi:10.1002/jnr.10351 · Cited by 517 · see citing works

High-Resolution Whole-Genome Association Study of Parkinson Disease

Maraganore, D. M., de Andrade, M., Lesnick, T. G., Strain, K. J., Farrer, M. J., Rocca, W. A., Pant, P. V. K., Frazer, K. A., Cox, D., & Ballinger, D. G. (2005) · The American Journal of Human Genetics · doi:10.1086/496902 · Cited by 508 · see citing works

Polyglutamine Pathogenesis

Ross, C. A. (2002) · Neuron · doi:10.1016/s0896-6273(02)00872-3 · Cited by 500 · see citing works

Toward genome-wide SNP genotyping

Syvänen, A. (2005) · Nature Genetics · doi:10.1038/ng1558 · Cited by 464 · see citing works

Model‐guided microarray implicates the retromer complex in Alzheimer's disease

Small, S. A., Kent, K., Pierce, A., Leung, C., Kang, M. S., Okada, H., Honig, L., Vonsattel, J., & Kim, T. (2005) · Annals of Neurology · doi:10.1002/ana.20667 · Cited by 440 · see citing works

Gene Expression Profiling Reveals Alterations of Specific Metabolic Pathways in Schizophrenia

Middleton, F. A., Mirnics, K., Pierri, J. N., Lewis, D. A., & Levitt, P. R. (2002) · Journal of Neuroscience · doi:10.1523/jneurosci.22-07-02718.2002 · Cited by 428 · see citing works

APPLICATIONS OF DNA MICROARRAYS IN BIOLOGY

Stoughton, R. B. (2005) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.74.082803.133212 · Cited by 390 · see citing works

Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA

Barrett, M. T., Scheffer-Wong, A., Ben‐Dor, A., Sampas, N., Lipson, D., Kincaid, R. H., Tsang, P. W. K., Curry, B., Baird, K., Meltzer, P. S., et al. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0407979101 · Cited by 367 · see citing works

Gene expression profiling of parkinsonian substantia nigra pars compacta; alterations in ubiquitin-proteasome, heat shock protein, iron and oxidative stress regulated proteins, cell adhesion/cellular matrix and vesicle trafficking genes

Grünblatt, E., Mandel, S. A., Jacob‐Hirsch, J., Zeligson, S., Amariglo, N., Rechavi, G., Li, J., Ravid, R., Roggendorf, W., Riederer, P. F., et al. (2004) · Journal of Neural Transmission · doi:10.1007/s00702-004-0212-1 · Cited by 358 · see citing works

Transcriptional profiling of a mouse model for Rett syndrome reveals subtle transcriptional changes in the brain

Tudor, M., Akbarian, S., Chen, R. Z., & Jaenisch, R. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.242566899 · Cited by 343 · see citing works

Gene expression profiles of transcripts in amyloid precursor protein transgenic mice: up-regulation of mitochondrial metabolism and apoptotic genes is an early cellular change in Alzheimer's disease

Reddy, P. H., McWeeney, S. K., Park, B. S., Mańczak, M., Gutala, R. V., Partovi, D., Jung, Y., Yau, V., Searles, R. P., Mori, M., et al. (2004) · Human Molecular Genetics · doi:10.1093/hmg/ddh140 · Cited by 327 · see citing works

Parallel Genotyping of Over 10,000 SNPs Using a One-Primer Assay on a High-Density Oligonucleotide ArrayPreprint

Matsuzaki, H., Loi, H., Dong, S., Tsai, Y.-Y., Fang, J., Law, J., Di, X., Liu, W., Yang, G., Liu, G., et al. (2004) · Genome Research · doi:10.1101/gr.2014904 · Cited by 320 · see citing works

A Gene Expression Profile of Alzheimer's Disease

Loring, J. F., Wen, X., Lee, J. M., Seilhamer, J. J., & Somogyi, R. (2001) · DNA and Cell Biology · doi:10.1089/10445490152717541 · Cited by 300 · see citing works

High-Throughput Variation Detection and Genotyping Using MicroarraysPreprint

Cutler, D. J., Zwick, M. E., Carrasquillo, M. M., Yohn, C. T., Tobin, K., Kashuk, C., Mathews, D., Shah, N. A., Eichler, E. E., Warrington, J. A., et al. (2001) · Genome Research · doi:10.1101/gr.197201 · Cited by 277 · see citing works

Differential expression of inflammation‐ and apoptosis‐related genes in spinal cords of a mutant SOD1 transgenic mouse model of familial amyotrophic lateral sclerosis

Yoshihara, T., Ishigaki, S., Yamamoto, M., Liang, Y., Jun, Niwa, I., Takeuchi, H., Doyu, M., & Sobue, G. (2001) · Journal of Neurochemistry · doi:10.1046/j.0022-3042.2001.00683.x · Cited by 275 · see citing works

Gene expression profile of spinal motor neurons in sporadic amyotrophic lateral sclerosis

Jiang, Y., Yamamoto, M., Kobayashi, Y., Yoshihara, T., Liang, Y., Terao, S., Takeuchi, H., Ishigaki, S., Katsuno, M., Adachi, H., et al. (2005) · Annals of Neurology · doi:10.1002/ana.20379 · Cited by 255 · see citing works

Gene expression analysis in N‐methyl‐4‐phenyl‐1,2,3,6‐tetrahydropyridine mice model of Parkinson's disease using cDNA microarray: effect of R‐apomorphine

Grünblatt, E., Mandel, S. A., Maor, G., & Youdim, M. B. H. (2001) · Journal of Neurochemistry · doi:10.1046/j.1471-4159.2001.00397.x · Cited by 246 · see citing works

Selectively Reduced Expression of Synaptic Plasticity-Related Genes in Amyloid Precursor Protein + Presenilin-1 Transgenic Mice

Dickey, C. A., Loring, J. F., Montgomery, J., Gordon, M. N., Eastman, P. S., & Morgan, D. (2003) · The Journal of Neuroscience · doi:10.1523/jneurosci.23-12-05219.2003 · Cited by 242 · see citing works

A Genetic Analysis of Neural Progenitor Differentiation

Geschwind, D. H., Ou, J., Easterday, M. C., Dougherty, J. D., Jackson, R. L., Chen, Z., Antoine, H. J., Terskikh, A. V., Weissman, I. L., Nelson, S. F., et al. (2001) · Neuron · doi:10.1016/s0896-6273(01)00209-4 · Cited by 242 · see citing works

The Human MitoChip: A High-Throughput Sequencing Microarray for Mitochondrial Mutation DetectionPreprint

Maitra, A., Cohen, Y., Gillespie, S. E. D., Mambo, E., Fukushima, N., Hoque, M. O., Shah, N., Goggins, M., Califano, J., Sidransky, D., et al. (2004) · Genome Research · doi:10.1101/gr.2228504 · Cited by 237 · see citing works

Early transcriptional profiles in huntingtin-inducible striatal cells by microarray analyses

Sipione, S., Rigamonti, D., Valenza, M., Zuccato, C., Conti, L., Pritchard, J., Kooperberg, C. L., Olson, J. M., & Cattaneo, E. F. (2014) · Human Molecular Genetics · doi:10.1093/hmg/ddu539 · Cited by 222 · see citing works

Friedreich ataxia: the oxidative stress paradox

Seznec, H., Simon, D., Bouton, C., Reutenauer, L., Hertzog, A., Golik, P., Procaccio, V., Patel, M., Drapier, J.-C., Koenig, M., et al. (2005) · Human Molecular Genetics · doi:10.1093/hmg/ddi042 · Cited by 219 · see citing works

DNA-microarray analysis of brain cancer: molecular classification for therapy

Mischel, P., Cloughesy, T., & Nelson, S. (2004) · Nature Reviews Neuroscience · doi:10.1038/nrn1518 · Cited by 218 · see citing works

Polyglutamine and transcription: gene expression changes shared by DRPLA and Huntington's disease mouse models reveal context-independent effects

Luthi‐Carter, R. (2002) · Human Molecular Genetics · doi:10.1093/hmg/11.17.1927 · Cited by 211 · see citing works

Early transcriptional profiles in huntingtin-inducible striatal cells by microarray analyses

Sipione, S. (2002) · Human Molecular Genetics · doi:10.1093/hmg/11.17.1953 · Cited by 209 · see citing works

Gene Expression Profiling in Postmortem Rett Syndrome Brain: Differential Gene Expression and Patient Classification

Colantuoni, C., Jeon, O., Hyder, K., Chenchik, A. A., Khimani, A. H., Narayanan, V., Hoffman, E. P., Kaufmann, W. E., Naidu, S., & Pevsner, J. (2001) · Neurobiology of Disease · doi:10.1006/nbdi.2001.0428 · Cited by 203 · see citing works

COMPARATIVE GENOMIC HYBRIDIZATION

Pinkel, D., & Albertson, D. G. (2005) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.6.080604.162140 · Cited by 202 · see citing works

Blood genomic responses differ after stroke, seizures, hypoglycemia, and hypoxia: Blood genomic fingerprints of disease

Tang, Y., Lu, A., Aronow, B. J., & Sharp, F. R. (2001) · Annals of Neurology · doi:10.1002/ana.10042 · Cited by 186 · see citing works

Gene profiling links SCA1 pathophysiology to glutamate signaling in Purkinje cells of transgenic mice

Serra, H. G., Byam, C. E., Lande, J. D., Tousey, S. K., Zoghbi, H. Y., & Orr, H. T. (2004) · Human Molecular Genetics · doi:10.1093/hmg/ddh268 · Cited by 176 · see citing works

Identification of an IMPDH1 mutation in autosomal dominant retinitis pigmentosa (RP10) revealed following comparative microarray analysis of transcripts derived from retinas of wild-type and Rho-/- mice

Kennan, A. (2002) · Human Molecular Genetics · doi:10.1093/hmg/11.5.547 · Cited by 167 · see citing works

Large-Scale Variation Among Human and Great Ape Genomes Determined by Array Comparative Genomic HybridizationPreprint

Locke, D. P., Segraves, R., Carbone, L., Archidiacono, N., Albertson, D. G., Pinkel, D., & Eichler, E. E. (2003) · Genome Research · doi:10.1101/gr.1003303 · Cited by 161 · see citing works

Gene expression in Huntington's disease skeletal muscle: a potential biomarker

Strand, A. D., Aragaki, A. K., Shaw, D., Bird, T. D., Holton, J. L., Turner, C., Tapscott, S. J., Tabrizi, S. J., Schapira, A. H. V., Kooperberg, C. L., et al. (2005) · Human Molecular Genetics · doi:10.1093/hmg/ddi192 · Cited by 160 · see citing works

Expression Profiling of Substantia Nigra in Parkinson Disease, Progressive Supranuclear Palsy, and Frontotemporal Dementia With Parkinsonism

Hauser, M. A., Li, Y., Xu, H., Noureddine, M., Shao, Y. S., Gullans, S. R., Scherzer, C. R., Jensen, R. V., McLaurin, A. C., Gibson, J., et al. (2005) · Archives of Neurology · doi:10.1001/archneur.62.6.917 · Cited by 158 · see citing works

Microarray analysis of gene expression in multiple sclerosis and EAE identifies 5-lipoxygenase as a component of inflammatory lesions

Whitney, L. W., Ludwin, S. K., McFarland, H. F., & Biddison, W. E. (2001) · Journal of Neuroimmunology · doi:10.1016/s0165-5728(01)00438-6 · Cited by 152 · see citing works

Progress in the use of microarray technology to study the neurobiology of disease

Mirnics, K., & Pevsner, J. (2004) · Nature Neuroscience · doi:10.1038/nn1230 · Cited by 150 · see citing works

Development of a comparative genomic hybridization microarray and demonstration of its utility with 25 well-characterized 1p36 deletions

Yu, W. (2003) · Human Molecular Genetics · doi:10.1093/hmg/ddg230 · Cited by 135 · see citing works

Microarray analysis identifies an aberrant expression of apoptosis and DNA damage-regulatory genes in multiple sclerosis

Satoh, J., Nakanishi, M., Koike, F., Miyake, S., Yamamoto, T., Kawai, M., Kikuchi, S., Nomura, K., Yokoyama, K., Ota, K., et al. (2005) · Neurobiology of Disease · doi:10.1016/j.nbd.2004.10.007 · Cited by 134 · see citing works

Mutational analysis using oligonucleotide microarrays

Hacia, J., & Collins, F. S. (1999) · Journal of Medical Genetics · doi:10.1136/jmg.36.10.730 · Cited by 129 · see citing works

Mapping of genetic and epigenetic regulatory networks using microarrays

van Steensel, B. (2005) · Nature Genetics · doi:10.1038/ng1559 · Cited by 118 · see citing works

Gene expression profile of oxidant stress and neurodegeneration in transgenic mice deficient in α-tocopherol transfer protein

Gohil, K., Schock, B. C., Chakraborty, A. A., Terasawa, Y., Raber, J., Farese, R. V., Packer, L., Cross, C. E., & Traber, M. G. (2003) · Free Radical Biology and Medicine · doi:10.1016/s0891-5849(03)00509-4 · Cited by 118 · see citing works

Gene expression patterns vary in clonal cell cultures from Rett syndrome females with eight different MECP2 mutations

Traynor, J., Agarwal, P., Lazzeroni, L. C., & Francke, U. (2002) · BMC Medical Genetics · doi:10.1186/1471-2350-3-12 · Cited by 109 · see citing works

Modulation of polyglutamine-induced cell death by genes identified by expression profiling

Kita, H. (2002) · Human Molecular Genetics · doi:10.1093/hmg/11.19.2279 · Cited by 104 · see citing works

Blood Gene Expression Profiling of Neurologic Diseases

Tang, Y., Gilbert, D. L., Glauser, T. A., Hershey, A. D., & Sharp, F. R. (2005) · Archives of Neurology · doi:10.1001/archneur.62.2.210 · Cited by 104 · see citing works

Altered expression of a-type but not b-type synapsin isoform in the brain of patients at high risk for Alzheimer's disease assessed by DNA microarray technique

Ho, L. (2001) · Neuroscience Letters · doi:10.1016/s0304-3940(00)01753-5 · Cited by 103 · see citing works

Detecting Gene Copy Number Fluctuations in Tumor Cells by Microarray Analysis of Genomic RepresentationsPreprint

Lucito, R. (2000) · Genome Research · doi:10.1101/gr.138300 · Cited by 102 · see citing works

Cystatin B-deficient mice have increased expression of apoptosis and glial activation genes

Lieuallen, K. (2001) · Human Molecular Genetics · doi:10.1093/hmg/10.18.1867 · Cited by 100 · see citing works

Genomewide High-Density SNP Linkage Analysis of 236 Japanese Families Supports the Existence of Schizophrenia Susceptibility Loci on Chromosomes 1p, 14q, and 20p

Arinami, T., Ohtsuki, T., Ishiguro, H., Ujike, H., Tanaka, Y., Morita, Y., Mineta, M., Takeichi, M., Yamada, S., Imamura, A., et al. (2005) · The American Journal of Human Genetics · doi:10.1086/498122 · Cited by 95 · see citing works

Modelling brain diseases in mice: the challenges of design and analysis

Watase, K., & Zoghbi, H. Y. (2003) · Nature Reviews Genetics · doi:10.1038/nrg1045 · Cited by 94 · see citing works

Mice, microarrays, and the genetic diversity of the brain

Geschwind, D. H. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.20.10676 · Cited by 92 · see citing works

[18F]Fluorodeoxyglucose positron emission tomography in the diagnosis of cancer in patients with paraneoplastic neurological syndrome and anti-Hu antibodies

Antoine, J.-C. G., Cinotti, L., Tilikete, C., Bouhour, F., Camdessanch�, J. P., Confavreux, C., Vighetto, A., Renault‐Mannel, V., Michel, D., & Honnorat, J. (2000) · Annals of Neurology · doi:10.1002/1531-8249(200007)48:1 · Cited by 86 · see citing works

Decreased expression of genes involved in sulfur amino acid metabolism in frataxin-deficient cells

Tan, G. (2003) · Human Molecular Genetics · doi:10.1093/hmg/ddg187 · Cited by 86 · see citing works

Gene Expression Profiling in Ataxin-3 Expressing Cell Lines Reveals Distinct Effects of Normal and Mutant Ataxin-3

Evert, B. O., Vogt, I. R., Vieira-Saecker, A. M. M., Ozimek, L., de Vos, R. A. I., Brunt, E. R. P., Klockgether, T., & Wüllner, U. (2003) · Journal of Neuropathology & Experimental Neurology · doi:10.1093/jnen/62.10.1006 · Cited by 81 · see citing works

A combination drug therapy improves cognition and reverses gene expression changes in a mouse model of Huntington's disease

Morton, A. J., Hunt, M. J., Hodges, A., Lewis, P. D., Redfern, A. J., Dunnett, S. B., & Jones, L. (2005) · European Journal of Neuroscience · doi:10.1111/j.1460-9568.2005.03895.x · Cited by 77 · see citing works

New developments in high-throughput resequencing and variation detection using high density microarrays

Warrington, J. A., Shah, N. A., Chen, X., Janis, M., Liu, C., Kondapalli, S., Reyes, V., Savage, M., Zhang, Z., Watts, R., et al. (2002) · Human Mutation · doi:10.1002/humu.10075 · Cited by 71 · see citing works

Systems biology 101—what you need to know

Ideker, T. (2004) · Nature Biotechnology · doi:10.1038/nbt0404-473 · Cited by 71 · see citing works

cDNA microarray analysis of individual Duchenne muscular dystrophy patients

Noguchi, S., Tsukahara, T., Fujita, M., Kurokawa, R., Tachikawa, M., Toda, T., Tsujimoto, A., Arahata, K., & Nishino, I. (2003) · Human Molecular Genetics · doi:10.1093/hmg/ddg065 · Cited by 69 · see citing works

Gene expression profile analysis of lymphocytes from Alzheimer??s patients

K??lm??n, J., Kitajka, K., ski, M. P. K., Zvara, ?., sz, A. J. A., Vincze, G., Janka, Z., & Pusk??s, L. G. (2005) · Psychiatric Genetics · doi:10.1097/00041444-200503000-00001 · Cited by 67 · see citing works

Neonatal screening by DNA microarray: spots and chips

Green, N., & Pass, K. A. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1526 · Cited by 66 · see citing works

DNA microarrays: translation of the genome from laboratory to clinic

Geschwind, D. H. (2003) · The Lancet Neurology · doi:10.1016/s1474-4422(03)00379-x · Cited by 59 · see citing works

Sequencing Arrays for Screening Multiple Genes Associated with Early-Onset Human Retinal Degenerations on a High-Throughput Platform

Mandal, M. N. A., Heckenlively, J. R., Burch, T., Chen, L., Vasireddy, V., Koenekoop, R. K., Sieving, P. A., & Ayyagari, R. (2005) · Investigative Ophthalmology & Visual Science · doi:10.1167/iovs.05-0007 · Cited by 59 · see citing works

Genomewide linkage searches for Mendelian disease loci can be efficiently conducted using high-density SNP genotyping arrays

Sellick, G. S. (2004) · Nucleic Acids Research · doi:10.1093/nar/gnh163 · Cited by 58 · see citing works

Gene Expression Phenotype in Heterozygous Carriers of Ataxia Telangiectasia

Watts, J. A., Morley, M. P., Burdick, J. T., Fiori, J. L., Ewens, W. J., Spielman, R. S., & Cheung, V. G. (2002) · The American Journal of Human Genetics · doi:10.1086/342974 · Cited by 57 · see citing works

Gene Expression Profiles in a Transgenic Animal Model of Fragile X Syndrome

D’Agata, V., Warren, S. T., Zhao, W., Torre, E. R., Alkon, D. L., & Cavallaro, S. (2002) · Neurobiology of Disease · doi:10.1006/nbdi.2002.0506 · Cited by 54 · see citing works

A unique gene expression signature discriminates familial Alzheimer's disease mutation carriers from their wild-type siblings

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DNA arrays and neurobiology — what's new and what's next?

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