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National Institute on Aging National Institutes of Health |
NIA Home Research Programs Intramural |
 | Gene Expression and Genomics Unit Research Resources Branch Baltimore, MD 21224-6825 Phone: 410-558-8360 Fax: 410-558-8281 Email: beckerk@grc.nia.nih.gov |
| Publications of the Gene Expression and Genomics Unit: |
| cDNA Microarrays and Gene Expression: |
| Mazan-Mamczarz, K., Hagner, P.R., Corl, S., Srikantan, S., Wood, W.H., Becker, K.G., Gorospe, M., Keene, J.D., Levenson, A.S., Gartenhaus, R.B. Post-transcriptional gene regulation by HuR promotes a more tumorigenic phenotype. Manuscript in preparation. [Data - Excel] |
| AGEMAP. [Data - Excel] |
| Xu, X., Duan, W., Brenneman, R., Zhan, M., Zhang, P., Ibe, C., Zonderman, A.B., Longo, D.L., Poosala, S., Becker, K.G., Mattson, M.P. Impact of age, energy intake and sex on central nervous system regional transcriptomes. 2005 (Submitted). |
| Baur, J.A., Pearson, K.J., Price, N.L., Jamieson, H.A., Lerin, C., Kalra, A., Prabhu, V.V., Allard, J.A., Lopez-Lluch, G., Lewis, K., Pistell, P.J., Poosala, S., Becker, K.G., Boss, O., Gwinn, D., Wang, M., Ramaswamy, S., Fishbein, K.W., Spencer, R.G., Lakatta, E.G., Le Couteur, D., Shaw, R.J., Navas, P., Puigserver, P., Ingram, D.K., de Cabo, R., Sinclair, D.A. Resveratrol improves health and survival of mice on a high-calorie diet. 2006 Nature. 444(7117): 337-342. [Data - Excel] - [Abs] |
| Zhang, Z., Fan, J., Becker, K.G., Graff, R.D., Lee, G.M., Francomano, C.A. Comparison of gene expression profile between human chondrons and chondrocytes:a cDNA microarray study. 2006 Osteoarthritis Cartilage. 14(5): 449-459. [Abs] |
| Ghorbel, M.T., Sharman, G., Hindmarch, C., Becker, K.G., Barrett, T., Murphy, D. Microarray screening of suppression subtractive hybridisation-PCR cDNA libraries identifies novel RNAs regulated by dehydration in the rat supraoptic nucleus. 2006 Physiol. Genomics. 24(2): 163-172. [Abs] |
| Pie, J.E., Park, J.H., Park, Y.H., Ryu, Y.M., Kim, K.N., Suh, S.W., Becker, K.G., Cho-Chung, Y.S., Kim, M.K. Effect of genistein on the expression of bone metabolism genes in ovariectomized mice using a cDNA microarray. 2006 J. Nutr. Biochem. 17(3): 157-164. [Abs] |
| Lee, P.R., Cohen, J.E., Becker, K.G., Fields, R.D. Gene expression in the conversion of early-phase to late-phase long-term potentiation. 2005 Ann. NY Acad. Sci. 1048: 259-271. [Abs] |
| Nadon,N.L., Mohr, D., Becker, K.G. National Institute on Aging microarray facility--resources for gerontology research. 2005 J. Gerontol. A Biol. Sci. Med. Sci. 60(4): 413-415. [Abs] |
| Cheadle, C., Fan, J., Cho-Chung, Y.S., Werner, T., Ray, J., Do, L., Gorospe, M., Becker, K.G. Control of gene expression during T cell activation: alternate regulation of mRNA transcription and mRNA stability. 2005 BMC Genomics. 6(1): 75. [Dataset - Excel files] [Abs] |
| Kyng, K.J., May, A., Stevnsner, T., Kolvraa, S., Becker, K.G., Bohr, V.A. Gene expression responses to DNA damage are altered in human aging and in Werner Syndrome. 2005 Oncogene. 24(32): 5026-5042. [Dataset - Excel files] [Abs] |
| Fann, M., Chiu, W.K., Wood, W.H. 3rd, Levine, B.L., Becker, K.G., Weng, N.P. Gene expression characteristics of CD28null memory phenotype CD8+ T cells and its implication in T-cell aging. 2005 Immunol. Rev. 205: 190-206. [Abs] |
| Ghorbel, M.T., Becker, K.G., Henley, J.M. Profile of changes in gene expression in cultured hippocampal neurones evoked by the GABAB receptor agonist baclofen. 2005 Physiol. Genomics. 22(1): 93-98. [Abs] |
| Hess, K., Yang, Y., Golech, S., Sharov, A., Becker, K.G., Weng, N.P. Kinetic assessment of general gene expression changes during human naive CD4+ T cell activation. 2004 Int. Immunol. 16(12): 1711-1721. [Abs] |
| Neary, C.L., Nesterova, M., Cho, Y.S., Cheadle, C., Becker, K.G., Cho-Chung, Y.S. Protein kinase A isozyme switching: eliciting differential cAMP signaling and tumor reversion. 2004 Oncogene. 23(54): 8847-8856. [Abs] |
| López de Silanes, I., Fan, J., Galban, C.J., Spencer, R.G., Becker, K.G., Gorospe, M. Global analysis of HuR-regulated gene expression in colon cancer systems of reducing complexity. 2004 Gene Expr. 12(1): 49-59. [Abs] |
| Hong, J.J., Loiselle, C.R., Yoon, D.Y., Lee, O., Becker, K.G., Singer, H.S. Microarray analysis in Tourette syndrome postmortem putamen. 2004 J. Neurol. Sci. 225(1-2): 57-64. [Abs] |
| Strunnikova, N., Zhang, C., Teichberg, D., Cousins, S.W., Baffi, J., Becker, K.G., Csaky, K.G. Survival of retinal pigment epithelium after exposure to prolonged oxidative injury: a detailed gene expression and cellular analysis. 2004 Invest. Ophthalmol. Vis. Sci. 45(10): 3767-3777. [Abs] |
| McLaren, P.J., Mayne, M., Rosser, S., Moffatt, T., Becker, K.G., Plummer, F.A., Fowke, K.R. Antigen-specific gene expression profiles of peripheral blood mononuclear cells do not reflect those of T-lymphocyte subsets. 2004 Clin. Diagn. Lab. Immunol. 11(5): 977-982. [Abs] |
| Xie, T., Tong, L., McCann, U.D., Yuan, J., Becker, K.G., Mechan, A.O., Cheadle, C., Donovan, D.M., Ricaurte, G.A. Identification and characterization of metallothionein-1 and -2 gene expression in the context of (+/-)3,4-methylenedioxymethamphetamine-induced toxicity to brain dopaminergic neurons. 2004 J. Neurosci. 24(32): 7043-7050. [Abs] |
| Becker, K.G., Barnes, K.C., Bright, T.J., Wang, S.A. The genetic association database. 2004 Nat. Genet. 36(5): 431-432. [Abs] |
| Wang, J., Cheng, C.M., Zhou, J., Smith, A., Weickert, C.S., Perlman, W.R., Becker, K.G., Powell, D., Bondy, C.A. Estradiol alters transcription factor gene expression in primate prefrontal cortex. 2004 J. Neurosci. Res. 76(3): 306-314. [Abs] |
| Mayne, M., Moffatt, T., Kong, H., McLaren, P.J., Fowke, K.R., Becker, K.G., Namaka, M., Schenck, A., Bardoni, B., Bernstein, C.N., Melanson, M. CYFIP2 is highly abundant in CD4+ cells from multiple sclerosis patients and is involved in T cell adhesion. 2004 Eur. J. Immunol. 34(4): 1217-1227. [Abs] |
| Becker, K.G. The common variants/multiple disease hypothesis of common complex genetic disorders. 2004 Med. Hypotheses. 62(2): 309-317. [Abs] |
| Kawai, T., Fan, J., Mazan-Mamczarz, K. and Gorospe, M. Global mRNA stabilization preferentially linked to translational repression during the endoplasmic reticulum stress response. 2004 Mol. Cell Biol. 24(15): 6773-6787. [Dataset - Excel files] [Abs] |
| López de Silanes, I., Olmo, N., Turnay, J., Gonzalez de Buitrago, G., Perez-Ramos, P., Guzman-Aranguez, A., Garcia, M., Lecona, E., Gorospe M., Lizarbe, M.A. Acquisition of resistance to butyrate enhances survival after stress and induces malignancy of human colon carcinoma cells. 2004 Cancer Res. 64(13): 4593-4600. [Dataset - Excel files] [Abs] |
| López de Silanes, I., Zhan, M., Lal, A., Yang, X., Gorospe, M. Identification of a target RNA motif for RNA-binding protein HuR. 2004 Proc. Natl. Acad. Sci. USA. 101(9): 2987-2992. [Dataset - Excel files] [Abs] |
| Hong, S.J., Li, H., Becker, K.G., Dawson, V.L., Dawson, T.M. Identification and analysis of plasticity-induced late-response genes. 2004 Proc. Natl. Acad. Sci. USA. 101(7): 2145-2150. [Abs] |
| Ermak, G., Cheadle, C., Becker, K.G., Harris, C.D., Davies, K.J. DSCR1(Adapt78) modulates expression of SOD1. 2004 FASEB J. 18(1): 62-69. [Abs] |
| Cheadle, C., Cho-Chung, Y.S., Becker, K., and M.P. Vawter. Application of z score transformation to Affymetrix data. 2003 Appl. Bioinformatics. 2(4): 209-217. [Dataset - Excel files] |
| Noailles, P.A., Becker, K.G., Wood, W.H., Teichberg, D., Cadet, J.L. Methamphetamine-induced gene expression profiles in the striatum of male rat pups exposed to the drug in utero. 2003 Brain Res Dev Brain Res. 147(1-2): 153-162. [Abs] |
| Becker, K.G., Hosack, D.A., Dennis, G. Jr., Lempicki, R.A., Bright, T., Cheadle, C., Engel, J.H. PubMatrix: a tool for multiplex literature mining. 2003 BMC Bioinformatics. 4(1):61. [Abs] |
| Kim, Y.H., Lee, J.H., Lim, do S., Shim, W.J., Ro, Y.M., Park, G.H., Becker, K.G., Cho-Chung, Y.S., Kim, M.K. Gene expression profiling of oxidative stress on atrial fibrillation in humans. 2003 Exp. Mol. Med. 35(5): 336-349. [Abs] |
| Lehrmann, E., Hyde, T.M., Vawter, M.P., Becker, K.G., Kleinman, J.E., Freed, W.J. The use of microarrays to characterize neuropsychiatric disorders: postmortem studies of substance abuse and schizophrenia. 2003 Curr. Mol. Med. 3(5): 437-446. [Abs] |
| López de Silanes, I., Fan, J., Yang, X., Zonderman, A.B., Potapova, O., Pizer, E.S., Gorospe, M. Role of the RNA-binding protein HuR in colon carcinogenesis. 2003 Oncogene. 22(46): 7146-7154. [Dataset - Excel files] |
| Kyng, K.J., May, A., Kolvraa, S., Bohr, V.A. Gene expression profiling in Werner syndrome closely resembles that of normal aging. 2003 Proc. Nat. Acad. Sci. USA. 100(21): 12259-12264. [Dataset - Excel files] |
| Cho-Chung, Y.S., Becker, K.G. A genome-wide view of antisense. 2003 Nat. Biotechnol. 21(5): 492. [Abs] |
| Ghorbel, M.T., Sharman, G., Leroux, M., Barrett, T., Donovan, D.M., Becker, K.G., Murphy, D. Microarray analysis reveals interleukin 6 as a novel secretory product of the hypothalamo-neurohypophyseal system. 2003 J. Biol. Chem. 278(21): 19280-19285. [Abs] |
| Lehrmann, E., Oyler, J., Vawter, M.P., Hyde, T.M., Kolachana, B., Kleinman, J.E., Huestis, M.A., Becker, K.G., Freed, W.J. Transcriptional profiling in the human prefrontal cortex: evidence for two activational states associated with cocaine abuse. 2003 Pharmacogenomics J. 3(1): 27-40. [Abs] |
| Comi, A.M., Hunt, P., Vawter, M.P., Pardo, C.A., Becker, K.G., Pevsner, J. Increased fibronectin expression in Sturge-Weber syndrome fibroblasts and brain tissue. 2003 Pediatr. Res. 53(5): 762-769. [Abs] |
| Miyashiro, K.Y., Beckel-Mitchener, A., Purk, T.P., Becker, K.G., Barret, T., Liu, L., Carbonetto, S., Weiler, I.J., Greenough, W.T., Eberwine, J. RNA cargoes associating with FMRP reveal deficits in cellular functioning in Fmr1 null mice. 2003 Neuron. 37(3): 417-431. [Abs] |
| Cheadle, C., Vawter, M.P., Freed, W.J., Becker, K.G. Analysis of microarray data using Z score transformation. 2003 J. Mol. Diagn. 5(2): 73-81. [Dataset - Excel zip file] [Abs] |
| Galbán, S., Fan, J., Martindale, J.L., Cheadle, C., Hoffman, B., Woods, M.P., Temeles, G., Brieger, J., Decker, J., Gorospe, M. VHL-mediated repression of TNFa translation revealed through use of cDNA arrays. 2003 Mol. Cell. Biol. 23(7): 2316-2328. [Dataset - Excel zip file] [Abs] |
| Kyng, K.J., May, A., Brosh, Jr., R.M., Cheng, W.H., Chen, C., Becker, K.G., Bohr, V.A. The transcriptional response after oxidative stress is defective in Cockayne Syndrome group B cells. 2003 Oncogene 22(8):1135-1149. [Dataset - Excel files] [Abs] |
| Vawter, M.P., Crook, J.M., Hyde, T.M., Kleinman, J.E., Weinberger, D.R., Becker, K.G., Freed, W.J. Microarray analysis of gene expression in the prefrontal cortex in schizophrenia: a preliminary study. 2002 Schizophr. Res. 58(1): 11-20. [Abs] |
| Cho, Y.S., Kim, M-K., Cheadle, C., Neary, C., Park, Y.G., Becker K.G., Cho-Chung, Y.S. A genomic-scale view of CRE enhancer decoy: a tumor target-based genetic tool. 2002 Proc. Natl. Acad. Sci. USA 99(24): 15626-15631. [Dataset - Supplementary Information] [Abs] |
| Fan, J., Yang, X., Wang, W., Wood, W.H. 3rd, Becker, K.G., Gorospe, M. Global analysis of stress-regulated mRNA turnover by using cDNA arrays. 2002 Proc Natl Acad Sci USA 99(16): 10611-10616. [Abs] |
| Donovan, D.M., Becker, K.G. Double round hybridization of membrane cDNA arrays: Improved background reduction and replication. 2002 J. Neurosci. Meth. 118(1):59.[Abs] |
| Li, M.D., Konu, O., Kane, J.K., Becker K.G. Microarray technology and its application on nicotine research. 2002 Mol. Neurobiol. 25(3): 265-285. [Abs] |
| Cho-Chung, Y.S., Nesterova, M., Becker, K.G., Srivastava, R., Park, Y.G., Lee, Y.N., Cho, Y.S., Kim, M-K., Neary, C., Cheadle, C. Dissecting the circuitry of protein kinase A and cAMP signaling in cancer genesis: Antisense, micorarray, gene overexpression, and transcription factor decoy. 2002 Annals. NY Acad. Sci. 968: 22-36. [Abs] |
| Truckenmiller, M.E., Vawter, M.P., Zhang, P., Conejero-Goldberg, C., Torres, A., Nouvier, M., Dillon-Carter, O., Cheadle, C., Becker, K.G., Freed, W.J. Af5, a CNS cell line immortalized with an N-terminal fragment of SV40 large T antigen: growth, differentiation, genetic stability and gene expression. 2002 Exp. Neurol. 175(2): 318-337. [Abs] |
| Becker, K.G., Cheadle, C. Nylon membrane-based arrays. Chapter in DNA Arrays: A Laboratory Manual. 2002 Cold Spring Harbor Laboratory Press. In press. |
| Freed, W.J., Hyde, T.M., Kleinman, J.E., Becker. K.G., Vawter, M.P. A hypothesis based on postmortem analysis of gene expression in schizophrenia using cDNA arrays with pooled samples. 2002 The Economics of Neuroscience 1: 48-57. |
| Sawiris, G.P., Becker, K.G., Cheadle, C., Teichberg, D., Morin, P.M. Development of a highly specialized cDNA array for the study and diagnosis of epithelial ovarian cancer. 2002 Cancer Res. 62(10): 2923-2928. [Abs] |
| Barrett, T., Cheadle, C., Wood, W.H., Donovan, D., Freed, W.J., Becker, K.G. Vawter, M.P. Assembly and use of a broadly applicable neural cDNA microarray. 2001 Restor. Neurol. Neurosci. 18(2-3): 127-135. [Abs] - List of Genes [Excel zip file] |
| Truckenmiller M.E., Vawter, M., Cheadle, C., Coggiano, M., Donovan, D.M., Freed, W.J., Becker, K.G. Gene expression profile in early stage of retinoic acid-induced differentiation of human SH-SY5Y neuroblastoma cells. 2001 Restor. Neurol. Neurosci. 18(2-3): 67-80. [Abs] |
| Mayne, M., Cheadle, C., Soldan, S.S., Cermelli, C., Yamano, Y., Akhyani, N., Nagel, J.E., Taub, D.D., Becker, K.G., Jacobson, S. Gene expression profile of herpesvirus-infected T cells obtained using immuno-microarrays: induction of pro-inflammatory mechanisms. 2001 J. Virol. 75(23): 11641-11650. [Abs] |
| Vawter, M.P., Barrett, T., Cheadle, C., Sokolov, B.P., Wood, W.H. III, Donovan, D.M., Webster, M., Freed, W.J., Becker, K.G. Application of cDNA microarrays to examine gene expression differences in schizophrenia. 2001 Brain. Res. Bull. 55(5): 641-650. [Abs] |
| Barrett, T., Xie, T., Piao, Y., Dillon-Carter, O., Kargul, G.J., Lim, M.K., Chrest, F.J., Wersto, R., Rowley, D.L., Juhaszova, M., Zhou, L., Vawter, M.P., Becker, K.G., Cheadle, C., Wood, W.H. 3rd, McCann, U.D., Freed, W.J., Ko, M.S., Ricaurte, G.A., Donovan, D.M. A murine dopamine neuron-specific cDNA library and microarray: increased COXI expression during methamphetamine neurotoxicity. 2001 Neurobiol. Dis. 8(5): 822-833. [Abs] [Dataset] |
| Cho, Y.S., Kim, M.K., Cheadle, C., Neary, C., Becker, K.G., Cho-Chung, Y.S. Antisense DNAs as multisite genomic modulators identified by DNA microarray. 2001 Proc. Natl. Acad. Sci. USA 98(17): 9819-9823. [Abs] - [Figure 4] |
| Konu, O., Kane, J.K., Barrett, T., Vawter, M.P., Chang, R., Ma, J.Z., Donovan, D.M., Sharp, B., Becker, K.G., Li, M.D. Region-specific transcriptional response to chronic nicotine in rat brain. 2001 Brain. Res. 909(1-2): 194-203. [Abs] |
| Liu, K., Li, Y., Prabhu, V., Young, L., Becker, K.G., Munson, P.J., Weng, N.P. Augmentation in expression of activation-induced genes differentiates memory from naive CD4+ T cells and is a molecular mechanism for enhanced cellular response of memory CD4+ T cells. 2001 J. Immunol. 166(12): 7335-7344. [Abs] [Dataset] |
| Becker, K.G. The sharing of cDNA microarray data. 2001 Nat. Rev. Neurosci. 2(6): 438-440. [Abs] |
| Eberwine, J., Kacharmina, J.E., Andrews, C., Miyashiro, K., McIntosh, T., Becker, K., Barrett, T., Hinkle, D., Dent, G., Marciano, P. mRNA expression analysis of tissue sections and single cells. 2001 J. Neurosci. 21(21): 8310-8314. [Abs] |
| Whitney, L.W., Becker K.G. Radioactive 33-P probes in hybridization to glass cDNA microarrays using neural tissues. 2001 J. Neurosci. Methods. 106(1): 9-13. [Abs] |
| Andrews, J., Bouffard, G.G., Cheadle, C., Lu, J., Becker, K.G., Oliver, B. Gene discovery using computational and microarray analysis of transcription in the drosophila melanogaster testis. 2000 Genome. Res. 10(12): 2030-2043. [Abs] |
| Becker, K.G., White, S.L., Muller, J., Engel, J. BBID: the biological biochemical image database. 2000 Bioinformatics. 16(8): 745-746. [Abs] [Database] |
| Ko, M.S.H., Becker, K.G. Current status of cDNA chip technology in the U.S. |
| Tanaka, T.S., Jaradat, S.A., Lim, M.K., Kargul, G.J., Wang, X., Grahovac, M.J., Pantano, S., Sano, Y., Piao, Y., Nagaraja, R., Doi, H., Wood, W.H., 3rd, Becker, K.G., Ko, M.S. Genome-wide expression profiling of mid-gestation placenta and embryo using a 15,000 mouse developmental cDNA microarray. 2000 Proc. Natl. Acad. Sci. USA 97(16): 9127-9132. [Abs] [Dataset] |
| Comparative Genomics: |
| Comparative Genomics Database |
Becker, K.G., Schultz, S.T. Similarities in features of autism and asthma and a possible link to acetaminophen use. |
| Zhang, Y., De, S., Garner, J.R., Smith, K., Wang, S.A., Becker, K.G. Systematic analysis, comparison, and integration of disease based human genetic association data and mouse genetic phenotypic information. Data-In preparation. |
| Becker, K.G. Autism, asthma, inflammation, and the hygiene hypothesis. 2007 Medical Hypothesis. 69(4): 731-740. [pdf] |
| Becker, K.G. The common variants/multiple disease hypothesis of common complex genetic disorders. 2004 Med. Hypotheses. 62(2): 309-317. [Abs] |
| Becker, K.G., Freidlin, B., and Simon, R.M. Comparative Genomics of Autism, Tourette syndrome and Autoimmune/ Inflammatory Disorders. 2003 Submitted. [pdf] |
| Jampol, L.M., Becker, K.G. White spot syndromes of the retina: a hypothesis based on the common genetic hypothesis of autoimmune/inflammatory disease. 2003 Am. J. Ophthalmol. 135(3): 376-379. [Abs] |
| Becker, K.G. The common genetic hypothesis of autoimmune/inflammatory disease. 2001 Curr. Opin. Allergy Clin. Immunol. 1(5): 399-405. [Dataset] [Abs] |
| Becker, K.G., Barnes, K.C. Underlying disease specificity of genetic loci in atopic dermatitis. 2001 J. Invest. Dermatol. 117(5): 1325-1327. [Abs] |
| Becker, K.G. APOE genotype is a major predictor of long-term progression of disability in multiple sclerosis. 2001 Neurology. 57(11): 2148-2149. [Abs] |
| Becker, K.G. Comparative genetics of type 1 diabetes and autoimmune disease: common loci, common pathways? 1999 Diabetes. 48(7): 1353-1358.[Abs] |
| Becker, K.G., Simon, R.M., Bailey-Wilson, J.E., Freidlin, B., Biddison, W.E., McFarland, H.F., Trent, J.M. Clustering of non-major histocompatibility complex susceptibility candidate loci in human autoimmune diseases. 1998 Proc. Natl. Acad. Sci. USA 95(17): 9979-9984. [Abs] |
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