 The public web presence of the Meltzer Lab
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Records found: 423 Transcriptional networks inferred from molecular signatures of breast cancer. Tongbai, R., Idelman, G., Nordgard, S.H., Cui, W., Jacobs, J.L., Haggerty, C.M., Chanock, S.J., Borresen-Dale, A.L., Livingston, G., Shaunessy, P., Chiang, C.H., Kristensen, V.N., Bilke, S., and Gardner, K. Am J Pathol 172, 495-509; 2008. PubMed EzArray: A web-based highly automated Affymetrix expression array data management and analysis system. Zhu, Y., Zhu, Y., and Xu, W. BMC bioinformatics 9, 46; 2008. PubMed A combined approach identifies a limited number of new thyroid hormone target genes in post-natal mouse cerebellum. Quignodon, L., Grijota-Martinez, C., Compe, E., Guyot, R., Allioli, N., Laperriere, D., Walker, R., Meltzer, P., Mader, S., Samarut, J., and Flamant, F. J Mol Endocrinol 39, 17-28; 2007. PubMed GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor. Davis, S., and Meltzer, P.S. Bioinformatics (Oxford, England), ; 2007. PubMed Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Birney, E., Stamatoyannopoulos, J.A., Dutta, A., Guigo, R., Gingeras, T.R., Margulies, E.H., Weng, Z., Snyder, M., Dermitzakis, E.T., Thurman, R.E., Kuehn, M.S., Taylor, C.M., Neph, S., Koch, C.M., Asthana, S., Malhotra, A., Adzhubei, I., Greenbaum, J.A., Andrews, R.M., Flicek, P., Boyle, P.J., Cao, H., Carter, N.P., Clelland, G.K., Davis, S., Day, N., Dhami, P., Dillon, S.C., Dorschner, M.O., Fiegler, H., Giresi, P.G., Goldy, J., Hawrylycz, M., Haydock, A., Humbert, R., James, K.D., Johnson, B.E., Johnson, E.M., Frum, T.T., Rosenzweig, E.R., Karnani, N., Lee, K., Lefebvre, G.C., Navas, P.A., Neri, F., Parker, S.C., Sabo, P.J., Sandstrom, R., Shafer, A., Vetrie, D., Weaver, M., Wilcox, S., Yu, M., Collins, F.S., Dekker, J., Lieb, J.D., Tullius, T.D., Crawford, G.E., Sunyaev, S., Noble, W.S., Dunham, I., Denoeud, F., Reymond, A., Kapranov, P., Rozowsky, J., Zheng, D., Castelo, R., Frankish, A., Harrow, J., Ghosh, S., Sandelin, A., Hofacker, I.L., Baertsch, R., Keefe, D., Dike, S., Cheng, J., Hirsch, H.A., Sekinger, E.A., Lagarde, J., Abril, J.F., Shahab, A., Flamm, C., Fried, C., Hackermuller, J., Hertel, J., Lindemeyer, M., Missal, K., Tanzer, A., Washietl, S., Korbel, J., Emanuelsson, O., Pedersen, J.S., Holroyd, N., Taylor, R., Swarbreck, D., Matthews, N., Dickson, M.C., Thomas, D.J., Weirauch, M.T., Gilbert, J., Drenkow, J., Bell, I., Zhao, X., Srinivasan, K.G., Sung, W.K., Ooi, H.S., Chiu, K.P., Foissac, S., Alioto, T., Brent, M., Pachter, L., Tress, M.L., Valencia, A., Choo, S.W., Choo, C.Y., Ucla, C., Manzano, C., Wyss, C., Cheung, E., Clark, T.G., Brown, J.B., Ganesh, M., Patel, S., Tammana, H., Chrast, J., Henrichsen, C.N., Kai, C., Kawai, J., Nagalakshmi, U., Wu, J., Lian, Z., Lian, J., Newburger, P., Zhang, X., Bickel, P., Mattick, J.S., Carninci, P., Hayashizaki, Y., Weissman, S., Hubbard, T., Myers, R.M., Rogers, J., Stadler, P.F., Lowe, T.M., Wei, C.L., Ruan, Y., Struhl, K., Gerstein, M., Antonarakis, S.E., Fu, Y., Green, E.D., Karaoz, U., Siepel, A., Taylor, J., Liefer, L.A., Wetterstrand, K.A., Good, P.J., Feingold, E.A., Guyer, M.S., Cooper, G.M., Asimenos, G., Dewey, C.N., Hou, M., Nikolaev, S., Montoya-Burgos, J.I., Loytynoja, A., Whelan, S., Pardi, F., Massingham, T., Huang, H., Zhang, N.R., Holmes, I., Mullikin, J.C., Ureta-Vidal, A., Paten, B., Seringhaus, M., Church, D., Rosenbloom, K., Kent, W.J., Stone, E.A., Batzoglou, S., Goldman, N., Hardison, R.C., Haussler, D., Miller, W., Sidow, A., Trinklein, N.D., Zhang, Z.D., Barrera, L., Stuart, R., King, D.C., Ameur, A., Enroth, S., Bieda, M.C., Kim, J., Bhinge, A.A., Jiang, N., Liu, J., Yao, F., Vega, V.B., Lee, C.W., Ng, P., Shahab, A., Yang, A., Moqtaderi, Z., Zhu, Z., Xu, X., Squazzo, S., Oberley, M.J., Inman, D., Singer, M.A., Richmond, T.A., Munn, K.J., Rada-Iglesias, A., Wallerman, O., Komorowski, J., Fowler, J.C., Couttet, P., Bruce, A.W., Dovey, O.M., Ellis, P.D., Langford, C.F., Nix, D.A., Euskirchen, G., Hartman, S., Urban, A.E., Kraus, P., Van Calcar, S., Heintzman, N., Kim, T.H., Wang, K., Qu, C., Hon, G., Luna, R., Glass, C.K., Rosenfeld, M.G., Aldred, S.F., Cooper, S.J., Halees, A., Lin, J.M., Shulha, H.P., Zhang, X., Xu, M., Haidar, J.N., Yu, Y., Ruan, Y., Iyer, V.R., Green, R.D., Wadelius, C., Farnham, P.J., Ren, B., Harte, R.A., Hinrichs, A.S., Trumbower, H., Clawson, H., Hillman-Jackson, J., Zweig, A.S., Smith, K., Thakkapallayil, A., Barber, G., Kuhn, R.M., Karolchik, D., Armengol, L., Bird, C.P., de Bakker, P.I., Kern, A.D., Lopez-Bigas, N., Martin, J.D., Stranger, B.E., Woodroffe, A., Davydov, E., Dimas, A., Eyras, E., Hallgrimsdottir, I.B., Huppert, J., Zody, M.C., Abecasis, G.R., Estivill, X., Bouffard, G.G., Guan, X., Hansen, N.F., Idol, J.R., Maduro, V.V., Maskeri, B., McDowell, J.C., Park, M., Thomas, P.J., Young, A.C., Blakesley, R.W., Muzny, D.M., Sodergren, E., Wheeler, D.A., Worley, K.C., Jiang, H., Weinstock, G.M., Gibbs, R.A., Graves, T., Fulton, R., Mardis, E.R., Wilson, R.K., Clamp, M., Cuff, J., Gnerre, S., Jaffe, D.B., Chang, J.L., Lindblad-Toh, K., Lander, E.S., Koriabine, M., Nefedov, M., Osoegawa, K., Yoshinaga, Y., Zhu, B., and de Jong, P.J. Nature 447, 799-816; 2007. PubMed Modeling synovial sarcoma: timing is everything. Davis, S.R., and Meltzer, P.S. Cancer Cell 11, 305-307; 2007. PubMed Expression of the cytoskeleton linker protein ezrin in human cancers. Bruce, B., Khanna, G., Ren, L., Landberg, G., Jirstrom, K., Powell, C., Borczuk, A., Keller, E.T., Wojno, K.J., Meltzer, P., Baird, K., McClatchey, A., Bretscher, A., Hewitt, S.M., and Khanna, C. Clin Exp Metastasis 24, 69-78; 2007. PubMed Claudin-1 overexpression in melanoma is regulated by PKC and contributes to melanoma cell motility. Leotlela, P.D., Wade, M.S., Duray, P.H., Rhode, M.J., Brown, H.F., Rosenthal, D.T., Dissanayake, S.K., Earley, R., Indig, F.E., Nickoloff, B.J., Taub, D.D., Kallioniemi, O.P., Meltzer, P., Morin, P.J., and Weeraratna, A.T. Oncogene 26, 3846-3856; 2007. PubMed Zoom-in comparative genomic hybridisation arrays for the characterisation of variable breakpoint contiguous gene syndromes. Johnston, J.J., Walker, R.L., Davis, S., Facio, F., Turner, J.T., Bick, D.P., Daentl, D.L., Ellison, J.W., Meltzer, P.S., and Biesecker, L.G. J Med Genet 44, e59; 2007. PubMed Detection of novel amplicons in prostate cancer by comprehensive genomic profiling of prostate cancer cell lines using oligonucleotide-based arrayCGH. Kamradt, J., Jung, V., Wahrheit, K., Tolosi, L., Rahnenfuehrer, J., Schilling, M., Walker, R., Davis, S., Stoeckle, M., Meltzer, P., and Wullich, B. PLoS ONE 2, e769; 2007. PubMed Constitutive Fms-like tyrosine kinase 3 activation results in specific changes in gene expression in myeloid leukaemic cells. Kim, K.T., Baird, K., Davis, S., Piloto, O., Levis, M., Li, L., Chen, P., Meltzer, P., and Small, D. Br J Haematol 138, 603-615; 2007. PubMed A single IGF1 allele is a major determinant of small size in dogs. Sutter, N.B., Bustamante, C.D., Chase, K., Gray, M.M., Zhao, K., Zhu, L., Padhukasahasram, B., Karlins, E., Davis, S., Jones, P.G., Quignon, P., Johnson, G.S., Parker, H.G., Fretwell, N., Mosher, D.S., Lawler, D.F., Satyaraj, E., Nordborg, M., Lark, K.G., Wayne, R.K., and Ostrander, E.A. Science 316, 112-115; 2007. PubMed The Wnt5A/protein kinase C pathway mediates motility in melanoma cells via the inhibition of metastasis suppressors and initiation of an epithelial to mesenchymal transition. Dissanayake, S.K., Wade, M., Johnson, C.E., O'Connell, M.P., Leotlela, P.D., French, A.D., Shah, K.V., Hewitt, K.J., Rosenthal, D.T., Indig, F.E., Jiang, Y., Nickoloff, B.J., Taub, D.D., Trent, J.M., Moon, R.T., Bittner, M., and Weeraratna, A.T. The Journal of biological chemistry 282, 17259-17271; 2007. PubMed A Cell Proliferation and Chromosomal Instability Signature in Anaplastic Thyroid Carcinoma. Salvatore, G., Nappi, T.C., Salerno, P., Jiang, Y., Garbi, C., Ugolini, C., Miccoli, P., Basolo, F., Castellone, M.D., Cirafici, A.M., Melillo, R.M., Fusco, A., Bittner, M.L., and Santoro, M. Cancer research 67, ; 2007. PubMed BP1 transcriptionally activates bcl-2 and inhibits TNFalpha-induced cell death in MCF7 breast cancer cells. Stevenson, H.S., Fu, S.W., Pinzone, J.J., Rheey, J., Simmens, S.J., and Berg, P.E. Breast Cancer Res 9, R60; 2007. PubMed Characterization of mismatch and high-signal intensity probes associated with Affymetrix genechips. Wang, Y., Miao, Z.H., Pommier, Y., Kawasaki, E.S., and Player, A. Bioinformatics (Oxford, England) 23, 2088-2095; 2007. PubMed Manufacturing of microarrays. Petersen, D.W., and Kawasaki, E.S. Advances in experimental medicine and biology 593, 1-11; 2007. PubMed Nonclassic functions of human topoisomerase I: genome-wide and pharmacologic analyses. Miao, Z.H., Player, A., Shankavaram, U., Wang, Y.H., Zimonjic, D.B., Lorenzi, P.L., Liao, Z.Y., Liu, H., Shimura, T., Zhang, H.L., Meng, L.H., Zhang, Y.W., Kawasaki, E.S., Popescu, N.C., Aladjem, M.I., Goldstein, D.J., Weinstein, J.N., and Pommier, Y. Cancer research 67, 8752-8761; 2007. PubMed Cyclin-dependent kinase 5 differentially regulates the transcriptional activity of the glucocorticoid receptor through phosphorylation: clinical implications for the nervous system response to glucocorticoids and stress. Kino, T., Ichijo, T., Amin, N.D., Kesavapany, S., Wang, Y., Kim, N., Rao, S., Player, A., Zheng, Y.L., Garabedian, M.J., Kawasaki, E., Pant, H.C., and Chrousos, G.P. Molecular endocrinology (Baltimore, Md 21, 1552-1568; 2007. PubMed Identification of arsenic-binding proteins in human breast cancer cells. Zhang, X., Yang, F., Shim, J.Y., Kirk, K.L., Anderson, D.E., and Chen, X. Cancer letters 255, 95-106; 2007. PubMed Global expression analysis of prostate cancer-associated stroma and epithelia. Richardson, A.M., Woodson, K., Wang, Y., Rodriguez-Canales, J., Erickson, H.S., Tangrea, M.A., Novakovic, K., Gonzalez, S., Velasco, A., Kawasaki, E.S., Emmert-Buck, M.R., Chuaqui, R.F., Player, A., Keenan, J., Liang, Y., and Clynes, M. Diagn Mol In press, ; 2007. PubMed Gene Expression Analysis of RNA Purified From Embryonic Stem Cells And Embryoidal Body Derived Cells Using A High-Throughput Microarray Platform. Player, A., Wang, Y., Rao, M., and Kawasaki, E.S. In: Current Protocols. John Wiley & Sons, Inc., ; 2007. Interagency White Paper on Prion Science. Edelman, D.C. Cyril Gay and Marcus Kehrli, editors. 2007. Meleady P and Clynes M. Co-ordinate upregulation of gene expression at the transcriptional level during BrdU-induced differentiation of DLKP lung cells may involve the transcription factor GATA-3. Doolan, P., Barron, N., and Liang, Y. Differentiation Submitted, ; 2007. PubMed Chromosome 8 BAC array comparative genomic hybridization and expression analysis identify amplification and overexpression of TRMT12 in breast cancer. Rodriguez, V., Chen, Y., Elkahloun, A., Dutra, A., Pak, E., and Chandrasekharappa, S. Genes, chromosomes & cancer 46, 694-707; 2007. PubMed | Supplement Gene expression profiling reveals potential biomarkers of human hepatocellular carcinoma. Jia, H.L., Ye, Q.H., Qin, L.X., Budhu, A., Forgues, M., Chen, Y., Liu, Y.K., Sun, H.C., Wang, L., Lu, H.Z., Shen, F., Tang, Z.Y., and Wang, X.W. Clin Cancer Res 13, 1133-1139; 2007. PubMed Sensitive and specific method for detecting G protein-coupled receptor mRNAs. Hansen, A., Chen, Y., Inman, J.M., Phan, Q.N., Qi, Z.Q., Xiang, C.C., Palkovits, M., Cherman, N., Kuznetsov, S.A., Robey, P.G., Mezey, E., and Brownstein, M.J. Nat Methods 4, 35-37; 2007. PubMed Mouse embryo fibroblasts lacking the tumor suppressor menin show altered expression of extracellular matrix protein genes. Ji, Y., Prasad, N.B., Novotny, E.A., Kaur, S., Elkahloun, A., Chen, Y., Zhang, R.Z., Chu, M.L., Agarwal, S.K., Marx, S.J., Collins, F.S., and Chandrasekharappa, S.C. Mol Cancer Res 5, 1041-1051; 2007. PubMed Human X-Box binding protein-1 confers both estrogen independence and antiestrogen resistance in breast cancer cell lines. Gomez, B.P., Riggins, R.B., Shajahan, A.N., Klimach, U., Wang, A., Crawford, A.C., Zhu, Y., Zwart, A., Wang, M., and Clarke, R. Faseb J, ; 2007. PubMed Analysis of comparative genomic hybridization data on cDNA microarrays. Bilke, S., and Khan, J. Methods in molecular biology (Clifton, NJ 377, 175-186; 2007. PubMed Functional profiling of uncommon VCAM1 promoter polymorphisms prevalent in African American populations. Idelman, G., Taylor, J.G., Tongbai, R., Chen, R.A., Haggerty, C.M., Bilke, S., Chanock, S.J., and Gardner, K. Human mutation 28, 824-829; 2007. PubMed Credentialing preclinical pediatric xenograft models using gene expression and tissue microarray analysis. Whiteford, C.C., Bilke, S., Greer, B.T., Chen, Q., Braunschweig, T.A., Cenacchi, N., Wei, J.S., Smith, M.A., Houghton, P., Morton, C., Reynolds, C.P., Lock, R., Gorlick, R., Khanna, C., Thiele, C.J., Takikita, M., Catchpoole, D., Hewitt, S.M., and Khan, J. Cancer research 67, 32-40; 2007. PubMed Proteomic expression profiling of thyroid neoplasms. Braunschweig, T., Kaserer, K., Chung, J.Y., Bilke, S., Krizman, D., Knezevic, V., and Hewitt, S.M. PROTEOMICS - Clinical Applications 1, 8; 2007. PubMed Lipid defect underlies selective skin barrier impairment of an epidermal-specific deletion of Gata-3. de Guzman Strong, C., Wertz, P.W., Wang, C., Yang, F., Meltzer, P.S., Andl, T., Millar, S.E., Ho, I.C., Pai, S.Y., and Segre, J.A. J Cell Biol 175, 661-670; 2006. PubMed The Synovial Sarcoma-Associated SS18-SSX2 Fusion Protein Induces Epigenetic Gene (De)Regulation. de Bruijn, D.R., Allander, S.V., van Dijk, A.H., Willemse, M.P., Thijssen, J., van Groningen, J.J., Meltzer, P.S., and Geurts van Kessel, A. Cancer research 66, 9474-9482; 2006. PubMed DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays. Crawford, G.E., Davis, S., Scacheri, P.C., Renaud, G., Halawi, M.J., Erdos, M.R., Green, R., Meltzer, P.S., Wolfsberg, T.G., and Collins, F.S. Nat Methods 3, 503-509; 2006. PubMed Ewing's sarcoma: general insights from a rare model. Davis, S., and Meltzer, P.S. Cancer Cell 9, 331-332; 2006. PubMed Molecular and cytogenetic changes involved in the immortalization of nasopharyngeal epithelial cells by telomerase. Li, H.M., Man, C., Jin, Y., Deng, W., Yip, Y.L., Feng, H.C., Cheung, Y.C., Lo, K.W., Meltzer, P.S., Wu, Z.G., Kwong, Y.L., Yuen, A.P., and Tsao, S.W. International journal of cancer 119, 1567-1576; 2006. PubMed Genome-wide analysis of menin binding provides insights into MEN1 tumorigenesis. Scacheri, P.C., Davis, S., Odom, D.T., Crawford, G.E., Perkins, S., Halawi, M.J., Agarwal, S.K., Marx, S.J., Spiegel, A.M., Meltzer, P.S., and Collins, F.S. PLoS Genet 2, e51; 2006. PubMed The epigenetic reprogramming of poorly aggressive melanoma cells by a metastatic microenvironment. Seftor, E.A., Meltzer, P.S., Kirschmann, D.A., Margaryan, N.V., Seftor, R.E., and Hendrix, M.J. J Cell Mol Med 10, 174-196; 2006. PubMed Statistics for ChIP-chip and DNase hypersensitivity experiments on NimbleGen arrays. Scacheri, P.C., Crawford, G.E., and Davis, S. Methods Enzymol 411, 270-282; 2006. PubMed Analysis of the quality of contact-pin fabricated oligonucleotide microarrays. Yang, A.X., Mejido, J., Bhattacharya, B., Petersen, D., Han, J., Kawasaki, E.S., and Puri, R.K. Molecular biotechnology 34, 303-315; 2006. PubMed The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Shi, L., Reid, L.H., Jones, W.D., Shippy, R., Warrington, J.A., Baker, S.C., Collins, P.J., de Longueville, F., Kawasaki, E.S., Lee, K.Y., Luo, Y., Sun, Y.A., Willey, J.C., Setterquist, R.A., Fischer, G.M., Tong, W., Dragan, Y.P., Dix, D.J., Frueh, F.W., Goodsaid, F.M., Herman, D., Jensen, R.V., Johnson, C.D., Lobenhofer, E.K., Puri, R.K., Schrf, U., Thierry-Mieg, J., Wang, C., Wilson, M., Wolber, P.K., Zhang, L., Amur, S., Bao, W., Barbacioru, C.C., Lucas, A.B., Bertholet, V., Boysen, C., Bromley, B., Brown, D., Brunner, A., Canales, R., Cao, X.M., Cebula, T.A., Chen, J.J., Cheng, J., Chu, T.M., Chudin, E., Corson, J., Corton, J.C., Croner, L.J., Davies, C., Davison, T.S., Delenstarr, G., Deng, X., Dorris, D., Eklund, A.C., Fan, X.H., Fang, H., Fulmer-Smentek, S., Fuscoe, J.C., Gallagher, K., Ge, W., Guo, L., Guo, X., Hager, J., Haje, P.K., Han, J., Han, T., Harbottle, H.C., Harris, S.C., Hatchwell, E., Hauser, C.A., Hester, S., Hong, H., Hurban, P., Jackson, S.A., Ji, H., Knight, C.R., Kuo, W.P., LeClerc, J.E., Levy, S., Li, Q.Z., Liu, C., Liu, Y., Lombardi, M.J., Ma, Y., Magnuson, S.R., Maqsodi, B., McDaniel, T., Mei, N., Myklebost, O., Ning, B., Novoradovskaya, N., Orr, M.S., Osborn, T.W., Papallo, A., Patterson, T.A., Perkins, R.G., Peters, E.H., Peterson, R., Philips, K.L., Pine, P.S., Pusztai, L., Qian, F., Ren, H., Rosen, M., Rosenzweig, B.A., Samaha, R.R., Schena, M., Schroth, G.P., Shchegrova, S., Smith, D.D., Staedtler, F., Su, Z., Sun, H., Szallasi, Z., Tezak, Z., Thierry-Mieg, D., Thompson, K.L., Tikhonova, I., Turpaz, Y., Vallanat, B., Van, C., Walker, S.J., Wang, S.J., Wang, Y., Wolfinger, R., Wong, A., Wu, J., Xiao, C., Xie, Q., Xu, J., Yang, W., Zhang, L., Zhong, S., Zong, Y., and Slikker, W., Jr. Nature biotechnology 24, 1151-1161; 2006. PubMed Comparisons between transcriptional regulation and RNA expression in human embryonic stem cell lines. Player, A., Wang, Y., Bhattacharya, B., Rao, M., Puri, R.K., and Kawasaki, E.S. Stem cells and development 15, 315-323; 2006. PubMed Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project. Patterson, T.A., Lobenhofer, E.K., Fulmer-Smentek, S.B., Collins, P.J., Chu, T.M., Bao, W., Fang, H., Kawasaki, E.S., Hager, J., Tikhonova, I.R., Walker, S.J., Zhang, L., Hurban, P., de Longueville, F., Fuscoe, J.C., Tong, W., Shi, L., and Wolfinger, R.D. Nature biotechnology 24, 1140-1150; 2006. PubMed The end of the microarray Tower of Babel: will universal standards lead the way? Kawasaki, E.S. J Biomol Tech 17, 200-206; 2006. PubMed Wnt-1 is dominant over neu in specifying mammary tumor expression profiles. Huang, S., Podsypanina, K., Chen, Y., Cai, W., Tsimelzon, A., Hilsenbeck, S., and Li, Y. Technol Cancer Res Treat 5, 565-571; 2006. PubMed Gene expression profiling of human placentas from preeclamptic and normotensive pregnancies. Hansson, S.R., Chen, Y., Brodszki, J., Chen, M., Hernandez-Andrade, E., Inman, J.M., Kozhich, O.A., Larsson, I., Marsal, K., Medstrand, P., Xiang, C.C., and Brownstein, M.J. Mol Hum Reprod 12, 169-179; 2006. PubMed Identification of molecular markers for endometriosis in blood lymphocytes by using deoxyribonucleic acid microarrays. Flores, I., Rivera, E., Mousses, S., Chen, Y., and Rozenblum, E. Fertil Steril 85, 1676-1683; 2006. PubMed A novel role of myosin VI in human prostate cancer. Dunn, T.A., Chen, S., Faith, D.A., Hicks, J.L., Platz, E.A., Chen, Y., Ewing, C.M., Sauvageot, J., Isaacs, W.B., De Marzo, A.M., and Luo, J. Am J Pathol 169, 1843-1854; 2006. PubMed Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Crawford, G.E., Holt, I.E., Whittle, J., Webb, B.D., Tai, D., Davis, S., Margulies, E.H., Chen, Y., Bernat, J.A., Ginsburg, D., Zhou, D., Luo, S., Vasicek, T.J., Daly, M.J., Wolfsberg, T.G., and Collins, F.S. Genome research 16, 123-131; 2006. PubMed Prediction of venous metastases, recurrence, and prognosis in hepatocellular carcinoma based on a unique immune response signature of the liver microenvironment. Budhu, A., Forgues, M., Ye, Q.H., Jia, H.L., He, P., Zanetti, K.A., Kammula, U.S., Chen, Y., Qin, L.X., Tang, Z.Y., and Wang, X.W. Cancer Cell 10, 99-111; 2006. PubMed Expression Technology – a Critical Review of the Nature, Performance, and Interpretation of Expression Micro arrays IEEE SPM review of white paper SPMGP.139, 2006. . Stafford, P., and Chen, Y. In: IEEE SPM review of white paper SPMGP. IEEE, 139; 2006. Microarray Data Analysis. Li, Y., and Chen, Y. In: Microarray Data Analysis. Chemical Industry Publish, ; 2006. Estrogen receptor alpha positive breast tumors and breast cancer cell lines share similarities in their transcriptome data structures. Zhu, Y., Wang, A., Liu, M.C., Zwart, A., Lee, R.Y., Gallagher, A., Wang, Y., Miller, W.R., Dixon, J.M., and Clarke, R. International journal of oncology 29, 1581-1589; 2006. PubMed Expression patterns among interferon regulatory factor-1, human X-box binding protein-1, nuclear factor kappa B, nucleophosmin, estrogen receptor-alpha and progesterone receptor proteins in breast cancer tissue microarrays. Zhu, Y., Singh, B., Hewitt, S., Liu, A., Gomez, B., Wang, A., and Clarke, R. International journal of oncology 28, 67-76; 2006. PubMed Increased WSB1 copy number correlates with its over-expression which associates with increased survival in neuroblastoma. Chen, Q.R., Bilke, S., Wei, J.S., Greer, B.T., Steinberg, S.M., Westermann, F., Schwab, M., and Khan, J. Genes, chromosomes & cancer 45, 856-862; 2006. PubMed BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Durinck, S., Moreau, Y., Kasprzyk, A., Davis, S., De Moor, B., Brazma, A., and Huber, W. Bioinformatics (Oxford, England) 21, 3439-3440; 2005. PubMed Genetic diversity in melanoma. Meltzer, P.S. N Engl J Med 353, 2104-2107; 2005. PubMed Gene expression profiling of human sarcomas: insights into sarcoma biology. Baird, K., Davis, S., Antonescu, C.R., Harper, U.L., Walker, R.L., Chen, Y., Glatfelter, A.A., Duray, P.H., and Meltzer, P.S. Cancer research 65, 9226-9235; 2005. PubMed Cancer genomics: small RNAs with big impacts. Meltzer, P.S. Nature 435, 745-746; 2005. PubMed Stress-specific signatures: expression profiling of p53 wild-type and -null human cells. Amundson, S.A., Do, K.T., Vinikoor, L., Koch-Paiz, C.A., Bittner, M.L., Trent, J.M., Meltzer, P., and Fornace, A.J., Jr. Oncogene 24, 4572-4579; 2005. 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Cancer Cell 2, 175-178; 2002. PubMed Ratio statistics of gene expression levels and applications to microarray data analysis. Chen, Y., Kamat, V., Dougherty, E.R., Bittner, M.L., Meltzer, P.S., and Trent, J.M. Bioinformatics (Oxford, England) 18, 1207-1215; 2002. PubMed | PDF | Supplement Human AML cells in NOD/SCID mice: engraftment potential and gene expression. Lumkul, R., Gorin, N.C., Malehorn, M.T., Hoehn, G.T., Zheng, R., Baldwin, B., Small, D., Gore, S., Smith, D., Meltzer, P.S., and Civin, C.I. Leukemia 16, 1818-1826; 2002. PubMed A genome-based strategy uncovers frequent BRAF mutations in melanoma. Pollock, P.M., and Meltzer, P.S. Cancer Cell 2, 5-7; 2002. PubMed Transgenic targeting of a dominant negative corepressor to liver and analyses by cDNA microarray. Feng, X., Meltzer, P., and Yen, P.M. Methods in molecular biology (Clifton, NJ 202, 31-54; 2002. PubMed Lucky draw in the gene raffle. Pollock, P.M., and Meltzer, P.S. Nature 417, 906-907; 2002. 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PubMed Hepatitis C virus transfusion-transmitted infection in Brazilian cardiac surgery patients. Nogueira, C.A., Edelman, D.C., Nogueira, C.M., Nogueira, S.A., Coelho, H.S., Abrahao, L.J., Vanderboght, B., Lambert, J.S., and Constantine, N.T. Clinical laboratory 48, 529-533; 2002. PubMed A lack of clinical correlation between the presence of HHV-8 DNA in PBMCs and staging of Kaposi's sarcoma. Edelman, D.C., and Sill, A. Dermatology (Basel, Switzerland) 205, 189; 2002. PubMed Strong feature sets from small samples. Kim, S., Dougherty, E.R., Barrera, J., Chen, Y., Bittner, M.L., and Trent, J.M. J Comput Biol 9, 127-146; 2002. PubMed | PDF Inference from clustering with application to gene-expression microarrays. Dougherty, E.R., Barrera, J., Brun, M., Kim, S., Cesar, R.M., Chen, Y., Bittner, M., and Trent, J.M. J Comput Biol 9, 105-126; 2002. PubMed | PDF Simulation of cDNA microarrays via a parameterized random signal model. 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Cancer research 61, 8624-8628; 2001. PubMed Application of molecular cytogenetic techniques in a case study of human cutaneous metastatic melanoma. Wiltshire, R.N., Dennis, T.R., Sondak, V.K., Meltzer, P.S., and Trent, J.M. Cancer Genet Cytogenet 131, 97-103; 2001. PubMed Detection of antisense and ribozyme accessible sites on native mRNAs: application to NCOA3 mRNA. Scherr, M., LeBon, J., Castanotto, D., Cunliffe, H.E., Meltzer, P.S., Ganser, A., Riggs, A.D., and Rossi, J.J. Mol Ther 4, 454-460; 2001. PubMed Disease fingerprinting with cDNA microarrays reveals distinct gene expression profiles in lethal type 1 and type 2 cytokine-mediated inflammatory reactions. Hoffmann, K.F., McCarty, T.C., Segal, D.H., Chiaramonte, M., Hesse, M., Davis, E.M., Cheever, A.W., Meltzer, P.S., Morse, H.C., 3rd, and Wynn, T.A. Faseb J 15, 2545-2547; 2001. PubMed Induction of gene expression as a monitor of exposure to ionizing radiation. 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PubMed Transgenic targeting of a dominant negative corepressor to liver blocks basal repression by thyroid hormone receptor and increases cell proliferation. Feng, X., Jiang, Y., Meltzer, P., and Yen, P.M. The Journal of biological chemistry 276, 15066-15072; 2001. PubMed Metastasis-associated differences in gene expression in a murine model of osteosarcoma. Khanna, C., Khan, J., Nguyen, P., Prehn, J., Caylor, J., Yeung, C., Trepel, J., Meltzer, P., and Helman, L. Cancer research 61, 3750-3759; 2001. PubMed The incidence of GB virus C / hepatitis G virus infection in Brazilian patients who received blood transfusion during cardiac surgery. Villela Nogueira, C.A., Nogueira, S.A., Nogueira, C.N., Coelho, H.S., Ketema, F., Edelman, D.C., Lambert, J.S., and Constantine, N.T. Journal of medical virology 63, 237-241; 2001. PubMed Transcription program of human herpesvirus 8 (kaposi's sarcoma-associated herpesvirus). 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Journal of human virology 4, 111; 2001. PubMed Chromosome arm-specific multicolor FISH. Karhu, R., Ahlstedt-Soini, M., Bittner, M., Meltzer, P., Trent, J.M., and Isola, J.J. Genes, chromosomes & cancer 30, 105-109; 2001. PubMed Failure of hormone therapy in prostate cancer involves systematic restoration of androgen responsive genes and activation of rapamycin sensitive signaling. Mousses, S., Wagner, U., Chen, Y., Kim, J.W., Bubendorf, L., Bittner, M., Pretlow, T., Elkahloun, A.G., Trepel, J.B., and Kallioniemi, O.P. Oncogene 20, 6718-6723; 2001. PubMed Comprehensive copy number and gene expression profiling of the 17q23 amplicon in human breast cancer. Monni, O., Barlund, M., Mousses, S., Kononen, J., Sauter, G., Heiskanen, M., Paavola, P., Avela, K., Chen, Y., Bittner, M.L., and Kallioniemi, A. Proceedings of the National Academy of Sciences of the United States of America 98, 5711-5716; 2001. PubMed Gastrointestinal stromal tumors with KIT mutations exhibit a remarkably homogeneous gene expression profile. Allander, S.V., Nupponen, N.N., Ringne?r, M., Hostetter, G., Maher, G.W., Goldberger, N., Chen, Y., Carpten, J., Elkahloun, A.G., and Meltzer, P.S. Cancer research 61, 8624-8628; 2001. PubMed Estrogen receptor status in breast cancer is associated with remarkably distinct gene expression patterns. Gruvberger, S., Ringne?r, M., Chen, Y., Panavally, S., Saal, L.H., Borg, A., Ferno, M., Peterson, C., and Meltzer, P.S. Cancer research 61, 5979-5984; 2001. PubMed Down-regulation of the desmosomal cadherin desmocollin 3 in human breast cancer. Klus, G.T., Rokaeus, N., Bittner, M.L., Chen, Y., Korz, D.M., Sukumar, S., Schick, A., and Szallasi, Z. International journal of oncology 19, 169-174; 2001. PubMed Human prostate cancer and benign prostatic hyperplasia: Molecular dissection by gene expression profiling. Luo, J., Duggan, D.J., Chen, Y., Sauvageot, J., Ewing, C.M., Bittner, M.L., Trent, J.M., and Isaacs, W.B. Cancer research 61, 4683-4688; 2001. PubMed Gene-expression profiles in hereditary breast cancer. Hedenfalk, I., Duggan, D., Chen, Y., Radmatcher, M., Bittner, M., Simon, R., Meltzer, P., Gusterson, B., Esteller, M., Kallioniemi, O.P., Wilfond, B., Borg, A., and Trent, J. New England Journal of Medicine 344, 539-548; 2001. PubMed Analysis of expression patterns: The scope of the problem, the problem of scope. Chen, Y., Yakhini, Z., Ben-Dor, A., Dougherty, E., Trent, J.M., and Bittner, M. Disease Markers 17, 59-65; 2001. PubMed Erratum: Molecular classification of cutaneous malignant melanoma by gene expression profiling. (Nature (2000) vol. 406 (536-540)). Bittner, M., Meltzer, P., and Chen, Y. Oncology Spectrums 2, 307; 2001. PubMed Expression profiling of medulloblastoma: PDGFRA and the RAS/MAPK pathway as therapeutic targets for metastatic disease. 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Forozan, F., Mahlamaki, E.H., Monni, O., Chen, Y., Veldman, R., Jiang, Y., Gooden, G.C., Ethier, S.P., Kallioniemi, A., and Kallioniemi, O.P. Cancer research 60, 4519-4525; 2000. PubMed Profiling Human Gene Expression with cDNA Microarrays. Jiang, Y., Lueders, J., Glatfelter, A., Gooden, C., and Bittner, M. In: Current Protocols in Human Genetics. John Wiley & Sons, Inc., 11.13.11-11.13.26; 2000. Lipid peroxidation is associated with the inhibitory action of all-trans-retinoic acid on mammary cell transformation. Kubow, S., Woodward, T.L., Turner, J.D., Nicodemo, A., Long, E., and Zhao, X. Anticancer research 20, 843-848; 2000. PubMed Detection of Kaposi's sarcoma-associated herpesvirus in oral and genital secretions of Zimbabwean women. 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