Publications

Microarray Core Manuscripts 2011:

Baine MJ, Chakraborty S, Smith LM, Mallya K, Sasson AR, Brand RE, and Batra SK, 2011. Transcriptional Profiling of Peripheral Blood Mononuclear Cells in Pancreatic Cancer Patients Identifies Novel Genes with Potential Diagnostic Utility. PloS One, In press.

Microarray Core Manuscripts 2010:

Parameswaran S, Balasubramanian S, Babai N, Qiu F, Eudy JD, Thoreson WB, Ahmad I. 2010. Induced pluripotent stem cells generate both retinal ganglion cells and photoreceptors: therapeutic implications in degenerative changes in glaucoma and age-related macular degeneration. Stem Cells. Apr;28(4):695-703.

Gao L, LI Y, Schultz HD, Wang WZ, Wang WW, Finch M, Smith LM, and Zucker IH. 2010. 2010. Downregulated Kv4.3 expression in the RVLM as a potential mechanism for sympathoexcitation in rats with chronic heart failure. Am J Physiol Heart Circ Physiol 298:H945-H955.

Deffenbacher KE, Iqbal J, Liu Z, Fu K, Chan WC. 2010. Recurrent chromosomal alternations in molecularly classified AIDS-related lymphomas: an integrated analysis of DNA copy number and gene expression. J Acquir Immune Defic Syndr. May 1;54(1):18-26.

Iqbal J, Weisenburger DD, Chowdhury A, Tsai MY, Srivastava G, Greiner TC, Kucuk C, Deffenbacher K, Vose J, Smith L, Au WY, Nakamura S, Seto M, Delabie J, Berger F, Loong F, Ko YH, Sng I, Liu X, Loughran TP, Armitage J, Chan WC. 2010. Natural killer cell lymphoma shares strikingly similar molecular features with a group of nonhepatosplenic T-cell lymphoma and is highly sensitive to a novel aurora kinase A inhibitor in vitro. Leukemia. 2010 Nov 5. Epub ahead of print.

Zhao X, Malhotra GK, Lele SM, Lele MS, West WW, Eudy JD, Band H, and Band V. 2010. Telomerase-immortalized human mammary stem/progenitor cells with ability to self-renew and differentiate. Proc Natl Acad Sci U.S.A. v107(32):14146-14151.

Sato T, Liu X, Nelson A, Nakanishi M, Kanaji N, Wang X, Kim M, Li Y, Sun J, Michalski J, Patil A, Basma H, Holz O, Magnussen H, Rennard SI. 2010. Reduced miR-146a increases prostaglandin E2 in chronic obstructive pulmonary disease fibroblasts. Am J Respir Crit Care Med. 2010 Oct 15;182(8):1020-9.

Yanai-Baiser GM, Duncan GA, Eudy JD, Wang D, Li X, Agarkova IV, Dunigan DD, Van Etten JL. “Microarray Analysis of Paramecium bursaria Chlorella Virus. Transcription”. J Virol 2010 Jan;84(1):532-42.

Microarray Core Manuscripts 2009:

Pavlinkova G, Salbaum JM, Kappen C. 2009. Maternal Diabetes alters Transcriptional Programs in the Developing Embryo. BMC Genomics. Jun 18;10(1):274.

Kou W, Banerjee S, Eudy J, Smith L, Persidsky R, Borgmann K, Wu L, Sakhuja N, Deshpande M, Walseth T, Ghorpade A. "CD38 regulation in activated astrocytes: implications for neuroinflammation and HIV-1 brain infection" Journal of Neuro Res 2009. Aug 1;87(10);2326-39.

Iqbal J, Kucuk C, Deleeuw RJ, Srivastava G, Tam W, Geng H, Klinkebiel, D, Christman JK, Patel K, Cao K, Shen L, Dybkaer K, Tsui IF, Ali H, Shimizu N, Au WY, Lam WL & Chan WC 2009. Genomic analyses reveal global functional alterations that promote tumor growth and novel tumor suppressor genes in natural killer-cell malignancies. Leukemia. Jun;23(6):1139-51

Iqbal J, Weisenburger DD, Greiner TC, Vose J, McKeithan T, Kucuk C, Geng H, Deffenbacher K, Smith L, Dybkaer K, Nakamura S, Seto M, Delabie J, Berger F, Loong F, Au WY, Ko YH, Sng I, Armitage J and Chan WC, 2009. Molecular signatures to improve diagnosis in peripheral T-cell lymphoma and prognostication in angioimmunoblastic T-cell lymphoma. for the International Peripheral T-cell Lymphoma Project. Blood. 2009 Nov 18.

Costanzo-Garvey DL, Pfluger PT, Dougherty MK, Stock JL, Boehm M, Chaika O, Fernandez MR, Fisher K, Kortum RL, Hong EG, Jun JY, Ko HJ, Schreiner A, Volle DJ, Treece T, Swift AL, Winer M, Chen D, Wu M, Leon LR, Shaw AS, McNeish J, Kim JK, Morrison DK, Tschöp MH, Lewis RE. 2009. KSR2 is an essential regulator of AMP kinase, energy expenditure, and insulin sensitivity. Cell Metab. 2009 Nov;10(5):366-78.

Abstracts 2009:

Christman, J. K., J. Yang, L. Tang, E. Rief, and D. L Klindebiel. Microarray analysis of CpG methylation and altered gene expression in the MCF10A model of breast cancer progression. U.S. Army Medical Research and Material Command Research Initiative Meeting. 

Christman, J. K., D. L. Klinkebiel, D. D. Weisenburger, W. C. Chan, and T. C. Greiner. Methylation analysis of mantle cell lymphoma: 1) Global methylation patterns of MCL patients, 2) Demethylating agent influence on cell line expression. Mantle Cell Lymphoma Research Initiative Annual Meeting.

Publications 2008:

Deffenbacher, K.E., G. Wright, J. Iqbal, H. Geng, D. O’Shea, T. A. Lister, J. Fitzgibbon, K. Fu, Z. Liu, D. D. Weisenburger,T. C. Greiner, R. D. Gascoyne, A. Rosenwald, E. Campo, L. M. Rimsza, J. Delabie, E. S. Jaffe, L. M. Staudt, and W. C. Chan. Genetic Abnormalities Involved in the Development and Progression of Follicular Lymphoma. Blood 112:2049.

Hegde, G.V., K. J. Peterson, K. Emanuel, A. K. Mittal, A. D. Joshi, J. D. Dickson, G. J. Kollessery, R. G. Bociek, P. J. Bierman,J. M. Vose, D. D. Weisenburger, and S. S. Joshi. Hedgehog-induced survival of B-CLL in a stromal cell microenvironment. Molecular Cancer Research 6:1928-1936.

Joshi, S.S., A. K. Mittal, A. D. Joshi, E. Vue, and W. Xioung. Differential gene expression in murine large B-cell lymphoma metastatic variants. Int. Immunopharmacology 8:1257-63.

Hegde, G. V., C. M. Munger, K. Emanuel, A. D. Joshi, D. D. Weisenburger, J. M. Vose, S. S. Joshi. Targeting GLI for the treatment of mantle cell lymphoma. Mol. Cancer Therapeutics, 7:1450-60.

Spresser, C. R., S. E. Marshall, and K. A. Carlson. Characterization of gene expression regulated by human OTK18 using Drosophila melanogaster as a model system for innate immunity J. Genet. 87.

Das, V.A., S. Bhattacharya, X. Zhao, G. Hegde, K. Mallya, J. D. Eudy, and I. Ahmad. The canonical Wnt pathway regulates retinal stem cells / progenitors in concert with notch signaling. Dev Neurosci. 30(6):389-409.

Bafna, S., A. P. Singh, N. Moniaux, J. D. Eudy, J. L. Meza, and S. K. Batra. MUC4, a multifunctional transmembrane glycoprotein, induces oncogenic transformation of NIH3T3 mouse fibroblast cells. Cancer Res. 68(22):9231-8.

Lenz, G., G. Wright, S. S. Dave, W. Xiao, J. Powell, H. Zhao, W. Xu, B. Tan, J. Iqbal, J. Vose, M. Bast, K Fu, D. D. Weisenburger,T. C. Greiner, J. O. Armitage, L. May, R. Gascoyne, J. M. Connors, G. Troen, H. Holte, S. Kvaloy, D. Dierickx, G. Verhoef, J. Delabie, E. B. Smeland, P. Jares, A. Martinez, A. Lopez-Guillermo, E. Montserrat, E. Campo, R. M. Braziel, T. Miller, L. M. Rimsza, J. Cook,

B. Pohlman, J. Sweetenham, R. Tubbs, R. I. Fisher, E. Hartmann, A. Rosenwald, G. Ott, H. K. Muller-Hermelink, D. Wrench, T. A. Lister, E. S. Jaffe, W. H. Wilson, W. C. Chan, and L. M. Staudt. A Gene Expression-based Survival Predictor For Diffuse Large B Cell Lymphoma Treated With Chemotherapy Plus Rituximab. NEJM 359(22):2313-23.

Bates, J. S., D. B. Petry, J. D. Eudy, L. S. Bough, and R. K. Johnson. Differential expression in lung and bronchial lymph node of pigs with high and low responses to infection with Porcine Reproductive and Respiratory Syndrome Virus. J Anim Sci. (12):3279-89.

Gelineau-van Waes, J., J. R. Maddox, L. M. Smith, M. van Waes, J. Wilberding, J. D. Eudy, L. K. Bauer, and R. H. Finnell. Microarray analysis of E9.5 reduced folate carrier (RFC1; Slc19a1) knockout embryos reveals altered expression of genes in the cubilin-megalin multiligand endocytic receptor complex. BMC Genomics. 9:156.

Langer, W.J., K. Devish, P.K. Carmines, and P. H. Lane. Prepubertal onset of diabetes prevents expression of renal cortical connective tissue growth factor. Pediatr Nephrol. (2):275-83.

Gelineau-van Waes, J., L. Smith, M. van Waes, J. Wilberding, J. D. Eudy, L. K. Bauer, and J. Maddox. Altered Expression of the Iron Transporter Nramp1 (slc11a1) During Fetal Eye Development in Microphthalmia-Associated Transcription Factor Mitfmi and Mitfvitiligo Mouse Mutants Experimental Eye Research 86(2):419-33.

Singh, A. P., S. Bafna, K. Chaudhary, G. Venkatraman, L. Smith, J. D. Eudy, S. L. Johansson, M. F. Lin, and S. K. Batra. Genome-wide expression profiling reveals transcriptomic variation and perturbed gene networks in androgen-dependent and androgen-independent prostate cancer cells. Cancer Letters 259(1):28-38.

Abstracts 2008:

Deffenbacher, K., Z. Liu, J. Iqbal, H. Geng, and W. C. Chan. High Resolution Profiling of DNA copy number and gene expression changes in AIDS-related Lymphoma. “11th International Conference on Malignancies in AIDS and other Acquired Immunodeficiencies”, NIH; October 6-7.

Christman, J. K, D. L. Klinkebiel, D. D. Weisenburger, W. C. Chan, and T. C. Greiner. Methylation analysis of mantle cell lymphoma: 1) Evaluation of methods to enhance detection of methylation changes using Affymetrix Promoter arrays, 2) Evaluation of agents to change gene expression patterns in vitro. Mantle Cell Lymphoma Research Initiative Annual Meeting.

Publications 2007:

Chaudhuri, A., F. Duan, B. Morsey, Y. Persidsky, and G. D. Kanmogne. HIV-1 activates proinflammatory and interferon-inducible genes in human brain microvascular endothelial cells: putative mechanisms of blood-brain barrier dysfunction. Journal of Cerebral Blood Flow and Metabolism 1-15.

Rocha-Sanchez, S., and K. Beisel. Pocket proteins and cell cycle regulation in inner ear development. Int. J. Dev. Biol. 51, 585-595.

Joshi, A. D., G. V. Hegde, J. D. Dickinson, A. K. Mittal, J. C. Lynch, J. D. Eudy, J. O. Armitage, P. J. Bierman, R. G. Bociek, M. P. Devetten, J. M. Vose, and S. S. Joshi. Divergent Role of ATM, CTLA4, MNDA and HEM1 in the Clinical Behavior of High versus Low CD38 Expressing CLL. Clin Cancer Res. 13(18 Pt 1):5295-304.

Dybkaer, K., J. Iqbal, G. Zhou, H. Geng, L. Xiao, A. Schmitz, F. d’Amore, and W. C. Chan. Genome wide transcriptional analysis of resting and IL2 activated human natural killer cells: Gene expression signatures indicative of novel molecular signaling pathways. BMC Genomics 8:230.

Joshi, A. D., J. D. Dickinson, G. V. Hegde, W. G. Sanger, J. O. Armitage, P. J. Bierman, R. G. Bociek, M. P. Devetten, J. M. Vose, and S. S. Joshi. Bulky lymphadenopathy with poor clinical outcome is associated with ATM downregulation in B-cell chronic lymphocytic leukemia patients irrespective of 11q23 deletion. Cancer Genet Cytogenet. 172(2): 120-126.

Jiang, C., J. Pecha, I. Hoshino, D. Ankrapp, and H. Xiao. TIP30 mutant derived from hepatocellular carcinoma specimens promotes growth of HepG2 cells through up-regulation of N-cadherin. Cancer Res. 67(8): 3574-3582.

Duan, F., E. R. Spindel, Y. H. Li, and R. Norgren. Intercenter reliability and validity of the rhesus macaque GeneChip. BMC Genomics 8:61.

Rosenquist, T. H., G. D. Bennett, P. R. Brauer, M. L. Stewart, T. R. Chaudoin, and R. H. Finnell. Microarray analysis of homocysteine-responsive genes in cardiac neural crest cells in vitro. Dev Dyn. 236(4): 1044-1054.

Publications 2006:

Weston, M. D., M. L. Pierce, S. Rocha-Sanchez, K. W. Beisel, and G. A. Soukup. MicroRNA gene expression in the mouse inner ear. Brain Res. 1111(1): 95-104.

Dickinson, J. D., A. Joshi, J. Iqbal, W. Sanger, P. J. Bierman, and S. S. Joshi. Genomic abnormalities in chronic lymphocytic leukemia influence gene expression by a gene dosage effect. Int J Mol Med. 17(5): 769-778.

Dickinson, J. D., J. Gilmore, J. Iqbal, W. Sanger, J. C. Lynch, J. Chan, P. J. Bierman, and S. S. Joshi. 11q22.3 deletion in B-chronic lymphocytic leukemia is specifically associated with bulky lymphadenopaty and ZAP-70 expression but not reduced expression of adhesion/cell surface receptor molecules. Leuk Lymphoma 47 (2): 231-244.

Schulz, J. S., N. Palmer, J. Steckelberg, S. J. Jones, and M. G. Zeece. Microarray profiling of skeletal muscle sarcoplasmic reticulum proteins. Biochim Biophys Acta. 1764 (9): 1429-1435.

Madson, J. G., D. T. Lynch, K. L. Tinkum, S. K. Putta, and L. A. Hansen. Erbb2 regulates inflammation and proliferation in the skin after ultraviolet irradiation. Am J Pathol. 169 (4): 1402-1414.

Publications 2005:

Dickinson, J. D., L. M. Smith, W. G. Sanger, G. Zhou, P. Townley, J. C. Lynch, Z. S. Pavletic, P. J. Bierman, and S. S. Joshi. Unique gene expression and clinical characteristics are associated with the 11q23 deletion in chronic lymphocytic leukemia. Br J Haematol. 128(4):460-471.

Ruthermund, C. A., V. K. Gopalakrishnan, J. D. Eudy, and J. K. Vishwanatha. Casodex treatment induces hypoxia-related gene expression in the LNCaP prostate cancer progression model. BMC Urology 5:5.

Lahue, E., J. Heckathorn, A. Meyer, J. Smith, and C. Wolfe. The Saccharomyces cerevisiae Sub2 protein suppresses heterochromatic silencing at telomeres and subtelomeric genes. Yeast 22 (7): 537-551.

Wei, M., L. Arnold, M. Cano, and S. M. Cohen. Effects of co-administration of antioxidants and arsenicals on the rat urinary bladder epithelium. Toxicol Sci. 83(2): 237-245.

Publications 2004:

Shen, Y., J. Iqbal, L. Xiao, R. C. Lynch, A. Rosenwald, L. M. Staudt, S. Sherman, K. Dybkaer, G. Zhou, J. D. Eudy, J. Delabie, T. W. McKeithan and W. C. Chan. Distinct gene expression profiles in different B-cell compartments in human peripheral lymphoid organs. BMC Immunology 5:20.

Caetano, A. R., R. K. Johnson, J. J. Ford, and D. Pomp. Microarray profiling for differential gene expression in ovaries and ovarian follicles of pigs selected for increased ovulation rate. Genetics 168 (3): 1529-1537.

Publications 2003:

Wiedmann, S., J. D. Eudy, and J. Zempleni. Biotin supplementation increases expression of genes encoding interferon-?, interleukin-1ß and 3-methylcrotonyl-CoA carboxylase, and decreases expression of the gene encoding interleukin-4 in human peripheral blood mononuclear cells. Journal of Nutrition 133 (3): 716-719.

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