Biomedical Informatics, 2006
This page lists 2006 publications by faculty and staff in the Division of Biomedical Informatics at Cincinnati Children's Research Foundation and the University of Cincinnati. Where possible, titles are linked to the article's PubMed abstract.
Kong S, Aronow BJ, Handwerger S. Gene expression microarray data analysis of decidual and placental cell differentiation. Methods Mol Med. 2006;121:425-38.
Mallakin A, Kutcher LW, McDowell SA, Kong S, Schuster R, Lentsch AB, Aronow BJ, et al. Gene expression profiles of Mst1r-deficient mice during nickel-induced acute lung injury. Am J Respir Cell Mol Biol. 2006 Jan;34(1):15-27.
Blanchard C, Wang N, Stringer KF, Mishra A, Fulkerson PC, Abonia JP, Jameson SC, Kirby C, Konikoff MR, Collins MH, Cohen MB, Akers R, Hogan SP, Assa'ad AH, Putnam PE, Aronow BJ, et al. Eotaxin-3 and a uniquely conserved gene-expression profile in eosinophilic esophagitis. J Clin Invest. 2006 Feb;116(2):536-47.
Oka T, Maillet M, Watt AJ, Schwartz RJ, Aronow BJ, Duncan SA, et al. Cardiac-specific deletion of Gata4 reveals its requirement for hypertrophy, compensation, and myocyte viability. Circ Res. 2006 Mar 31;98(6):837-45.
Xu J, Gong NL, Bodi I, Aronow BJ, Backx PH, Molkentin JD. Myocyte enhancer factors 2A and 2C induce dilated cardiomyopathy in transgenic mice. J Biol Chem. 2006 Apr 7;281(14):9152-62.
Imhof A, Charnay Y, Vallet PG, Aronow B, Kovari E, French LE, et al. Sustained astrocytic clusterin expression improves remodeling after brain ischemia. Neurobiol Dis. 2006 May;22(2):274-83.
Lowy AM, Clements WM, Bishop J, Kong L, Bonney T, Sisco K, Aronow B, et al. beta-Catenin/Wnt signaling regulates expression of the membrane type 3 matrix metalloproteinase in gastric cancer. Cancer Res. 2006 May 1;66(9):4734-41.
Schwab K, Hartman HA, Liang HC, Aronow BJ, Patterson LT, Potter SS. Comprehensive microarray analysis of Hoxa11/Hoxd11 mutant kidney development. Dev Biol. 2006 May 15;293(2):540-54.
McGraw DW, Fogel KM, Kong S, Litonjua AA, Kranias EG, Aronow BJ, et al. Transcriptional response to persistent {beta}2-adrenergic receptor signaling reveals regulation of phospholamban which alters airway contractility. Physiol Genomics. 2006 Jul 18.
Gerber LK, Aronow BJ, Matlib MA. Activation of a novel long-chain free fatty acid export system in mitochondria of diabetic rat hearts. Am J Physiol Cell Physiol. 2006 Jul 19.
Fink D, Fazli L, Aronow B, Gleave ME, Ong CJ. Clusterin is not essential for androgen-regulated involution and regeneration of the normal mouse prostate. The Prostate. 2006 Sep 15;66(13):1445-54.
Rajan S, Williams SS, Jagatheesan G, Ahmed RP, Fuller-Bicer G, Schwartz A, Aronow BJ, et al. Microarray analysis of gene expression during early stages of mild and severe cardiac hypertrophy. Physiol Genomics. 2006 Nov 27;27(3):309-17.
Jegga AG, Kong S, Zhang J, Moseley A, Gupta A, Williams SS, et al. Comparative genomics of tissue specific gene expression in gene expression and regulation. In: Ma J, editor. Gene Expression and Regulation: Higher Education Press/Springer; 2006.
Miller SJ, Rangwala F, Williams J, Ackerman P, Kong S, Jegga AG, et al. Large-scale molecular comparison of human schwann cells to malignant peripheral nerve sheath tumor cell lines and tissues. Cancer Res. 2006 Mar 1;66(5):2584-91.
Sartor MA, Zorn AM, Schwanekamp JA, Halbleib D, Karyala S, Howell ML, Dean GE, Medvedovic M, et al. A new method to remove hybridization bias for interspecies comparison of global gene expression profiles uncovers an association between mRNA sequence divergence and differential gene expression in Xenopus. Nucleic Acids Res. 2006;34(1):185-200.
Sartor MA, Tomlinson CR, Wesselkamper SC, Sivaganesan S, Leikauf GD, Medvedovic M. Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments. BMC bioinformatics. 2006;7:538.
Medvedovic M, Tomlinson CR, Call MK, Grogg M, Tsonis PA. Gene expression and discovery during lens regeneration in mouse: regulation of epithelial to mesenchymal transition and lens differentiation. Mol Vis. 2006;12:422-40.
Wesselkamper SC, McDowell SA, Medvedovic M, Dalton TP, Deshmukh HS, Sartor MA, et al. The role of metallothionein in the pathogenesis of acute lung injury. Am J Respir Cell Mol Biol. 2006 Jan;34(1):73-82.
Erwin CR, Jarboe MD, Sartor MA, Medvedovic M, Stringer KF, Warner BW, et al. Developmental characteristics of adapting mouse small intestine crypt cells. Gastroenterology. 2006 Apr;130(4):1324-32.
Gandhi M, Medvedovic M, Stringer JR, Nikiforov YE. Interphase chromosome folding determines spatial proximity of genes participating in carcinogenic RET/PTC rearrangements. Oncogene. 2006 Apr 13;25(16):2360-6.
Icenhour CR, Arnold J, Medvedovic M, Cushion MT. Competitive coexistence of two Pneumocystis species. Infect Genet Evol. 2006 May;6(3):177-86.
Liu X, Sivaganesan S, Yeung KY, Guo J, Bumgarner RE, Medvedovic M. Context-specific infinite mixtures for clustering gene expression profiles across diverse microarray dataset. Bioinformatics. 2006 May 18.
Mesa C, Jr., Mirza M, Mitsutake N, Sartor M, Medvedovic M, Tomlinson C, et al. Conditional activation of RET/PTC3 and BRAFV600E in thyroid cells is associated with gene expression profiles that predict a preferential role of BRAF in extracellular matrix remodeling. Cancer Res. 2006 Jul 1;66(13):6521-9.
Schwanekamp JA, Sartor MA, Karyala S, Halbleib D, Medvedovic M, Tomlinson CR. Genome-wide analyses show that nuclear and cytoplasmic RNA levels are differentially affected by dioxin. Biochimica et biophysica acta. 2006 Aug-Sep;1759(8-9):388-402.
Slaven BE, Porollo A, Sesterhenn T, Smulian AG, Cushion MT, Meller J. Large-scale characterization of introns in the Pneumocystis carinii genome. The Journal of eukaryotic microbiology. 2006;53 Suppl 1:S151-3.
Slaven BE, Meller J, Porollo A, Sesterhenn T, Smulian AG, Cushion MT. Draft assembly and annotation of the Pneumocystis carinii genome. The Journal of eukaryotic microbiology. 2006;53 Suppl 1:S89-91.
Cao B, Porollo A, Adamczak R, Jarrell M, Meller J. Enhanced recognition of protein transmembrane domains with prediction-based structural profiles. Bioinformatics. 2006 Feb 1;22(3):303-9.
Tan M, Meller J, Jiang X. C-terminal arginine cluster is essential for receptor binding of norovirus capsid protein. J Virol. 2006 Aug;80(15):7322-31.
Pestian JP, Itert L, Anderson C, Duch W. Preparing clinical text for use in biomedical research. J Database Manage. 2006 Apr-Jun;17(2):1-11.
McLachlan A, Borchers M, Velayutham P, Wagner M, Limbach PA. Characterizing the reproducibility of a protein profiling method for the analysis of mouse bronchoalveolar lavage fluid. Journal of proteome research. 2006 Nov;5(11):3059-65.
Bridges JP, Xu Y, Na CL, Wong HR, Weaver TE. Adaptation and increased susceptibility to infection associated with constitutive expression of misfolded SP-C. J Cell Biol. 2006 Jan 30;172(3):395-407.
Martis PC, Whitsett JA, Xu Y, Perl AK, Wan H, Ikegami M. C/EBPalpha is required for lung maturation at birth. Development (Cambridge, England). 2006 Mar;133(6):1155-64.
Xu Y, Liu C, Clark JC, Whitsett JA. Functional genomic responses to cystic fibrosis transmembrane conductance regulator (CFTR) and CFTR(delta508) in the lung. J Biol Chem. 2006 Apr 21;281(16):11279-91.
Matsuzaki Y, Xu Y, Ikegami M, Besnard V, Park KS, Hull WM, et al. Stat3 is required for cytoprotection of the respiratory epithelium during adenoviral infection. J Immunol. 2006 Jul 1;177(1):527-37.
Dave V, Childs T, Xu Y, Ikegami M, Besnard V, Maeda Y, et al. Calcineurin/Nfat signaling is required for perinatal lung maturation and function. J Clin Invest. 2006 Oct;116(10):2597-609.
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