Biomedical Informatics, 2004
This page lists 2004 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.
Bueno OF, Lips DJ, Kaiser RA, Wilkins BJ, Dai YS, Glascock BJ, Klevitsky R, Hewett TE, Kimball TR, Aronow BJ, et al. Calcineurin Abeta gene targeting predisposes the myocardium to acute ischemia-induced apoptosis and dysfunction. Circ Res. 2004 Jan 9;94(1):91-9.
DeMattos RB, Cirrito JR, Parsadanian M, May PC, O'Dell MA, Taylor JW, Harmony JA, Aronow BJ, et al. ApoE and clusterin cooperatively suppress Abeta levels and deposition: evidence that ApoE regulates extracellular Abeta metabolism in vivo. Neuron. 2004 Jan 22;41(2):193-202.
Gu G, Wells JM, Dombkowski D, Preffer F, Aronow B, Melton DA. Global expression analysis of gene regulatory pathways during endocrine pancreatic development. Development. 2004 Jan;131(1):165-79.
Zingarelli B, Hake PW, O'Connor M, Denenberg A, Wong HR, Kong S, Aronow BJ. Differential regulation of activator protein-1 and heat shock factor-1 in myocardial ischemia and reperfusion injury: role of poly(ADP-ribose) polymerase-1. Am J Physiol Heart Circ. Physiol. 2004 Apr;286(4):H1408-15.
Wu Y, Zhang D, Lou D, Fan Y, Aronow B, Xu M, et al. C-fos regulates neuropeptide Y expression in mouse dentate gyrus. Neurosci Lett. 2004 Jun 3;363(1):6-10.
Cheng YH, Aronow BJ, Hossain S, Trapnell B, Kong S, Handwerger S. Critical role for transcription factor AP-2alpha in human trophoblast differentiation. Physiol Genomics. 2004 Jun 17;18(1):99-107.
Schwab K, Witte DP, Aronow BJ, Devarajan P, Potter SS, Patterson LT. Microarray analysis of focal segmental glomerulosclerosis. Am J Nephrol. 2004 Jul-Aug;24(4):438-47.
Barnes MG, Aronow BJ, Luyrink LK, Moroldo MB, Pavlidis P, Passo MH, et al. Gene expression in juvenile arthritis and spondyloarthropathy: pro-angiogenic ELR+ chemokine genes relate to course of arthritis. Rheumatology (Oxford). 2004 Aug;43(8):973-9.
Kempster S, Collins ME, Aronow BJ, Simmons M, Green RB, Edington N. Clusterin shortens the incubation and alters the histopathology of bovine spongiform encephalopathy in mice. Neuroreport. 2004 Aug 6;15(11):1735-8.
Williams SS, Mear JP, Liang HC, Potter SS, Aronow BJ, Colbert MC. Large-scale reprogramming of cranial neural crest gene expression by retinoic acid exposure. Physiol Genomics. 2004 Oct 4;19(2):184-97.
Tang Y, Lu A, Ran R, Aronow BJ, Schorry EK, Hopkin RJ, et al. Human blood genomics: distinct profiles for gender, age and neurofibromatosis type 1. Brain Res Mol Brain Res. 2004 Dec 20;132(2):155-67.
Hutton JJ, Jegga AG, Kong S, Gupta A, Ebert C, Williams S, Katz JD, Aronow BJ. Microarray and comparative genomics-based identification of genes and gene regulatory regions of the mouse immune system. BMC Genomics. 2004 Oct 24;5(1):82.
Gu Y, Alvares CJ, Jasti AC, Jansen M, Bean J, Jegga AG, Aronow BJ, et al. Alteration of RhoH expression is associated with human diffuse large b-cell lymphoma. Blood. 2004 Nov 16;104(11).
Kim JW, Zeller KI, Wang Y, Jegga AG, Aronow BJ, O'Donnell KA, et al. Evaluation of myc E-box phylogenetic footprints in glycolytic genes by chromatin immunoprecipitation assays. Mol Cell Biol. 2004 Jul;24(13):5923-36.
Zhang J, Moseley A, Jegga AG, Gupta A, Witte DP, Sartor M, Medvedovic M, Williams SS, Ley-Ebert C, Coolen L, Egnaczyk G, Genter MB, Lehman M, Lingrel J, Maggio J, Parysek L, Walsh R, Xu M, Aronow BJ. Neural system-enriched gene expression, relationship to biological pathways and neurological diseases. Physiol Genomics 2004 Jul 8;18(2):167-83.
Bonizzi G, Bebien M, Otero DC, Johnson-Vroom KE, Cao Y, Vu D, Jegga AG, Aronow BJ, et al. Activation of IKKalpha target genes depends on recognition of specific kappaB binding sites by RelB:p52 dimers. Embo J. 2004 Oct 27;23(21):4202-10.
Livingston RJ, Von Niederhausern A, Jegga AG, Crawford DC, Carlson CS, Rieder MJ, Gowrisankar S, Aronow BJ, et al. Pattern of sequence variation across 213 environmental response genes. Genome Res. 2004 Oct;14(10A):1821-31.
Takemoto CM, Shahlaee AH, Ye Y, Zeller KI, Zablocki D, Huynh J, Huang S, DeKoter RP, Jegga AG, Aronow BJ, et al. Transcriptional regulation of a distinct GATA-1 isoform during selection of the mast and erythroid lineages. Blood. 2004 Nov 16;104(11).
Bahassi el M, Karyala S, Tomlinson CR, Sartor MA, Medvedovic M, Hennigan RF. Critical regulation of genes for tumor cell migration by AP-1. Clin Exp Metastasis. 2004;21(4):293-304.
Karyala S, Guo J, Sartor M, Medvedovic M, Kann S, Puga A, et al. Different global gene expression profiles in benzo[a]pyrene- and dioxin-treated vascular smooth muscle cells of AHR-knockout and wild-type mice. Cardiovasc Toxicol. 2004;4(1):47-73.
Puga A, Sartor MA, Huang MY, Kerzee JK, Wei YD, Tomlinson CR, Baxter CS, Medvedovic M. Gene expression profiles of mouse aorta and cultured vascular smooth muscle cells differ widely, yet show common responses to dioxin exposure. Cardiovasc Toxicol. 2004;4(4):385-404.
Vineis P, Schulte PA, Carreon T, Bailer AJ, Medvedovic M. Issues of design and analysis in studies of gene-environment interactions. IARC Sci Publ. 2004(157):417-35.
Yeung KY, Medvedovic M, Bumgarner RE. From co-expression to co-regulation: how many microarray experiments do we need? Genome Biol. 2004;5(7):R48.
Guo J, Sartor M, Karyala S, Medvedovic M, Kann S, Puga A, et al. Expression of genes in the TGF-beta signaling pathway is significantly deregulated in smooth muscle cells from aorta of aryl hydrocarbon receptor knockout mice. Toxicol Appl Pharmacol. 2004 Jan 1;194(1):79-89.
Medvedovic M, Yeung KY, Bumgarner RE. Bayesian mixture model based clustering of replicated microarray data. Bioinformatics. 2004 May 22;20(8):1222-32.
Sartor M, Schwanekamp J, Halbleib D, Mohamed I, Karyala S, Medvedovic M, et al. Microarray results improve significantly as hybridization approaches equilibrium. Biotechniques. 2004 May;36(5):790-6.
Whitsett JA, Bachurski CJ, Barnes KC, Bunn PA Jr, Case LM, Cook DN, Crooks D, Duncan MW, Dwyer-Nield L, Elston RC, Fessler MB, Franklin WA, Friedman N, Garcia JG, Geraci MW, Glasgow C, Glasser SW, Hardie WD, Henning LM, Johnson GL, Kawkitinarong K, Keith RL, Korfhagen TR, Leikauf GD, Liggett SB, Malcolm KC, Malkinson AM, Mariani TJ, McDowell SA, McGraw DW, Medvedovic M, Moss J, Nogee LM, Nonas S, Pacheco-Rodriguez G, Palmer LJ, Peters DG, Prows DR, Redline S, Regev A, Sartor MA, Schwartz DA, Silverman EK, Steagall WK, Stearman RS, Taveira-DaSilva A, Tichelaar JW, Tomlinson CR, Tsukada K, Weaver TE, Wert SE, Wesselkamper SC, Worthen GS, Xu Y, et al. Functional genomics of lung disease. Am J Respir Cell Mol Biol. 2004 Aug;31(2 Suppl):S1-S81.
Meller J. Advances in protein structure predictions: algorithms and ppplications. Warsaw. 2004.
Adamczak R, Meller J. On the transferability of folding and threading potentials and sequence-independent filters for protein folding simulations. Molecular Physics. 2004;102(11-12):1291-1305.
Czyzyk-Krzeska MF, Meller J. von Hippel-Lindau tumor suppressor: not only HIF's executioner. Trends Mol Med. 2004 Apr;10(4):146-9.
Filippi MD, Harris CE, Meller J, Gu Y, Zheng Y, Williams A. Localization of Rac2 viat the C terminus and aspartic acid 150 specifies superoxide generation, actin polarity and chemotaxis in neutrophils. Nat Immunology. 2004 Jul;5(7):744-51.
Wade SL, Wolfe CR, Pestian JP. A web-based family problem-solving intervention for families of children with traumatic brain injury. Behav Res Methods Instrum Comput. 2004 May;36(2):261-9.
Phillips JLM, Whalen C. Ask for passwords: Continuing to implement an LDAP suspicious path. Inside Solaris. 2004 Jan;10(1):5-7.
Phillips JLM, Whalen C. Completing the LDAP suspicious path. Inside Solaris. 2004 Feb;10(2):4-6.
Adamczak R, Porollo A, Meller J. Accurate prediction of solvent accessibility using neural networks-based regression. Proteins. 2004 Sep 1;56(4):753-67.
Porollo A, Adamczak R, Meller J. Polyview: a flexible visualization tool for structural and functional annotations of proteins. Bioinformatics. 2004 Oct 12:20(15):2460-2.
Wagner M, Meller J, Elber R. Large-scale linear programming techniques for the design of protein folding potentials. Mathematical Programming. 2004;101(2):301-318.
Wagner M, Naik DN, Pothen A, Kasukurti S, Devineni RR, Adam BL, et. al. Computational protein biomarker prediction: a case study for prostate cancer. BMC Bioinformatics 2004 Mar 11;5:26.
Guo M, Wagner M, West C. Outpatient scheduling: a simulation approach. In: Ingalls RG, Rossetti MD, Smith JS, Peters BA, editors. Proceedings of the 2004 Winter Simulation Conference; 2004 Dec 5-8; Washington, DC. Piscataway (NJ): IEEE; 2004. p. 1981-7.
Karp CL, Flick LM, Park KW, Softic S, Greer TM, Keledjian R, Yang R, Uddin J, Guggino WB, Atabani SF, Belkaid Y, Xu Y, et al. Defective lipoxin-mediated anti-inflammatory activity in the cystic fibrosis airway. Nat Immunol. 2004 Apr;5(4):388-92.
Lian X, Yan C, Yang L, Xu Y, Du H. Lysosomal acid lipase deficiency causes respiratory inflammation and destruction in the lung. Am J Physiol Lung Cell Mol Physiol. 2004 Apr;286(4):L801-7.
Miller LA, Wert SE, Clark JC, Xu Y, Perl AK, Whitsett JA. Role of Sonic hedgehog in patterning of tracheal-bronchial cartilage and the peripheral lung. Dev Dyn. 2004 Sep;231(1):57-71.
Wan H, Xu Y, Ikegami M, Stahlman MT, Kaestner KH, Ang SL, et al. Foxa2 is required for transition to air breathing at birth. Proc Natl Acad Sci USA. 2004 Oct 5;101(40):14449-54.
Contact Us
For more information about the Division of Biomedical Informatics, contact John Hutton, MD, director, 513-636-2051.
