Biomedical Informatics, 2007
This page lists 2007 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.
Liu X, Jessen WJ, Sivaganesan S, Aronow BJ, Medvedovic M. Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data. BMC bioinformatics. 2007;8:283.
Wells JM, Esni F, Boivin GP, Aronow BJ, Stuart W, Combs C, et al. Wnt/beta-catenin signaling is required for development of the exocrine pancreas. BMC developmental biology. 2007;7:4.
Liu C, Aronow BJ, Jegga AG, Wang N, Miethke A, Mourya R, et al. Novel resequencing chip customized to diagnose mutations in patients with inherited syndromes of intrahepatic cholestasis. Gastroenterology. 2007 Jan;132(1):119-26.
Bosco EE, Wang Y, Xu H, Zilfou JT, Knudsen KE, Aronow BJ, et al. The retinoblastoma tumor suppressor modifies the therapeutic response of breast cancer. The Journal of clinical investigation. 2007 Jan;117(1):218-28.
Liang Y, Jansen M, Aronow B, Geiger H, Van Zant G. The quantitative trait gene latexin influences the size of the hematopoietic stem cell population in mice. Nature genetics. 2007 Feb;39(2):178-88.
Schleiss MR, Aronow BJ, Handwerger S. Cytomegalovirus Infection of Human Syncytiotrophoblast Cells Strongly Interferes with Expression of Genes Involved in Placental Differentiation and Tissue Integrity. Pediatr Res. 2007 Mar 15.
Deane NG, Manning HC, Foutch AC, Washington MK, Aronow BJ, Bornhop DJ, et al. Targeted imaging of colonic tumors in smad3-/- mice discriminates cancer and inflammation. Mol Cancer Res. 2007 Apr;5(4):341-9.
Wong HR, Shanley TP, Sakthivel B, Cvijanovich N, Lin R, Allen GL, Thomas NJ, Doctor A, Kalyanaraman M, Tofil NM, Penfil S, Monaco M, Tagavilla MA, Odoms K, Dunsmore K, Barnes M, Aronow BJ. Genome-level expression profiles in pediatric septic shock indicate a role for altered zinc homeostasis in poor outcome. Physiol Genomics. 2007 Jul 18;30(2):146-55.
Deichmann A, Hacein-Bey-Abina S, Schmidt M, Garrigue A, Brugman MH, Hu J, Glimm H, Gyapay G, Prum B, Fraser CC, Fischer N, Schwarzwaelder K, Siegler ML, de Ridder D, Pike-Overzet K, Howe SJ, Thrasher AJ, Wagemaker G, Abel U, Staal FJ, Delabesse E, Villeval JL, Aronow B, et al. Vector integration is nonrandom and clustered and influences the fate of lymphopoiesis in SCID-X1 gene therapy. The Journal of clinical investigation. 2007 Aug;117(8):2225-32.
Oka T, Xu J, Kaiser RA, Melendez J, Hambleton M, Sargent MA, Lorts A, Brunskill EW, Dorn GW, Conway SJ, Aronow BJ, et al. Genetic manipulation of periostin expression reveals a role in cardiac hypertrophy and ventricular remodeling. Circ Res. 2007 Aug 3;101(3):313-21.
Shanley TP, Cvijanovich N, Lin R, Allen GL, Thomas NJ, Doctor A, Kalyanaraman M, Tofil NM, Penfil S, Monaco M, Odoms K, Barnes M, Sakthivel B, Aronow BJ, et al. Genome-level longitudinal expression of signaling pathways and gene networks in pediatric septic shock. Mol Med. 2007 Sep-Oct;13(9-10):495-508.
Jeong JW, Lee KY, Han SJ, Aronow BJ, Lydon JP, O'Malley BW, et al. The p160 steroid receptor coactivator 2, SRC-2, regulates murine endometrial function and regulates progesterone-independent and -dependent gene expression. Endocrinology. 2007 Sep;148(9):4238-50.
Mayhew CN, Carter SL, Fox SR, Sexton CR, Reed CA, Srinivasan SV, Liu X, Wikenheiser-Brokamp K, Boivin GP, Lee JS, Aronow BJ, et al. RB loss abrogates cell cycle control and genome integrity to promote liver tumorigenesis. Gastroenterology. 2007 Sep;133(3):976-84.
Banach-Petrosky W, Jessen WJ, Ouyang X, Gao H, Rao J, Quinn J, Aronow BJ, et al. Prolonged exposure to reduced levels of androgen accelerates prostate cancer progression in Nkx3.1; Pten mutant mice. Cancer Res. 2007 Oct 1;67(19):9089-96.
Chen J, Xu H, Aronow BJ, Jegga AG. Improved human disease candidate gene prioritization using mouse phenotype. BMC bioinformatics. 2007;8:392.
Heineke J, Auger-Messier M, Xu J, Oka T, Sargent MA, York A, Klevitsky R, Vaikunth S, Duncan SA, Aronow BJ, et al. Cardiomyocyte GATA4 functions as a stress-responsive regulator of angiogenesis in the murine heart. The Journal of clinical investigation. 2007 Nov;117(11):3198-210.
Hall ES, Thornton SN. Extracting nursing practice patterns from structured labor and delivery data sets. AMIA Annu Symp Proc. 2007:309-13.
Kaiser S, Park YK, Franklin JL, Halberg RB, Yu M, Jessen WJ, Freudenberg J, Chen X, Haigis K, Jegga AG, et al. Transcriptional recapitulation and subversion of embryonic colon development by mouse colon tumor models and human colon cancer. Genome Biol. 2007;8(7):R131.
Jegga AG, Chen J, Gowrisankar S, Deshmukh MA, Gudivada R, Kong S, et al. GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs. Nucleic acids research. 2007 Jan;35(Database issue):D116-21.
Jegga AG, Gowrisankar S, Chen J, Aronow BJ. PolyDoms: a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease. Nucleic acids research. 2007 Jan;35(Database issue):D700-6.
Diwan A, Koesters AG, Odley AM, Pushkaran S, Baines CP, Spike BT, Daria D, Jegga AG, et al. Unrestrained erythroblast development in Nix-/- mice reveals a mechanism for apoptotic modulation of erythropoiesis. Proceedings of the National Academy of Sciences of the United States of America. 2007 Apr 17;104(16):6794-9.
Markey MP, Bergseid J, Bosco EE, Stengel K, Xu H, Mayhew CN, Schwemberger SJ, Braden WA, Jiang Y, Babcock GF, Jegga AG, Aronow BJ, et al. Loss of the retinoblastoma tumor suppressor: differential action on transcriptional programs related to cell cycle control and immune function. Oncogene. 2007 Apr 23.
Flores SC, Lu LJ, Yang J, Carriero N, Gerstein MB. Hinge Atlas: relating protein sequence to sites of structural flexibility. BMC bioinformatics. 2007;8:167.
Lu LJ, Sboner A, Huang YJ, Lu HX, Gianoulis TA, Yip KY, et al. Comparing classical pathways and modern networks: towards the development of an edge ontology. Trends Biochem Sci. 2007 Jul;32(7):320-31.
Wu L, Hwang SI, Rezaul K, Lu LJ, Mayya V, Gerstein M, et al. Global survey of human T leukemic cells by integrating proteomics and transcriptomics profiling. Mol Cell Proteomics. 2007 Aug;6(8):1343-53.
Song Y, He F, Xie G, Guo X, Xu Y, Chen Y, Liang X, Stagljar I, Egli D, Ma J, et al. CAF-1 is essential for Drosophila development and involved in the maintenance of epigenetic memory. Dev Biol. 2007 Nov 1;311(1):213-22.
Hardie WD, Korfhagen TR, Sartor MA, Prestridge A, Medvedovic M, Le Cras TD, et al. Genomic profile of matrix and vasculature remodeling in TGF-alpha induced pulmonary fibrosis. Am J Respir Cell Mol Biol. 2007 Sep;37(3):309-21.
Popa I, Zubkova I, Medvedovic M, Romantseva T, Mostowski H, Boyd R, et al. Regeneration of the adult thymus is preceded by the expansion of K5+K8+ epithelial cell progenitors and by increased expression of Trp63, cMyc and Tcf3 transcription factors in the thymic stroma. Int Immunol. 2007 Nov;19(11):1249-60.
Ganguly K, Stoeger T, Wesselkamper SC, Reinhard C, Sartor MA, Medvedovic M, et al. Candidate genes controlling pulmonary function in mice: transcript profiling and predicted protein structure. Physiol Genomics. 2007 Nov 14;31(3):410-21.
Duch W, Swaminathan K, Meller J. Artificial intelligence approaches for rational drug design and discovery. Curr Pharm Des. 2007;13(14):1497-508.
Sinha AU, Meller J. Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms. BMC bioinformatics. 2007;8:82.
Cushion MT, Smulian AG, Slaven BE, Sesterhenn T, Arnold J, Staben C, Porollo A, Adamczak R, Meller J. Transcriptome of Pneumocystis carinii during Fulminate Infection: Carbohydrate Metabolism and the Concept of a Compatible Parasite. PLoS ONE. 2007;2:e423.
Porollo A, Meller J. Prediction-based fingerprints of protein-protein interactions. Proteins. 2007 Feb 15;66(3):630-45.
Porollo A, Meller J. Versatile annotation and publication quality visualization of protein complexes using POLYVIEW-3D. BMC bioinformatics. 2007;8:316.
Howarth JW, Meller J, Solaro RJ, Trewhella J, Rosevear PR. Phosphorylation-dependent conformational transition of the cardiac specific N-extension of troponin I in cardiac troponin. J Mol Biol. 2007 Oct 26;373(3):706-22.
Duch W, Matykiewicz P, Pestian J. Neurolinguistic approach to vector representation of medical concepts. IJCNN; 2007. p. 3110-15.
Pestian J, Brew C, Matykiewicz P, Hovermale DJ, Johnson N, Cohen KB, et al. A shared task involving multi-label classification of clinical free text. Proceedings of ACL BioNLP; 2007; Prague. p. 36-40.
Duch W, Matykiewicz P, Pestian J. Towards understanding of natural language: neurocognitive inspirations. Lecture notes in computer science. 2007:953-62.
Rajan J, Davis KC, Matykiewicz P, Duch W, Pestian JP. Medical acronym disambiguation using online sources. Enterprise Information Systems and Web Technologies 2007:123-30.
Stahlman MT, Besnard V, Wert SE, Weaver TE, Dingle S, Xu Y, et al. Expression of ABCA3 in developing lung and other tissues. J Histochem Cytochem. 2007 Jan;55(1):71-83.
Metzger DE, Xu Y, Shannon JM. Elf5 is an epithelium-specific, fibroblast growth factor-sensitive transcription factor in the embryonic lung. Dev Dyn. 2007 May;236(5):1175-92.
