OHSU

User Publications

2013

  • Iancu OD, Oberbeck D, Darakjian P, Metten P, McWeeney S, Crabbe JC, Hitzemann R. Selection for drinking in the dark alters brain gene coexpression networks. Alcohol Clin Exp Res 2013 Aug;37(8):1295-303. PubMed Link for this Article

  • Iancu OD, Oberbeck D, Darakjian P, Kawane S, Erk J, et al. Differential Network Analysis Reveals Genetic Effects on Catalepsy Modules. PLoS ONE 2013 8(3): e58951. PubMed Link for this Article

  • Davis MJ, Iancu OD, Acher FC, Stewart BM, Eiwaz MA, Duvoisin RM, Raber J. 2013. Role of mGlu4 in Acquisition of Fear Learning and Memory. Neuropharmacology 2012 March; 66:365-72. PubMed Link for this Article

2012

  • Iancu, O., Kawame, S., Bottomly, D., Searles, R., Hitzemann, R., and McWeeney, S. Utilizing RNA-Seq data for de Novo coexpression network inference.  Bioinformatics 2012 28: 1598- 1603. PubMed Link for this Article

  • O'Tierney, P.F., Lewis, R.M., McWeeney S.K., Hanson, M.A., Inskip, H.M., Morgan, T.K., Barker, D.J., Bagby, G., Cooper, C., Godfrey, K.M., Thornburg, K.L.  Immune response gene profiles in the term placenta depend upon maternal muscle mass.  Reprod Sci 2012. Epub ahead of print.  Pubmed Link for this abstract

  • Sampath H, Vartanian V, Rollins MR, Sakumi K, Nakabeppu Y, Lloyd RS. 8-Oxoguanine DNA Glycosylase (OGG1) Deficiency Increases Susceptibility to
    Obesity and Metabolic Dysfunction.
    PLoS One. 2012;7(12):e51697. PubMed Link for this Abstract

2011

  • Bishop CV, Bogan RL, Hennebold JD, Stouffer RL.  Analysis of microarray data from the macaque corpus luteum; the search for common themes in primate luteal regression.  Molecular Human Reproduction 2011 17(3): 143-151. PubMed Abstract for this article

  • Bottomly D, Walter NAR, Hunter JE, Darakjian P, Kawane S,  Buck KJ, Searles RP, Mooney M, McWeeney S, Hitzemann R.  Evaluating Gene Expression in C57BL/6J and DBA/2J Mouse Striatum Using RNASeqand Microarrays. PLoS ONE 2011 6(3). PubMed abstract for this article
  • Johnson EC, Doser TA, Cepurna WO, Dyck JA, Jia L, Guo Y, Lambert WS, Morrison JC.  Cell proliferation and interleukin-6-type cytokine signaling are implicated by gene expression responses in early optic nerve head injury in rat glaucoma.  Invest Ophthalmol Vis Sci. 2011 Jan 25;52(1):504-18. PubMed abstract for this article

  • Wahl-Jensen V, Kurz S, Feldmann F, Buehler LK, Kindrachuk J, Kindrachuk J, DeFilippis V, da Silva Correia J, Fruh K, Kuhn JH, Burton DR, Feldmann H.  Ebola Virion Attachment and Entry into Human Macrophages ProfoundlyEffects Early Cellular Gene Expression. PLoS Negl Trop Dis. 2011 5(10). PubMed abstract for this article

2010

  • Morimoto-Tochigi A, Walkup RD, Nakajima E, Shearer TR, Azuma M.  Mechanism for carbachol-induced secretion of lacritin in cultured monkey lacrimal acinar cells.  Invest Ophthalmol Vis Sci. 2010 Apr 7.  PubMed abstract for this article

2009

 

2008

  • Bogan RL, Murphy MJ, Stouffer RL, Hennebold JD.  Systematic determination of differential gene expression in the primate corpus luteum during the luteal phase of the menstrual cycle. Mol. Endocrinol. 2008 May;22(5):1260-73. Epub 2008 Feb 7.  PubMed abstract for this article
  • Choi D, Appukuttan B, Binek SJ, Planck SR, Stout JT, Rosenbaum JT, Smith JR. Prediction of Cis-Regulatory Elements Controlling Genes Differentially Expressed by Retinal and Choroidal Vascular Endothelial Cells. J Ocul Biol Dis Infor. 2008;1(1):37-45. PubMed abstract for this article
  • De La Chesnaye, E., Kerr, B., Paredes, A., Merchant_Larios, H., Mendez, JP, and Ojeda, SR. Fbxw15/Fbxo12J Is an F-Box Protein-Encoding Gene Selectively Expressed in Oocytes of the Mouse Ovary.  Biol Reprod 2008 Apr;78(4):714-25. Epub 2007 Dec 19.  PubMed abstract for this article
  • Farley SM, Purdy DE, Ryabinina OP, Schneider P, Magun BE, Iordanov MS.  Fas ligand-induced proinflammatory transcriptional responses in reconstructed human epidermis. Recruitment of the epidermal growth factor receptor and activation of MAP kinases.  J Biol Chem. 2008 Jan 11;283(2):919-28. Epub 2007 Oct 31.  PubMed abstract for this article
  • Orzechowska BU, Powers MF, Sprague J, Li H, Yen B, Searles RP, Axthelm MK, and Wong SW.  Rhesus macaque rhadinovirus-associated non-Hodgkin lymphoma: animal model for KSHV-associated malignancies.  Blood.  2008 Nov 15;112(10):4227-34. Epub 2008 Aug 29.  PubMed abstract for this article
  • Parent AS, Matagne V, Westphal M, Heger S, Ojeda S, Jung H.  Gene expression profiling of hypothalamic hamartomas: a search for genes associated with central precocious puberty.  Horm Res 2008; 69(2):114-23.  PubMed abstract for this article
  • Pelz CR, Kulesz-Martin M, Bagby G, Sears RC.  Global rank-invariant set normalization (GRSN) to reduce systematic distortions in microarray data.  BMC Bioinformatics. 2008 Dec 4;9:520.  PubMed abstract for this article
  • Ruby CE, Montler R, Shu S, Weinberg AD.  IL-12 is required for anti-OX40-mediated CD4 T cell survival.  J Immunol.  2008 180(4): 2140-8.  PubMed abstract for this article
  • Sitzmann BD, Lemos DR, Ottinger MA, Urbanski, HF.  Effects of age on clock gene expression in the rhesus macaque pituitary gland.  Neurobiol Aging 2008 Jul 7.  PubMed abstract for this article
  • Shaut CA, Keene DR, Sorensen LK, Li DY, Stadler HS.  HOXA13 Is essential for placental vascular patterning and labyrinth endothelial specification.  PLoS Genet. 2008 May 16;4(5):e1000073.  PubMed abstract for this article
  • Wilmot B, McWeeney SK, Nixon RR, Montine TJ, Laut J, Harrington CA, Kaye JA, and Kramer PL. Translational gene mapping of cognitive decline.  Neurobiol Aging.  2008 Apr;29(4):524-41. Epub 2006 Dec 14.  PubMed abstract for this article


2007

 

2006

  • DeFilippis, V.R., Robinson, B., Keck, T.M., Hansen, S.G., Nelson, J.A. and Früh, K.  Interferon regulatory factor 3 is necessary for induction of antiviral genes during human cytomegalovirus infectionJ Virol 2006 Jan; 80(2), 1032-1037.  PubMed abstract for this article
  • Farley SM, Dotson AD, Purdy DE, Sundholm AJ, Schneider P, Magun BE, Iordanov MS.  Fas ligand elicits a caspase-independent proinflammatory response in human keratinocytes: implications for dermatitis.  J Invest Dermatol. 2006 Nov;126(11):2438-51. Epub 2006 Jul 20.  PubMed abstract for this article
  • Huster D, Finegold MJ, Morgan CT, Burkhead JL, Nixon R, Vanderwerf SM, Gilliam CT, Lutsenko S.  Consequences of copper accumulation in the livers of the Atp7b-/- (Wilson disease gene) knockout mice.  Am J Pathol. 2006 Feb;168(2):423-34.  PubMed abstract for this article
  • Kuninger, D., Stewart, A. and Rotwein, P. Muscle cell survival mediated by the transcriptional co-activators p300 and PCAF displays different requirements for acetyl-transferase activity. Am J Physiol Cell Physiol. 2006 Oct;291(4):C699-709. Epub 2006 May 3.  Pubmed abstract for this article

 

2005

  • Crossman LC, Mori M, Hsieh YC, Lange T, Paschka P, Harrington CA, Krohn K, Niederwieser DW, Hehlmann R, Hochhaus A, Druker BJ, Deininger MW.  In chronic myeloid leukemia white cells from cytogenetic responders and non-responders to imatinib have very similar gene expression signatures. Haematologica 2005 Apr;90(4):459-64  PubMed abstract for this article
  • Fang Y, Choi D, Searles RP, Mathers WD  A time course microarray study of gene expression in the mouse lacrimal gland after acute corneal trauma.  Invest Ophthalmol Vis Sci 2005 Feb; 46(2):461-9.  PubMed abstract for this article
  • Howie HL, Glogauer M, So M.. The N. gonorrhoeae Type IV Pilus Stimulates Mechanosensitive Pathways and Cytoprotection through a pilT-Dependent Mechanism. PLoS Biol. 2005 Apr;3(4):e100. Epub 2005 Mar 22.  PubMed abstract for this article
  • Johnson J, Lagowski J, Sundberg A, Kulesz-Martin M.  P53 family activities in development and cancer: relationship to melanocyte and keratinocyte carcinogenesis.  J Invest Dermatol. 2005 Nov;125(5):857-64.  PubMed record for this article 
  • Raggo C, Ruhl R, McAllister S, Koon H, Dezube BJ, Fruh K, Moses AV. Novel cellular genes essential for transformation of endothelial cells by Kaposi's sarcoma-associated herpesvirus. Cancer Research 2005 Jun 15;65(12):5084-95  PubMed abstract for this article
  • Xu J, Stouffer RL, Searles RP, Hennebold JD  Discovery of LH-regulated genes in the primate corpus luteum.  Mol Hum Reprod. 2005 Mar;11(3):151-9. Epub 2005 Feb 21.   PubMed abstract for this article

 

2004

  • Hitzemann R, Reed C, Malmanger B, Lawler M, Hitzemann B, Cunningham B, McWeeney S, Belknap J, Harrington C, Buck K, Phillips T, Crabbe J.  On the integration of alcohol-related quantitative trait loci and gene expression analyses.   Alcohol Clin Exp Res. 2004 Oct;28(10):1437-48.  PubMed abstract for this article
  • Impey S, McCorkle SR, Cha-Molstad H, Dwyer JM, Yochum GS, Boss JM, McWeeney S, Dunn JJ, Mandel G, Goodman RH.  Defining the CREB regulon: a genome-wide analysis of transcription factor regulatory regions. Cell. 2004 Dec 29;119(7):1041-54 PubMed abstract for this article
  • Kuninger D, Kuzmickas R, Peng B, Pintar JE, Rotwein P.  Gene discovery by microarray: identification of novel genes induced during growth factor-mediated muscle cell survival and differentiation.  Genomics. 2004 Nov;84(5):876-89.  PubMed abstract for this article
  • Nakajima E, Nakajima T, Minagawa Y, Shearer TR, Azuma M.  Contribution of ROCK in contraction of trabecular meshwork: proposed mechanism for regulating aqueous outflow in monkey and human eyes.  J Pharm Sci. 2005 Apr; 94(4):701-8.  PubMed abstract for this article
  • Reddy PH, McWeeney S, Park BS, Manczak M, Gutala RV, Partovi D, Jung Y, Yau V, Searles R, Mori M, Quinn J.  Gene expression profiles of transcripts in amyloid precursor protein transgenic mice: up-regulation of mitochondrial metabolism and apoptotic genes is an early cellular change in Alzheimer's disease.  Hum Mol Genet. 2004 Jun 15;13(12):1225-40.
    PubMed abstract for this article
  • Stenzel-Poore MP, Stevens SL, Simon RP.. Genomics of preconditioning. Stroke 2004 Nov;35(11 Suppl 1):2683-6. Epub 2004 Sep 30.  PubMed abstract for this article
  • Weinberg AD, Evans DE, Thalhofer C, Shi T, Prell RA.  The generation of T cell memory: a review describing the molecular and cellular events following OX40 (CD134) engagement. J Leukoc Biol. 2004 Jun;75(6):962-72. Epub 2004 Mar 02.  PubMed abstract for this article

 

2003

  • Belusko PB, Nakajima T, Azuma M, Shearer TR  Expression changes in mRNAs and mitochondrial damage in lens epithelial cells with selenite.  Biochim Biophys Acta. 2003 Oct 13;1623(2-3):135-42.  PubMed abstract for this article
  • Fass DM, Butler JE, Goodman RH  Deacetylase activity is required for cAMP activation of a subset of CREB target genes.  J Biol Chem. 2003 Oct 31; 278(44):43014-9. Epub 2003 Aug. PubMed abstract for this article
  • Hitzemann R, Malmanger B, Reed C, Lawler M, Hitzemann B, Coulombe S, Buck K, Rademacher B, Walter N, Polyakov Y, Sikela J, Gensler B, Burgers S, Williams RW, Manly K, Flint J, Talbot C.  A strategy for the integration of QTL, gene expression, and sequence analyses.  Mamm Genome. 2003 Nov;14(11):733-47.  PubMed abstract for this article
  • Prell C, Evans DE, Thalfhofer C, Shi T, Funatake C, Weinberg AD.  OX40-mediated memory T cell generation is TNF receptor-associated factor 2 dependent.  J Immunol. 2003 171, 5997-6005.  PubMed abstract for this article
  • Stenzel-Poore MP, Stevens SL, Xiong Z, Lessov NS, Harrington CA, Mori M, Meller R, Rosenzweig HL, Tobar E, Shaw TE, Chu X, Simon RP.  Effect of ischaemic preconditioning on genomic response to cerebral ischaemia: similarity to neuroprotective strategies in hibernation and hypoxia-tolerant states.  Lancet. 2003 Sep 27;362(9389):1028-37.  PubMed abstract for this article

 

2002

  • Moses AV, Jarvis MA, Raggo C, Bell YC, Ruhl R, Luukkonen BG, Griffith DJ, Wait CL, Druker BJ, Heinrich MC, Nelson JA, Fruh K.  A functional genomics approach to Kaposi's sarcoma.  Ann N Y Acad Sci. 2002 Dec;975:180-91.  PubMed abstract for this article
  • Tian W, Cohen DM.  Urea stress more akin to epidermal growth factor exposure than to hypertonic stress in renal medullary cells.  Am J Physiol Renal Physiol. 2002 Sep;283(3):F388-98.  PubMed abstract for this article
  • Wang Z, Liu Y, Mori M, Kulesz-Martin M  Gene expression profiling of initiated epidermal cells with benign or malignant tumor fates.  Carcinogenesis. 2002 Apr;23(4):635-43.  PubMed abstract for this article.