OHSU

User Publications

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

  • Bethea, Cynthia L, Reddy, Arubala P, Pedersen, Darlene, and Tokuyama, Yukari.  Expression profile of differentiating serotonin neurons derived from rhesus embryonic stem cells and comparison to adult serotonin neurons.  Gene Expression Patterns, February 2009, Pages 94-108.  PubMed abstract for this article
  • Bishop, CV, Hennebold, JD, and Stouffer, RL.  The effects of luteinizing hormone ablation/replacement versus steroid ablation/replacement on gene expression in the primate corpus leteum.  Mol Hum Reprod.  2009 Mar; 15(3):181-93.  Epub 2009 Jan 24.  PubMed abstract for this article
  • Bogan RL, Murphy MJ, Hennebold JD.  Dynamic changes in gene expression that occur during the period of spontaneous functional regression in the rhesus macaque corpus luteum.  Endocrinology. 2009 Mar;150(3):1521-9. Epub 2008 Oct 23.  PubMed abstract for this article
  • Marsh BJ, Stevens SL, Hunter B, Stenzel-Poore MP. Inflammation and the emerging role of the toll-like receptor system in acute brain ischemia.  Stroke. 2009 Mar;40(3 Suppl):S34-7. Epub 2008 Dec 8.  PubMed abstract for this article
  • Marsh B, Stevens SL, Packard AE, Gopalan B, Hunter B, Leung PY, Harrington CA, Stenzel-Poore MP.  Systemic lipopolysaccharide protects the brain from ischemic injury by reprogramming the response of the brain to stroke: a critical role for IRF3.  J Neurosci. 2009 Aug 5;29(31):9839-49.  PubMed abstract for this article
  • Noriega NC, Eghlidi DH, Garyfallou VT, Kohama SG, Kryger SG, Urbanski HF.Influence of 17beta-estradiol and progesterone on GABAergic gene expression inthe arcuate nucleus, amygdala and hippocampus of the rhesus macaque. Brain Res.2009 Oct 13. PubMed abstract for this article
  • Noriega NC, Kohama SG, Urbanski HF. Gene expression profiling in the rhesus macaque: methodology, annotation and data interpretation. Methods. 2009 Sep;49(1):42-9. Epub 2009 May 23 PubMed abstract for this article
  • Pejovic T, Pande NT, Mori M, Mhawech-Fauceglia P, Harrington C, Mongoue-Tchokote S, Dim D, Andrews C, Beck A, Tarumi Y, Djilas J, Cappuccini F, Caballero O, Huang J, Levy S, Tsiamouri A, Cain J, Bagby GC, Strausberg RL, Simpson AJ, Odunsi KO.  Expression profiling of the ovarian surface kinome reveals candidate genes for early neoplastic changes.  Transl Oncol. 2009 Dec;2(4):341-9.  PubMed abstract for this article
  • Rosenbaum JT, Pasadhika S, Crouser ED, Choi D, Harrington CA, Lewis JA, Austin CR, Diebel TN, Vance EE, Braziel RM, Smith JR, Planck SR.  Hypothesis: sarcoidosis is a STAT-1mediated disease.  Clin Immunol.  2009 Aug; 132(2):174-83.  PubMed abstract for this article
  • Urbanski HF, Noriega NC, Lemos DR, Kohama SG. Gene expression profiling in therhesus macaque: experimental design considerations. Methods. 2009 Sep;49(1):26-31. Epub 2009 May 23 PubMed abstract for this article
  • Vanderwerf SM, Svahn J, Olson S, Rathbun RK, Harrington C, Yates J, Keeble W, Anderson DC, Anur P, Pereira NF, Pilonetto DV, Pasquini R, Bagby GC.  TLR8-dependent TNF-(alpha) overexpression in Fanconi anemia group C cells.  Blood. 2009 Dec 17;114(26):5290-8. Epub 2009 Oct 22.  PubMed abstract for this article
  • Vartanian K.A., Slottke R, Johnstone, T, Casale, A, Planck, S.R., Choi, D. Smith, J.R., Rosenbaum, J.T., and Harrington, C.A.  Gene expression profiling of whole blood: Comparison of target preparation methods for accurate and reproducible microarray analysis. BMC Genomics 2009,10:2. doi 10.1186/1471-2164-10-2.  PubMed abstract for this article
  • Walter NAR, Bottomly D, Laderas T, Mooney MA, Darakjian P, Searles RP, Harrington CA, McWeeney SK, Hitzemann, R, Buck, KJ.  High throughput sequencing in mice: a platform comparison identifies a preponderance of cryptic SNPs. 2009.  BMC Genomics 10, 379. PubMed abstract for this article

 

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

  • Byrne, JA, Pedersen, DA, Clepper, LL, Nelson, M, Sanger, WG, Gokhale, S., Wolf, DP and Mitalipov, SM.  Producing primate embryonic stem cells by somatic cell nuclear transfer.Nature.  2007 Nov 22;450(7169):497-502. Epub 2007 Nov 14.  PubMed abstract for this article
  • Cheng J, Alkayed NJ, Hurn PD.Deleterious effects of dihydrotestosterone on cerebral ischemic injury. J Cereb Blood Flow Metab. 2007 Sep;27(9):1553-62. Epub 2007 Feb 21. PubMed abstract for this article
  • Fish, D.J., Horne, T.M., Brewood, G.P., Goodarzi, J.P., Alemayehu, S., Bhandiwad, A., Searles, R.P., and Benight, A.S.  DNA multiplex hybridization on microarrays and thermodynamic stability in solution: a direct comparison.  Nucleic Acids Res., 2007;35(21):7197-208. Epub 2007 Oct 18.  PubMed abstract for this article
  • Fish, D.J., Horne, T.M., Searles, R.P., Brewood, G.P., and Benight, A.S.  Mulitplex SNP Discrimination.  Biophys. J., 2007 May 15;92(10):L89-91. Epub 2007 Mar 16.  PubMed abstract for this article
  • Li, Yanping, Zeng, Shelya X., Landais, Igor, and Lu, Hua.  Human SSRP1 has spt16-dependent and –independent roles in gene transcription.  J Biol Chem, 2007 Mar 9;282(10):6936-45. Epub 2007 Jan 5.  PubMed abstract for this article
  • Rose, PP, Carroll, JM, Carroll, PA, Defilippis, VR, Lagunoff, M, Moses, AV, Roberts, CT, Jr. and Fruh, K. The insulin receptor is essential for virus-induced tumorigenesis of Kaposi's sarcoma.  Oncogene 2007 Mar; 26(14):1995-2005.  Epub 2006 Sep 25.  PubMed abstract for this article 
  • Redmond WL, Gough MJ, Charbonneau B, Ratliff TL, Weinberg AD.  Defects in the acquisition of CD8 T cell effector function after priming with tumor or soluble antigen can be overcome by the addition of an OX40 agonist.  J Immunol.  2007 179(11):7244-53. PubMed abstract for this article
  • Smith JR, Choi D, Chipps TJ, Pan Y, Zamora DO, Davies MH, Babra B, Powers MR, Planck SR, Rosenbaum JT. Unique gene expression profiles of donor-matched human retinal and choroidal vascular endothelial cells. Invest Ophthalmol Vis Sci. 2007 Jun;48(6):2676-84.  PubMed abstract for this article
  • Streblow, DN, van Cleef, KWR., Kreklywich, CN, Meyer, C., Smith, P, Defilippis, V, Grey, F, Früh, K, Searles, R, Bruggeman, C, Vink, C, Nelson, JA, and Orloff, SL. Rat cytomegalovirus gene expression in cardiac allograft recipients is tissue specific and does not parallel the profiles detected in vitro.  J. Virol. 2007 Apr;81(8):3816-26. Epub 2007 Jan 24.  PubMed abstract for this article
  • Walter NA, McWeeney SK, Peters ST, Belknap JK, Hitzemann R, Buck KJ.SNPs matter: impact on detection of differential expression. Nat Methods. 2007 Sep;4(9):679-80.  PubMed abstract for this article
  • Wong J, Korcheva V, Jacoby DB, Magun BE.  Proinflammatory responses of human airway cells to ricin involve stress-activated protein kinases and NF-kappaB.  Am J Physiol Lung Cell Mol Physiol. 2007 Dec;293(6):L1385-94. Epub 2007 Sep 14.  PubMed abstract for this article
  • Wong J, Korcheva V, Jacoby DB, Magun B.  Intrapulmonary delivery of ricin at high dosage triggers a systemic inflammatory response and glomerular damage.  Am J Pathol. 2007 May;170(5):1497-510.  PubMed abstract for this article

 

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 infection.  J 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.