VMSR Publications

The following manuscripts utilized the VMSR for generation of microarray data. If you know of a publication not on this list or have collaborated with the VMSR for production of data, please contact us with the details of of your submissions.

If you have questions regarding how to acknowledge the VMSR for any involvement in data production, please use this summary or contact Dr. Shawn Levy with any other needs.

Supplemental Data for some of these papers can be found here

  1. Manicassamy S, Ravindran R, Deng J, Oluoch H, Denning TL, Kasturi SP, Rosenthal KM, Evavold BD, Pulendran B
    Toll-like receptor 2-dependent induction of vitamin A-metabolizing enzymes in dendritic cells promotes T regulatory responses and inhibits autoimmunity.
    Nat Med. 2009 Apr; 15(4):401-9 [Epub 2009 Mar 1]
  2. Zheng W, Long J, Gao YT, Li C, Zheng Y, Xiang YB, Wen W, Levy S, Deming SL, Haines JL, Gu K, Fair AM, Cai Q, Lu W, Shu XO
    Genome-wide association study identifies a new breast cancer susceptibility locus at 6q25.1.
    Nat Genet. 2009 Mar; 41(3):324-8 [Epub 2009 Feb 15]
  3. Maher CA, Kumar-Sinha C, Cao X, Kalyana-Sundaram S, Han B, Jing X, Sam L, Barrette T, Palanisamy N, Chinnaiyan AM
    Transcriptome sequencing to detect gene fusions in cancer.
    Nature. 2009 Mar 5; 458(7234):97-101 [Epub 2009 Jan 11]
  4. Derrick KL, Norbury K, Kieswetter K, Skaf J, McNulty AK
    Comparative analysis of global gene expression profiles between diabetic rat wounds treated with vacuum-assisted closure therapy, moist wound healing or gauze under suction.
    Int Wound J. 2008 Dec; 5(5):615-24
  5. Crawford LA, Guney MA, Oh YA, Deyoung RA, Valenzuela DM, Murphy AJ, Yancopoulos GD, Lyons KM, Brigstock DR, Economides A, Gannon M
    Connective tissue growth factor (CTGF) inactivation leads to defects in islet cell lineage allocation and beta-cell proliferation during embryogenesis.
    Mol Endocrinol. 2009 Mar; 23(3):324-36 [Epub 2009 Jan 8]
  6. Yang TL, Chen XD, Guo Y, Lei SF, Wang JT, Zhou Q, Pan F, Chen Y, Zhang ZX, Dong SS, Xu XH, Yan H, Liu X, Qiu C, Zhu XZ, Chen T, Li M, Zhang H, Zhang L, Drees BM, Hamilton JJ, Papasian CJ, Recker RR, Song XP, Cheng J, Deng HW
    Genome-wide copy-number-variation study identified a susceptibility gene, UGT2B17, for osteoporosis.
    Am J Hum Genet. 2008 Dec; 83(6):663-74 [Epub 2008 Nov 6]
  7. Qi M, Yang R, Aiken C
    Cyclophilin A-dependent restriction of human immunodeficiency virus type 1 capsid mutants for infection of nondividing cells.
    J Virol. 2008 Dec; 82(24):12001-8 [Epub 2008 Oct 1]
  8. Liu YZ, Wilson SG, Wang L, Liu XG, Guo YF, Li J, Yan H, Deloukas P, Soranzo N, Chinappen-Horsley U, Cervino A, Williams FM, Xiong DH, Zhang YP, Jin TB, Levy S, Papasian CJ, Drees BM, Hamilton JJ, Recker RR, Spector TD, Deng HW
    Identification of PLCL1 gene for hip bone size variation in females in a genome-wide association study.
    PLoS One. 2008 Sep 8; 3(9):e3160
  9. Xu B, Roos JL, Levy S, van Rensburg EJ, Gogos JA, Karayiorgou M
    Strong association of de novo copy number mutations with sporadic schizophrenia.
    Nat Genet. 2008 Jul; 40(7):880-5 [Epub 2008 May 30]
  10. Liu YJ, Liu XG, Wang L, Dina C, Yan H, Liu JF, Levy S, Papasian CJ, Drees BM, Hamilton JJ, Meyre D, Delplanque J, Pei YF, Zhang L, Recker RR, Froguel P, Deng HW
    Genome-wide association scans identified CTNNBL1 as a novel gene for obesity.
    Hum Mol Genet. 2008 Jun 15; 17(12):1803-13 [Epub 2008 Mar 5]
  11. Wilding Crawford L, Tweedie Ables E, Oh YA, Boone B, Levy S, Gannon M
    Gene expression profiling of a mouse model of pancreatic islet dysmorphogenesis.
    PLoS One. 2008 Feb 20; 3(2):e1611
  12. Watson JD, Wang S, Von Stetina SE, Spencer WC, Levy S, Dexheimer PJ, Kurn N, Heath JD, Miller DM 3rd
    Complementary RNA amplification methods enhance microarray identification of transcripts expressed in the C. elegans nervous system.
    BMC Genomics. 2008 Feb 19; 9:84
  13. Koontz T, Bralic M, Tomac J, Pernjak-Pugel E, Bantug G, Jonjic S, Britt WJ
    Altered development of the brain after focal herpesvirus infection of the central nervous system.
    J Exp Med. 2008 Feb 18; 205(2):423-35 [Epub 2008 Feb 11]
  14. Gimelbrant A, Hutchinson JN, Thompson BR, Chess A
    Widespread monoallelic expression on human autosomes.
    Science. 2007 Nov 16; 318(5853):1136-40
  15. Smith JC, Boone BE, Opalenik SR, Williams SM, Russell SB
    Gene profiling of keloid fibroblasts shows altered expression in multiple fibrosis-associated pathways.
    J Invest Dermatol. 2008 May; 128(5):1298-310 [Epub 2007 Nov 8]
  16. Buchanan FG, Holla V, Katkuri S, Matta P, DuBois RN
    Targeting cyclooxygenase-2 and the epidermal growth factor receptor for the prevention and treatment of intestinal cancer.
    Cancer Res. 2007 Oct 1; 67(19):9380-8
  17. Denning TL, Wang YC, Patel SR, Williams IR, Pulendran B
    Lamina propria macrophages and dendritic cells differentially induce regulatory and interleukin 17-producing T cell responses.
    Nat Immunol. 2007 Oct; 8(10):1086-94 [Epub 2007 Sep 16]
  18. Chung CH, Parker J, Levy S, Slebos RJ, Dicker AP, Rodeck U
    Gene expression profiles as markers of aggressive disease-EGFR as a factor.
    Int J Radiat Oncol Biol Phys. 2007; 69(2 Suppl):S102-5
  19. Fox RM, Watson JD, Von Stetina SE, McDermott J, Brodigan TM, Fukushige T, Krause M, Miller DM 3rd
    The embryonic muscle transcriptome of Caenorhabditis elegans.
    Genome Biol. 2007; 8(9):R188
  20. Jia H, King IN, Chopra SS, Wan H, Ni TT, Jiang C, Guan X, Wells S, Srivastava D, Zhong TP
    Vertebrate heart growth is regulated by functional antagonism between Gridlock and Gata5.
    Proc Natl Acad Sci U S A. 2007 Aug 28; 104(35):14008-13 [Epub 2007 Aug 21]
  21. Kaiser S, Park YK, Franklin JL, Halberg RB, Yu M, Jessen WJ, Freudenberg J, Chen X, Haigis K, Jegga AG, Kong S, Sakthivel B, Xu H, Reichling T, Azhar M, Boivin GP, Roberts RB, Bissahoyo AC, Gonzales F, Bloom GC, Eschrich S, Carter SL, Aronow JE, Kleimeyer J, Kleimeyer M, Ramaswamy V, Settle SH, Boone B, Levy S, Graff JM, Doetschman T, Groden J, Dove WF, Threadgill DW, Yeatman TJ, Coffey RJ Jr, Aronow BJ
    Transcriptional recapitulation and subversion of embryonic colon development by mouse colon tumor models and human colon cancer.
    Genome Biol. 2007; 8(7):R131
  22. Von Stetina SE, Watson JD, Fox RM, Olszewski KL, Spencer WC, Roy PJ, Miller DM 3rd
    Cell-specific microarray profiling experiments reveal a comprehensive picture of gene expression in the C. elegans nervous system.
    Genome Biol. 2007; 8(7):R135
  23. Yang L, Amann JM, Kikuchi T, Porta R, Guix M, Gonzalez A, Park KH, Billheimer D, Arteaga CL, Tai HH, DuBois R, Carbone DP, Johnson DH
    Inhibition of epidermal growth factor receptor signaling elevates 15-hydroxyprostaglandin dehydrogenase in non-small-cell lung cancer.
    Cancer Res. 2007 Jun 15; 67(12):5587-93
  24. Joshi S, Davies H, Sims LP, Levy SE, Dean J
    Ovarian gene expression in the absence of FIGLA, an oocyte-specific transcription factor.
    BMC Dev Biol. 2007 Jun 13; 7:67
  25. Perez CA, Ott J, Mays DJ, Pietenpol JA
    p63 consensus DNA-binding site: identification, analysis and application into a p63MH algorithm.
    Oncogene. 2007 Nov 15; 26(52):7363-70 [Epub 2007 Jun 11]
  26. Chin MH, Geng AB, Khan AH, Qian WJ, Petyuk VA, Boline J, Levy S, Toga AW, Smith RD, Leahy RM, Smith DJ
    A genome-scale map of expression for a mouse brain section obtained using voxelation.
    Physiol Genomics. 2007 Aug 20; 30(3):313-21 [Epub 2007 May 15]
  27. Schavolt KL, Pietenpol JA
    p53 and Delta Np63 alpha differentially bind and regulate target genes involved in cell cycle arrest, DNA repair and apoptosis.
    Oncogene. 2007 Sep 13; 26(42):6125-32 [Epub 2007 Apr 2]
  28. Von Stetina SE, Fox RM, Watkins KL, Starich TA, Shaw JE, Miller DM 3rd
    UNC-4 represses CEH-12/HB9 to specify synaptic inputs to VA motor neurons in C. elegans.
    Genes Dev. 2007 Feb 1; 21(3):332-46
  29. Muldowney JA 3rd, Stringham JR, Levy SE, Gleaves LA, Eren M, Piana RN, Vaughan DE
    Antiproliferative agents alter vascular plasminogen activator inhibitor-1 expression: a potential prothrombotic mechanism of drug-eluting stents.
    Arterioscler Thromb Vasc Biol. 2007 Feb; 27(2):400-6 [Epub 2006 Dec 7]
  30. Yazlovitskaya EM, Edwards E, Thotala D, Fu A, Osusky KL, Whetsell WO Jr, Boone B, Shinohara ET, Hallahan DE
    Lithium treatment prevents neurocognitive deficit resulting from cranial irradiation.
    Cancer Res. 2006 Dec 1; 66(23):11179-86
  31. Chung CH, Levy S, Chaurand P, Carbone DP
    Genomics and proteomics: emerging technologies in clinical cancer research.
    Crit Rev Oncol Hematol. 2007 Jan; 61(1):1-25 [Epub 2006 Oct 2]
  32. MAQC Consortium, Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, de Longueville F, Kawasaki ES, Lee KY, Luo Y, Sun YA, Willey JC, Setterquist RA, Fischer GM, Tong W, Dragan YP, Dix DJ, Frueh FW, Goodsaid FM, Herman D, Jensen RV, Johnson CD, Lobenhofer EK, Puri RK, Schrf U, Thierry-Mieg J, Wang C, Wilson M, Wolber PK, Zhang L, Amur S, Bao W, Barbacioru CC, Lucas AB, Bertholet V, Boysen C, Bromley B, Brown D, Brunner A, Canales R, Cao XM, Cebula TA, Chen JJ, Cheng J, Chu TM, Chudin E, Corson J, Corton JC, Croner LJ, Davies C, Davison TS, Delenstarr G, Deng X, Dorris D, Eklund AC, Fan XH, Fang H, Fulmer-Smentek S, Fuscoe JC, Gallagher K, Ge W, Guo L, Guo X, Hager J, Haje PK, Han J, Han T, Harbottle HC, Harris SC, Hatchwell E, Hauser CA, Hester S, Hong H, Hurban P, Jackson SA, Ji H, Knight CR, Kuo WP, LeClerc JE, Levy S, Li QZ, Liu C, Liu Y, Lombardi MJ, Ma Y, Magnuson SR, Maqsodi B, McDaniel T, Mei N, Myklebost O, Ning B, Novoradovskaya N, Orr MS, Osborn TW, Papallo A, Patterson TA, Perkins RG, Peters EH, Peterson R, Philips KL, Pine PS, Pusztai L, Qian F, Ren H, Rosen M, Rosenzweig BA, Samaha RR, Schena M, Schroth GP, Shchegrova S, Smith DD, Staedtler F, Su Z, Sun H, Szallasi Z, Tezak Z, Thierry-Mieg D, Thompson KL, Tikhonova I, Turpaz Y, Vallanat B, Van C, Walker SJ, Wang SJ, Wang Y, Wolfinger R, Wong A, Wu J, Xiao C, Xie Q, Xu J, Yang W, Zhang L, Zhong S, Zong Y, Slikker W Jr
    The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements.
    Nat Biotechnol. 2006 Sep; 24(9):1151-61
  33. Chung CH, Ely K, McGavran L, Varella-Garcia M, Parker J, Parker N, Jarrett C, Carter J, Murphy BA, Netterville J, Burkey BB, Sinard R, Cmelak A, Levy S, Yarbrough WG, Slebos RJ, Hirsch FR
    Increased epidermal growth factor receptor gene copy number is associated with poor prognosis in head and neck squamous cell carcinomas.
    J Clin Oncol. 2006 Sep 1; 24(25):4170-6
  34. Stanwood GD, Parlaman JP, Levitt P
    Genetic or pharmacological inactivation of the dopamine D1 receptor differentially alters the expression of regulator of G-protein signalling (Rgs) transcripts.
    Eur J Neurosci. 2006 Aug; 24(3):806-18
  35. Chung CH, Parker JS, Ely K, Carter J, Yi Y, Murphy BA, Ang KK, El-Naggar AK, Zanation AM, Cmelak AJ, Levy S, Slebos RJ, Yarbrough WG
    Gene expression profiles identify epithelial-to-mesenchymal transition and activation of nuclear factor-kappaB signaling as characteristics of a high-risk head and neck squamous cell carcinoma.
    Cancer Res. 2006 Aug 15; 66(16):8210-8
  36. Acuff HB, Sinnamon M, Fingleton B, Boone B, Levy SE, Chen X, Pozzi A, Carbone DP, Schwartz DR, Moin K, Sloane BF, Matrisian LM
    Analysis of host- and tumor-derived proteinases using a custom dual species microarray reveals a protective role for stromal matrix metalloproteinase-12 in non-small cell lung cancer.
    Cancer Res. 2006 Aug 15; 66(16):7968-75
  37. Barbieri CE, Tang LJ, Brown KA, Pietenpol JA
    Loss of p63 leads to increased cell migration and up-regulation of genes involved in invasion and metastasis.
    Cancer Res. 2006 Aug 1; 66(15):7589-97
  38. Ueda Y, Neel NF, Schutyser E, Raman D, Richmond A
    Deletion of the COOH-terminal domain of CXC chemokine receptor 4 leads to the down-regulation of cell-to-cell contact, enhanced motility and proliferation in breast carcinoma cells.
    Cancer Res. 2006 Jun 1; 66(11):5665-75
  39. Slebos RJ, Yi Y, Ely K, Carter J, Evjen A, Zhang X, Shyr Y, Murphy BM, Cmelak AJ, Burkey BB, Netterville JL, Levy S, Yarbrough WG, Chung CH
    Gene expression differences associated with human papillomavirus status in head and neck squamous cell carcinoma.
    Clin Cancer Res. 2006 Feb 1; 12(3 Pt 1):701-9
  40. Xie L, Xu BJ, Gorska AE, Shyr Y, Schwartz SA, Cheng N, Levy S, Bierie B, Caprioli RM, Moses HL
    Genomic and proteomic analysis of mammary tumors arising in transgenic mice.
    J Proteome Res. 2005 Nov-Dec; 4(6):2088-98
  41. West JD, Marnett LJ
    Alterations in gene expression induced by the lipid peroxidation product, 4-hydroxy-2-nonenal.
    Chem Res Toxicol. 2005 Nov; 18(11):1642-53
  42. Chung CH, Levy S, Yarbrough WG
    Clinical applications of genomics in head and neck cancer.
    Head Neck. 2006 Apr; 28(4):360-8
  43. Statnikov A, Tsamardinos I, Dosbayev Y, Aliferis CF
    GEMS: a system for automated cancer diagnosis and biomarker discovery from microarray gene expression data.
    Int J Med Inform. 2005 Aug; 74(7-8):491-503
  44. Jiang F, Shults K, Flye L, Hashimoto Y, Van Der Meer R, Xie J, Kravtsov V, Price J, Head DR, Briggs RC
    S100P is selectively upregulated in tumor cell lines challenged with DNA cross-linking agents.
    Leuk Res. 2005 Oct; 29(10):1181-90
  45. Touroutine D, Fox RM, Von Stetina SE, Burdina A, Miller DM 3rd, Richmond JE
    acr-16 encodes an essential subunit of the levamisole-resistant nicotinic receptor at the Caenorhabditis elegans neuromuscular junction.
    J Biol Chem. 2005 Jul 22; 280(29):27013-21 [Epub 2005 May 24]
  46. Stanwood GD, Parlaman JP, Levitt P
    Anatomical abnormalities in dopaminoceptive regions of the cerebral cortex of dopamine D1 receptor mutant mice.
    J Comp Neurol. 2005 Jul 4; 487(3):270-82
  47. Su YR, Dove DE, Major AS, Hasty AH, Boone B, Linton MF, Fazio S
    Reduced ABCA1-mediated cholesterol efflux and accelerated atherosclerosis in apolipoprotein E-deficient mice lacking macrophage-derived ACAT1.
    Circulation. 2005 May 10; 111(18):2373-81 [Epub 2005 Apr 25]
  48. McLaughlin JN, Mazzoni MR, Cleator JH, Earls L, Perdigoto AL, Brooks JD, Muldowney JA 3rd, Vaughan DE, Hamm HE
    Thrombin modulates the expression of a set of genes including thrombospondin-1 in human microvascular endothelial cells.
    J Biol Chem. 2005 Jun 10; 280(23):22172-80 [Epub 2005 Apr 7]
  49. Barbieri CE, Perez CA, Johnson KN, Ely KA, Billheimer D, Pietenpol JA
    IGFBP-3 is a direct target of transcriptional regulation by DeltaNp63alpha in squamous epithelium.
    Cancer Res. 2005 Mar 15; 65(6):2314-20
  50. Fox RM, Von Stetina SE, Barlow SJ, Shaffer C, Olszewski KL, Moore JH, Dupuy D, Vidal M, Miller DM 3rd
    A gene expression fingerprint of C. elegans embryonic motor neurons.
    BMC Genomics. 2005 Mar 21; 6(1):42
  51. Xie J, Shults K, Flye L, Jiang F, Head DR, Briggs RC
    Overexpression of GSTA2 protects against cell cycle arrest and apoptosis induced by the DNA inter-strand crosslinking nitrogen mustard, mechlorethamine.
    J Cell Biochem. 2005 May 15; 95(2):339-51
  52. Yi Y, Mirosevich J, Shyr Y, Matusik R, George AL Jr
    Coupled analysis of gene expression and chromosomal location.
    Genomics. 2005 Mar; 85(3):401-12
  53. Park YK, Franklin JL, Settle SH, Levy SE, Chung E, Jeyakumar LH, Shyr Y, Washington MK, Whitehead RH, Aronow BJ, Coffey RJ
    Gene expression profile analysis of mouse colon embryonic development.
    Genesis. 2005 Jan; 41(1):1-12
  54. Prasad RC, Herzog B, Boone B, Sims L, Waltner-Law M
    An extract of Syzygium aromaticum represses genes encoding hepatic gluconeogenic enzymes.
    J Ethnopharmacol. 2005 Jan 4; 96(1-2):295-301
  55. Statnikov A, Aliferis CF, Tsamardinos I, Hardin D, Levy S
    A comprehensive evaluation of multicategory classification methods for microarray gene expression cancer diagnosis.
    Bioinformatics. 2005 Mar 1; 21(5):631-43 [Epub 2004 Sep 16]
  56. Wu N, Davidson JM
    Migration inhibitory factor-related protein (MRP)8 and MRP14 are differentially expressed in free-electron laser and scalpel incisions.
    Wound Repair Regen. 2004 May-Jun; 12(3):327-36
  57. Sforza DM, Annese J, Liu D, Levy S, Toga AW, Smith DJ
    Anatomical methods for voxelation of the mammalian brain.
    Neurochem Res. 2004 Jun; 29(6):1299-306
  58. Turney MK, Nicholson WE, Kovacs WJ
    Gene expression phenotyping of an ACTH-producing small cell lung cancer line.
    Mol Cell Endocrinol. 2004 Apr 30; 219(1-2):105-13
  59. Friedman DB, Hill S, Keller JW, Merchant NB, Levy SE, Coffey RJ, Caprioli RM
    Proteome analysis of human colon cancer by two-dimensional difference gel electrophoresis and mass spectrometry.
    Proteomics. 2004 Mar; 4(3):793-811
  60. Xu L, Zhang L, Yi Y, Kang HK, Datta SK
    Human lupus T cells resist inactivation and escape death by upregulating COX-2.
    Nat Med. 2004 Apr; 10(4):411-5 [Epub 2004 Feb 29]
  61. McQuain MK, Seale K, Peek J, Fisher TS, Levy S, Stremler MA, Haselton FR
    Chaotic mixer improves microarray hybridization.
    Anal Biochem. 2004 Feb 15; 325(2):215-26
  62. Kokoszka JE, Waymire KG, Levy SE, Sligh JE, Cai J, Jones DP, MacGregor GR, Wallace DC
    The ADP/ATP translocator is not essential for the mitochondrial permeability transition pore.
    Nature. 2004 Jan 29; 427(6973):461-5
  63. Levy SE
    Microarray analysis in drug discovery: an uplifting view of depression.
    Sci STKE. 2003 Oct 28; 2003(206):pe46
  64. Yamagata N, Shyr Y, Yanagisawa K, Edgerton M, Dang TP, Gonzalez A, Nadaf S, Larsen P, Roberts JR, Nesbitt JC, Jensen R, Levy S, Moore JH, Minna JD, Carbone DP
    A training-testing approach to the molecular classification of resected non-small cell lung cancer.
    Clin Cancer Res. 2003 Oct 15; 9(13):4695-704
  65. Xie L, Law BK, Aakre ME, Edgerton M, Shyr Y, Bhowmick NA, Moses HL
    Transforming growth factor beta-regulated gene expression in a mouse mammary gland epithelial cell line.
    Breast Cancer Res. 2003; 5(6):R187-98 [Epub 2003 Aug 20]
  66. Hsia N, Cornwall GA
    DNA microarray analysis of region-specific gene expression in the mouse epididymis.
    Biol Reprod. 2004 Feb; 70(2):448-57 [Epub 2003 Oct 15]
  67. McQuain MK, Seale K, Peek J, Levy S, Haselton FR
    Effects of relative humidity and buffer additives on the contact printing of microarrays by quill pins.
    Anal Biochem. 2003 Sep 15; 320(2):281-91
  68. Nichols CD, Garcia EE, Sanders-Bush E
    Dynamic changes in prefrontal cortex gene expression following lysergic acid diethylamide administration.
    Brain Res Mol Brain Res. 2003 Mar 17; 111(1-2):182-8
  69. Levy SE, Muldowney JA 3rd
    Microarray analysis of neointima: flowing toward a clear future.
    Arterioscler Thromb Vasc Biol. 2002 Dec 1; 22(12):1946-7
  70. Moore JH, Parker JS, Olsen NJ, Aune TM
    Symbolic discriminant analysis of microarray data in autoimmune disease.
    Genet Epidemiol. 2002 Jun; 23(1):57-69