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Publications Utilizing Services and/or Support Provided by the Keck DNA Microarray Resource


  • Su N, He K, Jiao Y, Chen C, Zhou J, Li L, Bai S, Li X, Deng XW.(2007) Distinct reorganization of the genome transcription associates with organogenesis of somatic embryo, shoots, and roots in rice. Plant Mol Biol. 63:337-349
  • Zhou J, Wang X, Jiao Y, Qin Y, Liu X, He K, Chen C, Ma L, Wang J, Xiong L, Zhang Q, Fan L, Deng XW. Global genome expression analysis of rice in response to drought and high-salinity stresses in shoot, flag leaf, and panicle. Plant Mol Biol. 2007 Jan 16; [Epub ahead of print]


  • Zhang SS, Xu X, Liu MG, Zhao H, Soares MB, Barnstable CJ, Fu XY.(2006) A biphasic pattern of gene expression during mouse retina development. BMC Dev Biol.6(48)
  • Johung K, Goodwin EC, Dimaio D. Human papillomavirus E7 repression initiates a transcriptional cascade driven by the retinoblastoma family in senescing cervical carcinoma cells. J Virol. 2006 Dec 20; [Epub ahead of print]
  • Chimge NO, Mungunsukh O, Ruddle F, Bayarsaihan D. Gene expression analysis of TFII-I modulated genes in mouse embryonic fibroblasts. J Exp Zoolog B Mol Dev Evol. 2006 Nov 8; [Epub ahead of print]
  • Patterson, T.A., Lobenhofer, E.K., Fulmer-Smentek, S.B., Collins, P., Chu, T-M., Bao, W., Fang, H., Kawasaki, E.S., Hager, J., Tikhonova, I.R., Walker, S.J., Zhang, L., Hurban, P., de Longueville, F., Fuscoe, J.C., Tong, W., Shi, L., and Wolfinger, R.D. (2006) Performance Comparison of One-Color and Two-Color Platforms Within the Microarray Quality Control (MAQC) Project. Nature Biotechnology.24(9), 1140-50.
  • Shi, L. et al., MAQC Consortium. (2006) The MicroArray Quality Control (MAQC) project shows interplatform reproducibility of gene expression measurements. Nature Biotechnology, 24(9):1151-1161
  • Hager, J., (2006) Making and using spotted DNA Microarrays in an academic core laboratory In Methods in Enzymology Vol. 41 0: DNA Microarrays Part A: Array Platforms and Wet-Bench Protocols. (Kimmel, A.and Oliver, B. eds) Elsevier, San Diego, CA, in press.
  • Lei H, Juan AH, Kim MS, Ruddle FH. (2006) Identification of a Hoxc8-regulated transcriptional network in mouse embryo fibroblast cells. Proc Natl Acad Sci U S A. 103(27):10305-9.
  • Kim, K., Page, G.P., Beasley, T.M., Barnes, S., Scheirer, K.E., and Allison, D.B. (2006) A proposed metric for assessing the measurement quality of individual microarrays. BMC Bioinformatics. 7(1), 35.


  • Hunsberger, J.G., Bennett, A.H., Selvanayagam, E., Duman, R.S., and Newton, S.S. (2005) Gene profiling the response to kainic acid induced seizures. Brain Res Mol Brain Res. 141 (1):95-112.
  • Ma, L., Chen, C., Liu, X., Jiao, Y., Su, N., Li, L., Wang, X., Caa, M., Sun, N., Zhang, X., Bao, J., Li, J., Pedersen, S., Bolund, L., Zhao, H., Yuan, L., Wong, G.K., Wang, J., Deng, X.W., and Wang, J. (2005) A microarray analysis of the rice transcriptome and its comparison to Arabidopsis. Genome Res. 15(9),1274-1 283.
  • Lei, H., Wang, H., Juan, A.H., and Ruddle, F.H. (2005) The identification of Hoxc8 target genes. Proc Natl Acad Sci U S A., 102(7), 2420-4.
  • Kluger, H.M., Lev, D.C., Kluger, Y., McCarthy, M.M., Kiriakova, G., Camp, R.L., Rimm, D.L., and Price, J.E. (2005) Using a Xenograft Model of Human Breast Cancer Metastasis to Find Genes Associated with Clinically Aggressive Disease. Cancer Res., 65(13), 5578-5587.
  • Cook, H.L., Lytle, J.R., Mischo, H.E., Li, M.J., Rossi, J.J., Silva, D.P., Desrosiers, R.C., and Steitz, J.A. (2005) Small nuclear RNAs encoded by Herpesvirus saimiri upregulate the expression of genes linked to T cell activation in virally transformed T cells. Curr Biol., 15(10), 974-9.
  • Newton, S.S., Bennett, A., and Duman, R.S. (2005) Production of custom microarrays for neuroscience research. Methods 37(3), 238-246.
  • Ma, L., Sun, N., Liu, X., Jiao, Y., Zhao, H., and Deng, X.W. (2005) Organ-specific expression of Arabidopsis genome during development. Plant Physiol., 138(1), 80-91.
  • Feng, J.X., Liu, D., Pan, Y., Gong, W., Ma, L.G., Luo, J.C., Deng, X.W., and Zhu, Y.X. (2005) An annotation update via cDNA sequence analysis and comprehensive profiling of developmental, hormonal or environmental responsiveness of the Arabidopsis AP2JEREBP transcription factor gene family. Plant Mol Biol., 59(6), 853-868.
  • Jiao, Y., Ma, L., Strickland, E., and Deng, X.W. (2005) Conservation and divergence of light-regulated genome expression patterns during seedling development in rice and Arabidopsis. Plant Cell, 17(12), 3239-3256.
  • Yatsula B, Lin S, Read A, Poholek A, Yates K, Yue D, Hui P, Perkins A. (2005) Identification of binding sites of EVI1 in mammalian cells. J. Biol Chem. (In Press).
  • Amin DN, Tuck D, Stern DF. (2005) Neuregulin-regulated gene expression in mammary carcinoma cells. Exp Cell Res. Jun 15; [Epub ahead of print]
  • Grau M, Sole X, Obrador A, Tarafa G, Vandrell E, Valls J, Moreno V, Peinado MA, Capella G. (2005) Validation of RNA Arbitrarily Primed PCR Probes Hybridized to Glass cDNA Microarrays: Application to the analysis of limited samples. Clin Chem. 51(1): 93-101.
  • Zhang SS, Xu X, Li J, Liu MG, Zhao H, Soares MB, Barnstable CJ, Fu XY. (2005) Comprehensive in silico functional specification of mouse retina transcripts. BMC Genomics. 6(1):40.
  • Zhang WK, Shen YG, He XJ, Du BX, Xie ZM, Luo GZ, Zhang JS, Chen SY. (2005) Characterization of a novel cell cycle-related gene from Arabidopsis. J Exp Bot. 56(413):807-16.


  • Khil PP, Smirnova NA, Romanienko PJ, Camerini-Otero RD. (2004) The mouse X chromosome is enriched for sex-biased genes not subject to selection by meiotic sex chromosome inactivation. Nat Genet. 36(6):642-6.
  • Amin DN, Perkins AS, Stern DF. (2004) Gene expression profiling of ErbB receptor and ligand-dependent transcription. Oncogene. 23(7):1428-38.
  • Kluger, H.M., Kluger, Y., Gilmore-Hebert, M., Chang, J., Rodov, S., Mironenko, O., Kacinski, B., Perkins, A., and Eva Sapi. (2004) cDNA Microarray Analysis of Invasive and Tumorigenic Phenotypes in a Breast Cancer Model. Lab Invest. 84(3):320-31.
  • Chen, J., Newton, S.S., Zeng, L., Adams, D.H., Dow, A.L. Madsen, M., Nestler, E.J., and Duman, R.S. (2004) Downregulation of the CCAAT-enhancer binding protein beta in deltaFosB transgenic mice and by electroconvulsive seizures. Neuropsychopharmacology, 29(1): 23-31
  • Ueland, J.M., Gwira, J., Lui, ZX and Cantley, L.G. (2004) The chemokine KC regulates HGF-stimulated epithelial cell morphogenesis. Am J Physiol Renal Physiol. 286(3): F581-9.
  • Cook, H.L, Mischo, H.E. and Steitz, J.A. (2004) The Herpesvirus saimiri small nuclear RNAs recruit AU-rich element-binding proteins but do not alter host AU-rich element-containing mRNA levels in virally transformed T cells. Mol Cell Biol. 2004 24(10):4522-33.
  • Cheung, K.H., Hager, J., Pan, D., Srivastava, R., Mane, S., Li, Y., Miller, P., Williams, K. (2004) KARMA: A web server application for comparing and annotating heterogeneous microarray platforms. Nucleic Acids Research 32(Web Server issue):W441-W444.
  • Torpey N, Maher SE, Bothwell AL, Pober JS. (2004) Interferon alpha but not interleukin 12 activates STAT4 signaling in human vascular endothelial cells. J Biol Chem. 279(25):26789-96.
  • Wu Y, Zhang X, Bardag-Gorce F, Robel RC, Aguilo J, Chen L, Zeng Y, Hwang K, French SW, Lu SC, Wan YJ. (2004) Retinoid X receptor alpha regulates glutathione homeostasis and xenobiotic detoxification processes in mouse liver. Mol Pharmacol. 65(3):550-7.
  • Hoek, K., Rimm, D. L., Williams, K. R., Zhao, H., Ariyan, S., Lin, A., Kluger, H. M., Berger, A. J., Cheng, E., E. Trombetta, S., Wu, T., Niinobe, M., Yoshikawa, K., Hannigan, G. E., and Halaban, R. Expression profiling reveals novel pathways in the transformation of melanocytes to melanomas. Cancer Res., 64: in press, 2004. (Suppl. material)
  • Khil PP, Smirnova NA, Romanienko PJ, Camerini-Otero RD. (2004) The mouse X chromosome is enriched for sex-biased genes not subject to selection by meiotic sex chromosome inactivation. Nat Genet. 36(6):642-6.
  • Zhou D, Xue J, Gavrialov O, Haddad GG. (2004) Na+/H+ exchanger 1 deficiency alters gene expression in mouse brain. Physiol Genomics. 18(3):331-9.
  • Cheung, K.H., de Knikker, R., Guo, Y., Zhong G., Hager, J., Yip, K.Y., Kwan,A.K.H., Li, P. and Cheung, D.W. (2004) Biosphere: the interoperation of web services in microarray cluster analysis. Applied Bioinformatics (In Press).
  • Tangir J, Bonafe N, Gilmore-Hebert M, Henegariu O, Chambers SK. (2004) SGK1, a potential regulator of c-fms related breast cancer aggressiveness. Clin Exp Metastasis. 21(6):477-83.


  • Zik, M., and Irish, V.F. (2003) Global Identification of Target Genes Regulated by APETALA3 and PISTILLATA Floral Homeotic Gene Action, The Plant Cell 15, 1–17.
  • Ma, L., Zhao, H., and Deng, X. (2003) Analysis of the mutational effects of the COP/DET/FUS loci on genome expression profiles reveals their overlapping yet not identical roles in regulating Arabidopsis seedling development. Genes and Development, 130, 969-981.
  • Lage, J., Leamon, J., Pejovic, T., Hamann, S., Lacey, M., Dillon, D., Segraves, R., Vossbrinck, B., González, A., Pinkel, D., Albertson, D.G., Costa, J., and Lizardi, P.M. (2003) Whole genome analysis of genetic alterations in small DNA samples using hyperbranched strand displacement amplification and array-CGH. Genome Research 13, 294-307.
  • Savaldi-Goldstein, S., Aviv, D, Davydov, O., Fluhr, R. (2003) Alternative Splicing Modulation by a LAMMER Kinase Impinges on Developmental and Transcriptome Expression. Plant Cell. 15(4), 926-38.
  • Feng, S., Ma, L.G., Wang, X, Xie, D., Dinesh-Kumar, S. P., Wei, N, and Deng, X.W. (2003) The COP9 Signalosome Physically Interacts with SCFCOI1 and Modulates Jasmonate Responses. The Plant Cell. 15(5): 1083-94.
  • Wu, P, Ma, L.G., Hou, X, Liu, F, Deng, X.W. (2003) Phosphate Starvation Signal in Roots Triggers a Global Alteration of Cellular Metabolism and Genome Expression in Arabidopsis. Plant Physiology. 132(3): 1260-71
  • Page, G. P., Edwards, J. W., Barnes, S., Weindruch, R., Allison, D. B. (2003) A Design & Statistical Perspective on Microarray Gene Expression Studies in Nutrition: The Need for Playful Creativity and Scientific Hard-Mindedness. Nutrition 19(11-12):997-1000.
  • Gadbury, G. L., Page, G. P., Heo, M., Mountz, J. D., & Allison, D. B. (2003) Randomization tests for small samples: An application for genetic expression data. Journal of the Royal Statistical Society, Series C (Applied Statistics) in press.
  • Li, M., Zhang, S.S., and Barnstable, C.J. (2003) Developmental and tissue expression patterns of mouse Mpp4 gene. Biochem Biophys Res Commun. 2003 Jul 25;307(2):229-35.
  • Guda K, Cui H, Garg S, Dong M, Nambiar PR, Achenie LE, Rosenberg DW. (2003) Multistage gene expression profiling in a differentially susceptible mouse colon cancer model. Cancer Lett. 28; 191(1):17-25.
  • Guda K, Claffey KP, Dong M, Nambiar PR, Rosenberg DW. (2003) Defective processing of the transforming growth factor-beta1 in azoxymethane-induced mouse colon tumors. Mol Carcinog. 37(1): 51-9.
  • Sun N, Ma L, Pan D, Zhao H and Deng X-W. (2003) Evaluation of light regulatory potential of Calvin cycle steps based on large-scale gene expression profiling data. Plant Molecular Biology 53: 467–478.
  • Bais HP, Vepachedu R, Gilroy S, Callaway RM, Vivanco JM. (2003) Allelopathy and exotic plant invasion: from molecules and genes to species interactions. Science. 5;301(5638):1377-80.
  • Sun N, Ma L, Pan D, Zhao H and Deng X-W. (2003) Evaluation of light regulatory potential of Calvin cycle steps based on large-scale gene expression profiling data. Plant Molecular Biology 53: 467–478.
  • Weitzel JM, Hamann S, Jauk M, Lacey M, Filbry A, Radtke C, Iwen KA, Kutz S, Harneit A, Lizardi PM, Seitz HJ. (2003) Hepatic gene expression patterns in thyroid hormone-treated hypothyroid rats. J Mol Endocrinol. 31(2):291-303.


  • Wisnewski, A.V., Liu, Q., Miller, J.J., Magoski, N., Redlich, C.A. (2002) Effects of Hexamethylene Diisocyanate Exposure on Human Airway Epithelial Cells: In Vitro Cellular and Molecular Studies. Environmental Health Perspectives 110 (9) 901-907.
  • Lage, J.M., Hamann, S., Gribanov, O., Leamon, J.H., Pejovic, T., Lizardi, P.M. (2002) Microgel assessment of nucleic acid integrity and labeling quality in microarray experiments. Biotechniques; 32(2), 312-4.
  • Ma, X., Husain, T., Peng, H., Lin, S., Mironenko, O., Maun, N., Johnson, S., Tuck, D., Berliner, N., Krause, D.S., and Perkins, A.S. (2002) Development of a murine hematopoietic progenitor cDNA microarray using a subtracted cDNA library. Blood; 100(3): 833-844.
  • Wang, H., Ma, L., Habashi, J., Li, J., Zhao, H., and Deng, X. W. (2002) Analysis of far-red light-regulated genome expression profiles of phytochrome A pathway mutants in Arabidopsis. The Plant Journal 32, 723-733.
  • Ma, L., Gao, Y., Qu, L., Chen, Z., Li, J., Zhao, H., and Deng, X.W. (2002) Genomic Evidence for COP1 as a Repressor of Light-Regulated Gene Expression and Development in Arabidopsis. The Plant Cell 14, 2383–2398.
  • Cheung, K.H., White, K., Hager, J., Gerstein, M., Reinke, V., Nelson, K., Masiar, P., Srivastava, P., Li, Y., Li, J., Li, J.M., Allison, D.B., Snyder, M., Miller, P., Williams, K. (2002) YMD: A microarray database for large-scale gene expression analysis. Proceedings of the American Medical Informatics Association 2002 Annual Symposium, 140-144.
  • Allison, D.B., and Coffey, C.S. (2002) Two-Stage Testing in Microarray Analysis: What is Gained? Journal of Gerontology, Biological Sciences; 57(5), 189-92.
  • Allison, D. B., Gadbury, G., Heo, M, Fernandez, J, Lee, C-K, Prolla, T. A., & Weindruch, R. (2002). A Mixture Model Approach For The Analysis Of Microarray Gene Expression Data. Computational Statistics & Data Analysis, 39, 1-20.
  • Allison, D. B. (2002), Statistical Methods For Microarray Research For Drug Target Identification, 2002 Proceedings of the American Statistical Association, Biopharmaceutical Section [CD-ROM], Alexandria, VA: American Statistical Association.
  • Cheung, K.H., Hager, J., Nelson, K., White, K., Li, Y., Snyder, M., Williams, K., Miller, P. (2002) A dynamic approach to mapping coordinates between microplates and microarrays., J Biomed Inform. 35(5-6):306-12.


  • Ladner, D.P., Leamon, J.H., Hamann, S., Tarafa, G., Strugnell, T., Dillon, D., Lizardi, P., and Costa, J. (2001) Multiplex Detection of Hotspot Mutations by Rolling Circle-Enabled Universal Microarrays. Laboratory Investigation; 81:1079-1086.
  • Wang, H., Ma, L., Li, J., Zhao, H., Deng, X. (2001) Direct Interaction of Arabidopsis Cryptochromes with COP1 in Light Control Development. Science; 294:154-158.
  • Luo, C., Shent, B., Manley, J.l., and Zheng, L. (2001) Tehao functions in the Toll pathway in Drosophilia melanogaster: possible roles in development and innate immunity. Insect Molecular Biology; 10(5):457-464.
  • Ma, L., Li, J., Qu, L., Hager, J., Chen, Z., Zhao, H., Deng, X. (2001) Light control of Arabidopsis development entails coordinated regulation of genome expression and cellular pathways. Plant Cell; 13, 2589-2607.