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AECOM cDNA Microarray Facility - Supported Publications


Original Publications:

  1. Fan C, Iacobas DA, Zhou D, Chen Q, Lai JK, Gavrialov O, Haddad GG.
    Gene expression and phenotypic characterization of mouse heart after chronic constant or intermittent hypoxia.     Physiol Genomics. 2005 Aug 11;22(3):292-307. Epub 2005 May 31
  2. Brand-Schieber E, Werner P, Iacobas DA, Iacobas S, Beelitz M, Lowery SL, Spray DC, Scemes E.
    Connexin43, the major gap junction protein of astrocytes, is down-regulated in inflamed white matter in an animal model of multiple sclerosis.     J Neurosci Res. 2005 Jun 15;80(6):798-808.
  3. Iacobas DA, Iacobas S, Urban-Maldonado M, Spray DC.
    Sensitivity of the brain transcriptome to connexin ablation.     Biochim Biophys Acta. 2005 Jun 10;1711(2):183-96. Epub 2004 Dec 22.
  4. Iacobas DA, Iacobas S, Li WE, Zoidl G, Dermietzel R, Spray DC.
    Genes controlling multiple functional pathways are transcriptionally regulated in connexin43 null mouse heart.     Physiol Genomics. 2005 Feb 10;20(3):211-23. Epub 2004 Dec 7. PMID: 15585606 [PubMed - indexed for MEDLINE]
  5. Iacobas DA, Scemes E, Spray DC.
    Gene expression alterations in connexin null mice extend beyond the gap junction.     Neurochem Int. 2004 Aug-Sep;45(2-3):243-50. PMID: 15145539 [PubMed - in process]
  6. Charles E. Rogler, Tatyana Tchaikovskaya, Raquel Norel, Aldo Massimi, Christopher Plescia, Eugeny Rubashevsky, Paul Siebert, and Leslie E. Rogler
    RNA expression microarrays (REMs), a high-throughput method to measure differences in gene expression in diverse biological samples.     Nucleic Acids Res. 2004; 32(15): e120. Published online 2004 August 25 doi: 10.1093/nar/gnh116.
  7. Khabele D, Lopez-Jones M, Yang W, Arango D, Gross SJ, Augenlicht LH, Goldberg GL.
    Tumor necrosis factor-alpha related gene response to Epothilone B in ovarian cancer.     Gynecol Oncol. 2004 Apr;93(1):19-26. PMID: 15047209 [PubMed - indexed for MEDLINE]
  8. Susztak K, Bottinger E, Novetsky A, Liang D, Zhu Y, Ciccone E, Wu D, Dunn S, McCue P, Sharma K.
    Molecular profiling of diabetic mouse kidney reveals novel genes linked to glomerular disease.     Diabetes. 2004 Mar;53(3):784-94. PMID: 14988265 [PubMed - in process]
  9. Zhao H, Jhanwar-Uniyal M, Datta PK, Yemul S, Ho L, Khitrov G, Kupershmidt I, Pasinetti GM, Ray T, Athwal RS, Achary MP.
    Expression profile of genes associated with antimetastatic gene: nm23-mediated metastasis inhibition in breast carcinoma cells.     Int J Cancer. 2004 Mar10;109(1):65-70. PMID: 14735469 [PubMed - indexed for MEDLINE]
  10. Sotsky Kent T, Yuan Z, Miller A, Weber TK.
    Deleted in oral cancer-1 expression upregulates proapoptosis elements in microsatellite-unstable human colorectal cancer.     Ann Surg Oncol. 2004 Feb;11(2):192-6. PMID: 14761923 [PubMed - indexed for MEDLINE]
  11. Belbin TJ, Gaspar J, Haigentz M, Perez-Soler R, Keller SM, Prystowsky MB, Childs G, Socci ND.
    Indirect measurements of differential gene expression with cDNA microarrays.     Biotechniques. 2004 Feb;36(2):310-4. PMID: 14989096 [PubMed - in process]
  12. Mariadason JM, Arango D, Shi Q, Wilson AJ, Corner GA, Nicholas C, Aranes MJ, Lesser M, Schwartz EL, Augenlicht LH.
    Gene expression profiling-based prediction of response of colon carcinoma cells to 5-fluorouracil and camptothecin.     Cancer Res. 2003 Dec 15;63(24):8791-812. PMID: 14695196 [PubMed - indexed for MEDLINE]
  13. Rybicki AC, Fabry ME, Does MD, Kaul DK, Nagel RL.
    Differential gene expression in the kidney of sickle cell transgenic mice: upregulated genes.     Blood Cells Mol Dis. 2003 Nov-Dec;31(3):370-80. PMID: 14636654 [PubMed - in process]
  14. Arango D, Mariadason JM, Wilson AJ, Yang W, Corner GA, Nicholas C, Aranes MJ, Augenlicht LH.
    c-Myc overexpression sensitises colon cancer cells to camptothecin-induced apoptosis.     Br J Cancer. 2003 Nov 3;89(9):1757-65. PMID: 14583781 [PubMed - indexed for MEDLINE]
  15. Iyengar P, Combs TP, Shah SJ, Gouon-Evans V, Pollard JW, Albanese C, Flanagan L, Tenniswood MP, Guha C, Lisanti MP, Pestell RG, Scherer PE.
    Adipocyte-secreted factors synergistically promote mammary tumorigenesis through induction of anti-apoptotic transcriptional programs and proto-oncogene stabilization.     Oncogene. 2003 Sep 25;22(41):6408-23. PMID: 14508521 [PubMed - indexed for MEDLINE]
  16. Yuan Z, Sotsky Kent T, Weber TK.
    Differential expression of DOC-1 in microsatellite-unstable human colorectal cancer.     Oncogene. 2003 Sep 18;22(40):6304-10. PMID: 13679870 [PubMed - indexed for MEDLINE]
  17. Ohno H, Zhu G, Mohan VP, Chu D, Kohno S, Jacobs WR Jr, Chan J.
    The effects of reactive nitrogen intermediates on gene expression in Mycobacterium tuberculosis.     Cell Microbiol. 2003 Sep;5(9):637-48. PMID: 12925133 [PubMed - indexed for MEDLINE]
  18. Mukherjee S, Belbin TJ, Spray DC, Iacobas DA, Weiss LM, Kitsis RN, Wittner M, Jelicks LA, Scherer PE, Ding A, Tanowitz HB.
    Microarray analysis of changes in gene expression in a murine model of chronic chagasic cardiomyopathy.     Parasitol Res. 2003 Oct;91(3):187-96. Epub 2003 Aug 09. PMID: 12910413 [PubMed - indexed for MEDLINE]
  19. Iacobas DA, Urban-Maldonado M, Iacobas S, Scemes E, Spray DC.
    Array analysis of gene expression in connexin-43 null astrocytes.     Physiol Genomics. 2003 Nov 11;15(3):177-90. Epub 2003 Aug 19. PMID: 12928503 [PubMed - indexed for MEDLINE]
  20. Sanchez-Carbayo M, Socci ND, Lozano JJ, Li W, Charytonowicz E, Belbin TJ, Prystowsky MB, Ortiz AR, Childs G, Cordon-Cardo C.
    Gene discovery in bladder cancer progression using cDNA microarrays.     Am J Pathol. 2003 Aug;163(2):505-16. PMID: 12875971 [PubMed - indexed for MEDLINE]
  21. Locker J, Tian J, Carver R, Concas D, Cossu C, Ledda-Columbano GM, Columbano A.
    A common set of immediate-early response genes in liver regeneration and hyperplasia.     Hepatology. 2003 Aug;38(2):314-25. PMID: 12883475 [PubMed - indexed for MEDLINE]
  22. Augenlicht LH, Velcich A, Klampfer L, Huang J, Corner G, Aranes M, Laboisse C, Rigas B, Lipkin M, Yang K, Shi Q, Lesser M, Heerdt B, Arango D, Yang W, Wilson A, Mariadason JM.
    Application of gene expression profiling to colon cell maturation, transformation and chemoprevention.     J Nutr. 2003 Jul;133(7 Suppl):2410S-2416S. Review. PMID: 12840217 [PubMed - indexed for MEDLINE]
  23. Shankar SL, O'Guin K, Cammer M, McMorris FA, Stitt TN, Basch RS, Varnum B, Shafit-Zagardo B.
    The growth arrest-specific gene product Gas6 promotes the survival of human oligodendrocytes via a phosphatidylinositol 3-kinase-dependent pathway.     J Neurosci. 2003 May 15;23(10):4208-18. PMID: 12764109 [PubMed - indexed for MEDLINE]
  24. Supavekin S, Zhang W, Kucherlapati R, Kaskel FJ, Moore LC, Devarajan P.
    Differential gene expression following early renal ischemia/reperfusion.     Kidney Int. 2003 May;63(5):1714-24. PMID: 12675847 [PubMed - indexed for MEDLINE]
  25. Sanchez-Carbayo M, Belbin TJ, Scotlandi K, Prystowsky M, Baldini N, Childs G, Cordon-Cardo C.
    Expression profiling of osteosarcoma cells transfected with MDR1 and NEO genes: regulation of cell adhesion, apoptosis, and tumor suppression-related genes.     Lab Invest. 2003 Apr;83(4):507-17. PMID: 12695554 [PubMed - indexed for MEDLINE]
  26. Mariadason JM, Augenlicht LH, Arango D.
    Microarray analysis in the clinical management of cancer.     Hematol Oncol Clin North Am. 2003 Apr;17(2):377-87. Review. PMID: 12737394 [PubMed - indexed for MEDLINE]
  27. Goswami S, Sheets NL, Zavadil J, Chauhan BK, Bottinger EP, Reddy VN, Kantorow M, Cvekl A.
    Spectrum and range of oxidative stress responses of human lens epithelial cells to H2O2 insult.     Invest Ophthalmol Vis Sci. 2003 May;44(5):2084-93. PMID: 12714647 [PubMed - indexed for MEDLINE]
  28. Chauhan BK, Reed NA, Yang Y, Cermak L, Reneker L, Duncan MK, Cvekl A.
    A comparative cDNA microarray analysis reveals a spectrum of genes regulated by Pax6 in mouse lens.     Genes Cells 2002 Dec;7(12):1267-83
  29. Sanchez-Carbayo M, Socci ND, Charytonowicz E, Lu M, Prystowsky M, Childs G, Cordon-Cardo C.
    Molecular profiling of bladder cancer cell lines using cDNA microarrays: defining histogenesis and biological phenotypes.     Cancer Research 2002 Dec 1;62(23):6973-80
  30. Wang W, Wyckoff JB, Frohlich VC, Oleynikov Y, Huttelmaier S, Zavadil J, Cermak L, Bottinger EP, Singer RH, White JG, Segall JE, Condeelis JS.
    Single cell behavior in metastatic primary mammary tumors correlated with gene expression patterns revealed by molecular profiling.     Cancer Res 2002 Dec 1;62(23):7132
  31. Bourdon V, Naef F, Rao PH, Reuter V, Mok SC, Bosl GJ, Koul S, Murty VV, Kucherlapati RS, Chaganti RS.
    Genomic and Expression analysis of the 12p11p12 amplicon using EST array identifies two novel amplified and over-expressed genes.     Cancer Res, 2002, Nov 1, vol 62(21).
  32. John GR, Shankar SL, Shafit-Zagardo B, Massimi A, Lee SC, Raine CS, Brosnan CF.
    Multiple sclerosis: re-expression of a developmental pathway that restricts oligodendrocyte maturation.     Nat Med. 2002 Oct;8(10):1115-21.
  33. Shin CH, Liu ZP, Passier R, Zhang CL, Wang DZ, Harris TM, Yamagishi H, Richardson JA, Childs G, Olson EN.
    Modulation of cardiac development by HOP, an unusual homeodomain protein.     Cell 2002 Sep 20;110(6):725-35
  34. Iacobas A.D., Massimi A.B., Urban M., Iacobas S., Spray D.C.
    Hits and Misses from Gene Expression Ratio Measurements in cDNA microarray studies.     Invited review. J Biomol. Tech. 13(3), Sept.2002.
  35. Gross SJ, Ferreira JC, Morrow B, Dar P, Funke B, Khabele D, Merkatz I.
    Gene expression profile of trisomy 21 placentas: a potential approach for designing noninvasive techniques of renatal diagnosis.     Am J Obstet Gynecol. 2002 Aug;187(2):457-62. PMID: 12193943 [PubMed - indexed for MEDLINE]
  36. Harris TM, Childs G.
    Global gene expression patterns during differentiation of F9 embryonal carcinoma cells into parietal endoderm.     Functional and Integrative Genomics, 2002 Aug;2(3):105-19
  37. Mariadason JM, Arango D, Corner GA, Aranes MJ, Hotchkiss KA, Yang W, Augenlicht LH.
    A gene expression profile that defines colon cell maturation in vitro.     Cancer Res 2002 Aug 15;62(16):4791-804
  38. Wei Y, Harris T, Childs G.
    Global expression patterns during neural differentiation of P19 embryonic carcinoma cells.     Differentiation 2002 Jun;70(4-5):204-19
  39. Peng CF, Wei Y, Levsky JM, McDonald TV, Childs G, Kitsis RN.
    Microarray analysis of global changes in gene expression during cardiac myocyte differentiation.     Physiol Genomics. 2002;9(3):145-55.
  40. Chauhan BK, Reed NA, Zhang W, Duncan MK, Kilimann MW, Cvekl A.
    Identification of genes downstream of Pax6 in the mouse lens using cDNA microarrays.     J Biol Chem 2002 Mar 29;277(13):11539-48
  41. Iacobas, A.D., Urban, M., Massimi, A., and Spray, D.C.
    Improved procedures to mine data obtained from spotted cDNA arrays.     J Biomol Tech. 13(1), March 2002
  42. Belbin TJ, Singh B, Barber I, Socci N, Wenig B, Smith R, Prystowsky MB, Childs G.
    Molecular classification of head and neck squamous cell carcinoma using cDNA microarrays.     Cancer Res 2002 Feb 15;62(4):1184-90
  43. Yuan R, Fan S, Achary M, Stewart DM, Goldberg ID, Rosen EM.
    Altered gene expression pattern in cultured human breast cancer cells treated with hepatocyte growth factor/scatter factor in the setting of DNA damage.     Cancer Res. 2001 Nov 1;61(21):8022-31.
  44. Plescia C, Rogler C, Rogler L.
    Genomic expression analysis implicates Wnt signaling pathway and extracellular matrix alterations in hepatic specification and differentiation of murine hepatic stem cells.     Differentiation 2001 Oct;68(4-5):254-69
  45. Zhang W, Bardwell PD, Woo CJ, Poltoratsky V, Scharff MD, Martin A.
    Clonal instability of V-region hypermutation in the Ramos Burkitt's lymphoma cell line.     Int Immunol 2001 Sep;13(9):1175-84
  46. Yang W, Velcich A, Mariadason J, Nicholas C, Corner G, Houston M, Edelmann W, Kucherlapati R, Holt PR, Augenlicht LH.
    p21(WAF1/cip1) is an important determinant of intestinal cell response to sulindac in vitro and in vivo.     Cancer Res. 2001 Aug 15;61(16):6297-302.
  47. Zavadil J, Bitzer M, Liang D, Yang YC, Massimi A, Kneitz S, Piek E, Bottinger EP.
    Genetic programs of epithelial cell plasticity directed by transforming growth factor-beta.     Proc Natl Acad Sci U S A. 2001 Jun 5;98(12):6686-91.
  48. Gonzalez J, Harris T, Childs G, Prystowsky MB.
    Abstract Rapamycin blocks IL-2-driven T cell cycle progression while preserving T cell survival.     Blood Cells Mol Dis. 2001 May-Jun;27(3):572-85.
  49. Iacobas A.D., Marcia Urban, Sanda Iacobas, D.C. Spray. (2001).
    The "patholog" of the genes expression profile in evaluating the ecotoxin effects.     Advances in Ecological Sciences. 10: 733-742.
  50. Achary MP, Jaggernauth W, Gross E, Alfieri A, Klinger HP, Vikram B.
    Cell lines from the same cervical carcinoma but with different radiosensitivities exhibit different cDNA microarray patterns of gene expression.     Cytogenet Cell Genet. 2000;91(1-4):39-43.
  51. Mariadason JM, Corner GA, Augenlicht LH.
    Genetic reprogramming in pathways of colonic cell maturation induced by short chain fatty acids: comparison with trichostatin A, sulindac, and curcumin and implications for chemoprevention of colon cancer.     Cancer Res. 2000 Aug 15;60(16):4561-72.
  52. Harris TM, Massimi A, Childs G.
    Injecting new ideas into microarray printing.     Nat Biotechnol. 2000 Apr;18(4):384-5.
  53. Wang C, Francis R, Harirchian S, Batlle D, Mayhew B, Bassett M, Rainey WE, Pestell RG.
    The application of high density microarray for analysis of mitogenic signaling and cell-cycle in the adrenal.     Endocr Res. 2000 Nov;26(4):807-23.
  54. Cheung VG, Morley M, Aguilar F, Massimi A, Kucherlapati R, Childs G.
    Making and reading microarrays.     Nat Genet. 1999 Jan;21(1 Suppl):15-9. Review.


Books, Chapters in Books, Surveys and Review Articles:

  1. In press:
    Iacobas DA, Iacobas S, Spray DC.
    Use of cDNA arrays to explore gene expression in genetically manipulated mice and cell lines.
    In Methods in Cardiovascular Research, S. Dhein & M. Delmar (editors), Springer-Verlag.
  2. Knudson K, Brooks AI, Griffin C, Iacobas DA, Johnson K, Khitrov G, Levy S, Massimi A, Nowak N, Viale A., Grills G. (2003).
    A current profile of microarray laboratories: 2002-2003 Microarray Research Group Survey of laboratories using microarray technologies.
  3. Knudson KL, Griffin C, Brooks A, Iacobas DA, Johnson K, Khitrov G, Lilley K, Massimi A, Viale A, Zhang W, Bao Y, Grills G. (2002).
    Factors contributing to variability in DNA microarray results: the ABRF Microarray Research Group 2002 Study.
  4. Childs G., DeRisi J., Harris T., Holloway A., Hou BH, Massimi A., Murphy M., Somerville S.
    Printing Spotted Glass Microarrays.
    In DNA Microarrays, A Molecular Cloning Manual. David Bowtell and Joseph Sambrook editors, Cold Spring Harbor Laboratory Press, (2002) Section 2, 61-100.

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