James Eudy, Ph.D.


James Eudy, Ph.D.Director of UNMC DNA Microarray and Sequencing Core Facilities

University of Nebraska Medical Center
(Biochemistry and Molecular Biology)

Phone: 402-559-3940
Fax: 402-559-4001

Teaching: Cell and Molecular Processes Core: I provide yearly lectures to first year medical students involving several areas of human genetics and molecular biology including gene mapping, gene therapy, DNA Microarrays, Next Generation DNA Sequencing and functional genomics. Pharmacology 820: I present a lecture in this course offered by the Department of Pharmacology at UNMC. This lecture covers the history, laboratory techniques, and fundamental research applications of DNA Microarray Technology.

Research Interests: Next Generation DNA Sequencing strategies for rare Mendelian disease gene identification and functional genomic technologies in general. I also collaborate on a number of research projects at UNMC involving many different areas of biomedical interest including cancer, cardiovascular disease, and virology.

Microarray Core Facility: This facility is comprehensive in scope and provides microarray service and support for both the Affymetrix GeneChip System and spotted DNA array platforms. The laboratory routinely processes many of the gene expression and genotyping arrays offered by Affymetrix. The facility is also fully equipped with all the necessary instrumentation for hybridizing, scanning and analyzing spotted arrays. Collectively, the Affymetrix and spotted array platforms allow researchers to measure the genome-wide activity of tens of thousands of genes in parallel in a variety of model organisms.

DNA Sequencing Core Facility: Our DNA Sequencing Core Facility serves the role of the UNMC research DNA sequencing facility. In addition to traditional sequencing of PCR fragments and plasmid inserts, we have also employed Next Generation Sequencing technology. In 2010 I was awarded a Shared Instrumentation Grant from the NIH General Medical Sciences (formally National Center for Research Resources or NCRR). This Illumina Genome Analyzer IIx instrument will be operated in the context of a Next Generation Sequencing Core facility and service a variety of projects related to biomedical research; including cancer, diseases of the retina, HIV, inherited neurological disorders and others. In 2011, the GAIIx instrument was upgraded to an Illumina HiSeq2000 with funds obtained from a Nebraska Research Initiative grant. In addition, we are looking forward to upgrading the HiSeq2000 to a HiSeq2500 instrument in November of 2012 utilizing funds obtained from a Nebraska Research Foundation grant.

Through a collaborative and interactive relationship with the newly established Center for Bioinformatics and Systems Biology, we aim to provide functional genomics technological support for the UNMC campus.

Publications listed in PubMed

Research Publications

  1. Lada AG, Stepchenkova EI, Waisertreiger IS, Noskov VN, Dhar A, Eudy JD, Boissy RJ, Hirano M, Rogozin IB, Pavlov YI. 2013.  Genome-wide mutation avalanches induced in diploid yeast cells by a base analog or an APOBEC deaminase. PLoS Genet. 2013 Sep; 9(9):e1003736. doi: 10.1371/journal.pgen.1003736. Epub 2013 Sep 5.

  2. Carlson MA, Smith LM, Cordes CM, Chao J, Eudy JD. 2013.  Attachment-regulated signaling networks in the fibroblast-populated 3D collagen matrix. Sci Rep. 2013; 3:1880. doi: 10.1038/srep01880

  3. Mohibi S, Gurumurthy CB, Nag A, Wang J, Mirza S, Mian Y, Quinn M, Katafiasz B, Eudy J, Pandey S, Guda C, Naramura M, Band H, Band V.  Mammalian alteration/deficiency in activation 3 (ada3) is essential for embryonic development and cell cycle progression. J Biol Chem. 2012 Aug 24;287 (35):29442-56.

  4. Workman A, Eudy JD, Smith L, da Silva LF, Sinani D, Bricker H, Cook E, Doster A, and Jones C.  Cellular transcription factors induced in trigeminal ganglia during dexamethasone-induced reactivation from latency stimulate bovine herpesvirus 1 productive infection and certain viral promoters J Virol. 2012 Mar;86(5):2459-73.

  5. Pathak S, Ma S, Trinh L, Eudy J, Wagner KU, Joshi SS, Lu R.  IRF4 is a suppressor of c-Myc induced B cell leukemia. PLoS One. 2011. 6(7):e22628. Epub 2011 Jul 27

  6. Thulasingam S, Massilamany C, Gangaplara A, Dai H, Yarbaeva S, Subramaniam S, Riethoven JJ, Eudy J, Lou M, Reddy J.  miR-27b*, an oxidative stress-responsive microRNA modulates nuclear factor-kB pathway in RAW 264.7 cells. Mol Cell Biochem. 2011. Jun;352(1-2):181-8.

  7. Zhao X, Malhotra GK, Lele SM, Lele MS, West WW, Eudy JD, Band H, Band V.  Telomerase-immortalized human mammary stem/progenitor cells with ability to self-renew and differentiate. Proc Natl Acad Sci U S A. 2010 Aug 10;107(32):14146-51.

  8. Eudy JD, Pickering DL, Lutz R, Platt K, Dave BJ, Olney AH, Sanger,WG.  18q22.3 to 18q23 Deletion Syndrome and Cleft Palate Am J Med Genet A. 2010 Apr;152A(4):1046-8.
  9. Parameswaran S, Balasubramanian S, Babai N, Qiu F, Eudy JD, Thoreson WB, Ahmad I.  Induced pluripotent stem cells (iPSCs) generate both retinal ganglion cells and photoreceptors:Therapeutic implications in degenerative changes in glaucoma and age-related macular degeneration. Stem Cells2010 Apr;28(4):695-703.
  10. Yanai-Balser GM, Duncan GA, Eudy JD, Wang D, Li X, Agarkova IV, Dunigan DD, Van Etten JL.  Microarray analysis of Paramecium bursaria chlorella virus 1 transcription. J Virol 2010 Jan;84(1):532-42.
  11. Kou W, Banerjee S, Eudy JDSmith L, Persidsky R, Borgmann K, Wu L, Sakhuja N, Deshpande M, Walseth T, Ghorpade A.  CD38 regulation in activated astrocytes: implications for neuroinflammation and HIV-1 brain infection. Journ of Neuro Res2009 Aug 1;87(10):2326-39.
  12. Das VA, Bhattacharya S, Zhao X, Hegde G, Mallya K, Eudy JD, and Ahmad I.  The canonical Wnt pathway regulates retinal stem cells / progenitors in concert with notch signaling. Dev Neurosci. 2008;30(6):389-409.
  13. Bafna S, Singh AP, Moniaux N, Eudy JD, Meza JL, and Batra SK.  MUC4, a multifunctional transmembrane glycoprotein, induces oncogenic transformation of NIH3T3 mouse fibroblast cells. Cancer Res. 2008 Nov 15;68(22):9231-8.
  14. Bates JS , Petry DB, Eudy J, Bough L, and Johnson RK.  Differential expression in lung and bronchial lymph node of pigs with high and low responses to infection with Porcine Reproductive and Respiratory Syndrome VirusJ Anim Sci. 2008 Dec;86(12):3279-89.
  15. Pickering DL, Eudy JD, Olney AH, Dave BJ, Golden D, Stevens J, Sanger WG.  Array-cGH Analysis of 1176 Consecutive Clinical Genetics Investigations Genet Med. 2008 Apr;10(4):262-6.
  16. Gelineau-van Waes J, Maddox J, Smith L, van Waes M, Wilberding J, Eudy JD, Bauer LK, and Finnell RH.  Microarray Analysis Of E9.5 Reduced Folate Carrier Knockout Embryos Reveals Altered Expression Of Genes In The Cubulin-Megalin Multiligand Endocytic Receptor Complex. BMC Genomics. 2008 Apr 9;9(1):156.
  17. Gelineau-van Waes J, Smith L, van Waes M, Wilberding J, Eudy JD, Bauer LK,and Maddox J (2007)  Altered Expression of the Iron Transporter Nramp1 (slc11a1) During Fetal Eye Development in Microphthalmia-Associated Transcription Factor Mitfmi and Mitfvitiligo Mouse Mutants Exp Eye Res. Feb;86(2):419-33 (2008).
  18. Singh APBafna SChaudhary KVenkatraman GSmith LEudy JDJohansson SLLin MFBatra SK.  Genome-wide expression profiling reveals transcriptomic variation and perturbed gene networks in androgen-dependent and androgen-independent prostate cancer cells. Cancer Lett. Jan 18;259(1):28-38 (2008).
  19. Joshi AD, Hegde GV, Dickinson JD, Mittal AK, Lynch JC, Eudy JD, Armitage JO, Bierman PJ, Bociek RG, Devetten MP, Vose JM, Joshi SS. ATM, CTLA4, MNDA and HEM1 in High versus Low CD38-Expressing B-Cell Chronic Lymphocytic Leukemia. Clinical Cancer Research 13(18) 5295-5304 (2007).
  20. Ruthermund CA, Gopalakrishnan VK, Eudy JD, and Vishwanatha JK.  Casodex treatment induces Hypoxia-related gene expression in the LNcAP prostate cancer progression model. BMC Urology5(1) 5, 2005.
  21. Shen, Y, Iqbal J, Xiao, L, Lynch, RC, Rosenqald, A, Staudt LM, Sherman, S, Dybkaer, K, Zhou, G, Eudy JD, Delabie, J, McKeithan TW, Chang WC.  Distinct gene expression profiles in different B-cell compartments in human peripheral lymphoid organs. BMC Immunology 5-20, 2004.
  22. Wiedmann S, Eudy JD, Zempleni J.  Biotin supplementation causes increased expression of genes encoding interferon-γ, interleukin-1β, and 3-methylcrotonyl-CoA carboxylase, and causes decreased expression of the gene encoding interleukin-4 in human peripheral blood mononuclear cells. Journal of Nutrition 133:716-9, 2003.
  23. Huang DH, Eudy JD, Uzvolgyi E, Davis JR, Talmadge CB, Pretto D, Weston MD, Lehman JE, Zhou M, Seemayer TA, Ahmad I, Kimberling WJ, Sumegi J.  Identification of the mouse and rat orthologs of the gene mutated in Usher syndrome type IIA and the cellular source of USH2A mRNA in retina: a target tissue of the disease. Genomics 80:195-203, 2002.
  24. Finnell RH, Gelineau-van Waes J, Eudy JD, Rosenquist TH.  Molecular Basis of Environmentally-Induced Birth Defects. Annual Review of Pharmacology and Toxicology. 42:181-208, 2002.
  25. Weston MD, Eudy JD, Fujita S, Yao SF, Sumegi J, Kimberling WJ.  Genomic structure and identification of novel mutations in usherin, the gene responsible for usher syndrome type IIa. American Journal of Human Genetics. First two authors contributed equally to this manuscript. 66:1199-1210, 2000.
  26. Spiegelstein O, Eudy JD, and Finnell, RH.  Identification of two novel folate receptor genes in mouse and humans. Gene. First two authors contributed equally to this manuscript. 27;258:117-25, 2000.
  27. Eudy JD, Spiegelstein O, Barber RC, Wlodarczyk BJ, Talbot J, Finnell, RH.  Identification and characterization of the human and mouse SLC19A3 gene: a novel member of the reduced folate family of micronutrient transporter genes. Molecular Genetics and Metabolism. First two authors contributed equally to this manuscript. 71:581-590, 2000.
  28. Eudy JD, Sumegi J.  Cellular and molecular aspects of Usher Syndrome. Cellular and Molecular Life Sciences 56:258-267, 1999.
  29. Eudy JD, Yao SF, Ma-Edmonds M, Talmadge C, Weston MD, Kimberling W, Sumegi J.  Isolation of a gene encoding a novel member of the orphan hormone receptor superfamily from the Usher Syndrome Type 2a locus on Chr 1q41.Genomics 50:382-384, 1998.
  30. Eudy JD, Weston MD, Yao SF, Hoover DM, Ma-Edmonds M, Yan D, Cheng JJ, Beisel K, Ayuso C, Cremers C, Davenport S, Moller C, Talmadge C, Tamayo M, Swaroop A, Kimberling WJ, Sumegi J.  A novel gene encoding a protein with extracellular matrix motifs is mutated in Usher syndrome type 2a. Science 280:1753-1757, 1998.