Jonathan D Wren

Summary

Publications

  1. ncbi request reprint Meta-analysis of published transcriptional and translational fold changes reveals a preference for low-fold inductions
    Jonathan D Wren
    Advanced Center for Genome Technology, Department of Botany and Microbiology, The University of Oklahoma, Norman, 73019, USA
    OMICS 10:15-27. 2006
  2. ncbi request reprint A system-wide analysis of differentially expressed genes in ectopic and eutopic endometrium
    Jonathan D Wren
    Arthritis and Immunology Research Program, Oklahoma Medical Research Foundation, 825 N E 13th Street, Oklahoma City, OK 73104 5005, USA
    Hum Reprod 22:2093-102. 2007
  3. pmc Large-scale directional relationship extraction and resolution
    Cory B Giles
    Arthritis and Immunology Research Program, Oklahoma Medical Research Foundation, 825 N, E, 13th Street, Oklahoma City, Oklahoma 73104 5005, USA
    BMC Bioinformatics 9:S11. 2008
  4. pmc A global meta-analysis of microarray expression data to predict unknown gene functions and estimate the literature-data divide
    Jonathan D Wren
    Arthritis and Immunology Research Program, Oklahoma Medical Research Foundation, 825 N E 13th Street, Oklahoma City, OK 73104 5005, USA
    Bioinformatics 25:1694-701. 2009
  5. pmc Experimental validation of 5 in-silico predicted glioma biomarkers
    Rheal A Towner
    Corresponding author Rheal A Towner, PhD, Director, Advanced Magnetic Resonance Center, Oklahoma Medical Research Foundation, 825 N E 13th Street, Oklahoma City, OK 73104 USA
    Neuro Oncol 15:1625-34. 2013
  6. pmc Circulating IGF-1 deficiency exacerbates hypertension-induced microvascular rarefaction in the mouse hippocampus and retrosplenial cortex: implications for cerebromicrovascular and brain aging
    Stefano Tarantini
    Reynolds Oklahoma Center on Aging, Donald W Reynolds Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
    Age (Dordr) 38:273-289. 2016
  7. pmc GenomeRunner: automating genome exploration
    Mikhail G Dozmorov
    Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104 5005, USA
    Bioinformatics 28:419-20. 2012
  8. pmc Functional characterization of the MECP2/IRAK1 lupus risk haplotype in human T cells and a human MECP2 transgenic mouse
    Kristi A Koelsch
    Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
    J Autoimmun 41:168-74. 2013
  9. pmc GFP affects human T cell activation and cytokine production following in vitro stimulation
    Kristi A Koelsch
    Oklahoma Medical Research Foundation, Arthritis and Clinical Immunology Program, Oklahoma City, Oklahoma, USA
    PLoS ONE 8:e50068. 2013
  10. pmc Predicting gene ontology from a global meta-analysis of 1-color microarray experiments
    Mikhail G Dozmorov
    Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation 825 NE 13th Street, Oklahoma City, Oklahoma 73104 5005, USA
    BMC Bioinformatics 12:S14. 2011

Collaborators

Detail Information

Publications32

  1. ncbi request reprint Meta-analysis of published transcriptional and translational fold changes reveals a preference for low-fold inductions
    Jonathan D Wren
    Advanced Center for Genome Technology, Department of Botany and Microbiology, The University of Oklahoma, Norman, 73019, USA
    OMICS 10:15-27. 2006
    ..All extracted regulation and response patterns can be downloaded at the following website: www.ou.edu/microarray/ oumcf/Meta_analysis.xls...
  2. ncbi request reprint A system-wide analysis of differentially expressed genes in ectopic and eutopic endometrium
    Jonathan D Wren
    Arthritis and Immunology Research Program, Oklahoma Medical Research Foundation, 825 N E 13th Street, Oklahoma City, OK 73104 5005, USA
    Hum Reprod 22:2093-102. 2007
    ..Thus, it is difficult to see 'the big picture' without first integrating these multiple, heterogeneous sources of high-quality information for analysis...
  3. pmc Large-scale directional relationship extraction and resolution
    Cory B Giles
    Arthritis and Immunology Research Program, Oklahoma Medical Research Foundation, 825 N, E, 13th Street, Oklahoma City, Oklahoma 73104 5005, USA
    BMC Bioinformatics 9:S11. 2008
    ..Because of the size and growth of biomedical literature, it is increasingly important to be able to automate this process as much as possible...
  4. pmc A global meta-analysis of microarray expression data to predict unknown gene functions and estimate the literature-data divide
    Jonathan D Wren
    Arthritis and Immunology Research Program, Oklahoma Medical Research Foundation, 825 N E 13th Street, Oklahoma City, OK 73104 5005, USA
    Bioinformatics 25:1694-701. 2009
    ..If we are to better understand human/mammalian biology and complete the catalog of human gene function, it is important to finish predicting putative functions for these genes based upon existing experimental evidence...
  5. pmc Experimental validation of 5 in-silico predicted glioma biomarkers
    Rheal A Towner
    Corresponding author Rheal A Towner, PhD, Director, Advanced Magnetic Resonance Center, Oklahoma Medical Research Foundation, 825 N E 13th Street, Oklahoma City, OK 73104 USA
    Neuro Oncol 15:1625-34. 2013
    ....
  6. pmc Circulating IGF-1 deficiency exacerbates hypertension-induced microvascular rarefaction in the mouse hippocampus and retrosplenial cortex: implications for cerebromicrovascular and brain aging
    Stefano Tarantini
    Reynolds Oklahoma Center on Aging, Donald W Reynolds Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
    Age (Dordr) 38:273-289. 2016
    ....
  7. pmc GenomeRunner: automating genome exploration
    Mikhail G Dozmorov
    Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104 5005, USA
    Bioinformatics 28:419-20. 2012
    ..Our goal is to provide partial automation of this process to begin examining associations between experimental features and annotated genomic regions in a hypothesis-free, data-driven manner...
  8. pmc Functional characterization of the MECP2/IRAK1 lupus risk haplotype in human T cells and a human MECP2 transgenic mouse
    Kristi A Koelsch
    Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
    J Autoimmun 41:168-74. 2013
    ....
  9. pmc GFP affects human T cell activation and cytokine production following in vitro stimulation
    Kristi A Koelsch
    Oklahoma Medical Research Foundation, Arthritis and Clinical Immunology Program, Oklahoma City, Oklahoma, USA
    PLoS ONE 8:e50068. 2013
    ..These findings indicate that the utilization of GFP-tagged vectors may negatively impact in vitro experiments in T cells, emphasizing the critical importance of controls to identify any GFP-induced effects...
  10. pmc Predicting gene ontology from a global meta-analysis of 1-color microarray experiments
    Mikhail G Dozmorov
    Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation 825 NE 13th Street, Oklahoma City, Oklahoma 73104 5005, USA
    BMC Bioinformatics 12:S14. 2011
    ..Our goal here is to define how sample, dataset size and ranking parameters affect prediction performance...
  11. pmc High-throughput processing and normalization of one-color microarrays for transcriptional meta-analyses
    Mikhail G Dozmorov
    Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation 825 NE 13th Street, Oklahoma City, Oklahoma 73104 5005, USA
    BMC Bioinformatics 12:S2. 2011
    ..Methods to automatically process large repositories of microarray data into a standardized, directly comparable format will enable easier and more reliable access to microarray data to conduct meta-analyses...
  12. pmc Elevated AKR1C3 expression promotes prostate cancer cell survival and prostate cell-mediated endothelial cell tube formation: implications for prostate cancer progression
    Mikhail G Dozmorov
    Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, 825 N, E, 13th Street, Oklahoma City, Oklahoma 73104, USA
    BMC Cancer 10:672. 2010
    ..Here we propose a novel pathological function of AKR1C3 in tumor angiogenesis and its potential role in promoting PCa progression...
  13. pmc IGF-1 deficiency in a critical period early in life influences the vascular aging phenotype in mice by altering miRNA-mediated post-transcriptional gene regulation: implications for the developmental origins of health and disease hypothesis
    Stefano Tarantini
    Reynolds Oklahoma Center on Aging, Donald W Reynolds Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
    Age (Dordr) 38:239-258. 2016
    ....
  14. pmc Absence of genomic hypomethylation or regulation of cytosine-modifying enzymes with aging in male and female mice
    Niran Hadad
    Oklahoma Center for Neuroscience, Oklahoma City, OK USA Reynolds Oklahoma Center on Aging, SLY BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA
    Epigenetics Chromatin 9:30. 2016
    ..Furthermore, existing data are limited to only male animals...
  15. pmc ELTD1, a potential new biomarker for gliomas
    Rheal A Towner
    Advanced Magnetic Resonance Center, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma 73104, USA
    Neurosurgery 72:77-90; discussion 91. 2013
    ..Glioblastoma multiforme (GBM), a high-grade glioma, is characterized by being diffuse, invasive, and highly angiogenic and has a very poor prognosis. Identification of new biomarkers could help in the further diagnosis of GBM...
  16. pmc Novel protein ADTRP regulates TFPI expression and function in human endothelial cells in normal conditions and in response to androgen
    Cristina Lupu
    Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
    Blood 118:4463-71. 2011
    ..We conclude that the ADTRP-dependent up-regulation of TFPI expression and activity by androgen represents a novel mechanism of increasing the anticoagulant protection of the endothelium...
  17. ncbi request reprint ELTD1, an effective anti-angiogenic target for gliomas: preclinical assessment in mouse GL261 and human G55 xenograft glioma models
    Jadith Ziegler
    Advanced Magnetic Resonance Center, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma J Z, R P, P C d S, B E, D S, N S, S M, C N, J D, O M, R A T Comparative Medicine, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma S T Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma J D W Vascular Biology Program, Boston Children s Hospital and Harvard Medical School, Karp Family Research Laboratories, Boston, Massachusetts Y D, H C Department of Pathology, Oklahoma City, Oklahoma J Z, K M F, R A T Department of Biochemistry and Molecular Biology, Oklahoma City, Oklahoma J D W Department of Surgery Research Laboratory, Oklahoma City, Oklahoma M L The Stephenson Cancer Center, Oklahoma City, Oklahoma J B, K M F, Feinberg School of Medicine of Northwestern University
    Neuro Oncol . 2016
    ..The focus of this study was to assess the effect on tumor growth of an antibody against ELTD1 in orthotopic, GL261, and G55 xenograft glioma models...
  18. pmc Bisulfite oligonucleotide-capture sequencing for targeted base- and strand-specific absolute 5-methylcytosine quantitation
    Dustin R Masser
    Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
    Age (Dordr) 38:49. 2016
    ..This oligonucleotide capture targeting approach and quantitative validation workflow can also be applied to any genome of interest. ..
  19. pmc PDGFRα signaling drives adipose tissue fibrosis by targeting progenitor cell plasticity
    Tomoaki Iwayama
    Immunobiology and Cancer Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma 73104, USA
    Genes Dev 29:1106-19. 2015
    ..These results identify perivascular cells as fibro/adipogenic progenitors in WAT and show that PDGFRα targets progenitor cell plasticity as a profibrotic mechanism. ..
  20. pmc Ska3 is required for spindle checkpoint silencing and the maintenance of chromosome cohesion in mitosis
    John R Daum
    Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
    Curr Biol 19:1467-72. 2009
    ..We suggest that this network plays a major role in silencing the spindle checkpoint when chromosomes are aligned at metaphase to allow timely anaphase onset and mitotic exit...
  21. pmc Proceedings of the 2008 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference
    Jonathan D Wren
    Arthritis and Immunology Research Program, Oklahoma Medical Research Foundation 825 N E 13th Street, Oklahoma City, OK 73104 5005, USA
    BMC Bioinformatics 9:S1. 2008
  22. pmc Proceedings of the Fourth Annual Conference of the MidSouth Computational Biology and Bioinformatics Society
    Dawn Wilkins
    Computer and Information Science Department, The University of Mississippi, University, MS, USA
    BMC Bioinformatics 8:S1. 2007
  23. ncbi request reprint Clustering microarray-derived gene lists through implicit literature relationships
    Mark F Burkart
    Department of Internal Medicine, The McDermott Center for Human Growth and Development, Division of Translational Research, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
    Bioinformatics 23:1995-2003. 2007
    ..New methods that can identify functionally related genes via shared literature concepts will be useful in addressing these needs...
  24. ncbi request reprint ARROGANT: an application to manipulate large gene collections
    Amit V Kulkarni
    Program in Biomedical Engineering, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
    Bioinformatics 18:1410-7. 2002
    ....
  25. ncbi request reprint Simulated annealing of microarray data reduces noise and enables cross-experimental comparisons
    Jonathan D Wren
    Advanced Center for Genome Technology, The University of Oklahoma, Norman, Oklahoma 73019, USA
    DNA Cell Biol 23:695-700. 2004
    ..Testing SA on a published dataset, we find that it significantly reduces interexperimental variation, suggesting it holds promise to accomplish this goal...
  26. ncbi request reprint Differential activation profiles of multiple transcription factors during dendritic cell maturation
    Norikatsu Mizumoto
    Department of Dermatology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
    J Invest Dermatol 124:718-24. 2005
    ..We propose that differential TF usage represents a previously unrecognized mechanism regulating the direction of DC maturation...
  27. ncbi request reprint Cross-hybridization on PCR-spotted microarrays
    Jonathan D Wren
    IEEE Eng Med Biol Mag 21:71-5. 2002