Chris Cheadle

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc PubMatrix: a tool for multiplex literature mining
    Kevin G Becker
    Gene Expression and Genomics Unit, National Institutes of Health, Baltimore, MD, USA
    BMC Bioinformatics 4:61. 2003
  2. ncbi request reprint Application of z-score transformation to Affymetrix data
    Chris Cheadle
    Cellular Biochemistry Section, Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Appl Bioinformatics 2:209-17. 2003
  3. pmc GSMA: Gene Set Matrix Analysis, An Automated Method for Rapid Hypothesis Testing of Gene Expression Data
    Chris Cheadle
    Genomics Core, Division of Allergy and Clinical Immunology, School of Medicine, Johns Hopkins University, 5200 Eastern Avenue, Baltimore, MD 21224
    Bioinform Biol Insights 1:49-62. 2009
  4. pmc Control of gene expression during T cell activation: alternate regulation of mRNA transcription and mRNA stability
    Chris Cheadle
    Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, NIH, 9000 Rockville Pike, Bethesda, MD 20892, USA
    BMC Genomics 6:75. 2005
  5. ncbi request reprint Stability regulation of mRNA and the control of gene expression
    Chris Cheadle
    Cellular Biochemistry Section, Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
    Ann N Y Acad Sci 1058:196-204. 2005
  6. doi request reprint Transcriptional analysis of kidneys during repair from AKI reveals possible roles for NGAL and KIM-1 as biomarkers of AKI-to-CKD transition
    Gang Jee Ko
    Nephrology Division, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Am J Physiol Renal Physiol 298:F1472-83. 2010
  7. pmc Transcriptional analysis of infiltrating T cells in kidney ischemia-reperfusion injury reveals a pathophysiological role for CCR5
    Gang Jee Ko
    Division of Nephrology, Department of Medicine, Johns Hopkins University School of Medicine, Ross Bldg, Rm 965, 720 Rutland Ave, Baltimore, MD 21205, USA
    Am J Physiol Renal Physiol 302:F762-73. 2012
  8. pmc A genomic-scale view of the cAMP response element-enhancer decoy: a tumor target-based genetic tool
    Yee Sook Cho
    Cellular Biochemistry Section, Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 99:15626-31. 2002
  9. pmc The local and systemic inflammatory transcriptome after acute kidney injury
    Dmitry N Grigoryev
    Division of Allergy and Clinical Immunology, 5501 Hopkins Bayview Circle, JHAAC 3A 62, Baltimore, Maryland, 21224, USA
    J Am Soc Nephrol 19:547-58. 2008
  10. pmc Analysis of microarray data using Z score transformation
    Chris Cheadle
    DNA Array Unit, Research Resources Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21221, USA
    J Mol Diagn 5:73-81. 2003

Detail Information

Publications37

  1. pmc PubMatrix: a tool for multiplex literature mining
    Kevin G Becker
    Gene Expression and Genomics Unit, National Institutes of Health, Baltimore, MD, USA
    BMC Bioinformatics 4:61. 2003
    ..PubMatrix is a web-based tool that allows simple text based mining of the NCBI literature search service PubMed using any two lists of keywords terms, resulting in a frequency matrix of term co-occurrence...
  2. ncbi request reprint Application of z-score transformation to Affymetrix data
    Chris Cheadle
    Cellular Biochemistry Section, Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Appl Bioinformatics 2:209-17. 2003
    ..Z-score transformation provides a useful tool for comparisons between experiments and between laboratories that use the Affymetrix platform...
  3. pmc GSMA: Gene Set Matrix Analysis, An Automated Method for Rapid Hypothesis Testing of Gene Expression Data
    Chris Cheadle
    Genomics Core, Division of Allergy and Clinical Immunology, School of Medicine, Johns Hopkins University, 5200 Eastern Avenue, Baltimore, MD 21224
    Bioinform Biol Insights 1:49-62. 2009
    ..Methods which allow the rapid and robust evaluation of multiple functional hypotheses increase the power of individual researchers to data mine gene expression data more efficiently...
  4. pmc Control of gene expression during T cell activation: alternate regulation of mRNA transcription and mRNA stability
    Chris Cheadle
    Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, NIH, 9000 Rockville Pike, Bethesda, MD 20892, USA
    BMC Genomics 6:75. 2005
    ..One reason for this difficulty may result from the intricate convergence of both transcriptional and mRNA turnover events which, together, directly influence steady-state mRNA levels...
  5. ncbi request reprint Stability regulation of mRNA and the control of gene expression
    Chris Cheadle
    Cellular Biochemistry Section, Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
    Ann N Y Acad Sci 1058:196-204. 2005
    ..It is proposed that the regulation of mRNA stability in response to external stimuli contributes significantly to observed changes in gene expression as measured by high throughput systems...
  6. doi request reprint Transcriptional analysis of kidneys during repair from AKI reveals possible roles for NGAL and KIM-1 as biomarkers of AKI-to-CKD transition
    Gang Jee Ko
    Nephrology Division, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Am J Physiol Renal Physiol 298:F1472-83. 2010
    ....
  7. pmc Transcriptional analysis of infiltrating T cells in kidney ischemia-reperfusion injury reveals a pathophysiological role for CCR5
    Gang Jee Ko
    Division of Nephrology, Department of Medicine, Johns Hopkins University School of Medicine, Ross Bldg, Rm 965, 720 Rutland Ave, Baltimore, MD 21205, USA
    Am J Physiol Renal Physiol 302:F762-73. 2012
    ..Using discovery techniques to identify transcriptional responses in purified kidney-infiltrating cells enabled the elucidation of novel mechanisms and therapeutic targets for IRI...
  8. pmc A genomic-scale view of the cAMP response element-enhancer decoy: a tumor target-based genetic tool
    Yee Sook Cho
    Cellular Biochemistry Section, Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 99:15626-31. 2002
    ..The CRE-decoy ODN, therefore, may serve as a target-based genetic tool to treat cancer and other diseases in which CRE-directed transcription is abnormally used...
  9. pmc The local and systemic inflammatory transcriptome after acute kidney injury
    Dmitry N Grigoryev
    Division of Allergy and Clinical Immunology, 5501 Hopkins Bayview Circle, JHAAC 3A 62, Baltimore, Maryland, 21224, USA
    J Am Soc Nephrol 19:547-58. 2008
    ..Functional genomic analysis identified potential mediators that connect local and systemic inflammation, suggesting that this type of analysis may be a useful discovery tool for novel biomarkers and therapeutic drug development...
  10. pmc Analysis of microarray data using Z score transformation
    Chris Cheadle
    DNA Array Unit, Research Resources Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21221, USA
    J Mol Diagn 5:73-81. 2003
    ..The results provided by these methods can be as rigorous and are no more arbitrary than other test methods, and, in addition, they have the advantage that they can be easily adapted to standard spreadsheet programs...
  11. ncbi request reprint A rapid method for microarray cross platform comparisons using gene expression signatures
    Chris Cheadle
    Genomics Core, Division of Allergy and Clinical Immunology, School of Medicine, Johns Hopkins University, Mason Lord Bldg, Center Tower, Rm 664, 5200 Eastern Avenue, Baltimore, MD 21224, USA
    Mol Cell Probes 21:35-46. 2007
    ....
  12. pmc Activation of cyclic AMP signaling leads to different pathway alterations in lesions of the adrenal cortex caused by germline PRKAR1A defects versus those due to somatic GNAS mutations
    Madson Q Almeida
    Section on Endocrinology and Genetics, Program on Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Building 10, CRC, Room 1 3330, 10 Center Drive, MSC1103, Bethesda, Maryland 20892, USA
    J Clin Endocrinol Metab 97:E687-93. 2012
    ....
  13. pmc Differentially expressed genes in MHC-compatible rat strains that are susceptible or resistant to experimental autoimmune uveitis
    Mary J Mattapallil
    Laboratory of Immunology, National Eye Institute, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA
    Invest Ophthalmol Vis Sci 49:1957-70. 2008
    ..The primary objective of this study was to identify the non-MHC genes involved in the pathogenesis of EAU, to identify potential drug targets and possibly to target their protein products for immunotherapy...
  14. pmc Hypoxia-induced mitogenic factor (HIMF/FIZZ1/RELMĪ±) in chronic hypoxia- and antigen-mediated pulmonary vascular remodeling
    Daniel J Angelini
    Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Respir Res 14:1. 2013
    ..We investigate the nature of the vascular remodeling and the expression and role of hypoxia-induced mitogenic factor (HIMF/FIZZ1/RELMĪ±) in explaining this differential response...
  15. pmc Time-dependent c-Myc transactomes mapped by Array-based nuclear run-on reveal transcriptional modules in human B cells
    Jinshui Fan
    Lowe Family Genomics Core, Division of Allergy and Clinical Immunology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
    PLoS ONE 5:e9691. 2010
    ....
  16. pmc Renal ischemia-reperfusion leads to long term infiltration of activated and effector-memory T lymphocytes
    Miguel Ascon
    Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
    Kidney Int 75:526-35. 2009
    ..Our study demonstrates that moderate or severe kidney ischemia induces long-term T lymphocyte infiltration and cytokine/chemokine upregulation, leading to kidney structural changes...
  17. pmc Pulmonary endothelial cell activation during experimental acute kidney injury
    Carolyn M Feltes
    Departments of Anesthesia and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
    Shock 36:170-6. 2011
    ..Further mechanistic analysis of EC-specific events in the lung during AKI might reveal potential novel therapeutic targets for the deleterious kidney-lung crosstalk in the critically ill patient...
  18. pmc Chemokine transcripts as targets of the RNA-binding protein HuR in human airway epithelium
    Jinshui Fan
    Division of Allergy and Clinical Immunology, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
    J Immunol 186:2482-94. 2011
    ..HuR-mediated regulation in airway epithelium appears broader than previously appreciated, coordinating numerous inflammatory genes through multiple posttranscriptional mechanisms...
  19. doi request reprint Effects of anti-adhesive therapy on kidney biomarkers of ischemia reperfusion injury in human deceased donor kidney allografts
    Chris Cheadle
    Lowe Family Genomics Core, Johns Hopkins University, Baltimore, MD, USA
    Clin Transplant 25:766-75. 2011
    ..Molecular biomarkers validated previously in animal models are increasingly being studied in conjunction with traditional clinical endpoints in therapeutic trials...
  20. pmc Array-based nuclear run-on analysis
    Jinshui Fan
    Lowe Family Genomics Core, Division of Allergy and Clinical Immunology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
    Methods Mol Biol 809:505-17. 2012
    ..It involves the genome-wide labeling of nascent transcripts using nonradioactive modified nucleotides, their isolation for amplification, and their hybridization and analysis using commercial microarrays...
  21. pmc Protein kinase A regulates caspase-1 via Ets-1 in bone stromal cell-derived lesions: a link between cyclic AMP and pro-inflammatory pathways in osteoblast progenitors
    Madson Q Almeida
    PDEGEN, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
    Hum Mol Genet 20:165-75. 2011
    ....
  22. pmc Transcription of proteinase 3 and related myelopoiesis genes in peripheral blood mononuclear cells of patients with active Wegener's granulomatosis
    Chris Cheadle
    Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
    Arthritis Rheum 62:1744-54. 2010
    ..The aim of this study was to understand the biology underlying WG and to discover markers of disease activity that would be useful for prognosis and treatment guidance...
  23. doi request reprint Hypoxia-induced mitogenic factor (HIMF/FIZZ1/RELMalpha) increases lung inflammation and activates pulmonary microvascular endothelial cells via an IL-4-dependent mechanism
    Kazuyo Yamaji-Kegan
    Department of Anesthesiology and Critical Care Medicine, The Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA
    J Immunol 185:5539-48. 2010
    ..These findings suggest that IL-4 signaling may play a significant role in HIMF-induced lung inflammation and vascular remodeling...
  24. ncbi request reprint Protein kinase A isozyme switching: eliciting differential cAMP signaling and tumor reversion
    Catherine L Neary
    Cellular Biochemistry Section, Basic Research Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 1750, USA
    Oncogene 23:8847-56. 2004
    ..Differential expression of PKA R subunits may therefore serve as a tumor-target-based gene therapy for PC3M prostate and other cancers...
  25. pmc von Hippel-Lindau protein-mediated repression of tumor necrosis factor alpha translation revealed through use of cDNA arrays
    Stefanie Galban
    Laboratory of Cellular and Molecular Biology, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
    Mol Cell Biol 23:2316-28. 2003
    ..Our findings uncover a novel function for the pVHL tumor suppressor protein as regulator of protein translation...
  26. pmc Mouse Prkar1a haploinsufficiency leads to an increase in tumors in the Trp53+/- or Rb1+/- backgrounds and chemically induced skin papillomas by dysregulation of the cell cycle and Wnt signaling
    Madson Q Almeida
    Section on Endocrinology and Genetics, Program on Developmental Endocrinology and Genetics, Eunice KennedyShriver, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
    Hum Mol Genet 19:1387-98. 2010
    ....
  27. pmc Role of the RNA-binding protein tristetraprolin in glucocorticoid-mediated gene regulation
    Faoud T Ishmael
    Division of Allergy and Clinical Immunology, Johns Hopkins University, Baltimore, MD 21224, USA
    J Immunol 180:8342-53. 2008
    ..These results reveal a strong and previously unrecognized contribution of PTR to the anti-inflammatory action of GCs and point at TTP as a key factor mediating this process through a complex mechanism of action...
  28. pmc Erythroid-specific transcriptional changes in PBMCs from pulmonary hypertension patients
    Chris Cheadle
    Division of Allergy and Clinical Immunology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
    PLoS ONE 7:e34951. 2012
    ..The hypothesis tested in this study was that chronic exposure of PBMCs to a hypertensive environment in remodeled pulmonary vessels would be reflected by specific transcriptional changes in these cells...
  29. pmc Integrated genomic analysis of nodular tissue in macronodular adrenocortical hyperplasia: progression of tumorigenesis in a disorder associated with multiple benign lesions
    Madson Q Almeida
    Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Clin Endocrinol Metab 96:E728-38. 2011
    ..Massive macronodular adrenocortical disease or ACTH-independent macronodular adrenal hyperplasia (AIMAH) is a clinically and genetically heterogeneous disorder...
  30. pmc Vaccinia virus-specific molecular signature in atopic dermatitis skin
    Dmitry N Grigoryev
    Division of Allergy and Clinical Immunology, Johns Hopkins University, Baltimore, MD, USA
    J Allergy Clin Immunol 125:153-159.e28. 2010
    ..However, the precise mechanism or mechanisms and key factor or factors of EV are unknown...
  31. pmc Late stage erythroid precursor production is impaired in mice with chronic inflammation
    Olivier D Prince
    Geriatric Medicine and Gerontology, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
    Haematologica 97:1648-56. 2012
    ....
  32. ncbi request reprint Dissecting the circuitry of protein kinase A and cAMP signaling in cancer genesis: antisense, microarray, gene overexpression, and transcription factor decoy
    Yoon S Cho-Chung
    Cellular Biochemistry Section, BRL, CCR, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892 1750, USA
    Ann N Y Acad Sci 968:22-36. 2002
    ..Thus, a complex circuitry of cAMP signaling comprises cAMP growth regulatory function, and deregulation of the effector molecule by this circuitry may underlie cancer genesis and tumor progression...
  33. ncbi request reprint Ischemic acute kidney injury induces a distant organ functional and genomic response distinguishable from bilateral nephrectomy
    Heitham T Hassoun
    Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
    Am J Physiol Renal Physiol 293:F30-40. 2007
    ..Further investigation using this lung molecular signature induced by kidney IRI will provide mechanistic insights and new therapies for critically ill patients with AKI...
  34. ncbi request reprint AF5, a CNS cell line immortalized with an N-terminal fragment of SV40 large T: growth, differentiation, genetic stability, and gene expression
    M E Truckenmiller
    Cellular Neurobiology Research Branch, National Institute on Drug Abuse, 5500 Nathan Shock Drive, Baltimore, Maryland 21224, USA
    Exp Neurol 175:318-37. 2002
    ..These data suggest that the AF5 cell line may be useful as an in vitro model system for studies of neural differentiation...
  35. pmc Precise probes of type II interferon activity define the origin of interferon signatures in target tissues in rheumatic diseases
    John C Hall
    Division of Rheumatology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
    Proc Natl Acad Sci U S A 109:17609-14. 2012
    ..Precise probes of the different IFN pathways active in tissues of complex rheumatic diseases will be critical to classify disease, elucidate pathogenesis, and select therapy...
  36. ncbi request reprint Development of a highly specialized cDNA array for the study and diagnosis of epithelial ovarian cancer
    G Peter Sawiris
    Laboratory of Cellular and Molecular Biology, Gerontology Research Center, National Institute on Aging NIH, 5600 Nathan Shock Drive, Baltimore, MD 21224, USA
    Cancer Res 62:2923-8. 2002
    ....
  37. ncbi request reprint DSCR1(Adapt78) modulates expression of SOD1
    Gennady Ermak
    Ethel Percy Andrus Gerontology Center, University of Southern California, 3715 McClintock Avenue, Los Angeles, CA 90089 0191, USA
    FASEB J 18:62-9. 2004
    ..These data also have importance for our understanding of Down's syndrome, Alzheimer's disease, and other human pathologies...