Sean Davis

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc SRAdb: query and use public next-generation sequencing data from within R
    Yuelin Zhu
    Genetics Branch, National Cancer Institute, National Institutes of HealthBethesda, MD 20892, USA
    BMC Bioinformatics 14:19. 2013
  2. ncbi request reprint GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor
    Sean Davis
    Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
    Bioinformatics 23:1846-7. 2007
  3. doi request reprint Genome-wide methylation profiling in archival formalin-fixed paraffin-embedded tissue samples
    J Keith Killian
    Cancer Genetics Branch, National Institutes of Health National Cancer Institute, Bethesda, MD, USA
    Methods Mol Biol 823:107-18. 2012
  4. pmc DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays
    Gregory E Crawford
    National Human Genome Research Institute, National Institutes of Health, Building 31, Room 4B09, Bethesda, Maryland 20892, USA
    Nat Methods 3:503-9. 2006
  5. pmc GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus
    Yuelin Zhu
    Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Bioinformatics 24:2798-800. 2008
  6. pmc Canine tumor cross-species genomics uncovers targets linked to osteosarcoma progression
    Melissa Paoloni
    Comparative Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    BMC Genomics 10:625. 2009
  7. pmc Comparative exome sequencing of metastatic lesions provides insights into the mutational progression of melanoma
    Jared J Gartner
    The Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    BMC Genomics 13:505. 2012
  8. pmc A methyl-deviator epigenotype of estrogen receptor-positive breast carcinoma is associated with malignant biology
    J Keith Killian
    Genetics Branch, National Cancer Institute, Bethesda, MD 20892, USA
    Am J Pathol 179:55-65. 2011
  9. pmc Identification of an inhibitor of the EWS-FLI1 oncogenic transcription factor by high-throughput screening
    Patrick J Grohar
    Molecular Oncology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr MSC 1104, 10 CRC 1W 3816, Bethesda, MD 20892 1104, USA
    J Natl Cancer Inst 103:962-78. 2011
  10. pmc Archival fine-needle aspiration cytopathology (FNAC) samples: untapped resource for clinical molecular profiling
    J Keith Killian
    Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Bethesda, MD 20892 4265, USA
    J Mol Diagn 12:739-45. 2010

Detail Information

Publications29

  1. pmc SRAdb: query and use public next-generation sequencing data from within R
    Yuelin Zhu
    Genetics Branch, National Cancer Institute, National Institutes of HealthBethesda, MD 20892, USA
    BMC Bioinformatics 14:19. 2013
    ..etc), Roche 454 GS System, Applied Biosystems SOLiD System, Helicos Heliscope, PacBio RS, and others...
  2. ncbi request reprint GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor
    Sean Davis
    Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
    Bioinformatics 23:1846-7. 2007
    ..Availability: GEOquery is available as part of the BioConductor project...
  3. doi request reprint Genome-wide methylation profiling in archival formalin-fixed paraffin-embedded tissue samples
    J Keith Killian
    Cancer Genetics Branch, National Institutes of Health National Cancer Institute, Bethesda, MD, USA
    Methods Mol Biol 823:107-18. 2012
    ..This chapter takes the reader step by step through a biomarker discovery experiment to identify phenotype-correlated DNA methylation signatures in routine pathology specimens...
  4. pmc DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays
    Gregory E Crawford
    National Human Genome Research Institute, National Institutes of Health, Building 31, Room 4B09, Bethesda, Maryland 20892, USA
    Nat Methods 3:503-9. 2006
    ..This method can be applied globally or in a targeted fashion to any tissue from any species with a sequenced genome...
  5. pmc GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus
    Yuelin Zhu
    Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Bioinformatics 24:2798-800. 2008
    ..abcc.ncifcrf.gov/geo/. The Bioconductor package is available via the Bioconductor project. The corresponding MATLAB implementation is also available at the same website...
  6. pmc Canine tumor cross-species genomics uncovers targets linked to osteosarcoma progression
    Melissa Paoloni
    Comparative Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    BMC Genomics 10:625. 2009
    ....
  7. pmc Comparative exome sequencing of metastatic lesions provides insights into the mutational progression of melanoma
    Jared J Gartner
    The Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    BMC Genomics 13:505. 2012
    ..Here we performed whole exome sequencing of two sets of matched normal and metastatic tumor DNAs...
  8. pmc A methyl-deviator epigenotype of estrogen receptor-positive breast carcinoma is associated with malignant biology
    J Keith Killian
    Genetics Branch, National Cancer Institute, Bethesda, MD 20892, USA
    Am J Pathol 179:55-65. 2011
    ..Finally, a comparison between metastases and primary tumors suggests methylation patterns are established early and maintained through disease progression for both ER(+) and ER(-) tumors...
  9. pmc Identification of an inhibitor of the EWS-FLI1 oncogenic transcription factor by high-throughput screening
    Patrick J Grohar
    Molecular Oncology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr MSC 1104, 10 CRC 1W 3816, Bethesda, MD 20892 1104, USA
    J Natl Cancer Inst 103:962-78. 2011
    ....
  10. pmc Archival fine-needle aspiration cytopathology (FNAC) samples: untapped resource for clinical molecular profiling
    J Keith Killian
    Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Bethesda, MD 20892 4265, USA
    J Mol Diagn 12:739-45. 2010
    ..Overall, this study identifies a largely untapped reserve of human pathology specimens for molecular profiling studies, with ramifications for the prospective collection of clinical biospecimens...
  11. pmc In vivo role of alternative splicing and serine phosphorylation of the microphthalmia-associated transcription factor
    Julien Debbache
    Mammalian Development Section, National Institute of Neurological Disorders and Stroke NINDS, National Institutes of Health, Bethesda, MD 20892, USA
    Genetics 191:133-44. 2012
    ..These results underscore, in vivo, the importance of the link between alternative splicing and post-translational modifications and may bear on the recent observation that exon 2B skipping can be found in metastatic melanoma...
  12. doi request reprint Large-scale profiling of archival lymph nodes reveals pervasive remodeling of the follicular lymphoma methylome
    J Keith Killian
    Genetics Branch, Laboratory of Pathology, NIH National Cancer Institute, Bethesda, Maryland, USA
    Cancer Res 69:758-64. 2009
    ..Analysis of the DMT profile is consistent with a pervasive epigenomic remodeling process in FL that affects predominantly nonlymphoid genes...
  13. pmc Genome-wide analysis of menin binding provides insights into MEN1 tumorigenesis
    Peter C Scacheri
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
    PLoS Genet 2:e51. 2006
    ..Our findings expand the realm of menin-targeted genes several hundred-fold beyond that previously described and provide potential insights to the endocrine tumor bias observed in MEN1 patients...
  14. pmc Preferential localization of human origins of DNA replication at the 5'-ends of expressed genes and at evolutionarily conserved DNA sequences
    Manuel S Valenzuela
    Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 6:e17308. 2011
    ....
  15. doi request reprint Vorinostat inhibits brain metastatic colonization in a model of triple-negative breast cancer and induces DNA double-strand breaks
    Diane Palmieri
    Women s Cancers Section, Laboratory of Molecular Pharmacology, Genetics Branch, National Cancer Institute NIH, Bethesda, Maryland, USA
    Clin Cancer Res 15:6148-57. 2009
    ..We report the pharmacokinetic, efficacy, and mechanism of action studies for the histone deactylase inhibitor vorinostat (suberoylanilide hydroxamic acid) in a preclinical model of brain metastasis of triple-negative breast cancer...
  16. pmc Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma
    Jared J Gartner
    National Human Genome Research Institute and National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
    Proc Natl Acad Sci U S A 110:13481-6. 2013
    ..Our data indicate that silent alterations have a role to play in human cancer, emphasizing the importance of their investigation in future cancer genome studies. ..
  17. pmc Exome sequencing identifies GRIN2A as frequently mutated in melanoma
    Xiaomu Wei
    The Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
    Nat Genet 43:442-6. 2011
    ..Our study provides, to our knowledge, the most comprehensive map of genetic alterations in melanoma to date and suggests that the glutamate signaling pathway is involved in this disease...
  18. pmc Analyses of resected human brain metastases of breast cancer reveal the association between up-regulation of hexokinase 2 and poor prognosis
    Diane Palmieri
    Women s Cancers Section, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892 7322, USA
    Mol Cancer Res 7:1438-45. 2009
    ..028). The data suggest that HK2 overexpression is associated with metastasis to the brain in breast cancer and it may be a therapeutic target...
  19. ncbi request reprint Ewing's sarcoma: general insights from a rare model
    Sean Davis
    Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Cancer Cell 9:331-2. 2006
    ..Using this strategy, Smith et al. have identified a homeobox gene, NKX2.2, which is both highly expressed in Ewing's sarcoma and essential for the transforming activity of EWS/FLI...
  20. pmc NCBI GEO: archive for functional genomics data sets--update
    Tanya Barrett
    National Center for Biotechnology Information, National Library of Medicine and Molecular Genetics Section, Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Nucleic Acids Res 41:D991-5. 2013
    ..This article reports current status and recent database developments, including the release of GEO2R, an R-based web application that helps users analyse GEO data...
  21. doi request reprint Chromothripsis and focal copy number alterations determine poor outcome in malignant melanoma
    Daniela Hirsch
    Genetics Branch, Center for Cancer Research, National Cancer Institute NIH, Bethesda, Maryland 20892, USA
    Cancer Res 73:1454-60. 2013
    ..Our study therefore links focal copy number alterations and chromothripsis with poor outcome in patients with malignant melanomas (P = 0.0002) and provides a genetic approach to predict outcome in malignant melanomas...
  22. pmc Advanced bone formation in mice with a dominant-negative mutation in the thyroid hormone receptor β gene due to activation of Wnt/β-catenin protein signaling
    Patrick J O'Shea
    Gene Regulation Section, Laboratory of Molecular Biology, NCI, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Biol Chem 287:17812-22. 2012
    ..These studies demonstrate novel interactions between T(3) and Wnt signaling pathways in the regulation of skeletal development and bone formation...
  23. pmc Interferon-γ links ultraviolet radiation to melanomagenesis in mice
    M Raza Zaidi
    Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
    Nature 469:548-53. 2011
    ..Our data reveal an unanticipated role for IFN-γ in promoting melanocytic cell survival/immunoevasion, identifying a novel candidate therapeutic target for a subset of melanoma patients...
  24. ncbi request reprint Constitutive Fms-like tyrosine kinase 3 activation results in specific changes in gene expression in myeloid leukaemic cells
    Kyu Tae Kim
    Department of Oncology, Johns Hopkins University School of Medicine, Bethesda, MD, USA
    Br J Haematol 138:603-15. 2007
    ..The alterations of the gene expression profiles in these cells help to further elucidate the mechanisms of FLT3-mediated leukaemogenesis...
  25. pmc Assessment of automated image analysis of breast cancer tissue microarrays for epidemiologic studies
    Kelly L Bolton
    Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland, USA
    Cancer Epidemiol Biomarkers Prev 19:992-9. 2010
    ..We assessed agreement between automated and pathologist scores of a diverse set of immunohistochemical assays done on breast cancer tissue microarrays (TMA)...
  26. pmc Database of mRNA gene expression profiles of multiple human organs
    Chang Gue Son
    Advanced Technology Center, Oncogenomics Section, Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health, Gaithersburg, Maryland 20877, USA
    Genome Res 15:443-50. 2005
    ..We expect this database will be of utility for developing rationally designed molecularly targeted therapeutics in diseases such as cancer, as well as for exploring the functions of genes...
  27. pmc Exclusion of the 750-kb genetically unstable region at Xq27 as a candidate locus for prostate malignancy in HPCX1-linked families
    Natalay Kouprina
    Laboratory of Molecular Pharmacology, NCI, NIH, Bethesda, MD, USA
    Genes Chromosomes Cancer 51:933-48. 2012
    ..Our results exclude the 750-kb genetically unstable region at Xq27 as a candidate locus for prostate malignancy. Adjacent regions appear to be the most likely candidates to identify the elusive HPCX1 locus...
  28. pmc A single IGF1 allele is a major determinant of small size in dogs
    Nathan B Sutter
    National Human Genome Research Institute, Building 50, Room 5349, 50 South Drive MSC 8000, Bethesda, MD 20892 8000, USA
    Science 316:112-5. 2007
    ..A single IGF1 single-nucleotide polymorphism haplotype is common to all small breeds and nearly absent from giant breeds, suggesting that the same causal sequence variant is a major contributor to body size in all small dogs...
  29. pmc Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)
    Gregory E Crawford
    National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Res 16:123-31. 2006
    ..This strategy, which can be applied to any cell line or tissue, will enable a better understanding of how chromatin structure dictates cell function and fate...