Research Topics
Genomes and Genes | Sean DavisSummaryAffiliation: National Institutes of Health Country: USA Publications
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Publications
SRAdb: query and use public next-generation sequencing data from within RYuelin Zhu
Genetics Branch, National Cancer Institute, National Institutes of HealthBethesda, MD 20892, USA
BMC Bioinformatics 14:19. 2013..abstract:..
GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductorSean 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...
Genome-wide methylation profiling in archival formalin-fixed paraffin-embedded tissue samplesJ 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...- DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarraysGregory 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... - GEOmetadb: powerful alternative search engine for the Gene Expression OmnibusYuelin 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... - Canine tumor cross-species genomics uncovers targets linked to osteosarcoma progressionMelissa Paoloni
Comparative Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
BMC Genomics 10:625. 2009.... - A methyl-deviator epigenotype of estrogen receptor-positive breast carcinoma is associated with malignant biologyJ 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... - Identification of an inhibitor of the EWS-FLI1 oncogenic transcription factor by high-throughput screeningPatrick 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..quot;.. - Archival fine-needle aspiration cytopathology (FNAC) samples: untapped resource for clinical molecular profilingJ 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... - In vivo role of alternative splicing and serine phosphorylation of the microphthalmia-associated transcription factorJulien 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... - Preferential localization of human origins of DNA replication at the 5'-ends of expressed genes and at evolutionarily conserved DNA sequencesManuel 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.... - Large-scale profiling of archival lymph nodes reveals pervasive remodeling of the follicular lymphoma methylomeJ 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... - Genome-wide analysis of menin binding provides insights into MEN1 tumorigenesisPeter 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... - Comparative exome sequencing of metastatic lesions provides insights into the mutational progression of melanomaJared 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... - Vorinostat inhibits brain metastatic colonization in a model of triple-negative breast cancer and induces DNA double-strand breaksDiane 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... - Analyses of resected human brain metastases of breast cancer reveal the association between up-regulation of hexokinase 2 and poor prognosisDiane 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... - Ewing's sarcoma: general insights from a rare modelSean 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... - Exome sequencing identifies GRIN2A as frequently mutated in melanomaXiaomu 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... - 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 signalingPatrick 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... - Interferon-γ links ultraviolet radiation to melanomagenesis in miceM 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... - Assessment of automated image analysis of breast cancer tissue microarrays for epidemiologic studiesKelly 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)... - Constitutive Fms-like tyrosine kinase 3 activation results in specific changes in gene expression in myeloid leukaemic cellsKyu 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... - Database of mRNA gene expression profiles of multiple human organsChang 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... - Exclusion of the 750-kb genetically unstable region at Xq27 as a candidate locus for prostate malignancy in HPCX1-linked familiesNatalay 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... - A single IGF1 allele is a major determinant of small size in dogsNathan 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... - 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...