All Stories

  1. BiocPkgTools: Toolkit for mining the Bioconductor package ecosystem

    Article • F1000Research, May 2019, Faculty of 1000, Ltd.

    Sean Davis, Dr Matthew E Ritchie, Martin Morgan

  2. BiocPkgTools: Toolkit for Mining the Bioconductor Package Ecosystem

    Article • May 2019, Cold Spring Harbor Laboratory Press

    Sean Davis

  3. recount-brain: a curated repository of human brain RNA-seq datasets metadata

    Article • April 2019, Cold Spring Harbor Laboratory Press

    Sean Davis

  4. restfulSE: A semantically rich interface for cloud-scale genomics with Bioconductor

    Article • F1000Research, January 2019, Faculty of 1000, Ltd.

    Sean Davis, Martin Morgan, Shweta Gopaulakrishnan

  5. Orchestrating a community-developed computational workshop and accompanying training materials

    Article • F1000Research, October 2018, Faculty of 1000, Ltd.

    Marcel Ramos, Dr Benjamin Haibe-Kains, Levi Waldron, Martin Morgan, Sean Davis

  6. Resources for Interpreting Variants in Precision Genomic Oncology Applications

    Article • July 2017, Cold Spring Harbor Laboratory Press

    Sean Davis

  7. Software For The Integration Of Multi-Omics Experiments In Bioconductor

    Article • June 2017, Cold Spring Harbor Laboratory Press

    Sean Davis

  8. GenomicDataCommons: a Bioconductor Interface to the NCI Genomic Data Commons

    Article • March 2017, Cold Spring Harbor Laboratory Press

    Sean Davis

  9. RARRES2 functions as a tumor suppressor by promoting β-catenin phosphorylation/degradation and inhibiting p38 phosphorylation in adrenocortical carcinoma

    Article • Oncogene, January 2017, Springer Science + Business Media

    Sean Davis

  10. Upregulation of IFN-Inducible and Damage-Response Pathways in Chronic Graft-versus-Host Disease

    Article • The Journal of Immunology, September 2016, The American Association of Immunologists

    Sean Davis

  11. On the Selective Packaging of Genomic RNA by HIV-1

    Article • Viruses, September 2016, MDPI AG

    Sean Davis

  12. The Bioconductor channel in F1000Research

    Article • F1000Research, April 2016, Faculty of 1000, Ltd.

    Sean Davis

  13. Statistical Genomics

    Article • January 2016, Springer Science + Business Media

    Sean Davis

  14. The Bioconductor channel in F1000Research

    Article • F1000Research, July 2015, Faculty of 1000, Ltd.

    Sean Davis

  15. Integrated analysis of DNA methylation, immunohistochemistry and mRNA expression, data identifies a methylation expression index (MEI) robustly associated with survival of ER-positive breast cancer patients

    Article • Breast Cancer Research and Treatment, March 2015, Springer Science + Business Media

    Sean Davis

  16. Super-enhancers delineate disease-associated regulatory nodes in T cells

    Article • Nature, February 2015, Springer Science + Business Media

    Sean Davis

  17. Orchestrating high-throughput genomic analysis with Bioconductor

    Article • Nature Methods, January 2015, Springer Science + Business Media

    Sean Davis

  18. Antagonistic Cross-Regulation between Sox9 and Sox10 Controls an Anti-tumorigenic Program in Melanoma

    Article • PLoS Genetics, January 2015, PLOS

    Sean Davis

  19. miR30a Inhibits LOX Expression and Anaplastic Thyroid Cancer Progression

    Article • Cancer Research, December 2014, American Association for Cancer Research (AACR)

    Sean Davis

  20. NCI-60 Whole Exome Sequencing and Pharmacological CellMiner Analyses

    Article • PLoS ONE, July 2014, PLOS

    Sean Davis

  21. Lineage of origin in rhabdomyosarcoma informs pharmacological response

    Article • Genes & Development, July 2014, Cold Spring Harbor Laboratory Press

    Sean Davis

  22. Genome-Wide Methylation Patterns in Papillary Thyroid Cancer Are Distinct Based on Histological Subtype and Tumor Genotype

    Article • The Journal of Clinical Endocrinology & Metabolism, February 2014, Endocrine Society

    Sean Davis

  23. Downregulation of IGFBP2 is associated with resistance to IGF1R therapy in rhabdomyosarcoma

    Article • Oncogene, December 2013, Springer Science + Business Media

    Sean Davis

  24. Prohibitin expression is associated with high grade breast cancer but is not a driver of amplification at 17q21.33

    Article • Pathology, December 2013, Elsevier

    Sean Davis

  25. High prevalence of MAP2K1 mutations in variant and IGHV4-34–expressing hairy-cell leukemias

    Article • Nature Genetics, November 2013, Springer Science + Business Media

    Sean Davis

  26. A Polymorphism in IRF4 Affects Human Pigmentation through a Tyrosinase-Dependent MITF/TFAP2A Pathway

    Article • Cell, November 2013, Elsevier

    Sean Davis

  27. Oncogenic ETS fusions deregulate E2F3 target genes in Ewing sarcoma and prostate cancer

    Article • Genome Research, August 2013, Cold Spring Harbor Laboratory Press

    Sean Davis

  28. Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma

    Article • Proceedings of the National Academy of Sciences, July 2013, Proceedings of the National Academy of Sciences

    Sean Davis

  29. The Exomes of the NCI-60 Panel: A Genomic Resource for Cancer Biology and Systems Pharmacology

    Article • Cancer Research, July 2013, American Association for Cancer Research (AACR)

    Sean Davis

  30. Whole Genome and Transcriptome Sequencing of a B3 Thymoma

    Article • PLoS ONE, April 2013, PLOS

    Sean Davis

  31. Harnessing genomics to identify environmental determinants of heritable disease

    Article • Mutation Research/Reviews in Mutation Research, January 2013, Elsevier

    Dr Francesco Marchetti, Sean Davis

  32. RCircos: an R package for Circos 2D track plots

    Article • BMC Bioinformatics, January 2013, Springer Science + Business Media

    Sean Davis

  33. Rb1 loss modifies but does not initiate alveolar rhabdomyosarcoma

    Article • Skeletal Muscle, January 2013, Springer Science + Business Media

    Sean Davis

  34. SRAdb: query and use public next-generation sequencing data from within R

    Article • BMC Bioinformatics, January 2013, Springer Science + Business Media

    Sean Davis

  35. Chromothripsis and Focal Copy Number Alterations Determine Poor Outcome in Malignant Melanoma

    Article • Cancer Research, December 2012, American Association for Cancer Research (AACR)

    Sean Davis

  36. NCBI GEO: archive for functional genomics data sets—update

    Article • Nucleic Acids Research, November 2012, Oxford University Press (OUP)

    Sean Davis

  37. Exclusion of the 750-kb genetically unstable region at Xq27 as a candidate locus for prostate malignancy in HPCX1-linked families

    Article • Genes Chromosomes and Cancer, June 2012, Wiley

    Sean Davis

  38. 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

    Article • Journal of Biological Chemistry, March 2012, American Society for Biochemistry & Molecular Biology (ASBMB)

    Sean Davis

  39. In Vivo Role of Alternative Splicing and Serine Phosphorylation of the Microphthalmia-Associated Transcription Factor

    Article • Genetics, February 2012, Genetics Society of America

    Sean Davis

  40. Comparative exome sequencing of metastatic lesions provides insights into the mutational progression of melanoma

    Article • BMC Genomics, January 2012, Springer Science + Business Media

    Sean Davis

  41. Genome-Wide Methylation Profiling in Archival Formalin-Fixed Paraffin-Embedded Tissue Samples

    Article • October 2011, Springer Science + Business Media

    Sean Davis

  42. Genome-wide depletion of replication initiation events in highly transcribed regions

    Article • Genome Research, August 2011, Cold Spring Harbor Laboratory Press

    Sean Davis

  43. CHEK2 genomic and proteomic analyses reveal genetic inactivation or endogenous activation across the 60 cell lines of the US National Cancer Institute

    Article • Oncogene, July 2011, Springer Science + Business Media

    Sean Davis

  44. A Methyl-Deviator Epigenotype of Estrogen Receptor–Positive Breast Carcinoma Is Associated with Malignant Biology

    Article • American Journal Of Pathology, July 2011, Elsevier

    Sean Davis

  45. Identification of an Inhibitor of the EWS-FLI1 Oncogenic Transcription Factor by High-Throughput Screening

    Article • JNCI Journal of the National Cancer Institute, June 2011, Oxford University Press (OUP)

    Sean Davis

  46. Preferential Localization of Human Origins of DNA Replication at the 5′-Ends of Expressed Genes and at Evolutionarily Conserved DNA Sequences

    Article • PLoS ONE, May 2011, PLOS

    Sean Davis

  47. Exome sequencing identifies GRIN2A as frequently mutated in melanoma

    Article • Nature Genetics, April 2011, Springer Science + Business Media

    Sean Davis

  48. Evidence for an Unanticipated Relationship between Undifferentiated Pleomorphic Sarcoma and Embryonal Rhabdomyosarcoma

    Article • Cancer Cell, February 2011, Elsevier

    Sean Davis

  49. Interferon-γ links ultraviolet radiation to melanomagenesis in mice

    Article • Nature, January 2011, Nature

    Dr Howard A Young, Sean Davis

  50. Archival Fine-Needle Aspiration Cytopathology (FNAC) Samples

    Article • Journal of Molecular Diagnostics, November 2010, Elsevier

    Sean Davis

  51. High frequencies of leukemia stem cells in poor-outcome childhood precursor-B acute lymphoblastic leukemias

    Article • Leukemia, August 2010, Springer Science + Business Media

    Sean Davis

  52. Epigenomic alterations and gene expression profiles in respiratory epithelia exposed to cigarette smoke condensate

    Article • Oncogene, May 2010, Springer Science + Business Media

    Sean Davis

  53. Assessment of Automated Image Analysis of Breast Cancer Tissue Microarrays for Epidemiologic Studies

    Article • Cancer Epidemiology Biomarkers & Prevention, March 2010, American Association for Cancer Research (AACR)

    Dr Stephen M Hewitt, Sean Davis

  54. Vorinostat Inhibits Brain Metastatic Colonization in a Model of Triple-Negative Breast Cancer and Induces DNA Double-Strand Breaks

    Article • Clinical Cancer Research, September 2009, American Association for Cancer Research (AACR)

    Sean Davis

  55. Analyses of Resected Human Brain Metastases of Breast Cancer Reveal the Association between Up-Regulation of Hexokinase 2 and Poor Prognosis

    Article • Molecular Cancer Research, September 2009, American Association for Cancer Research (AACR)

    Sean Davis

  56. A Molecular Function Map of Ewing's Sarcoma

    Article • PLoS ONE, April 2009, PLOS

    Sean Davis

  57. Kinetic Complexity of the Global Response to Glucocorticoid Receptor Action

    Article • Endocrinology, April 2009, Endocrine Society

    Sean Davis

  58. Analysis of the matrix metalloproteinase family reveals that MMP8 is often mutated in melanoma

    Article • Nature Genetics, March 2009, Springer Science + Business Media

    Sean Davis

  59. Large-Scale Profiling of Archival Lymph Nodes Reveals Pervasive Remodeling of the Follicular Lymphoma Methylome

    Article • Cancer Research, January 2009, American Association for Cancer Research (AACR)

    Sean Davis

  60. Canine tumor cross-species genomics uncovers targets linked to osteosarcoma progression

    Article • BMC Genomics, January 2009, Springer Science + Business Media

    Dr Stephen M Hewitt, Sean Davis

  61. Molecular Grading of Ductal Carcinoma In situ of the Breast

    Article • Clinical Cancer Research, December 2008, American Association for Cancer Research (AACR)

    Sean Davis

  62. GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus

    Article • Bioinformatics, October 2008, Oxford University Press (OUP)

    Sean Davis

  63. Rare Structural Variants Disrupt Multiple Genes in Neurodevelopmental Pathways in Schizophrenia

    Article • Science, April 2008, American Association for the Advancement of Science

    Sean Davis

  64. Interaction of the Glucocorticoid Receptor with the Chromatin Landscape

    Article • Molecular Cell, March 2008, Elsevier

    Sean Davis

  65. TRAIL induces apoptosis in triple-negative breast cancer cells with a mesenchymal phenotype

    Article • Breast Cancer Research and Treatment, February 2008, Springer Science + Business Media

    Sean Davis

  66. Suppressor role of activating transcription factor 2 (ATF2) in skin cancer

    Article • Proceedings of the National Academy of Sciences, February 2008, Proceedings of the National Academy of Sciences

    Sean Davis

  67. High-Resolution Mapping and Characterization of Open Chromatin across the Genome

    Article • Cell, January 2008, Elsevier

    Sean Davis

  68. Constitutive Fms-like tyrosine kinase 3 activation results in specific changes in gene expression in myeloid leukaemic cells

    Article • British Journal of Haematology, September 2007, Wiley

    Sean Davis

  69. Detection of Novel Amplicons in Prostate Cancer by Comprehensive Genomic Profiling of Prostate Cancer Cell Lines Using Oligonucleotide-Based ArrayCGH

    Article • PLoS ONE, August 2007, PLOS

    Sean Davis

  70. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

    Article • Nature, June 2007, Nature

    Dr Stefan Enroth, Piero Carninci, Sean Davis, Jonghwan Kim

  71. A Single IGF1 Allele Is a Major Determinant of Small Size in Dogs

    Article • Science, April 2007, American Association for the Advancement of Science

    Sean Davis

  72. Modeling Synovial Sarcoma: Timing Is Everything

    Article • Cancer Cell, April 2007, Elsevier

    Sean Davis

  73. DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays

    Article • Nature Methods, June 2006, Springer Science + Business Media

    Sean Davis

  74. Ewing's sarcoma: General insights from a rare model

    Article • Cancer Cell, May 2006, Elsevier

    Sean Davis

  75. Genome-Wide Analysis of Menin Binding Provides Insights into MEN1 Tumorigenesis

    Article • PLoS Genetics, January 2006, PLOS

    Sean Davis

  76. [14] Statistics for ChIP‐chip and DNase Hypersensitivity Experiments on NimbleGen Arrays

    Article • January 2006, Elsevier

    Sean Davis

  77. Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)

    Article • Genome Research, December 2005, Cold Spring Harbor Laboratory Press

    Sean Davis

  78. Gene Expression Profiling of Human Sarcomas: Insights into Sarcoma Biology

    Article • Cancer Research, October 2005, American Association for Cancer Research (AACR)

    Sean Davis

  79. BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis

    Article • Bioinformatics, August 2005, Oxford University Press (OUP)

    Sean Davis

  80. Database of mRNA gene expression profiles of multiple human organs

    Article • Genome Research, February 2005, Cold Spring Harbor Laboratory Press

    Sean Davis

  81. Impact of overlapping recruitment on linkage analysis of complex disorders: Simulation studies

    Article • American Journal of Medical Genetics, January 2001, Wiley

    Sean Davis

  82. Linkage and Association between Inflammatory Bowel Disease and a Locus on Chromosome 12

    Article • The American Journal of Human Genetics, July 1998, Elsevier

    Dr M Michael Barmada, Sean Davis

  83. Comparison of Nonparametric Statistics for Detection of Linkage in Nuclear Families: Single-Marker Evaluation

    Article • The American Journal of Human Genetics, December 1997, Elsevier

    Sean Davis

  84. Genetic Susceptibility for Human Familial Essential Hypertension in a Region of Homology with Blood Pressure Linkage on Rat Chromosome 10

    Article • Human Molecular Genetics, November 1997, Oxford University Press (OUP)

    Sean Davis

  85. Analysis of bipolar disorder using affected relatives

    Article • Genetic Epidemiology, January 1997, Wiley

    Sean Davis

  86. Analysis of bipolar disorder using affected relatives

    Article • Genetic Epidemiology, January 1997, Wiley

    Sean Davis

  87. Analysis of complex oligogenic disease

    Article • Genetic Epidemiology, January 1997, Wiley

    Sean Davis

  88. Analysis of complex oligogenic disease

    Article • Genetic Epidemiology, January 1997, Wiley

    Sean Davis

  89. Homozygosity mapping of Hallervorden–Spatz syndrome to chromosome 20p12.3–p13

    Article • Nature Genetics, December 1996, Springer Science + Business Media

    Sean Davis