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. Software For The Integration Of Multi-Omics Experiments In Bioconductor. 2017.


. Resources for Interpreting Variants in Precision Genomic Oncology Applications. Frontiers in Oncology, 2017.


. RARRES2 functions as a tumor suppressor by promoting $beta$-catenin phosphorylation/degradation and inhibiting p38 phosphorylation in adrenocortical carcinoma. Oncogene, 2017.

. Autoreactive T Cells and Chronic Fungal Infection Drive Esophageal Carcinogenesis . *Cell Host & Microbe *, 2017.


. ASXL3 is a Novel Pluripotency Factor in Human Respiratory Epithelial Cells and a Potential Therapeutic Target in Small Cell Lung Cancer. Cancer Research, 2017.

. Upregulation of IFN-Inducible and Damage-Response Pathways in Chronic Graft-versus-Host Disease. J. Immunol., 2016.

. Public data and open source tools for multi-assay genomic investigation of disease. Brief. Bioinformatics, 2016.

. Point Mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis Variant. Am. J. Hum. Genet., 2016.

. caOmicsV: an R package for visualizing multidimensional cancer genomic data. BMC Bioinformatics, 2016.

. Whole Genome Sequencing of Newly Established Pancreatic Cancer Lines Identifies Novel Somatic Mutation (c.2587G>A) in Axon Guidance Receptor Plexin A1 as Enhancer of Proliferation and Invasion. PLoS ONE, 2016.

. Statistical Genomics. 2016.


. On the Selective Packaging of Genomic RNA by HIV-1. Viruses, 2016.

. Inhibition of Survivin with YM155 Induces Durable Tumor Response in Anaplastic Thyroid Cancer. Clin. Cancer Res., 2015.

. A Genome-Wide Scan Identifies Variants in NFIB Associated with Metastasis in Patients with Osteosarcoma. Cancer Discov, 2015.

. Super-enhancers delineate disease-associated regulatory nodes in T cells. Nature, 2015.

. 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. Breast Cancer Res. Treat., 2015.

. Dual inhibition of HDAC and EGFR signaling with CUDC-101 induces potent suppression of tumor growth and metastasis in anaplastic thyroid cancer. Oncotarget, 2015.

. Dual inhibition of HDAC and EGFR signaling with CUDC-101 induces potent suppression of tumor growth and metastasis in anaplastic thyroid cancer. Oncotarget, 2015.

. Orchestrating high-throughput genomic analysis with Bioconductor. Nat. Methods, 2015.

. miR30a inhibits LOX expression and anaplastic thyroid cancer progression. Cancer Res., 2015.

. The Bioconductor channel in F1000Research. F1000Res, 2015.

. Characterization of genomic alterations in radiation-associated breast cancer among childhood cancer survivors, using comparative genomic hybridization (CGH) arrays. PLoS ONE, 2015.

. Antagonistic cross-regulation between Sox9 and Sox10 controls an anti-tumorigenic program in melanoma. PLoS Genet., 2015.

. Downregulation of IGFBP2 is associated with resistance to IGF1R therapy in rhabdomyosarcoma. Oncogene, 2014.

. Lineage of origin in rhabdomyosarcoma informs pharmacological response. Genes Dev., 2014.

. Genome-wide methylation patterns in papillary thyroid cancer are distinct based on histological subtype and tumor genotype. J. Clin. Endocrinol. Metab., 2014.

. NCI-60 whole exome sequencing and pharmacological CellMiner analyses. PLoS ONE, 2014.

. High prevalence of MAP2K1 mutations in variant and IGHV4-34-expressing hairy-cell leukemias. Nat. Genet., 2014.

. Prohibitin expression is associated with high grade breast cancer but is not a driver of amplification at 17q21.33. Pathology, 2013.

. Oncogenic ETS fusions deregulate E2F3 target genes in Ewing sarcoma and prostate cancer. Genome Res., 2013.

. A polymorphism in IRF4 affects human pigmentation through a tyrosinase-dependent MITF/TFAP2A pathway. Cell, 2013.

. Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma. Proc. Natl. Acad. Sci. U.S.A., 2013.

. The exomes of the NCI-60 panel: a genomic resource for cancer biology and systems pharmacology. Cancer Res., 2013.

. Chromothripsis and focal copy number alterations determine poor outcome in malignant melanoma. Cancer Res., 2013.

. Whole genome and transcriptome sequencing of a B3 thymoma. PLoS ONE, 2013.

. SRAdb: query and use public next-generation sequencing data from within R. BMC Bioinformatics, 2013.

. Rb1 loss modifies but does not initiate alveolar rhabdomyosarcoma. Skelet Muscle, 2013.

. RCircos: an R package for Circos 2D track plots. BMC Bioinformatics, 2013.

. NCBI GEO: archive for functional genomics data sets--update. Nucleic Acids Res., 2013.

. Harnessing genomics to identify environmental determinants of heritable disease. Mutat. Res., 2013.

. Exclusion of the 750-kb genetically unstable region at Xq27 as a candidate locus for prostate malignancy in HPCX1-linked families. Genes Chromosomes Cancer, 2012.

. In vivo role of alternative splicing and serine phosphorylation of the microphthalmia-associated transcription factor. Genetics, 2012.

. 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. J. Biol. Chem., 2012.

. Genome-wide methylation profiling in archival formalin-fixed paraffin-embedded tissue samples. Methods Mol. Biol., 2012.

. Comparative exome sequencing of metastatic lesions provides insights into the mutational progression of melanoma. BMC Genomics, 2012.

. CHEK2 genomic and proteomic analyses reveal genetic inactivation or endogenous activation across the 60 cell lines of the US National Cancer Institute. Oncogene, 2012.

. Genome-wide depletion of replication initiation events in highly transcribed regions. Genome Res., 2011.

. A methyl-deviator epigenotype of estrogen receptor-positive breast carcinoma is associated with malignant biology. Am. J. Pathol., 2011.

. Identification of an inhibitor of the EWS-FLI1 oncogenic transcription factor by high-throughput screening. J. Natl. Cancer Inst., 2011.

. Exome sequencing identifies GRIN2A as frequently mutated in melanoma. Nat. Genet., 2011.

. Evidence for an unanticipated relationship between undifferentiated pleomorphic sarcoma and embryonal rhabdomyosarcoma. Cancer Cell, 2011.

. Preferential localization of human origins of DNA replication at the 5'-ends of expressed genes and at evolutionarily conserved DNA sequences. PLoS ONE, 2011.

. Interferon-γlinks ultraviolet radiation to melanomagenesis in mice. Nature, 2011.

. High frequencies of leukemia stem cells in poor-outcome childhood precursor-B acute lymphoblastic leukemias. Leukemia, 2010.

. Archival fine-needle aspiration cytopathology (FNAC) samples: untapped resource for clinical molecular profiling. J Mol Diagn, 2010.

. Epigenomic alterations and gene expression profiles in respiratory epithelia exposed to cigarette smoke condensate. Oncogene, 2010.

. Assessment of automated image analysis of breast cancer tissue microarrays for epidemiologic studies. Cancer Epidemiol. Biomarkers Prev., 2010.

. Vorinostat inhibits brain metastatic colonization in a model of triple-negative breast cancer and induces DNA double-strand breaks. Clin. Cancer Res., 2009.

. Analyses of resected human brain metastases of breast cancer reveal the association between up-regulation of hexokinase 2 and poor prognosis. Mol. Cancer Res., 2009.

. Analysis of the matrix metalloproteinase family reveals that MMP8 is often mutated in melanoma. Nat. Genet., 2009.

. Kinetic complexity of the global response to glucocorticoid receptor action. Endocrinology, 2009.

. Large-scale profiling of archival lymph nodes reveals pervasive remodeling of the follicular lymphoma methylome. Cancer Res., 2009.

. TRAIL induces apoptosis in triple-negative breast cancer cells with a mesenchymal phenotype. Breast Cancer Res. Treat., 2009.

. Canine tumor cross-species genomics uncovers targets linked to osteosarcoma progression. BMC Genomics, 2009.

. A molecular function map of Ewing's sarcoma. PLoS ONE, 2009.

. Molecular grading of ductal carcinoma in situ of the breast. Clin. Cancer Res., 2008.

. GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus. Bioinformatics, 2008.

. Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science, 2008.

. Interaction of the glucocorticoid receptor with the chromatin landscape. Mol. Cell, 2008.

. Suppressor role of activating transcription factor 2 (ATF2) in skin cancer. Proc. Natl. Acad. Sci. U.S.A., 2008.

. High-resolution mapping and characterization of open chromatin across the genome. Cell, 2008.

. Constitutive Fms-like tyrosine kinase 3 activation results in specific changes in gene expression in myeloid leukaemic cells. Br. J. Haematol., 2007.

. GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor. Bioinformatics, 2007.

. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 2007.

. Modeling synovial sarcoma: timing is everything. Cancer Cell, 2007.

. A single IGF1 allele is a major determinant of small size in dogs. Science, 2007.

. Zoom-in comparative genomic hybridisation arrays for the characterisation of variable breakpoint contiguous gene syndromes. J. Med. Genet., 2007.

. Detection of novel amplicons in prostate cancer by comprehensive genomic profiling of prostate cancer cell lines using oligonucleotide-based arrayCGH. PLoS ONE, 2007.

. DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays. Nat. Methods, 2006.

. Ewing's sarcoma: general insights from a rare model. Cancer Cell, 2006.

. Genome-wide analysis of menin binding provides insights into MEN1 tumorigenesis. PLoS Genet., 2006.

. Statistics for ChIP-chip and DNase hypersensitivity experiments on NimbleGen arrays. Meth. Enzymol., 2006.

. Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res., 2006.

. Gene expression profiling of human sarcomas: insights into sarcoma biology. Cancer Res., 2005.

. BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics, 2005.

. Database of mRNA gene expression profiles of multiple human organs. Genome Res., 2005.

. Linkage and association between inflammatory bowel disease and a locus on chromosome 12. Am. J. Hum. Genet., 1998.

. Genetic susceptibility for human familial essential hypertension in a region of homology with blood pressure linkage on rat chromosome 10. Hum. Mol. Genet., 1997.

. Nonparametric simulation based linkage statistics for general pedigrees. J. Rheumatol., 1997.

. Analysis of bipolar disorder using affected relatives. Genet. Epidemiol., 1997.

. Analysis of a complex oligogenic disease. Genet. Epidemiol., 1997.

. Nonparametric simulation-based statistics for detecting linkage in general pedigrees. Am. J. Hum. Genet., 1996.