Publications

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GenomicDataCommons: a Bioconductor Interface to the NCI Genomic Data Commons

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

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

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

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Point Mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis Variant.

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caOmicsV: an R package for visualizing multidimensional cancer genomic data.

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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.

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Public data and open source tools for multi-assay genomic investigation of disease.

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A Genome-Wide Scan Identifies Variants in NFIB Associated with Metastasis in Patients with Osteosarcoma.

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Inhibition of Survivin with YM155 Induces Durable Tumor Response in Anaplastic Thyroid Cancer.

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

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

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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.

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

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

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Orchestrating high-throughput genomic analysis with Bioconductor.

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

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The Bioconductor channel in F1000Research.

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miR30a inhibits LOX expression and anaplastic thyroid cancer progression.

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NCI-60 whole exome sequencing and pharmacological CellMiner analyses.

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Lineage of origin in rhabdomyosarcoma informs pharmacological response.

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Genome-wide methylation patterns in papillary thyroid cancer are distinct based on histological subtype and tumor genotype.

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

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Rb1 loss modifies but does not initiate alveolar rhabdomyosarcoma.

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

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

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

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

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

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

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

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Whole genome and transcriptome sequencing of a B3 thymoma.

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

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Chromothripsis and focal copy number alterations determine poor outcome in malignant melanoma.

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NCBI GEO: archive for functional genomics data sets--update.

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

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Harnessing genomics to identify environmental determinants of heritable disease.

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

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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.

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

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Genome-wide methylation profiling in archival formalin-fixed paraffin-embedded tissue samples.

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

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

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Identification of an inhibitor of the EWS-FLI1 oncogenic transcription factor by high-throughput screening.

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A methyl-deviator epigenotype of estrogen receptor-positive breast carcinoma is associated with malignant biology.

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

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Exome sequencing identifies GRIN2A as frequently mutated in melanoma.

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Evidence for an unanticipated relationship between undifferentiated pleomorphic sarcoma and embryonal rhabdomyosarcoma.

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Interferon-γ links ultraviolet radiation to melanomagenesis in mice.

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Archival fine-needle aspiration cytopathology (FNAC) samples: untapped resource for clinical molecular profiling.

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

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

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Assessment of automated image analysis of breast cancer tissue microarrays for epidemiologic studies.

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Chemical analysis of four capsules containing the controlled substance analogues 4-methylmethcathinone, 2-fluoromethamphetamine, alpha-phthalimidopropiophenone and N-ethylcathinone.

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

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

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

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A molecular function map of Ewing's sarcoma.

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

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

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Kinetic complexity of the global response to glucocorticoid receptor action.

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Molecular grading of ductal carcinoma in situ of the breast.

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

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Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia.

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Interaction of the glucocorticoid receptor with the chromatin landscape.

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

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

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

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

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

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GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor

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

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

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Modeling synovial sarcoma: timing is everything.

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

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Zoom-in comparative genomic hybridisation arrays for the characterisation of variable breakpoint contiguous gene syndromes.

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Statistics for ChIP-chip and DNase hypersensitivity experiments on NimbleGen arrays.

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

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Ewing's sarcoma: general insights from a rare model.

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Genome-wide analysis of menin binding provides insights into MEN1 tumorigenesis.

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

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Gene expression profiling of human sarcomas: insights into sarcoma biology.

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

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Database of mRNA gene expression profiles of multiple human organs.

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

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Linkage and association between inflammatory bowel disease and a locus on chromosome 12.

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Comparison of nonparametric statistics for detection of linkage in nuclear families: single-marker evaluation.

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

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Nonparametric simulation based linkage statistics for general pedigrees.

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Analysis of bipolar disorder using affected relatives.

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Analysis of a complex oligogenic disease.

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Nonparametric simulation-based statistics for detecting linkage in general pedigrees.

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