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SUMMARY geWorkbench (genomics Workbench) is an open source Java desktop application that provides access to an integrated suite of tools for the analysis and visualization of data from a wide range of genomics domains (gene expression, sequence, protein structure and systems biology). More than 70 distinct plug-in modules are currently available(More)
CONTEXT Pituitary tumor-transforming gene (PTTG) is a multifunctional protein involved in several tumorigenic mechanisms, including angiogenesis. PTTG has been shown to promote angiogenesis, a key rate-limiting step in tumor progression, by up-regulation of fibroblast growth factor-2 and vascular endothelial growth factor. OBJECTIVE To investigate whether(More)
BACKGROUND Despite extensive research, the details of the biological mechanisms by which cancer cells acquire motility and invasiveness are largely unknown. This study identifies an invasion associated gene signature shedding light on these mechanisms. METHODS We analyze data from multiple cancers using a novel computational method identifying sets of(More)
BACKGROUND Analysis of microarray data has been used for the inference of gene-gene interactions. If, however, the aim is the discovery of disease-related biological mechanisms, then the criterion for defining such interactions must be specifically linked to disease. RESULTS Here we present a computational methodology that jointly analyzes two sets of(More)
SUMMARY We present a visualization tool applied on genome-wide association data, revealing disease-associated haplotypes, epistatically interacting loci, as well as providing visual signatures of multivariate correlations of genetic markers with respect to a phenotype. AVAILABILITY Freely available on the web at:(More)
Light emitting diode (LED) forward lighting systems soon will become a reality on today's roadways. One aspect of LED sources that will differ significantly from tungsten halogen (TH) or high intensity discharge (HID) lamps is their spectral power distribution (SPD). Lamp SPD can have considerable impacts on a driver's visual performance. Recent studies(More)
The human leukocyte antigen (HLA) class II genes HLA-DRB1, -DQA1 and -DQB1 are the strongest genetic factors for type 1 diabetes (T1D). Additional loci in the major histocompatibility complex (MHC) are difficult to identify due to the region's high gene density and complex linkage disequilibrium (LD). To facilitate the association analysis, two novel(More)
Analysis of large gene expression data sets in the presence and absence of a phenotype can lead to the selection of a group of genes serving as biomarkers jointly predicting the phenotype. Among gene selection methods, filter methods derived from ranked individual genes have been widely used in existing products for diagnosis and prognosis. Univariate(More)