Gregory E. Gonye

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We have developed a bioinformatics tool named PAINT that automates the promoter analysis of a given set of genes for the presence of transcription factor binding sites. Based on coincidence of regulatory sites, this tool produces an interaction matrix that represents a candidate transcriptional regulatory network. This tool currently consists of (1) a(More)
Gene expression profiles are an increasingly common data source that can yield insights into the functions of cells at a system-wide level. The present work considers the limitations in information content of gene expression data for reverse engineering regulatory networks. An in silico genetic regulatory network was constructed for this purpose. Using the(More)
A model genetic regulatory network for the evaluation of genetic regulatory network identification methods is described in the present work. This model is novel because of its mechanistic basis and its relatively large (10 gene) scale. The model is used to evaluate several simple techniques from the literature for identifying genetic regulatory networks(More)
A genetically engineered cardiac TnC mutant labeled at Cys-84 with tetramethylrhodamine-5-iodoacetamide dihydroiodide was passively exchanged for the endogenous form in skinned guinea pig trabeculae. The extent of exchange averaged nearly 70%, quantified by protein microarray of individual trabeculae. The uniformity of its distribution was verified by(More)
Several lines of evidence suggest that nonspecific drug interaction with the lipid bilayer plays an important role in subsequent recognition and binding to specific receptor sites in the membrane. The interaction of Bay K 8644, a 1,4-dihydropyridine (DHP) calcium channel agonist, with model and biological membranes was examined at the molecular level using(More)
The expression of protein phosphatase 32 (PP32, ANP32A) is low in poorly differentiated pancreatic cancers and is linked to the levels of HuR (ELAV1), a predictive marker for gemcitabine response. In pancreatic cancer cells, exogenous overexpression of pp32 inhibited cell growth, supporting its long-recognized role as a tumor suppressor in pancreatic(More)
Understanding regulation of fetal and embryonic hemoglobin expression is critical, since their expression decreases clinical severity in sickle cell disease and beta-thalassemia. K562 cells, a human erythroleukemia cell line, can differentiate along erythroid or megakaryocytic lineages and serve as a model for regulation of fetal/embryonic globin(More)
BACKGROUND Adaptation to chronic ethanol (EtOH) treatment of rats results in a changed functional state of the liver and greatly inhibits its regenerative ability, which may contribute to the progression of alcoholic liver disease. METHODS In this study, we investigated the effect of chronic EtOH intake on hepatic microRNA (miRNA) expression in male(More)
Most partition-based cluster analysis methods (e.g., kmeans) will partition any dataset D into k subsets, regardless of the inherent appropriateness of such a partitioning. This paper presents a family of permutation-based procedures to determine both the number of clusters k best supported by the available data and the weight of evidence in support of this(More)
The broad conceptual postulate that systems engineering techniques developed for complex chemical processes may be applicable to complex cell biological processes is very compelling. However, a naïve, "direct" application of systems engineering techniques to biological problems of practical significance may be rendered virtually ineffective by fundamental(More)