In this paper, a similarity measure between genes with protein-protein interactions is proposed. The chip-chip data are converted into the same form of gene expression data with pearson correlation as its similarity measure. On the basis of the similarity measures of proteinprotein interaction data and chip-chip data, the combined dissimilarity measure is defined. The combined distance measure ...

Multiple studies have illustrated that gene expression profiling of primary breast cancers throughout the final stages of tumor development can provide valuable markers for risk prediction of metastasis and disease sub typing. However, the identification of a biologically interpretable and universally shared set of markers proved to be difficult. Here, we propose a method for de novo grouping o...

Cells and organisms are governed by networks of genetic, physical and metabolic interactions between proteins and other their substrates, such as DNA, RNA, and other biologically important molecules. Large scale experimental studies of interactions between components of biological systems have been performed for a variety of eukaryotic organisms. However, there is a dearth of such data for plan...

This report summarizes the participation of the Tsujii-lab group in the 2006 BioCreative2 text mining challenge. It describes the systems used, the results attained, and the lessons learned. The basic idea was to see how well the AKANE system could perform on a full-text ProteinProtein Interaction (PPI) Information Extraction (IE) task. AKANE system is a recently developed, sentence-level PPI s...

Title of Document: CHARACTERIZATION OF THE INTERACTION OF THE HPV8 E2 TETHERING PROTEIN WITH HOST CHROMOSOMES. Vandana Sekhar, Doctor of Philosophy, 2011 Directed By: Dr. Alison A McBride, DNA Tumor Virus Section, Laboratory of Viral Diseases, NIAID, NIH and Dr. Leslie Pick, MOCB, UMD One of the mechanisms by which papillomaviruses establish persistent infection of the host is by tethering thei...

Murgia, Chiara, Isabella Vespignani, Joanna Cerase, Fabio Nobili, and Giuditta Perozzi. Cloning, expression, and vesicular localization of zinc transporter Dri 27/ZnT4 in intestinal tissue and cells. Am. J. Physiol. 277 (Gastrointest. Liver Physiol. 40): G1231–G1239, 1999.—We have identified the Dri 27 cDNA on the basis of its upregulated expression during rat intestinal development. It encodes...

Understanding the molecular mechanisms of life requires decoding the functions of the proteins in an organism. Various high-throughput experimental techniques have been developed to characterize biological systems at the genome scale. A fundamental challenge of the post-genomic era is to assign biological functions to all the proteins encoded by the genome using high-throughput biological data....

Protein-protein interactions (PPIs) are broadly recognized as an emerging target class for a whole new era in drug discovery. They show significant differences to classical target classes and have been regarded as “undruggable” for a long time. Priaxon AG has developed a unique, proprietary technology platform for PPI drug discovery. PriaXplore employs novel computational and synthetic approach...

This vignette provides examples of how to use the package FEM to identify interactome hotspots of differential promoter methylation and differential expression, where an inverse association between promoter methylation and gene expression is assumed [1]. By “interactome hotspot” we mean a connected subnetwork of the protein interaction network (PIN) with an exceptionally large average edge-weig...

Understanding the mathematical properties of graphs underling biological systems could give hints on the evolutionary mechanisms behind these structures. In this article we perform a complete statistical analysis over thousands of graphs representing metabolic and proteinprotein interaction (PPI) networks. The focus of the analysis is, apart from the description of the main properties of the gr...