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BACKGROUND In the post-genomic era, the rapid increase in high-throughput data calls for computational tools capable of integrating data of diverse types and facilitating recognition of biologically meaningful patterns within them. For example, protein-protein interaction data sets have been clustered to identify stable complexes, but scientists lack easily(More)
MOTIVATION Assembling the relevant information needed to interpret the output from high-throughput, genome scale, experiments such as gene expression microarrays is challenging. Analysis reveals genes that show statistically significant changes in expression levels, but more information is needed to determine their biological relevance. The challenge is to(More)
The glxR (cg0350) gene of Corynebacterium glutamicum ATCC 13032 encodes a DNA-binding transcription regulator of the CRP/FNR protein family. Five genomic DNA regions known to be bound by GlxR provided the seed information for DNA binding site discovery by expectation maximization and Gibbs sampling approaches. The detection of additional motifs in the(More)
Transitivity Clustering is a method for the partitioning of biological data into groups of similar objects, such as genes, for instance. It provides integrated access to various functions addressing each step of a typical cluster analysis. To facilitate this, Transitivity Clustering is accessible online and offers three user-friendly interfaces: a powerful(More)
BACKGROUND Detecting groups of functionally related proteins from their amino acid sequence alone has been a long-standing challenge in computational genome research. Several clustering approaches, following different strategies, have been published to attack this problem. Today, new sequencing technologies provide huge amounts of sequence data that has to(More)
(Supplementary Table 1). The average bead displacement and the ratio between correspondence candidates and true correspondences is a quantitative measure of the reconstruction success, which is crucial for automatic validation of registration results in long time-lapse recordings. The beads can be removed optically or com-putationally from the sample(More)
The adaptability of pathogenic bacteria to hosts is influenced by the genomic plasticity of the bacteria, which can be increased by such mechanisms as horizontal gene transfer. Pathogenicity islands play a major role in this type of gene transfer because they are large, horizontally acquired regions that harbor clusters of virulence genes that mediate the(More)
BACKGROUND Transcriptional regulation of gene activity is essential for any living organism. Transcription factors therefore recognize specific binding sites within the DNA to regulate the expression of particular target genes. The genome-scale reconstruction of the emerging regulatory networks is important for biotechnology and human medicine but(More)
Introduction: With the so-called OMICS technology the scientific community has generated huge amounts of data that allow us to reconstruct the interplay of all kinds of biological entities. The emerging interaction networks are usually modeled as graphs with thousands of nodes and tens of thousands of edges between them. In addition to sequence alignment,(More)
Motivation: We address the problem of multiple protein-protein interaction (PPI) network alignment. Given a set of such networks for different species we might ask how much the network topology is conserved throughout evolution. Solving this problem will help to derive a subset of interactions that is conserved over multiple species thus forming a 'core(More)