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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: 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)
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)
BACKGROUND The application of DNA microarray technology in post-genomic analysis of bacterial genome sequences has allowed the generation of huge amounts of data related to regulatory networks. This data along with literature-derived knowledge on regulation of gene expression has opened the way for genome-wide reconstruction of transcriptional regulatory(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)
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)
UNLABELLED We investigated the problem of imprecisely determined prokaryotic transcription factor (TF) binding sites (TFBSs). We found that the identification and reinvestigation of questionable binding motifs may result in improved models of these motifs. Subsequent modelbased predictions of gene regulatory interactions may be performed with increased(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)
Alternative splicing is an important mechanism for increasing protein diversity. However, its functional effects are largely unknown. Here, we present our new software workflow composed of the open-source application AltAnalyze and the Cytoscape plugin DomainGraph. Both programs provide an intuitive and comprehensive end-to-end solution for the analysis and(More)
Clustering objects according to given similarity or distance values is a ubiquitous problem in computational biology with diverse applications, e.g., in defining families of orthologous genes, or in the analysis of microarray experiments. While there exists a plenitude of methods, many of them produce clusterings that can be further improved. "Cleaning up"(More)