Konstantin Halachev

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Epigenome mapping consortia are generating resources of tremendous value for studying epigenetic regulation. To maximize their utility and impact, new tools are needed that facilitate interactive analysis of epigenome datasets. Here we describe EpiExplorer, a web tool for exploring genome and epigenome data on a genomic scale. We demonstrate EpiExplorer's(More)
The EpiGRAPH web service http://epigraph.mpi-inf.mpg.de/ enables biologists to uncover hidden associations in vertebrate genome and epigenome datasets. Users can upload sets of genomic regions and EpiGRAPH will test multiple attributes (including DNA sequence, chromatin structure, epigenetic modifications and evolutionary conservation) for enrichment or(More)
Modern life sciences are becoming increasingly data intensive, posing a significant challenge for most researchers and shifting the bottleneck of scientific discovery from data generation to data analysis. As a result, progress in genome research is increasingly impeded by bioinformatic hurdles. A new generation of powerful and easy-to-use genome analysis(More)
MOTIVATION Recurrent DNA breakpoints in cancer genomes indicate the presence of critical functional elements for tumor development. Identifying them can help determine new therapeutic targets. High-dimensional DNA microarray experiments like arrayCGH afford the identification of DNA copy number breakpoints with high precision, offering a solid basis for(More)
The eROSE plugin for ECLIPSE uses version archives to guide programmers: You changed fKeys[] and eROSE suggests you to change initDefaults(), because both items always have been changed together in the past. In addition, eROSE points out item coupling that is undetectable by program analysis, for instance between fKeys[] and a properties file. All eROSE(More)
This chapter describes bioinformatic tools for analyzing epigenome differences between species and in diseased versus normal cells. We illustrate the interplay of several Web-based tools in a case study of CpG island evolution between human and mouse. Starting from a list of orthologous genes, we use the Galaxy Web service to obtain gene coordinates for(More)
Epigenetic marks, such as DNA methylation and histone modifications, are important regulatory mechanisms that allow a single genomic sequence to give rise to a complex multicellular organism. When studying mechanisms of epigenetic regulation, the analyses depend on the experimental technologies and the available data. Recent advancements in sequencing(More)
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