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The ENCODE Project has generated a wealth of experimental information mapping diverse chromatin properties in several human cell lines. Although each such data track is independently informative toward the annotation of regulatory elements, their interrelations contain much richer information for the systematic annotation of regulatory elements. To uncover(More)
Gene regulation at functional elements (e.g., enhancers, promoters, insulators) is governed by an interplay of nucleosome remodeling, histone modifications, and transcription factor binding. To enhance our understanding of gene regulation, the ENCODE Consortium has generated a wealth of ChIP-seq data on DNA-binding proteins and histone modifications. We(More)
The advent of high-throughput DNA sequencing has enabled the measurement of many types of chemical phenomena in the human genome [2]. These methods have enabled the location of both punctate phenomena, such as transcription factor binding sites (TFBSs), and broad phenomena, such as the location of chemical modification of the histone proteins that wrap DNA.(More)
Understanding the mechanisms of gene expression is a central problem in biology. Important to gene expression is the binding of RNA polymerase at transcription start sites (TSSs). TSS detection from sequence is a well-studied problem, but recent innovations in data collection have made a much richer feature set available. Furthermore, these innovations(More)
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