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Understanding epigenetic changes across various conditions is a fundamental problem to epigenome annotation. With more high-throughput epigenomic data available, computational methods have been developed to quantify various types of epigenetic modification signals, to compare epigenetic marks between different conditions and to understand the functional consequences of epigenetic changes. However,...
It is important to develop computational methods to predict target genes of a transcription factor. In this paper, we developed a phylogenetic footprinting method to effectively identify target genes on the whole genome scale. Appling the method to 31 transcription factors, we improved the quality of the initial motifs, and predicted additional target genes that are supported by gene ontology analysis...
With an overwhelming amount of expression data available, many interesting problems have been studied, such as identifying cancer signatures, constructing gene regulatory networks, analyzing activity of pathways, and so on. Here we show another fascinating aspect of using expression data, constructing the hierarchical order of gene expression levels. We found that there is an order of expression levels...
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