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Tiling array is one type production of Affymetrix short oligonucleotide microarrays to map transcriptional factor binding sites (TFBS) at a high resolution. In order to estimate the quantity of target sequences of probes, we model the binding behavior between probes and DNA sequences at molecular interaction level and term it hybridization model for tiling array analysis (HMT). In our model, the binding...
With the increase in genome-wide experiments and sequenced genomes, the analysis of large data sets has become commonplace in biology. It is often the case that thousands of features in a genome-wide data set are tested against null hypotheses, where only a small number of features are expected to be significant. The empirical Bayesian method (EB) is one of the most powerful methods to address such...
Rapid and accurate identification of potentially interested pathways through the analysis of genome-wide expression profiles remains an important challenge in bioinformatics. Most existing methods are based on hypothesis testing, such as GSEA. These methods mainly focus on individual pathways and rank them based on their individual strengths. However, biological pathways often work together to function...
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