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Recent development of MeRIP-Seq enabled the global unbiased profiling of transcriptome-wide N6-Adenosine. With this technique, it is now possible to detect the RNA methylation sites under a specific condition or the differential methylation sites between two experimental conditions. However, as an affinity-based approach, MeRIP-Seq has yet provided base-pair resolution. A single methylation site reported...
Methyl-CpG binding domain-based capture followed by sequencing (MBDCap-seq) is a cost-effective method for genome-wide methylation analyses especially in CpG-rich regions. In this study, we developed BIMMER, a BI-layer hidden Markov model for differential Methylation Regions (DMRs) identification BIMMER using MBDCap-seq samples derived from two different phenotypes. BIMMER models and generates a posterior...
Statistical models for reverse engineering gene regulatory networks are surveyed in this article. To provide readers with a system-level view of the modeling issues in this research, a graphical modeling framework is proposed. This framework serves as the scaffolding on which the review of different models can be systematically assembled. Based on the framework, we review many existing models for...
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