This document discusses the ins and outs of an analysis of a whole-genome shotgun bisulfite sequencing (WGBS) dataset, using the BSmooth algorithm, which was first used in [1] and more formally presented and evaluated in [2]. The intention with the document is to focus on analysis-related tasks and questions. Basic usage of the bsseq package is covered in “The bsseq user’s guide”. It may be use...

The p14(ARF) protein directly inhibits the MDM-2 oncoprotein, which mediates degradation of the p53 protein. It has been shown that p14(ARF) expression is frequently down-regulated by p14(ARF) gene hypermethylation in colorectal cancer. To determine whether p14(ARF) inactivation was involved in ulcerative colitis (UC)-associated carcinogenesis, the frequency and timing of p14(ARF) methylation w...

Aspergillus flavus first gained scientific attention for its production of aflatoxin. The underlying regulation of aflatoxin biosynthesis has been serving as a theoretical model for biosynthesis of other microbial secondary metabolites. Nevertheless, for several decades, the DNA methylation status, one of the important epigenomic modifications involved in gene regulation, in A. flavus remains t...

OBJECTIVE Increased risk of psychopathology is observed in children exposed to maternal prenatal distress, and elevated maternal cortisol and epigenetic regulation of placental glucocorticoid-pathway genes are potential mechanisms. The authors examined maternal distress and salivary cortisol in relation to fetal movement and heart rate ("coupling") and DNA methylation of three glucocorticoid pa...

Read mapping is a fundamental part of next-generation genomic research but is complicated by genome duplication in many plants. Categorizing DNA sequence reads into their respective genomes enables current methods to analyze polyploid genomes as if they were diploid. We present PolyCat-a pipeline for mapping and categorizing all types of next-generation sequence data produced from allopolyploid...