Background Protein-DNA interaction constitutes a basic mechanism for the genetic
regulation of target gene expression. Deciphering this mechanism has been a daunting task …

Aberrant DNA methylation is known as an important cause of human cancers, along with
mutations. Although aberrant methylation was initially speculated to be similar to mutations …

Chromatin structure and transcription factor localization can be assayed genome-wide by
sequencing genomic DNA fractionated by protein occupancy or other properties, but current …

Abstract Motivation: The Illumina BeadArray is a popular platform for profiling DNA
methylation, an important epigenetic event associated with gene silencing and …

Epigenetics describes the study of stable, reversible alterations to the genome that affect
gene expression and genome function, the most studied mechanisms are DNA methylation …

Cytosine methylation is a com-mon DNA modification found in most eukaryotic organisms
including plants, animals, and fungi (1, 2). The addition of a methyl group to cytosine …

Using the type III restriction-modification enzyme EcoP15I, we isolated sequences flanking
sites digested by the methylation-sensitive HpaII enzyme or its methylation-insensitive MspI …

Embryonic stem cells (ESCs) are pluripotent, self‐renewing cells. These cells can be used in
applications such as cell therapy, drug development, disease modeling, and the study of …

DNA cytosine methylation is a central epigenetic modification which plays critical roles in
cellular processes including genome regulation, development and disease. Here, we review …

Motivation: New generation sequencing technologies producing increasingly complex
datasets demand new efficient and specialized sequence analysis algorithms. Often, it is …