Epigenetic research aims to understand heritable gene regulation that is not directly
encoded in the DNA sequence. Epigenetic mechanisms such as DNA methylation and …

Recent advances in technology have led to a dramatic increase in the number of available
transcription factor ChIP-seq and ChIP-chip data sets. Understanding the motif content of …

Recent progress in massively parallel sequencing platforms has enabled genome-wide
characterization of DNA-associated proteins using the combination of chromatin …

The term “transcriptional network” refers to the mechanism (s) that underlies coordinated
expression of genes, typically involving transcription factors (TFs) binding to the promoters of …

Regulation of gene expression is integral to the development and survival of all organisms.
Transcription begins with the assembly of a pre-initiation complex at the gene promoter …

DNA methylation is an indispensible epigenetic modification required for regulating the
expression of mammalian genomes. Immunoprecipitation-based methods for DNA …

We present CisGenome, a software system for analyzing genome-wide chromatin
immunoprecipitation (ChIP) data. CisGenome is designed to meet all basic needs of ChIP …

Markov Chain Monte Carlo (MCMC) methods are now an indispensable tool in scientific
computing. This book discusses recent developments of MCMC methods with an emphasis …

We demonstrate that the binding sites for highly conserved transcription factors vary
extensively between human and mouse. We mapped the binding of four tissue-specific …

Next-generation DNA sequencing coupled with chromatin immunoprecipitation (ChIP-seq)
is revolutionizing our ability to interrogate whole genome protein-DNA interactions …