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ChIP–seq: advantages and challenges of a maturing technology
Chromatin immunoprecipitation followed by sequencing (ChIP–seq) is a technique for
genome-wide profiling of DNA-binding proteins, histone modifications or nucleosomes …
genome-wide profiling of DNA-binding proteins, histone modifications or nucleosomes …
Identifying and mitigating bias in next-generation sequencing methods for chromatin biology
Next-generation sequencing (NGS) technologies have been used in diverse ways to
investigate various aspects of chromatin biology by identifying genomic loci that are bound …
investigate various aspects of chromatin biology by identifying genomic loci that are bound …
The androgen receptor is a tumor suppressor in estrogen receptor–positive breast cancer
The role of the androgen receptor (AR) in estrogen receptor (ER)-α-positive breast cancer is
controversial, constraining implementation of AR-directed therapies. Using a diverse …
controversial, constraining implementation of AR-directed therapies. Using a diverse …
Identifying ChIP-seq enrichment using MACS
Abstract Model-based analysis of ChIP-seq (MACS) is a computational algorithm that
identifies genome-wide locations of transcription/chromatin factor binding or histone …
identifies genome-wide locations of transcription/chromatin factor binding or histone …
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
Chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-
seq) has become a valuable and widely used approach for map** the genomic location of …
seq) has become a valuable and widely used approach for map** the genomic location of …
GREAT improves functional interpretation of cis-regulatory regions
Abstract We developed the Genomic Regions Enrichment of Annotations Tool (GREAT) to
analyze the functional significance of cis-regulatory regions identified by localized …
analyze the functional significance of cis-regulatory regions identified by localized …
Software for computing and annotating genomic ranges
We describe Bioconductor infrastructure for representing and computing on annotated
genomic ranges and integrating genomic data with the statistical computing features of R …
genomic ranges and integrating genomic data with the statistical computing features of R …
Measuring reproducibility of high-throughput experiments
Supplementary materials for Measuring reproducibility of high-throughput experiments. This
supplement consists of four parts. Part 1 describes the algorithm for estimating parameters in …
supplement consists of four parts. Part 1 describes the algorithm for estimating parameters in …
Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies
Background During the past 5 years, high-throughput technologies have been successfully
used by epidemiology studies, but almost all have focused on sequence variation through …
used by epidemiology studies, but almost all have focused on sequence variation through …
TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity
Enzymes catalysing the methylation of the 5-position of cytosine (mC) have essential roles in
regulating gene expression and maintaining cellular identity. Recently, TET1 was found to …
regulating gene expression and maintaining cellular identity. Recently, TET1 was found to …