ChIP–seq: advantages and challenges of a maturing technology

PJ Park - Nature reviews genetics, 2009‏ - nature.com
Chromatin immunoprecipitation followed by sequencing (ChIP–seq) is a technique for
genome-wide profiling of DNA-binding proteins, histone modifications or nucleosomes …

Identifying and mitigating bias in next-generation sequencing methods for chromatin biology

CA Meyer, XS Liu - Nature Reviews Genetics, 2014‏ - nature.com
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 …

The androgen receptor is a tumor suppressor in estrogen receptor–positive breast cancer

TE Hickey, LA Selth, KM Chia, G Laven-Law… - Nature medicine, 2021‏ - nature.com
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 …

Identifying ChIP-seq enrichment using MACS

J Feng, T Liu, B Qin, Y Zhang, XS Liu - Nature protocols, 2012‏ - nature.com
Abstract Model-based analysis of ChIP-seq (MACS) is a computational algorithm that
identifies genome-wide locations of transcription/chromatin factor binding or histone …

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

SG Landt, GK Marinov, A Kundaje… - Genome …, 2012‏ - genome.cshlp.org
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 …

GREAT improves functional interpretation of cis-regulatory regions

CY McLean, D Bristor, M Hiller, SL Clarke… - Nature …, 2010‏ - nature.com
Abstract We developed the Genomic Regions Enrichment of Annotations Tool (GREAT) to
analyze the functional significance of cis-regulatory regions identified by localized …

Software for computing and annotating genomic ranges

M Lawrence, W Huber, H Pagès… - PLoS computational …, 2013‏ - journals.plos.org
We describe Bioconductor infrastructure for representing and computing on annotated
genomic ranges and integrating genomic data with the statistical computing features of R …

Measuring reproducibility of high-throughput experiments

Q Li, JB Brown, H Huang, PJ Bickel - 2011‏ - projecteuclid.org
Supplementary materials for Measuring reproducibility of high-throughput experiments. This
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

AE Jaffe, P Murakami, H Lee, JT Leek… - International journal …, 2012‏ - academic.oup.com
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 …

TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity

K Williams, J Christensen, MT Pedersen, JV Johansen… - Nature, 2011‏ - nature.com
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 …