Targeted in situ genome-wide profiling with high efficiency for low cell numbers

Complex multi-enhancer contacts captured by genome architecture mapping

(2017) Robert A. Beagrie et al.   NATURE

Epigenetics, cellular memory and gene regulation

(2016) Steven Henikoff et al.   CURRENT BIOLOGY

S1-DRIP-seq identifies high expression and polyA tracts as major contributors to R-loop formation

(2016) Lamia Wahba et al.   GENES & DEVELOPMENT

Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution

(2016) M Ryan Corces et al.   NATURE GENETICS

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

(2016) Maxwell R Mumbach et al.   NATURE METHODS

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

(2015) Zhonghui Tang et al.   CELL

ChIP bias as a function of cross-linking time

(2015) Laura Baranello et al.   CHROMOSOME RESEARCH

The Overlooked Fact: Fundamental Need for Spike-In Control for Virtually All Genome-Wide Analyses

(2015) Kaifu Chen et al.   MOLECULAR AND CELLULAR BIOLOGY

Active promoters give rise to false positive ‘Phantom Peaks’ in ChIP-seq experiments

(2015) Dhawal Jain et al.   NUCLEIC ACIDS RESEARCH

ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo

(2015) Gabriel E. Zentner et al.   Nature Communications

An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations

(2015) Julie Brind’Amour et al.   Nature Communications

A simple method for generating high-resolution maps of genome-wide protein binding

(2015) Peter J Skene et al.   eLife

Nucleosome loss leads to global transcriptional up-regulation and genomic instability during yeast aging

(2014) Z. Hu et al.   GENES & DEVELOPMENT

High-resolution digital profiling of the epigenome

(2014) Gabriel E. Zentner et al.   NATURE REVIEWS GENETICS

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

(2014) Clifford A. Meyer et al.   NATURE REVIEWS GENETICS

Quantitative ChIP-Seq Normalization Reveals Global Modulation of the Epigenome

(2014) David A. Orlando et al.   Cell Reports

High-resolution mapping of transcription factor binding sites on native chromatin

(2013) Sivakanthan Kasinathan et al.   NATURE METHODS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Widespread Misinterpretable ChIP-seq Bias in Yeast

(2013) Daechan Park et al.   PLoS One

Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins

(2013) L. Teytelman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

MLL-Rearranged Leukemia Is Dependent on Aberrant H3K79 Methylation by DOT1L

(2011) Kathrin M. Bernt et al.   CANCER CELL

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

(2011) Ho Sung Rhee et al.   CELL

Epigenome characterization at single base-pair resolution

(2011) J. G. Henikoff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Method to Separate Nuclear, Cytosolic, and Membrane-Associated Signaling Molecules in Cultured Cells

(2011) X. Liu et al.   Science Signaling

Chromatin particle spectrum analysis: a method for comparative chromatin structure analysis using paired-end mode next-generation DNA sequencing

(2010) N. A. Kent et al.   NUCLEIC ACIDS RESEARCH

The Effect of Micrococcal Nuclease Digestion on Nucleosome Positioning Data

(2010) Ho-Ryun Chung et al.   PLoS One

Impact of Chromatin Structures on DNA Processing for Genomic Analyses

(2009) Leonid Teytelman et al.   PLoS One

Mapping accessible chromatin regions using Sono-Seq

(2009) R. K. Auerbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Genome-wide profiling of salt fractions maps physical properties of chromatin

(2008) S. Henikoff et al.   GENOME RESEARCH

Extensive chromatin fragmentation improves enrichment of protein binding sites in chromatin immunoprecipitation experiments

(2008) X. Fan et al.   NUCLEIC ACIDS RESEARCH