MNase titration reveals differences between nucleosome occupancy and chromatin accessibility

Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming

(2015) Abdenour Soufi et al.   CELL

Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains

(2015) Sergey V. Ulianov et al.   GENOME RESEARCH

MPE-seq, a new method for the genome-wide analysis of chromatin structure

(2015) Haruhiko Ishii et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription

(2014) Britta Knight et al.   GENES & DEVELOPMENT

Comparative analysis of metazoan chromatin organization

(2014) Joshua W. K. Ho et al.   NATURE

Nucleosomal occupancy changes locally over key regulatory regions during cell differentiation and reprogramming

(2014) Jason A. West et al.   Nature Communications

Multiplexed Illumina sequencing libraries from picogram quantities of DNA

(2013) Sarah K Bowman et al.   BMC GENOMICS

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

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

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

(2013) Simon Anders et al.   Nature Protocols

Standardized collection of MNase-seq experiments enables unbiased dataset comparisons

(2012) Jason M Rizzo et al.   BMC MOLECULAR BIOLOGY

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

(2012) A. Kundaje et al.   GENOME RESEARCH

GC-Content Normalization for RNA-Seq Data

(2011) Davide Risso et al.   BMC BIOINFORMATICS

High-Resolution Genome-wide Mapping of the Primary Structure of Chromatin

(2011) Zhenhai Zhang et al.   CELL

Nucleosome fragility reveals novel functional states of chromatin and poises genes for activation

(2011) Y. Xi et al.   GENOME RESEARCH

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 Region of the Human HOXD Cluster that Confers Polycomb-Group Responsiveness

(2010) Caroline J. Woo et al.   CELL

Polycomb preferentially targets stalled promoters of coding and noncoding transcripts

(2010) D. Enderle et al.   GENOME RESEARCH

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

Accessibility of the Drosophila genome discriminates PcG repression, H4K16 acetylation and replication timing

(2010) Oliver Bell et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Effect of Micrococcal Nuclease Digestion on Nucleosome Positioning Data

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

Analysis of the primary structure of chromatin with next-generation sequencing

(2010) Michael Y Tolstorukov et al.   Epigenomics

Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology

(2010) Noam Kaplan et al.   GENOME BIOLOGY

The Biology of Chromatin Remodeling Complexes

(2009) Cedric R. Clapier et al.   Annual Review of Biochemistry

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

High-resolution nucleosome mapping reveals transcription-dependent promoter packaging

(2009) A. Weiner et al.   GENOME RESEARCH

H3.3/H2A.Z double variant–containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions

(2009) Chunyuan Jin et al.   NATURE GENETICS

What controls nucleosome positions?

(2009) Eran Segal et al.   TRENDS IN GENETICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

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

(2008) S. Henikoff et al.   GENOME RESEARCH

Nucleosome organization in the Drosophila genome

(2008) Travis N. Mavrich et al.   NATURE

Activator Control of Nucleosome Occupancy in Activation and Repression of Transcription

(2008) Gene O Bryant et al.   PLOS BIOLOGY