Coupling transcription factor occupancy to nucleosome architecture with DNase-FLASH

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

(2012) A. Kundaje et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

Genome-wide structure and organization of eukaryotic pre-initiation complexes

(2012) Ho Sung Rhee et al.   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Controls of Nucleosome Positioning in the Human Genome

(2012) Daniel J. Gaffney et al.   PLoS Genetics

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis

(2011) R. Yamashita et al.   GENOME RESEARCH

Determinants of nucleosome organization in primary human cells

(2011) Anton Valouev et al.   NATURE

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

(2009) Jay R Hesselberth et al.   NATURE METHODS

Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo

(2009) Yong Zhang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

DNase I footprinting of the nucleosome in whole nuclei

(2008) D.Z. Staynov   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Dynamic Regulation of Nucleosome Positioning in the Human Genome

(2008) Dustin E. Schones et al.   CELL

Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains

(2008) S. Cuddapah et al.   GENOME RESEARCH

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome

(2008) T. N. Mavrich et al.   GENOME RESEARCH

The Insulator Binding Protein CTCF Positions 20 Nucleosomes around Its Binding Sites across the Human Genome

(2008) Yutao Fu et al.   PLoS Genetics