Genome-wide nucleosome positioning during embryonic stem cell development

Short nucleosome repeats impose rotational modulations on chromatin fibre folding

(2012) Sarah J Correll et al.   EMBO JOURNAL

Chromatin and Transcription in Yeast

(2012) Oliver J. Rando et al.   GENETICS

Micrococcal Nuclease Does Not Substantially Bias Nucleosome Mapping

(2012) James Allan et al.   JOURNAL OF MOLECULAR BIOLOGY

Chromatin organization is a major influence on regional mutation rates in human cancer cells

(2012) Benjamin Schuster-Böckler et al.   NATURE

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Widespread remodeling of mid-coding sequence nucleosomes by Isw1

(2012) Itay Tirosh et al.   GENOME BIOLOGY

Targeting chromatin remodelers: Signals and search mechanisms

(2011) Fabian Erdel et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Genome-wide “Re”-Modeling of Nucleosome Positions

(2011) Ronen Sadeh et al.   CELL

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

(2011) Zhenhai Zhang et al.   CELL

Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells

(2011) I. M. Min et al.   GENES & DEVELOPMENT

Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1

(2011) G. Hu et al.   GENOME RESEARCH

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

(2011) Y. Xi et al.   GENOME RESEARCH

Stable and dynamic nucleosome states during a meiotic developmental process

(2011) L. Zhang et al.   GENOME RESEARCH

Remodelers Organize Cellular Chromatin by Counteracting Intrinsic Histone-DNA Sequence Preferences in a Class-Specific Manner

(2011) Y. M. Moshkin et al.   MOLECULAR AND CELLULAR BIOLOGY

Determinants of nucleosome organization in primary human cells

(2011) Anton Valouev et al.   NATURE

Control of Drosophila endocycles by E2F and CRL4CDT2

(2011) Norman Zielke et al.   NATURE

CTCF-mediated functional chromatin interactome in pluripotent cells

(2011) Lusy Handoko et al.   NATURE GENETICS

Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes

(2011) David Martin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The nucleosome map of the mammalian liver

(2011) Zhaoyu Li et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Nucleosome occupancy reveals regulatory elements of the CFTR promoter

(2011) Christopher J. Ott et al.   NUCLEIC ACIDS RESEARCH

Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells

(2011) Chao Cheng et al.   NUCLEIC ACIDS RESEARCH

Statistical mechanics of nucleosome ordering by chromatin-structure-induced two-body interactions

(2011) Răzvan V. Chereji et al.   PHYSICAL REVIEW E

Multiple Distinct Stimuli Increase Measured Nucleosome Occupancy around Human Promoters

(2011) Chuong D. Pham et al.   PLoS One

Coding RNAs with a non-coding function: Maintenance of open chromatin structure

(2011) Maïwen Caudron-Herger et al.   Nucleus

Next generation sequencing in functional genomics

(2010) T. Werner   BRIEFINGS IN BIOINFORMATICS

The Effect of Micrococcal Nuclease Digestion on Nucleosome Positioning Data

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

Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3'-end formation

(2010) X. Fan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CHD7 Targets Active Gene Enhancer Elements to Modulate ES Cell-Specific Gene Expression

(2010) Michael P. Schnetz et al.   PLoS Genetics

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

A novel mechanism of epigenetic regulation: Nucleosome-space occupancy

(2009) Peng Cui et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Poly(dA:dT) tracts: major determinants of nucleosome organization

(2009) Eran Segal et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

High-resolution nucleosome mapping reveals transcription-dependent promoter packaging

(2009) A. Weiner et al.   GENOME RESEARCH

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

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

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

Predicting nucleosome positions on the DNA: combining intrinsic sequence preferences and remodeler activities

(2009) Vladimir B. Teif et al.   NUCLEIC ACIDS RESEARCH

An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network

(2009) L. Ho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Dynamic Regulation of Nucleosome Positioning in the Human Genome

(2008) Dustin E. Schones et al.   CELL

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning

(2008) A. Valouev et al.   GENOME RESEARCH

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

Nucleosome organization in the Drosophila genome

(2008) Travis N. Mavrich et al.   NATURE

The DNA-encoded nucleosome organization of a eukaryotic genome

(2008) Noam Kaplan et al.   NATURE

Genomewide Analysis of PRC1 and PRC2 Occupancy Identifies Two Classes of Bivalent Domains

(2008) Manching Ku et al.   PLoS Genetics

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

(2008) Yutao Fu et al.   PLoS Genetics

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY