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

Multiplexed Illumina sequencing libraries from picogram quantities of DNA

(2013) Sarah K Bowman et al.   BMC GENOMICS

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Epigenetics of Reprogramming to Induced Pluripotency

(2013) Bernadett Papp et al.   CELL

Understanding impediments to cellular conversion to pluripotency by assessing the earliest events in ectopic transcription factor binding to the genome

(2013) Abdenour Soufi et al.   CELL CYCLE

Swi/Snf chromatin remodeling/tumor suppressor complex establishes nucleosome occupancy at target promoters

(2013) M. Y. Tolstorukov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Foxa2 and H2A.Z Mediate Nucleosome Depletion during Embryonic Stem Cell Differentiation

(2012) Zhaoyu Li et al.   CELL

Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome

(2012) Abdenour Soufi et al.   CELL

H2A.Z Facilitates Access of Active and Repressive Complexes to Chromatin in Embryonic Stem Cell Self-Renewal and Differentiation

(2012) Gangqing Hu et al.   Cell Stem Cell

DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencing

(2012) K. Chen et al.   GENOME RESEARCH

Micrococcal Nuclease Does Not Substantially Bias Nucleosome Mapping

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

Histone Variant H2A.Bbd Is Associated with Active Transcription and mRNA Processing in Human Cells

(2012) Michael Y. Tolstorukov et al.   MOLECULAR CELL

Genome-wide nucleosome positioning during embryonic stem cell development

(2012) Vladimir B Teif et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

Controls of Nucleosome Positioning in the Human Genome

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

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

Mbd3/NURD Complex Regulates Expression of 5-Hydroxymethylcytosine Marked Genes in Embryonic Stem Cells

(2011) Ozlem Yildirim et al.   CELL

Constitutive heterochromatin reorganization during somatic cell reprogramming

(2011) Eden Fussner et al.   EMBO JOURNAL

CpG islands and the regulation of transcription

(2011) A. M. Deaton 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

Determinants of nucleosome organization in primary human cells

(2011) Anton Valouev et al.   NATURE

The nucleosome map of the mammalian liver

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

Systematic bias in high-throughput sequencing data and its correction by BEADS

(2011) Ming-Sin Cheung et al.   NUCLEIC ACIDS 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

Concise Review: Induced Pluripotent Stem Cells Versus Embryonic Stem Cells: Close Enough or Yet Too Far Apart?

(2011) Josipa Bilic et al.   STEM CELLS

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

(2010) Caroline J. Woo et al.   CELL

Distinct Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells

(2010) R. David Hawkins et al.   Cell Stem Cell

Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells

(2010) Matthias Stadtfeld et al.   NATURE

Open chromatin in pluripotency and reprogramming

(2010) Alexandre Gaspar-Maia et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Effect of Micrococcal Nuclease Digestion on Nucleosome Positioning Data

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

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The transcriptional foundation of pluripotency

(2009) I. Chambers et al.   DEVELOPMENT

Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes

(2009) M. Y. Tolstorukov et al.   GENOME RESEARCH

High-resolution nucleosome mapping reveals transcription-dependent promoter packaging

(2009) A. Weiner et al.   GENOME RESEARCH

Interaction of Transcriptional Regulators with Specific Nucleosomes across the Saccharomyces Genome

(2009) R. Thomas Koerber et al.   MOLECULAR CELL

A reprogrammable mouse strain from gene-targeted embryonic stem cells

(2009) Matthias Stadtfeld et al.   NATURE METHODS

The SWI/SNF complex and cancer

(2009) D Reisman et al.   ONCOGENE

An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency

(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

Nucleosome positioning in human HOX gene clusters

(2008) P. V. Kharchenko et al.   GENOME RESEARCH

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

ES cell pluripotency and germ-layer formation require the SWI/SNF chromatin remodeling component BAF250a

(2008) X. Gao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Activator Control of Nucleosome Occupancy in Activation and Repression of Transcription

(2008) Gene O Bryant et al.   PLOS BIOLOGY

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

(2008) Yutao Fu et al.   PLoS Genetics