Widespread changes in nucleosome accessibility without changes in nucleosome occupancy during a rapid transcriptional induction

MNase-Sensitive Complexes in Yeast: Nucleosomes and Non-histone Barriers

(2017) Răzvan V. Chereji et al.   MOLECULAR CELL

Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping

(2016) Lilien N. Voong et al.   CELL

The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation

(2016) Makiko Iwafuchi-Doi et al.   MOLECULAR CELL

MNase titration reveals differences between nucleosome occupancy and chromatin accessibility

(2016) Jakub Mieczkowski et al.   Nature Communications

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

(2015) Abdenour Soufi et al.   CELL

Nucleosome Stability Distinguishes Two Different Promoter Types at All Protein-Coding Genes in Yeast

(2015) Slawomir Kubik et al.   MOLECULAR CELL

Genome-wide profiling of nucleosome sensitivity and chromatin accessibility inDrosophila melanogaster

(2015) Răzvan V. Chereji et al.   NUCLEIC ACIDS RESEARCH

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS 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

Pioneer transcription factors in cell reprogramming

(2014) Makiko Iwafuchi-Doi et al.   GENES & DEVELOPMENT

Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development

(2014) Vladimir B. Teif et al.   GENOME RESEARCH

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

The spring-loaded genome: Nucleosome redistributions are widespread, transient, and DNA-directed

(2013) B. S. Sexton et al.   GENOME RESEARCH

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

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

The Unfolded Protein Response: From Stress Pathway to Homeostatic Regulation

(2011) P. Walter et al.   SCIENCE

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

(2010) Michael Y Tolstorukov et al.   Epigenomics

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

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

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

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Nucleosome organization in the Drosophila genome

(2008) Travis N. Mavrich et al.   NATURE

Design and analysis of ChIP-seq experiments for DNA-binding proteins

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY