Nucleosome remodeling at origins of global genome–nucleotide excision repair occurs at the boundaries of higher-order chromatin structure

Understanding nucleosome dynamics and their links to gene expression and DNA replication

(2017) William K. M. Lai et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Variants of core histones and their roles in cell fate decisions, development and cancer

(2017) Marcus Buschbeck et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Histone degradation in response to DNA damage enhances chromatin dynamics and recombination rates

(2017) Michael H Hauer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Histone degradation in response to DNA damage enhances chromatin dynamics and recombination rates

(2017) Michael H Hauer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Global genome nucleotide excision repair is organized into domains that promote efficient DNA repair in chromatin

(2016) Shirong Yu et al.   GENOME RESEARCH

Micro-C XL: assaying chromosome conformation from the nucleosome to the entire genome

(2016) Tsung-Han S Hsieh et al.   NATURE METHODS

Histone variants on the move: substrates for chromatin dynamics

(2016) Paul B. Talbert et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Chromosomal landscape of UV damage formation and repair at single-nucleotide resolution

(2016) Peng Mao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C

(2015) Tsung-Han S. Hsieh et al.   CELL

Chromatin plasticity in response to DNA damage: The shape of things to come

(2015) Salomé Adam et al.   DNA REPAIR

Chromatin dynamics after DNA damage: The legacy of the access–repair–restore model

(2015) Sophie E. Polo et al.   DNA REPAIR

Reshaping Chromatin after DNA Damage: The Choreography of Histone Proteins

(2015) Sophie E. Polo   JOURNAL OF MOLECULAR BIOLOGY

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

(2015) Adrian L. Sanborn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo

(2015) Gabriel E. Zentner et al.   Nature Communications

3D-DIP-Chip: a microarray-based method to measure genomic DNA damage

(2015) James Rees Powell et al.   Scientific Reports

Nucleosomes Are Context-Specific, H2A.Z-Modulated Barriers to RNA Polymerase

(2014) Christopher M. Weber et al.   MOLECULAR CELL

Understanding nucleotide excision repair and its roles in cancer and ageing

(2014) Jurgen A. Marteijn et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Histone variant Htz1 promotes histone H3 acetylation to enhance nucleotide excision repair in Htz1 nucleosomes

(2013) Yachuan Yu et al.   NUCLEIC ACIDS RESEARCH

Nucleosome Free Regions in Yeast Promoters Result from Competitive Binding of Transcription Factors That Interact with Chromatin Modifiers

(2013) Evgeniy A. Ozonov et al.   PLoS Computational Biology

A Compendium of Nucleosome and Transcript Profiles Reveals Determinants of Chromatin Architecture and Transcription

(2013) Harm van Bakel et al.   PLoS Genetics

DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencing

(2012) K. Chen et al.   GENOME RESEARCH

Functions of Protosilencers in the Formation and Maintenance of Heterochromatin in Saccharomyces cerevisiae

(2012) Xinmin Zhang et al.   PLoS One

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

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

(2011) Zhenhai Zhang et al.   CELL

Chromatin and the DNA damage response: The cancer connection

(2011) Martijn S. Luijsterburg et al.   Molecular Oncology

How Chromatin Is Remodelled during DNA Repair of UV-Induced DNA Damage in Saccharomyces cerevisiae

(2011) Shirong Yu et al.   PLoS Genetics

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

(2010) Lihua J Zhu et al.   BMC BIOINFORMATICS

Chromatin Remodeling around Nucleosome-Free Regions Leads to Repression of Noncoding RNA Transcription

(2010) A. N. Yadon et al.   MOLECULAR AND CELLULAR BIOLOGY

The DNA Damage Response: Making It Safe to Play with Knives

(2010) Alberto Ciccia et al.   MOLECULAR CELL

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

A novel method for the genome-wide high resolution analysis of DNA damage

(2010) Yumin Teng et al.   NUCLEIC ACIDS RESEARCH

Extensive role of the general regulatory factors, Abf1 and Rap1, in determining genome-wide chromatin structure in budding yeast

(2010) Mythily Ganapathi et al.   NUCLEIC ACIDS RESEARCH

Chromatin particle spectrum analysis: a method for comparative chromatin structure analysis using paired-end mode next-generation DNA sequencing

(2010) N. A. Kent et al.   NUCLEIC ACIDS RESEARCH

Mechanisms that Specify Promoter Nucleosome Location and Identity

(2009) Paul D. Hartley et al.   CELL

Bidirectional promoters generate pervasive transcription in yeast

(2009) Zhenyu Xu et al.   NATURE

Nucleosome positioning and gene regulation: advances through genomics

(2009) Cizhong Jiang et al.   NATURE REVIEWS GENETICS

ABF1-binding Sites Promote Efficient Global Genome Nucleotide Excision Repair

(2008) Shirong Yu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Genome-wide Expression Profiling, In Vivo DNA Binding Analysis, and Probabilistic Motif Prediction Reveal Novel Abf1 Target Genes during Fermentation, Respiration, and Sporulation in Yeast

(2008) Ulrich Schlecht et al.   MOLECULAR BIOLOGY OF THE CELL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY