Active promoters give rise to false positive ‘Phantom Peaks’ in ChIP-seq experiments

Locus-Specific Targeting to the X Chromosome Revealed by the RNA Interactome of CTCF

(2015) Johnny T. Kung et al.   MOLECULAR CELL

Reproducibility: Standardize antibodies used in research

(2015) Andrew Bradbury et al.   NATURE

Chromatin Immunoprecipitation Indirect Peaks Highlight Long-Range Interactions of Insulator Proteins and Pol II Pausing

(2014) Jun Liang et al.   MOLECULAR CELL

Identifying and mitigating bias in next-generation sequencing methods for chromatin biology

(2014) Clifford A. Meyer et al.   NATURE REVIEWS GENETICS

Optimization of transcription factor binding map accuracy utilizing knockout-mouse models

(2014) Wolfgang Krebs et al.   NUCLEIC ACIDS RESEARCH

Phosphorylation-Regulated Binding of RNA Polymerase II to Fibrous Polymers of Low-Complexity Domains

(2013) Ilmin Kwon et al.   CELL

Two new and distinct roles for Drosophila Argonaute-2 in the nucleus: alternative pre-mRNA splicing and transcriptional repression

(2013) J. M. Taliaferro et al.   GENES & DEVELOPMENT

A Network Model of the Molecular Organization of Chromatin in Drosophila

(2013) Joke G. van Bemmel et al.   MOLECULAR CELL

High-resolution mapping of transcription factor binding sites on native chromatin

(2013) Sivakanthan Kasinathan et al.   NATURE METHODS

The CRAPome: a contaminant repository for affinity purification–mass spectrometry data

(2013) Dattatreya Mellacheruvu et al.   NATURE METHODS

Overlapping chromatin-remodeling systems collaborate genome wide at dynamic chromatin transitions

(2013) Stephanie A Morris et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Widespread Misinterpretable ChIP-seq Bias in Yeast

(2013) Daechan Park et al.   PLoS One

Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins

(2013) L. Teytelman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ISWI and CHD Chromatin Remodelers Bind Promoters but Act in Gene Bodies

(2013) Gabriel E. Zentner et al.   PLoS Genetics

An effective statistical evaluation of ChIPseq dataset similarity

(2012) Maria D. Chikina et al.   BIOINFORMATICS

Solution-based targeted genomic enrichment for precious DNA samples

(2012) Aiden Shearer et al.   BMC BIOTECHNOLOGY

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Genome-wide Nucleosome Specificity and Directionality of Chromatin Remodelers

(2012) Kuangyu Yen et al.   CELL

Different chromatin interfaces of the Drosophila dosage compensation complex revealed by high-shear ChIP-seq

(2012) T. Straub et al.   GENOME RESEARCH

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

Systematic evaluation of factors influencing ChIP-seq fidelity

(2012) Yiwen Chen et al.   NATURE METHODS

Genome-wide copy number analysis of single cells

(2012) Timour Baslan et al.   Nature Protocols

Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange

(2012) Michaela Smolle et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Quantifying transient binding of ISWI chromatin remodelers in living cells by pixel-wise photobleaching profile evolution analysis

(2012) F. Erdel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions

(2011) Joseph K. Pickrell et al.   BIOINFORMATICS

ATP-dependent chromatin remodeling: genetics, genomics and mechanisms

(2011) Diana C Hargreaves et al.   CELL RESEARCH

Genome-wide characterization of chromatin binding and nucleosome spacing activity of the nucleosome remodelling ATPase ISWI

(2011) Anna Sala et al.   EMBO JOURNAL

Calling Cards enable multiplexed identification of the genomic targets of DNA-binding proteins

(2011) H. Wang 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

Identification of a Rapidly Formed Nonnucleosomal Histone-DNA Intermediate that Is Converted into Chromatin by ACF

(2011) Sharon E. Torigoe et al.   MOLECULAR CELL

A cis-regulatory map of the Drosophila genome

(2011) Nicolas Nègre et al.   NATURE

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

Binding kinetics of human ISWI chromatin-remodelers to DNA repair sites elucidate their target location mechanism

(2011) Fabian Erdel et al.   Nucleus

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

(2010) Lihua J Zhu et al.   BMC BIOINFORMATICS

ChIP on Chip: surprising results are often artifacts

(2010) Torsten Waldminghaus et al.   BMC GENOMICS

Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

(2010) Guillaume J. Filion et al.   CELL

Developmental role for ACF1-containing nucleosome remodellers in chromatin organisation

(2010) M. Chioda et al.   DEVELOPMENT

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

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

The developmental transcriptome of Drosophila melanogaster

(2010) Brenton R. Graveley et al.   NATURE

Human ISWI chromatin-remodeling complexes sample nucleosomes via transient binding reactions and become immobilized at active sites

(2010) F. Erdel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Biology of Chromatin Remodeling Complexes

(2009) Cedric R. Clapier et al.   Annual Review of Biochemistry

The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets

(2009) J. W. Nicol et al.   BIOINFORMATICS

Betulin Is a Potent Anti-Tumor Agent that Is Enhanced by Cholesterol

(2009) Franziska B. Mullauer et al.   PLoS One

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

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY

A large genome center's improvements to the Illumina sequencing system

(2008) Michael A Quail et al.   NATURE METHODS

RSF Governs Silent Chromatin Formation via Histone H2Av Replacement

(2008) Kazuma Hanai et al.   PLoS Genetics