Standardizing chromatin research: a simple and universal method for ChIP-seq

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors

(2015) Christian Schmidl et al.   NATURE METHODS

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Monocyte to Macrophage Differentiation Goes along with Modulation of the Plasmalogen Pattern through Transcriptional Regulation

(2014) Stefan Wallner et al.   PLoS One

An Optimized Protocol for Isolating Primary Epithelial Cell Chromatin for ChIP

(2014) James A. Browne et al.   PLoS One

Chromatin state dynamics during blood formation

(2014) D. Lara-Astiaso et al.   SCIENCE

Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity

(2014) S. Saeed et al.   SCIENCE

Fully automated high-throughput chromatin immunoprecipitation for ChIP-seq: Identifying ChIP-quality p300 monoclonal antibodies

(2014) William C. Gasper et al.   Scientific Reports

Recent advances in 2D and 3D in vitro systems using primary hepatocytes, alternative hepatocyte sources and non-parenchymal liver cells and their use in investigating mechanisms of hepatotoxicity, cell signaling and ADME

(2013) Patricio Godoy et al.   ARCHIVES OF TOXICOLOGY

In Vivo Epigenomic Profiling of Germ Cells Reveals Germ Cell Molecular Signatures

(2013) Jia-Hui Ng et al.   DEVELOPMENTAL CELL

The UCSC Genome Browser database: 2014 update

(2013) Donna Karolchik et al.   NUCLEIC ACIDS RESEARCH

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

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

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA

(2012) Jeremy M Simon et al.   Nature Protocols

ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions

(2012) Terrence S. Furey   NATURE REVIEWS GENETICS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

ChIP-Seq: technical considerations for obtaining high-quality data

(2011) Benjamin L Kidder et al.   NATURE IMMUNOLOGY

Single-tube linear DNA amplification (LinDA) for robust ChIP-seq

(2011) Pattabhiraman Shankaranarayanan et al.   NATURE METHODS

Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq

(2011) Mazhar Adli et al.   Nature Protocols

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors

(2010) Mazhar Adli et al.   NATURE METHODS

An assessment of histone-modification antibody quality

(2010) Thea A Egelhofer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Exploring DNA-Binding Proteins with In Vivo Chemical Cross-Linking and Mass Spectrometry

(2009) Haibo Qiu et al.   JOURNAL OF PROTEOME RESEARCH

Studying physical chromatin interactions in plants using Chromosome Conformation Capture (3C)

(2009) Marieke Louwers et al.   Nature Protocols

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

An integrated software system for analyzing ChIP-chip and ChIP-seq data

(2008) Hongkai Ji et al.   NATURE BIOTECHNOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY