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

Fast gapped-read alignment with Bowtie 2

Ben Langmead, Steven L. Salzberg · Nature Methods · 2012 · 58.3K citations · Full text

Long-read Sequencing, Sequence Assembly, Natural Sciences +7

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan, Ira M. Hall · Bioinformatics · 2010 · 28.9K citations · Full text

Model-based Analysis of ChIP-Seq (MACS)

Yong Zhang, Tao Liu, Clifford A. Meyer et al. · Genome biology · 2008 · 19.1K citations · Full text

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

Sven Heinz, Christopher Benner, Nathanael J. Spann et al. · Molecular Cell · 2010 · 14K citations · Full text

Transcriptional Regulation, B Cell Identities, Cell Lineage +9

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

Jason D. Buenrostro, Paul G. Giresi, Lisa C. Zaba et al. · Nature Methods · 2013 · 6.8K citations · Full text

Chromatin, Native Chromatin, Chromatin Remodeling +15