ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data

motifStack for the analysis of transcription factor binding site evolution

(2018) Jianhong Ou et al.   NATURE METHODS

The Short Isoform of BRD4 Promotes HIV-1 Latency by Engaging Repressive SWI/SNF Chromatin-Remodeling Complexes

(2017) Ryan J. Conrad et al.   MOLECULAR CELL

Robust Identification of Developmentally Active Endothelial Enhancers in Zebrafish Using FANS-Assisted ATAC-Seq

(2017) Aurelie Quillien et al.   Cell Reports

Integration of ATAC-seq and RNA-seq identifies human alpha cell and beta cell signature genes

(2016) Amanda M. Ackermann et al.   Molecular Metabolism

ATAC-seq on biobanked specimens defines a unique chromatin accessibility structure in naïve SLE B cells

(2016) Christopher D. Scharer et al.   Scientific Reports

Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions

(2015) Alicia N. Schep et al.   GENOME RESEARCH

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Discovery of Transcription Factors and Regulatory Regions Driving In Vivo Tumor Development by ATAC-seq and FAIRE-seq Open Chromatin Profiling

(2015) Kristofer Davie et al.   PLoS Genetics

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Chromatin accessibility: a window into the genome

(2014) Maria Tsompana et al.   Epigenetics & Chromatin

SRAdb: query and use public next-generation sequencing data from within R

(2013) Yuelin Zhu et al.   BMC BIOINFORMATICS

Predicting the molecular complexity of sequencing libraries

(2013) Timothy Daley et al.   NATURE METHODS

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

Human housekeeping genes, revisited

(2013) Eli Eisenberg et al.   TRENDS IN GENETICS

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

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

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

DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencing

(2012) K. Chen et al.   GENOME RESEARCH

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

Nucleosome distribution and linker DNA: connecting nuclear function to dynamic chromatin structureThis paper is one of a selection of papers published in a Special Issue entitled 31st Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process.

(2011) Heather J. Szerlong et al.   Biochemistry and Cell Biology

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Large Scale Library Generation for High Throughput Sequencing

(2011) Erik Borgström et al.   PLoS One

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

(2010) Lihua J Zhu et al.   BMC BIOINFORMATICS

Increased Throughput by Parallelization of Library Preparation for Massive Sequencing

(2010) Sverker Lundin et al.   PLoS One

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition

(2010) Andrew Adey et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Dynamic Regulation of Nucleosome Positioning in the Human Genome

(2008) Dustin E. Schones et al.   CELL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY