ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation

Chromatin accessibility and the regulatory epigenome

(2019) Sandy L. Klemm et al.   NATURE REVIEWS GENETICS

Specific chromatin changes mark lateral organ founder cells in the Arabidopsis thaliana inflorescence meristem

(2019) Anneke Frerichs et al.   JOURNAL OF EXPERIMENTAL BOTANY

Transcriptomic and epigenetic regulation of hair cell regeneration in the mouse utricle and its potentiation by Atoh1

(2019) Hsin-I Jen et al.   eLife

Defining the dynamic chromatin landscape of mouse nephron progenitors

(2019) Sylvia Hilliard et al.   Biology Open

An ATAC-seq atlas of chromatin accessibility in mouse tissues

(2019) Chuanyu Liu et al.   Scientific Data

Transcription Restart Establishes Chromatin Accessibility after DNA Replication

(2019) Kathleen R. Stewart-Morgan et al.   MOLECULAR CELL

HMMRATAC: a Hidden Markov ModeleR for ATAC-seq

(2019) Evan D Tarbell et al.   NUCLEIC ACIDS RESEARCH

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

ARID1A and PI3-kinase pathway mutations in the endometrium drive epithelial transdifferentiation and collective invasion

(2019) Mike R. Wilson et al.   Nature Communications

A mouse model of endometriosis mimicking the natural spread of invasive endometrium

(2019) Mike R Wilson et al.   HUMAN REPRODUCTION

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

(2018) Jianhong Ou et al.   BMC GENOMICS

Chromatin Accessibility-Based Characterization of the Gene Regulatory Network Underlying Plasmodium falciparum Blood-Stage Development

(2018) Christa Geeke Toenhake et al.   Cell Host & Microbe

Global dynamics of stage-specific transcription factor binding during thymocyte development

(2018) Tomonori Hosoya et al.   Scientific Reports

GUAVA: A Graphical User Interface for the Analysis and Visualization of ATAC-seq Data

(2018) Mayur Divate et al.   Frontiers in Genetics

ATAC2GRN: optimized ATAC-seq and DNase1-seq pipelines for rapid and accurate genome regulatory network inference

(2018) Thomas J. F. Pranzatelli et al.   BMC GENOMICS

The Histone Demethylase LSD1 Regulates B Cell Proliferation and Plasmablast Differentiation

(2018) Robert R. Haines et al.   JOURNAL OF IMMUNOLOGY

The chromatin accessibility landscape of primary human cancers

(2018) M. Ryan Corces et al.   SCIENCE

Single cell RNA-seq and ATAC-seq analysis of cardiac progenitor cell transition states and lineage settlement

(2018) Guangshuai Jia et al.   Nature Communications

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

Ensembl 2018

(2017) Daniel R Zerbino et al.   NUCLEIC ACIDS RESEARCH

Universal correction of enzymatic sequence bias reveals molecular signatures of protein/DNA interactions

(2017) André L Martins et al.   NUCLEIC ACIDS RESEARCH

Chromatin accessibility underlies synthetic lethality of SWI/SNF subunits in ARID1A-mutant cancers

(2017) Timothy W R Kelso et al.   eLife

I-ATAC: interactive pipeline for the management and pre-processing of ATAC-seq samples

(2017) Zeeshan Ahmed et al.   PeerJ

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Analysis of computational footprinting methods for DNase sequencing experiments

(2016) Eduardo G Gusmao et al.   NATURE METHODS

MNase titration reveals differences between nucleosome occupancy and chromatin accessibility

(2016) Jakub Mieczkowski et al.   Nature Communications

PRROC: computing and visualizing precision-recall and receiver operating characteristic curves in R

(2015) Jan Grau et al.   BIOINFORMATICS

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

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

The Overlooked Fact: Fundamental Need for Spike-In Control for Virtually All Genome-Wide Analyses

(2015) Kaifu Chen et al.   MOLECULAR AND CELLULAR BIOLOGY

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows

(2015) Aaron T.L. Lun et al.   NUCLEIC ACIDS RESEARCH

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

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

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

Chromatin accessibility: a window into the genome

(2014) Maria Tsompana et al.   Epigenetics & Chromatin

Quantitative ChIP-Seq Normalization Reveals Global Modulation of the Epigenome

(2014) David A. Orlando et al.   Cell Reports

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

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

Widespread Misinterpretable ChIP-seq Bias in Yeast

(2013) Daechan Park et al.   PLoS One

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

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

MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets

(2012) Zhen Shao et al.   GENOME BIOLOGY

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Epigenome characterization at single base-pair resolution

(2011) J. G. Henikoff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions

(2011) Naim U Rashid et al.   GENOME BIOLOGY

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

Principles and challenges of genome-wide DNA methylation analysis

(2010) Peter W. Laird   NATURE REVIEWS GENETICS

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Comparative study on ChIP-seq data: normalization and binding pattern characterization

(2009) Cenny Taslim et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

BioMart – biological queries made easy

(2009) Damian Smedley et al.   BMC GENOMICS

Dynamic and complex transcription factor binding during an inducible response in yeast

(2009) L. Ni et al.   GENES & DEVELOPMENT

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

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY