BRG1 governs glucocorticoid receptor interactions with chromatin and pioneer factors across the genome

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Conventional and pioneer modes of glucocorticoid receptor interaction with enhancer chromatin in vivo

(2017) Thomas A Johnson et al.   NUCLEIC ACIDS RESEARCH

The BRG1 ATPase of human SWI/SNF chromatin remodeling enzymes as a driver of cancer

(2017) Qiong Wu et al.   Epigenomics

Single-molecule analysis of steroid receptor and cofactor action in living cells

(2017) Ville Paakinaho et al.   Nature Communications

Glucocorticoid Receptor Binding Induces Rapid and Prolonged Large-Scale Chromatin Decompaction at Multiple Target Loci

(2017) Alasdair W. Jubb et al.   Cell Reports

Steroid Receptors Reprogram FoxA1 Occupancy through Dynamic Chromatin Transitions

(2016) Erin E. Swinstead et al.   CELL

Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome

(2016) Christopher M. Vockley et al.   CELL

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Downstream Antisense Transcription Predicts Genomic Features That Define the Specific Chromatin Environment at Mammalian Promoters

(2016) Christopher A. Lavender et al.   PLoS Genetics

ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors

(2015) Stephan R. Starick et al.   GENOME RESEARCH

Glucocorticoid Receptor Transcriptional Activation via the BRG1-Dependent Recruitment of TOP2β and Ku70/86

(2015) Kevin W. Trotter et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2014) Charity W Law et al.   GENOME BIOLOGY

C/EBP maintains chromatin accessibility in liver and facilitates glucocorticoid receptor recruitment to steroid response elements

(2013) Lars Grøntved et al.   EMBO JOURNAL

Proteomic and bioinformatic analysis of mammalian SWI/SNF complexes identifies extensive roles in human malignancy

(2013) Cigall Kadoch et al.   NATURE GENETICS

The Spectrum of SWI/SNF Mutations, Ubiquitous in Human Cancers

(2013) A. Hunter Shain et al.   PLoS One

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Analysis of Chromatin Dynamics during Glucocorticoid Receptor Activation

(2012) C. J. Burd et al.   MOLECULAR AND CELLULAR BIOLOGY

The Stat3/GR Interaction Code: Predictive Value of Direct/Indirect DNA Recruitment for Transcription Outcome

(2012) David Langlais et al.   MOLECULAR CELL

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Coactivation of GR and NFKB alters the repertoire of their binding sites and target genes

(2011) N. A. S. Rao et al.   GENOME RESEARCH

Transcription Factor AP1 Potentiates Chromatin Accessibility and Glucocorticoid Receptor Binding

(2011) Simon C. Biddie et al.   MOLECULAR CELL

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data

(2010) Robert C McLeay et al.   BMC BIOINFORMATICS

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

FOXA1 is a key determinant of estrogen receptor function and endocrine response

(2010) Antoni Hurtado et al.   NATURE GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Glucocorticoid Receptor Activation of theCiz1-Lcn2Locus by Long Range Interactions

(2009) Ofir Hakim et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Chromatin Remodeling Complexes Interact Dynamically with a Glucocorticoid Receptor–regulated Promoter

(2008) Thomas A. Johnson et al.   MOLECULAR BIOLOGY OF THE CELL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY