Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity

Stepwise androgen receptor dimerization

(2012) M. E. van Royen et al.   JOURNAL OF CELL SCIENCE

Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection

(2012) Yoichiro Shibata et al.   PLoS Genetics

A Comprehensive View of Nuclear Receptor Cancer Cistromes

(2011) Q. Tang et al.   CANCER RESEARCH

Dynamic Exchange at Regulatory Elements during Chromatin Remodeling Underlies Assisted Loading Mechanism

(2011) Ty C. Voss et al.   CELL

AP-2γ regulates oestrogen receptor-mediated long-range chromatin interaction and gene transcription

(2011) Si Kee Tan et al.   EMBO JOURNAL

The androgen receptor fuels prostate cancer by regulating central metabolism and biosynthesis

(2011) Charles E Massie et al.   EMBO JOURNAL

Structure and function of active chromatin and DNase I hypersensitive sites

(2011) Peter N. Cockerill   FEBS Journal

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

(2011) L. Song et al.   GENOME RESEARCH

Energy Restriction-mimetic Agents Induce Apoptosis in Prostate Cancer Cells in Part through Epigenetic Activation of KLF6 Tumor Suppressor Gene Expression

(2011) Chun-Han Chen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Dynamic Nucleosome-Depleted Regions at Androgen Receptor Enhancers in the Absence of Ligand in Prostate Cancer Cells

(2011) C. Andreu-Vieyra et al.   MOLECULAR AND CELLULAR BIOLOGY

Opposing effects of Tcf3 and Tcf1 control Wnt stimulation of embryonic stem cell self-renewal

(2011) Fei Yi et al.   NATURE CELL BIOLOGY

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

CENTDIST: discovery of co-associated factors by motif distribution

(2011) Zhizhuo Zhang et al.   NUCLEIC ACIDS RESEARCH

An Integrated Network of Androgen Receptor, Polycomb, and TMPRSS2-ERG Gene Fusions in Prostate Cancer Progression

(2010) Jindan Yu et al.   CANCER CELL

Androgen receptor responsive enhancers are flanked by consistently-positioned H3-acetylated nucleosomes

(2010) Benjamin P. Berman et al.   CELL CYCLE

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

(2010) A. P. Boyle et al.   GENOME RESEARCH

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

(2010) R. Pique-Regi et al.   GENOME RESEARCH

Nucleosome dynamics define transcriptional enhancers

(2010) Housheng Hansen He et al.   NATURE GENETICS

Identification of a Cell of Origin for Human Prostate Cancer

(2010) A. S. Goldstein et al.   SCIENCE

Evidence-ranked motif identification

(2010) Stoyan Georgiev et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

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

Histone Deacetylases Are Required for Androgen Receptor Function in Hormone-Sensitive and Castrate-Resistant Prostate Cancer

(2009) D. S. Welsbie et al.   CANCER RESEARCH

Androgen Receptor Regulates a Distinct Transcription Program in Androgen-Independent Prostate Cancer

(2009) Qianben Wang et al.   CELL

Aberrant ERG expression cooperates with loss of PTEN to promote cancer progression in the prostate

(2009) Brett S Carver et al.   NATURE GENETICS

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

(2009) Jay R Hesselberth et al.   NATURE METHODS

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

(2009) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Yin Yang 1 regulates the transcriptional activity of androgen receptor

(2009) Z Deng et al.   ONCOGENE

ETS family transcription factors collaborate with alternative signaling pathways to induce carcinoma from adult murine prostate cells

(2009) Y. Zong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

What controls nucleosome positions?

(2009) Eran Segal et al.   TRENDS IN GENETICS

An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data

(2009) Daniel Ramsköld et al.   PLoS Computational Biology

F-Seq: a feature density estimator for high-throughput sequence tags

(2008) A. P. Boyle et al.   BIOINFORMATICS

Evolutionary conservation of zinc finger transcription factor binding sites in promoters of genes co-expressed with WT1 in prostate cancer

(2008) Kurtis Eisermann et al.   BMC GENOMICS

FoxA1 Translates Epigenetic Signatures into Enhancer-Driven Lineage-Specific Transcription

(2008) Mathieu Lupien et al.   CELL

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

(2008) Alan P. Boyle et al.   CELL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY