Genome-wide analysis of androgen receptor binding and transcriptomic analysis in mesenchymal subsets during prostate development

Genome-wide analysis of AR binding and comparison with transcript expression in primary human fetal prostate fibroblasts and cancer associated fibroblasts

(2018) Claire Nash et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

Loss of androgen receptor signaling in prostate cancer-associated fibroblasts (CAFs) promotes CCL2- and CXCL8-mediated cancer cell migration

(2018) Bianca Cioni et al.   Molecular Oncology

Bias, robustness and scalability in single-cell differential expression analysis

(2018) Charlotte Soneson et al.   NATURE METHODS

ZNRF3 functions in mammalian sex determination by inhibiting canonical WNT signaling

(2018) Abigail Harris et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Cellular Anatomy of the Normal Adult Human Prostate and Prostatic Urethra

(2018) Gervaise H. Henry et al.   Cell Reports

Single cell proteomics in biomedicine: High-dimensional data acquisition, visualization, and analysis

(2017) Yapeng Su et al.   PROTEOMICS

Identification of genes expressed in a mesenchymal subset regulating prostate organogenesis using tissue and single cell transcriptomics

(2017) Nadia Boufaied et al.   Scientific Reports

On the Dependency of Cellular Protein Levels on mRNA Abundance

(2016) Yansheng Liu et al.   CELL

Nfib Regulates Transcriptional Networks That Control the Development of Prostatic Hyperplasia

(2016) Magdalena M. Grabowska et al.   ENDOCRINOLOGY

An illustrated anatomical ontology of the developing mouse lower urogenital tract

(2015) K. M. Georgas et al.   DEVELOPMENT

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

The androgen receptor cistrome is extensively reprogrammed in human prostate tumorigenesis

(2015) Mark M Pomerantz et al.   NATURE GENETICS

NFI Transcription Factors Interact with FOXA1 to Regulate Prostate-Specific Gene Expression

(2014) Magdalena M. Grabowska et al.   MOLECULAR ENDOCRINOLOGY

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Formation of Human Prostate Epithelium Using Tissue Recombination of Rodent Urogenital Sinus Mesenchyme and Human Stem Cells

(2013) Yi Cai et al.   Jove-Journal of Visualized Experiments

Reduced prostate branching morphogenesis in stromal fibroblast, but not in epithelial, estrogen receptor α knockout mice

(2012) Ming Chen et al.   ASIAN JOURNAL OF ANDROLOGY

The Androgen Receptor Induces a Distinct Transcriptional Program in Castration-Resistant Prostate Cancer in Man

(2012) Naomi L. Sharma et al.   CANCER CELL

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Persistent androgen receptor-mediated transcription in castration-resistant prostate cancer under androgen-deprived conditions

(2012) Keith F. Decker et al.   NUCLEIC ACIDS RESEARCH

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

(2011) Hanbo Chen et al.   BMC BIOINFORMATICS

Atlas of Wnt and R-spondin gene expression in the developing male mouse lower urogenital tract

(2011) Vatsal Mehta et al.   DEVELOPMENTAL DYNAMICS

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

(2011) Charles E Massie et al.   EMBO JOURNAL

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

Androgen receptor-mediated gene repression

(2011) Andreas Grosse et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

Identification of stromally expressed molecules in the prostate by tag-profiling of cancer-associated fibroblasts, normal fibroblasts and fetal prostate

(2011) B Orr et al.   ONCOGENE

Effects of Androgen Receptor and Androgen on Gene Expression in Prostate Stromal Fibroblasts and Paracrine Signaling to Prostate Cancer Cells

(2011) Matthew J. Tanner et al.   PLoS One

A flexible R package for nonnegative matrix factorization

(2010) Renaud Gaujoux et al.   BMC BIOINFORMATICS

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

(2010) Jindan Yu et al.   CANCER CELL

Nfix Regulates Fetal-Specific Transcription in Developing Skeletal Muscle

(2010) Graziella Messina et al.   CELL

Expression of pleiotrophin in the prostate is androgen regulated and it functions as an autocrine regulator of mesenchyme and cancer associated fibroblasts and as a paracrine regulator of epithelia

(2010) Brigid Orr et al.   PROSTATE

The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets

(2009) J. W. Nicol et al.   BIOINFORMATICS

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

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

Conserved Gene Expression Programs Integrate Mammalian Prostate Development and Tumorigenesis

(2009) C. Pritchard et al.   CANCER RESEARCH

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

The transcription factor Nfix is essential for normal brain development

(2008) Christine E Campbell et al.   BMC DEVELOPMENTAL BIOLOGY

Mesenchymal mechanisms in prostate organogenesis

(2008) Axel A. Thomson   DIFFERENTIATION

Defects of Prostate Development and Reproductive System in the Estrogen Receptor-α Null Male Mice

(2008) Ming Chen et al.   ENDOCRINOLOGY

Androgen-induced programs for prostate epithelial growth and invasion arise in embryogenesis and are reactivated in cancer

(2008) E M Schaeffer et al.   ONCOGENE