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

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

SC3: consensus clustering of single-cell RNA-seq data

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

De novo MEIS2 mutation causes syndromic developmental delay with persistent gastro-esophageal reflux

(2016) Atsushi Fujita et al.   JOURNAL OF HUMAN GENETICS

MEIS2involvement in cardiac development, cleft palate, and intellectual disability

(2015) Jacoba J. Louw et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART A

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

MEIS2 is essential for neuroblastoma cell survival and proliferation by transcriptional control of M-phase progression

(2014) Y Zha et al.   Cell Death & Disease

Bmp4regulates chickEbf2andEbf3gene expression in somite development

(2013) Mohammed A. El-Magd et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

RNA-SeQC: RNA-seq metrics for quality control and process optimization

(2012) David S. DeLuca et al.   BIOINFORMATICS

Reduction of pro-tumorigenic activity of human prostate cancer-associated fibroblasts using Dlk1 or SCUBE1

(2012) B. Orr et al.   Disease Models & Mechanisms

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

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

Stromal Expression of Decorin, Semaphorin6D, SPARC, Sprouty1 and Tsukushi in Developing Prostate and Decreased Levels of Decorin in Prostate Cancer

(2012) Alexander Henke et al.   PLoS One

A high-resolution molecular atlas of the fetal mouse lower urogenital tract

(2011) Lisa L. Abler et al.   DEVELOPMENTAL DYNAMICS

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

A High Throughput in situ Hybridization Method to Characterize mRNA Expression Patterns in the Fetal Mouse Lower Urogenital Tract

(2011) Lisa L. Abler et al.   Jove-Journal of Visualized Experiments

Identification of EphrinB1 expression in prostatic mesenchyme and a role for EphB–EphrinB signalling in prostate development

(2010) George R. Ashley et al.   DIFFERENTIATION

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

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell 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

Molecular signaling pathways that regulate prostate gland development

(2008) Gail S. Prins et al.   DIFFERENTIATION

Mesenchymal mechanisms in prostate organogenesis

(2008) Axel A. Thomson   DIFFERENTIATION

A Role for Notch Signaling in Stromal Survival and Differentiation during Prostate Development

(2008) Brigid Orr 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