Gene regulatory mechanisms underpinning prostate cancer susceptibility

The androgen receptor cistrome is extensively reprogrammed in human prostate tumorigenesis

(2015) Mark M Pomerantz et al.   NATURE GENETICS

Recurrent somatic mutations in regulatory regions of human cancer genomes

(2015) Collin Melton et al.   NATURE GENETICS

Integration of copy number and transcriptomics provides risk stratification in prostate cancer: A discovery and validation cohort study

(2015) H. Ross-Adams et al.   EBioMedicine

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

(2014) Hongshan Jiang et al.   BMC BIOINFORMATICS

Association of Prostate Cancer Risk Variants with Gene Expression in Normal and Tumor Tissue

(2014) K. L. Penney et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

Expression QTL-based analyses reveal candidate causal genes and loci across five tumor types

(2014) Qiyuan Li et al.   HUMAN MOLECULAR GENETICS

Androgens and androgen receptor signaling in prostate tumorigenesis

(2014) Ye Zhou et al.   JOURNAL OF MOLECULAR ENDOCRINOLOGY

A meta-analysis of 87,040 individuals identifies 23 new susceptibility loci for prostate cancer

(2014) Ali Amin Al Olama et al.   NATURE GENETICS

A prostate cancer susceptibility allele at 6q22 increases RFX6 expression by modulating HOXB13 chromatin binding

(2014) Qilai Huang et al.   NATURE GENETICS

Three-tiered role of the pioneer factor GATA2 in promoting androgen-dependent gene expression in prostate cancer

(2014) Dayong Wu et al.   NUCLEIC ACIDS RESEARCH

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

Comprehensive Functional Annotation of 77 Prostate Cancer Risk Loci

(2014) Dennis J. Hazelett et al.   PLoS Genetics

Ion Channels and Transporters in Cancer: Pathophysiology, Regulation, and Clinical Potential

(2013) S. F. Pedersen et al.   CANCER RESEARCH

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

A rare variant, which destroys a FoxA1 site at 8q24, is associated with prostate cancer risk

(2013) Dennis J. Hazelett et al.   CELL CYCLE

Variants at IRX4 as prostate cancer expression quantitative trait loci

(2013) Xing Xu et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers

(2013) A. Jankowski et al.   GENOME RESEARCH

Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals

(2013) A. Battle et al.   GENOME RESEARCH

Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model

(2013) Robin P Smith et al.   NATURE GENETICS

Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array

(2013) Rosalind A Eeles et al.   NATURE GENETICS

An Erythroid Enhancer of BCL11A Subject to Genetic Variation Determines Fetal Hemoglobin Level

(2013) D. E. Bauer et al.   SCIENCE

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Exome Sequencing of Prostate Cancer Supports the Hypothesis of Independent Tumour Origins

(2012) Johan Lindberg et al.   EUROPEAN UROLOGY

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

P-value-based regulatory motif discovery using positional weight matrices

(2012) H. Hartmann et al.   GENOME RESEARCH

Linking disease associations with regulatory information in the human genome

(2012) M. A. Schaub et al.   GENOME RESEARCH

Annotation of functional variation in personal genomes using RegulomeDB

(2012) A. P. Boyle et al.   GENOME RESEARCH

Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q24.3 prostate cancer risk locus

(2012) X. Zhang et al.   GENOME RESEARCH

IRX4 at 5p15 suppresses prostate cancer growth through the interaction with vitamin D receptor, conferring prostate cancer susceptibility

(2012) Hai Ha Nguyen et al.   HUMAN MOLECULAR GENETICS

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Genetic and functional analyses implicate the NUDT11, HNF1B, and SLC22A3 genes in prostate cancer pathogenesis

(2012) C. Grisanzio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Method for sampling tissue for research which preserves pathological data in radical prostatectomy

(2012) Anne Y. Warren et al.   PROSTATE

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

A Genome-Wide Survey over the ChIP-On-Chip Identified Androgen Receptor-Binding Genomic Regions Identifies a Novel Prostate Cancer Susceptibility Locus at 12q13.13

(2011) J. Feng et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Inferring transcription factor complexes from ChIP-seq data

(2011) Tom Whitington et al.   NUCLEIC ACIDS RESEARCH

Cistrome: an integrative platform for transcriptional regulation studies

(2011) Tao Liu et al.   GENOME BIOLOGY

Elevated serum matrix metalloproteinase 7 levels predict poor prognosis after radical prostatectomy

(2010) Tibor Szarvas et al.   INTERNATIONAL JOURNAL OF CANCER

Understanding mechanisms underlying human gene expression variation with RNA sequencing

(2010) Joseph K. Pickrell et al.   NATURE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The Homeodomain Protein HOXB13 Regulates the Cellular Response to Androgens

(2009) John D. Norris et al.   MOLECULAR CELL

The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling

(2009) Sari Tuupanen et al.   NATURE GENETICS

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional Enhancers at the Gene-Poor 8q24 Cancer-Linked Locus

(2009) Li Jia et al.   PLoS Genetics

A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies

(2009) Bryan N. Howie et al.   PLoS Genetics

Matrilysin (MMP-7) Is a Novel Broadly Expressed Tumor Antigen Recognized by Antigen-Specific T Cells

(2008) Y. Yokoyama et al.   CLINICAL CANCER RESEARCH

The human keratins: biology and pathology

(2008) Roland Moll et al.   HISTOCHEMISTRY AND CELL BIOLOGY

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions

(2008) D. E. Newburger et al.   NUCLEIC ACIDS RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY