Translational Bioinformatics for Diagnostic and Prognostic Prediction of Prostate Cancer in the Next-Generation Sequencing Era

SOXs in human prostate cancer: implication as progression and prognosis factors

(2012) Wei-de Zhong et al.   BMC CANCER

A transcriptional repressor co-regulatory network governing androgen response in prostate cancers

(2012) Kern Rei Chng et al.   EMBO JOURNAL

Targeted Next-generation Sequencing of Advanced Prostate Cancer Identifies Potential Therapeutic Targets and Disease Heterogeneity

(2012) Himisha Beltran et al.   EUROPEAN UROLOGY

Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics

(2012) Housheng Hansen He et al.   GENOME RESEARCH

Rearrangement of the ETS genes ETV-1, ETV-4, ETV-5, and ELK-4 is a clonal event during prostate cancer progression

(2012) Zaki Shaikhibrahim et al.   HUMAN PATHOLOGY

Prostate Cancer Screening: Facts, Statistics, and Interpretation in Response to the US Preventive Services Task Force Review

(2012) Sigrid Carlsson et al.   JOURNAL OF CLINICAL ONCOLOGY

Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer

(2012) Chunxiao Wu et al.   JOURNAL OF PATHOLOGY

Next Generation Sequencing of Prostate Cancer from a Patient Identifies a Deficiency of Methylthioadenosine Phosphorylase, an Exploitable Tumor Target

(2012) C. C. Collins et al.   MOLECULAR CANCER THERAPEUTICS

The mutational landscape of lethal castration-resistant prostate cancer

(2012) Catherine S. Grasso et al.   NATURE

Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer

(2012) Christopher E Barbieri et al.   NATURE GENETICS

Methylome analysis using MeDIP-seq with low DNA concentrations

(2012) Oluwatosin Taiwo et al.   Nature Protocols

Oncogene-mediated alterations in chromatin conformation

(2012) D. S. Rickman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High NRBP1 expression in prostate cancer is linked with poor clinical outcomes and increased cancer cell growth

(2012) Christian Ruiz et al.   PROSTATE

PSA-based prostate cancer screening: the role of active surveillance and informed and shared decision making

(2011) Lionne DF Venderbos et al.   ASIAN JOURNAL OF ANDROLOGY

Randomized studies of PSA screening: an opinion

(2011) Oliver Sartor   ASIAN JOURNAL OF ANDROLOGY

A pipeline for RNA-seq data processing and quality assessment

(2011) Angela Goncalves et al.   BIOINFORMATICS

SeqWare Query Engine: storing and searching sequence data in the cloud

(2011) Brian D O’Connor et al.   BMC BIOINFORMATICS

PeakRanger: A cloud-enabled peak caller for ChIP-seq data

(2011) Xin Feng et al.   BMC BIOINFORMATICS

Monocarboxylate transporter 4 (MCT4) and CD147 overexpression is associated with poor prognosis in prostate cancer

(2011) Nelma Pértega-Gomes et al.   BMC CANCER

A network-based biomarker approach for molecular investigation and diagnosis of lung cancer

(2011) Yu-Chao Wang et al.   BMC Medical Genomics

Common Structural and Epigenetic Changes in the Genome of Castration-Resistant Prostate Cancer

(2011) T. W. Friedlander et al.   CANCER RESEARCH

Identifying novel prostate cancer associated pathways based on integrative microarray data analysis

(2011) Ying Wang et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer

(2011) J. H. Kim et al.   GENOME RESEARCH

Integration of Regulatory Networks by NKX3-1 Promotes Androgen-Dependent Prostate Cancer Survival

(2011) P. Y. Tan et al.   MOLECULAR AND CELLULAR BIOLOGY

The genomic complexity of primary human prostate cancer

(2011) Michael F. Berger et al.   NATURE

Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression

(2011) John R Prensner et al.   NATURE BIOTECHNOLOGY

CENTDIST: discovery of co-associated factors by motif distribution

(2011) Zhizhuo Zhang et al.   NUCLEIC ACIDS RESEARCH

Genome-wide Runx2 occupancy in prostate cancer cells suggests a role in regulating secretion

(2011) Gillian H. Little et al.   NUCLEIC ACIDS RESEARCH

Overexpression of androgen receptor enhances the binding of the receptor to the chromatin in prostate cancer

(2011) A Urbanucci et al.   ONCOGENE

Identification of Clinically Relevant Protein Targets in Prostate Cancer with 2D-DIGE Coupled Mass Spectrometry and Systems Biology Network Platform

(2011) Ramesh Ummanni et al.   PLoS One

MicroRNAs Associated with Metastatic Prostate Cancer

(2011) Akira Watahiki et al.   PLoS One

A Systems Biology-Based Classifier for Hepatocellular Carcinoma Diagnosis

(2011) Yanqiong Zhang et al.   PLoS One

Exome sequencing identifies a spectrum of mutation frequencies in advanced and lethal prostate cancers

(2011) A. Kumar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recurrent chimeric RNAs enriched in human prostate cancer identified by deep sequencing

(2011) K. Kannan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Urine TMPRSS2:ERG Fusion Transcript Stratifies Prostate Cancer Risk in Men with Elevated Serum PSA

(2011) S. A. Tomlins et al.   Science Translational Medicine

Integrative Genomic Profiling of Human Prostate Cancer

(2010) Barry S. Taylor et al.   CANCER CELL

Distinct Genomic Alterations in Prostate Cancers in Chinese and Western Populations Suggest Alternative Pathways of Prostate Carcinogenesis

(2010) X. Mao et al.   CANCER RESEARCH

Cost-Effective Cloud Computing: A Case Study Using the Comparative Genomics Tool, Roundup

(2010) Parul Kudtarkar et al.   Evolutionary Bioinformatics

Copy number and targeted mutational analysis reveals novel somatic events in metastatic prostate tumors

(2010) C. M. Robbins et al.   GENOME RESEARCH

Biomedical informatics and translational medicine

(2010) Indra N Sarkar   Journal of Translational Medicine

Diverse somatic mutation patterns and pathway alterations in human cancers

(2010) Zhengyan Kan et al.   NATURE

Up in a cloud?

(2010) Clare Sansom   NATURE BIOTECHNOLOGY

Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma

(2010) Nallasivam Palanisamy et al.   NATURE MEDICINE

DDPC: Dragon Database of Genes associated with Prostate Cancer

(2010) M. Maqungo et al.   NUCLEIC ACIDS RESEARCH

Cloud-scale RNA-sequencing differential expression analysis with Myrna

(2010) Ben Langmead et al.   GENOME BIOLOGY

hCAP-D3 Expression Marks a Prostate Cancer Subtype With Favorable Clinical Behavior and Androgen Signaling Signature

(2009) Jacques Lapointe et al.   AMERICAN JOURNAL OF SURGICAL PATHOLOGY

CloudBurst: highly sensitive read mapping with MapReduce

(2009) M. C. Schatz   BIOINFORMATICS

High-throughput next-generation sequencing technologies foster new cutting-edge computing techniques in bioinformatics

(2009) Mary Yang et al.   BMC GENOMICS

Genetic and Epigenetic SLC18A2 Silencing in Prostate Cancer Is an Independent Adverse Predictor of Biochemical Recurrence after Radical Prostatectomy

(2009) K. D. Sorensen et al.   CLINICAL CANCER RESEARCH

Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver

(2009) A. L. Brunner et al.   GENOME RESEARCH

Cross-platform method for identifying candidate network biomarkers for prostate cancer

(2009) G. Jin et al.   IET Systems Biology

Multicenter Evaluation of an Investigational Prostate Cancer Methylation Assay

(2009) Jonathan Baden et al.   JOURNAL OF UROLOGY

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Dynamic modularity in protein interaction networks predicts breast cancer outcome

(2009) Ian W Taylor et al.   NATURE BIOTECHNOLOGY

Copy number analysis indicates monoclonal origin of lethal metastatic prostate cancer

(2009) Wennuan Liu et al.   NATURE MEDICINE

Searching for SNPs with cloud computing

(2009) Ben Langmead et al.   GENOME BIOLOGY

An integrative approach to characterize disease-specific pathways and their coordination: a case study in cancer

(2008) Min Xu et al.   BMC GENOMICS

TEAD1 and c-Cbl are novel prostate basal cell markers that correlate with poor clinical outcome in prostate cancer

(2008) J F Knight et al.   BRITISH JOURNAL OF CANCER

Two Unique Novel Prostate-Specific and Androgen-Regulated Fusion Partners of ETV4 in Prostate Cancer

(2008) K. G. Hermans et al.   CANCER RESEARCH

Genomic Alterations Indicate Tumor Origin and Varied Metastatic Potential of Disseminated Cells from Prostate Cancer Patients

(2008) I. N. Holcomb et al.   CANCER RESEARCH

Characterization of TMPRSS2:ETV5 and SLC45A3:ETV5 Gene Fusions in Prostate Cancer

(2008) B. E. Helgeson et al.   CANCER RESEARCH

Biomedical and Health Informatics in Translational Medicine

(2008) Casimir A. Kulikowski et al.   METHODS OF INFORMATION IN MEDICINE

KLF6 and TP53 mutations are a rare event in prostate cancer: distinguishing between Taq polymerase artifacts and true mutations

(2008) Laia Agell et al.   MODERN PATHOLOGY