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List of works by Paul C. Boutros

A Partner in Crime: Tumor-associated Stroma and Metastatic Prostate Cancer

scientific article published on 21 December 2017

A Pilot Study Comparing HPV-Positive and HPV-Negative Head and Neck Squamous Cell Carcinomas by Whole Exome Sequencing

scientific article

A Progesterone-CXCR4 Axis Controls Mammary Progenitor Cell Fate in the Adult Gland

scientific article published on 19 February 2015

A Progesterone-CXCR4 Axis Controls Mammary Progenitor Cell Fate in the Adult Gland.

scientific article published on 10 March 2015

A Prostate Cancer "Nimbosus": Genomic Instability and SChLAP1 Dysregulation Underpin Aggression of Intraductal and Cribriform Subpathologies

scientific article published on 13 May 2017

A bedr way of genomic interval processing

scientific article published on 15 December 2016

A case report and genetic characterization of a massive acinic cell carcinoma of the parotid with delayed distant metastases

scientific article published on 3 April 2013

A community effort to create standards for evaluating tumor subclonal reconstruction

scientific article published on 09 January 2020

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.

scientific article

A comprehensive multicenter comparison of whole genome sequencing pipelines using a uniform tumor-normal sample pair

A proteomic investigation of isogenic radiation resistant prostate cancer cell lines

scientific article published on 30 June 2021

A robust benchmark for detection of germline large deletions and insertions

scientific article published on 15 June 2020

A transcriptome-based signature of pathological angiogenesis predicts breast cancer patient survival

scientific article published on 17 December 2019

A tree-based approach for motif discovery and sequence classification.

scientific article published on 17 June 2011

Abstract 3184: Whole genome sequencing of low-input fresh frozen prostate cancer biopsies

Activation of the aryl hydrocarbon receptor by dioxin disrupts Wnt signaling in the developing mouse kidney

Analysis of the TCGA Dataset Reveals that Subsites of Laryngeal Squamous Cell Carcinoma are Molecularly Distinct

scientific article published on 31 December 2020

Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue

scientific article

Appropriateness of using patient-derived xenograft models for pharmacologic evaluation of novel therapies for esophageal/gastro-esophageal junction cancers

scientific article

Aryl hydrocarbon receptor (AHR)-regulated transcriptomic changes in rats sensitive or resistant to major dioxin toxicities

scientific article

Aryl hydrocarbon receptor is a transcriptional activator of the human breast cancer resistance protein (BCRP/ABCG2).

scientific article published on 11 May 2010

Aryl hydrocarbon receptor regulates distinct dioxin-dependent and dioxin-independent gene batteries

scientific article

Aryl hydrocarbon receptor-dependent induction of flavin-containing monooxygenase mRNAs in mouse liver

scientific article published on 02 September 2008

Author Correction: A robust benchmark for detection of germline large deletions and insertions

scientific article published on 22 July 2020

Author Correction: Best practices for benchmarking germline small-variant calls in human genomes

scientific article published on 01 May 2019

BAMQL: a query language for extracting reads from BAM files.

scientific article

BPG: Seamless, automated and interactive visualization of scientific data

scientific article published on 21 January 2019

Best practices for benchmarking germline small-variant calls in human genomes

scientific article published on 11 March 2019

C-Terminal region of teneurin-1 co-localizes with dystroglycan and modulates cytoskeletal organization through an extracellular signal-regulated kinase-dependent stathmin- and filamin A-mediated mechanism in hippocampal cells

scientific journal article

CRISPRi screens reveal a DNA methylation-mediated 3D genome dependent causal mechanism in prostate cancer

scientific article published on 19 March 2021

CUL7 is a novel antiapoptotic oncogene

scientific article

Changes in gene expression induced by tienilic Acid and sulfamethoxazole: testing the danger hypothesis

scientific journal article

Characterisation of retinoblastomas without RB1 mutations: genomic, gene expression, and clinical studies

scientific article published on 13 March 2013

Characterization of the apoptotic response of human leukemia cells to organosulfur compounds

scientific article

Cistrome Partitioning Reveals Convergence of Somatic Mutations and Risk Variants on Master Transcription Regulators in Primary Prostate Tumors

scientific article published on 14 November 2019

Clonality of localized and metastatic prostate cancer

scientific article published on 16 February 2016

Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection

scientific article published on 06 November 2018

Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection

scientific article published on 18 May 2015

Comparative toxicoproteogenomics of mouse and rat liver identifies TCDD-resistance genes

scientific article published on 11 September 2019

Comparing continuous and discrete analyses of breast cancer survival information

scientific article published on 13 June 2016

Comparison of Pre-processing Methods for Infinium HumanMethylation450 BeadChip Array

scientific article published on 10 June 2017

Comparison of toxicity and outcomes of concurrent radiotherapy with carboplatin/paclitaxel or cisplatin/etoposide in stage III non-small cell lung cancer.

scientific article

Compendium of TCDD-mediated transcriptomic response datasets in mammalian model systems

scientific article

Computational approaches to identify functional genetic variants in cancer genomes

scientific article published on August 2013

Computational approaches to support comparative analysis of multiparametric tests: Modelling versus Training

scientific article published on 03 September 2020

Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction

scientific article published on 28 March 2013

CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome

scientific article

Cribriform and intraductal prostate cancer are associated with increased genomic instability and distinct genomic alterations.

scientific article published on 2 January 2018

Cross-species transcriptomic analysis elucidates constitutive aryl hydrocarbon receptor activity

scientific article

Data-driven identification of inherent features of eukaryotic stress-responsive genes

scientific article published on 07 March 2022

Determinants of sensitivity to lovastatin-induced apoptosis in multiple myeloma

scientific article published on 01 June 2007

Determining the Impact of Spatial Heterogeneity on Genomic Prognostic Biomarkers for Localized Prostate Cancer

scientific article published on 27 June 2020

Developing a prognostic micro-RNA signature for human cervical carcinoma

scientific article published on 16 April 2015

Development and Validation of a 28-gene Hypoxia-related Prognostic Signature for Localized Prostate Cancer.

scientific article

Differential expression profiling of the hepatic proteome in a rat model of dioxin resistance: correlation with genomic and transcriptomic analyses.

scientific article published on 23 February 2006

Differential interactions between statins and P-glycoprotein: implications for exploiting statins as anticancer agents

scientific article published on December 2010

Dioxin-dependent and dioxin-independent gene batteries: comparison of liver and kidney in AHR-null mice

scientific article published on 16 September 2009

Dioxin-responsive AHRE-II gene battery: identification by phylogenetic footprinting

scientific article

Divergent mutational processes distinguish hypoxic and normoxic tumours

scientific article published on 05 February 2020

Downregulation of histone H2A and H2B pathways is associated with anthracycline sensitivity in breast cancer

scientific article published on 6 February 2016

Dysregulation of the mevalonate pathway promotes transformation

scientific article

Ensemble analyses improve signatures of tumour hypoxia and reveal inter-platform differences

scientific article

Epigenetic markers of prostate cancer in plasma circulating DNA.

scientific article

Epigenetics in radiotherapy: where are we heading?

scientific article published on 23 May 2014

Erratum: Corrigendum: Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue

scholarly article by Colin S Cooper et al published June 2015 in Nature Genetics

Erratum: Robust global micro-RNA profiling with formalin-fixed paraffin-embedded breast cancer tissues

scholarly article published in Laboratory Investigation

Evaluation of various housekeeping genes for their applicability for normalization of mRNA expression in dioxin-treated rats.

scientific article

Exploiting high-throughput cell line drug screening studies to identify candidate therapeutic agents in head and neck cancer

scientific article

Exploiting the mevalonate pathway to distinguish statin-sensitive multiple myeloma

scientific article published on April 2010

Exploiting the noise: improving biomarkers with ensembles of data analysis methodologies

scientific article

Expression profiling during mammary epithelial cell three-dimensional morphogenesis identifies PTPRO as a novel regulator of morphogenesis and ErbB2-mediated transformation

scientific article

Flavopiridol causes cell cycle inhibition and demonstrates anti-cancer activity in anaplastic thyroid cancer models

scientific article published on 24 September 2020

Frequent Amplification of a chr19q13.41 MicroRNA Polycistron in Aggressive Primitive Neuroectodermal Brain Tumors

article

Frequent amplification of a chr19q13.41 microRNA polycistron in aggressive primitive neuroectodermal brain tumors

scientific article published on December 2009

From sequence to molecular pathology, and a mechanism driving the neuroendocrine phenotype in prostate cancer

scientific article published on July 2012

Gene expression profiling in a model of D-penicillamine-induced autoimmunity in the Brown Norway rat: predictive value of early signs of danger

scientific article published in August 2005

Gene expression profiling in cervical cancer: an exploration of intratumor heterogeneity

scientific article published on October 2006

Genome-wide effects of acute progressive feed restriction in liver and white adipose tissue.

scientific article published on 14 February 2008

Genome-wide gene expression profiling of stress response in a spinal cord clip compression injury model

scientific article

Genome-wide germline correlates of the epigenetic landscape of prostate cancer

scientific article published on 07 October 2019

Genomic Classifier for Guiding Treatment of Intermediate-Risk Prostate Cancers to Dose-Escalated Image Guided Radiation Therapy Without Hormone Therapy

scientific article published in January 2019

Genomic hallmarks of localized, non-indolent prostate cancer.

scientific article published on 9 January 2017

Germline BRCA2 mutations drive prostate cancers with distinct evolutionary trajectories.

scientific article published on 09 January 2017

Germline Mutations in the Kallikrein 6 Region and Predisposition for Aggressive Prostate Cancer

scientific article published on April 2017

Global optimization of somatic variant identification in cancer genomes with a global community challenge

scientific article

Haploinsufficiency of an RB-E2F1-Condensin II complex leads to aberrant replication and aneuploidy

scientific article published on 16 April 2014

Hepatic transcriptomic responses to TCDD in dioxin-sensitive and dioxin-resistant rats during the onset of toxicity

scientific article published on 5 January 2011

Hotspot activating PRKD1 somatic mutations in polymorphous low-grade adenocarcinomas of the salivary glands.

scientific article

How do changes in the mtDNA and mitochondrial dysfunction influence cancer and cancer therapy? Challenges, opportunities and models

scientific article

Hypoxia promotes stem cell phenotypes and poor prognosis through epigenetic regulation of DICER.

scientific article

ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles.

scientific article published on 14 May 2015

Identification of a novel brain derived neurotrophic factor (BDNF)-inhibitory factor: regulation of BDNF by teneurin C-terminal associated peptide (TCAP)-1 in immortalized embryonic mouse hypothalamic cells

scientific journal article

Identification of differentially expressed proteins in direct expressed prostatic secretions of men with organ-confined versus extracapsular prostate cancer

scientific article

Identification of genes expressed by immune cells of the colon that are regulated by colorectal cancer-associated variants

scientific article

Identification of intraductal carcinoma of the prostate on tissue specimens using Raman micro-spectroscopy: A diagnostic accuracy case-control study with multicohort validation

scientific article published on 14 August 2020

Identification of reference proteins for Western blot analyses in mouse model systems of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) toxicity

scientific article (publication date: 2014)

Identifying gene locus associations with promyelocytic leukemia nuclear bodies using immuno-TRAP.

scientific article published on April 2013

Identifying molecular features that distinguish fluvastatin-sensitive breast tumor cells

scientific article published on 17 December 2013

Immune-focused multi-omics analysis of prostate cancer: leukocyte Ig-Like receptors are associated with disease progression

scientific article published on 01 December 2020

In-depth proteomics of ovarian cancer ascites: combining shotgun proteomics and selected reaction monitoring mass spectrometry.

scientific article

Inhibition of the sodium/potassium ATPase impairs N-glycan expression and function

scientific article

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

scientific article published on 21 March 2012

Integrated omic analysis of oropharyngeal carcinomas reveals human papillomavirus (HPV)-dependent regulation of the activator protein 1 (AP-1) pathway

scientific article

Integrated single-nucleotide and structural variation signatures of DNA-repair deficient human cancers

Integrating RAS status into prognostic signatures for adenocarcinomas of the lung

scientific article published on 21 January 2015

Integrative pathway enrichment analysis of multivariate omics data

scientific article published on 05 February 2020

Inter-strain heterogeneity in rat hepatic transcriptomic responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD).

scientific article published on 9 February 2012

International network of cancer genome projects

scientific article

LSD1-Mediated Epigenetic Reprogramming Drives CENPE Expression and Prostate Cancer Progression.

scientific article

Landscape of transcriptomic interactions between breast cancer and its microenvironment

scientific article published on 15 July 2019

Lestaurtinib is a potent inhibitor of anaplastic thyroid cancer cell line models

scientific article published in PLoS ONE

Log::ProgramInfo: A Perl module to collect and log data for bioinformatics pipelines

scientific article

Long-term hemodynamic and molecular effects persist after discontinued renin-angiotensin system blockade in patients with type 1 diabetes mellitus

scientific article published on 12 June 2013

MEDULLOBLASTOMA

MYC Interacts with the G9a Histone Methyltransferase to Drive Transcriptional Repression and Tumorigenesis

article

MYC dephosphorylation by the PP1/PNUTS phosphatase complex regulates chromatin binding and protein stability

scientific article published in Nature Communications

MYC interaction with the tumor suppressive SWI/SNF complex member INI1 regulates transcription and cellular transformation

scientific article published on 07 June 2016

MYC phosphorylation at novel regulatory regions suppresses transforming activity

scientific article published on 12 September 2013

Mapping genomic and transcriptomic alterations spatially in epithelial cells adjacent to human breast carcinoma.

scientific article published in November 2017

Matching Kidneys and Urines: Establishing Noninvasive Surrogates of Intrarenal Events in Primary Glomerulonephritis

scientific article published on May 2015

MiRNA-106a and prostate cancer radioresistance: a novel role for LITAF in ATM regulation.

scientific article

MicroRNA-196b regulates the homeobox B7-vascular endothelial growth factor axis in cervical cancer.

scientific article published on 4 July 2013

Microarray analysis of the developing cortex

scientific article published in December 2006

Mitochondrial mutations drive prostate cancer aggression

scientific article published on 22 September 2017

Modelling the MYC-driven normal-to-tumour switch in breast cancer

scientific article published on 26 July 2019

Modulation of long noncoding RNAs by risk SNPs underlying genetic predispositions to prostate cancer.

scientific article published on 15 August 2016

Molecular landmarks of tumor hypoxia across cancer types

scientific article published on 14 January 2019

Molecular markers of injury in kidney biopsy specimens of patients with lupus nephritis

scientific article published on March 2011

Mutations in Mitochondrial DNA From Pancreatic Ductal Adenocarcinomas Associate With Survival Times of Patients and Accumulate as Tumors Progress

scientific article published on 25 January 2018

NanoStringNorm: an extensible R package for the pre-processing of NanoString mRNA and miRNA data

scientific article

NanoStringNormCNV: Pre-processing of NanoString CNV data

scientific article

Nanocall: An Open Source Basecaller for Oxford Nanopore Sequencing Data

Next-generation Sequencing of Urologic Cancers: Next Is Now

scientific article published on 05 April 2014

Noncoding mutations target cis-regulatory elements of the FOXA1 plexus in prostate cancer

scientific article published on 23 January 2020

Novel PRKD gene rearrangements and variant fusions in cribriform adenocarcinoma of salivary gland origin.

scientific article

ONECUT2 is a driver of neuroendocrine prostate cancer

scientific article published in Nature Communications

Onco-proteogenomics: cancer proteomics joins forces with genomics

scientific article

Optimization of experimental design parameters for high-throughput chromatin immunoprecipitation studies

scientific article published on 21 October 2008

PDGFRα stromal adipocyte progenitors transition into epithelial cells during lobulo-alveologenesis in the murine mammary gland

scientific article published on 15 April 2019

PUNS: transcriptomic- and genomic-in silico PCR for enhanced primer design

scientific article

Pathway and network analysis of cancer genomes

scientific article (publication date: July 2015)

Pathway-based subnetworks enable cross-disease biomarker discovery

scientific article published in Nature Communications

Pdxdc1 modulates prepulse inhibition of acoustic startle in the mouse

scientific article published on 9 May 2017

Pharmacogenomics

Predicting outcomes in radiation oncology--multifactorial decision support systems

scientific article

Prediction of early breast cancer patient survival using ensembles of hypoxia signatures

scientific article published in PLoS ONE

Prediction of early breast cancer patient survival using ensembles of hypoxia signatures

Prognostic gene signatures for non-small-cell lung cancer

scientific article

Prophylactic valproic acid treatment prevents schizophrenia-related behaviour in Disc1-L100P mutant mice

scientific article

Prospective comparison of restriction spectrum imaging and non-invasive biomarkers to predict upgrading on active surveillance prostate biopsy

scientific article published in 2022

Quantifying the influence of mutation detection on tumour subclonal reconstruction

scientific article published on 07 December 2020

Re: Gene expression-based prognostic signatures in lung cancer: ready for clinical use?

scientific article

Rethinking Lupus Nephritis Classification on a Molecular Level

scientific article published on 23 September 2019

Risk factors for voriconazole hepatotoxicity at 12 weeks in lung transplant recipients.

scientific article published on 5 April 2012

Robust global micro-RNA profiling with formalin-fixed paraffin-embedded breast cancer tissues

scientific article

Role of Nek2 on centrosome duplication and aneuploidy in breast cancer cells.

scientific article published on 27 May 2013

Role of Pirh2 in mediating the regulation of p53 and c-Myc

scientific article

SeqControl: process control for DNA sequencing

scientific article published on 31 August 2014

Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets

scientific article published on 16 April 2018

Serine racemase is associated with schizophrenia susceptibility in humans and in a mouse model.

scientific article

Sex differences in oncogenic mutational processes

scientific article published on 28 August 2020

Sex-related differences in murine hepatic transcriptional and proteomic responses to TCDD.

scientific article published on 20 February 2015

ShatterProof: operational detection and quantification of chromothripsis

scientific article

Somatic driver mutation prevalence in 1844 prostate cancers identifies ZNRF3 loss as a predictor of metastatic relapse

scientific article published on 29 October 2021

Spatial genomic heterogeneity within localized, multifocal prostate cancer

scientific article published on 25 May 2015

Subnetwork-based prognostic biomarkers exhibit performance and robustness superior to gene-based biomarkers in breast cancer

article

Systematic analysis of 18F-FDG PET and metabolism, proliferation and hypoxia markers for classification of head and neck tumors

scientific article

Systematic evaluation of medium-throughput mRNA abundance platforms

scientific article

TCDD dysregulation of 13 AHR-target genes in rat liver

scientific article published on 16 December 2013

TMPRSS2-ERG fusion co-opts master transcription factors and activates NOTCH signaling in primary prostate cancer.

scientific article published on 07 August 2017

TMPRSS2-ERG status is not prognostic following prostate cancer radiotherapy: implications for fusion status and DSB repair

scientific article published on 5 August 2013

Targeted proteomics identifies liquid-biopsy signatures for extracapsular prostate cancer

scientific article published on 28 June 2016

Temporal Stability and Prognostic Biomarker Potential of the Prostate Cancer Urine miRNA Transcriptome

scientific article published on 01 March 2020

Teneurin C-terminal associated peptide (TCAP)-1 modulates dendritic morphology in hippocampal neurons and decreases anxiety-like behaviors in rats

scientific article published on 23 March 2011

The Clinical Genomics of Prostate Cancer

The DNA methylation landscape of advanced prostate cancer

scientific article published on 13 July 2020

The Evolutionary Landscape of Localized Prostate Cancers Drives Clinical Aggression

The Immune Microenvironment, Genome-wide Copy Number Aberrations, and Survival in Mesothelioma

scientific article published on 28 February 2017

The Proteogenomic Landscape of Curable Prostate Cancer

scientific article published on 01 March 2019

The c-Myc oncogene directly induces the H19 noncoding RNA by allele-specific binding to potentiate tumorigenesis

scientific article (publication date: 15 May 2006)

The genomic landscape of metastatic castration-resistant prostate cancers reveals multiple distinct genotypes with potential clinical impact

scientific article published on 20 November 2019

The influence of BRCA2 mutation on localized prostate cancer

scientific article published on 01 May 2019

The parameter sensitivity of random forests

scientific article

The path to routine use of genomic biomarkers in the cancer clinic

scientific article

The prognostic value of temporal in vitro and in vivo derived hypoxia gene-expression signatures in breast cancer

scientific article published on 20 February 2012

The role of Cancer-Testis antigens as predictive and prognostic markers in non-small cell lung cancer.

scientific article

The transcriptomic profile of ovarian cancer grading

scientific article

Three-Gene Prognostic Classifier for Early-Stage Non–Small-Cell Lung Cancer

article

Toward better benchmarking: challenge-based methods assessment in cancer genomics

scientific article

Toxicological implications of polymorphisms in receptors for xenobiotic chemicals: the case of the aryl hydrocarbon receptor

scientific article

Transcriptional profiling of rat hypothalamus response to 2,3,7,8-tetrachlorodibenzo-ρ-dioxin

scientific article published on 18 December 2014

Transcriptional profiling of rat white adipose tissue response to 2,3,7,8-tetrachlorodibenzo-ρ-dioxin

scientific article published on 29 July 2015

Transcriptomic Impact of IMA-08401, a Novel AHR Agonist Resembling Laquinimod, on Rat Liver ⬇️

scientific article published on 19 March 2019

Transcriptomic responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in liver: comparison of rat and mouse

scientific article

Translating a Prognostic DNA Genomic Classifier into the Clinic: Retrospective Validation in 563 Localized Prostate Tumors

scientific article

Tumour genomic and microenvironmental heterogeneity for integrated prediction of 5-year biochemical recurrence of prostate cancer: a retrospective cohort study

scientific article

Two phases of disulfide bond formation have differing requirements for oxygen.

scientific article

Unsupervised detection of genes of influence in lung cancer using biological networks

scientific article

Unsupervised pattern recognition: an introduction to the whys and wherefores of clustering microarray data

scientific article

Use of Sequenom sample ID Plus® SNP genotyping in identification of FFPE tumor samples

scientific article

Valection: design optimization for validation and verification studies

scholarly article by Christopher I Cooper published in September 2018

Validating reference genes within a mouse model system of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) toxicity

scientific article published on 19 June 2013

VennDIS: a JavaFX-based Venn and Euler diagram software to generate publication quality figures

scientific article published on 23 January 2015

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

scientific article

Virally programmed extracellular vesicles sensitize cancer cells to oncolytic virus and small molecule therapy

scientific article published on 07 April 2022

What Is Oligometastatic Prostate Cancer?

scientific article published on 12 January 2019

Widespread and Functional RNA Circularization in Localized Prostate Cancer

scientific article published on 01 February 2019

dbZach: A MIAME-compliant toxicogenomic supportive relational database

scientific article published on 10 January 2006

mRNA levels in control rat liver display strain-specific, hereditary, and AHR-dependent components

scientific article

miR-620 promotes tumor radioresistance by targeting 15-hydroxyprostaglandin dehydrogenase (HPGD).

scientific article

microRNAs in Adult Rodent Liver Are Refractory to Dioxin Treatment

scientific article published on 13 August 2007

novoBreak: local assembly for breakpoint detection in cancer genomes

scientific article

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