Paul C. Boutros

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

Inna Y. Gong, Natalie S. Fox, Paul C. Boutros, 2017 .

Network-Based Biomarkers Enable Cross-Disease Biomarker Discovery

Syed Haider, Jianxin Wang, Paul C. Boutros, 2018, bioRxiv.

Optimization and expansion of non-negative matrix factorization

Paul C. Boutros, Xihui Lin, P. Boutros, 2020, BMC Bioinformatics.

A comparative study of survival models for breast cancer prognostication revisited: the benefits of multi-gene models

Vincent Huang, Paul C. Boutros, Michal R. Grzadkowski, 2018, BMC Bioinformatics.

A robust benchmark for detection of germline large deletions and insertions

Ken Chen, Adam M. Phillippy, Iman Hajirasouliha, 2020, Nature Biotechnology.

An Introduction to Effective BLASTing

Paul C. Boutros, P. Boutros, 2008 .

To Cluster Or Not To Cluster: The Uses and Misuses of Clustering Algorithms

Paul C. Boutros, 2008 .

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

Paul C. Boutros, Allan B. Okey, P. Boutros, 2004, Bioinform..

Kronos: a workflow assembler for genome analytics and informatics

Sohrab P. Shah, Ali Bashashati, Paul C. Boutros, 2016 .

Nanocall: an open source basecaller for Oxford Nanopore sequencing data

Matei David, Paul C. Boutros, Jared T. Simpson, 2016, bioRxiv.

BAMQL: a query language for extracting reads from BAM files

Paul C. Boutros, Michael Fraser, Andre P. Masella, 2016, BMC Bioinformatics.

Comparison of pre‐processing methods for Infinium HumanMethylation450 BeadChip array

Paul C. Boutros, Michael Fraser, Robert G. Bristow, 2017, Bioinform..

A Crowdsourcing Approach to Developing and Assessing Prediction Algorithms for AML Prognosis

Li Liu, Raquel Norel, Paul C. Boutros, 2016, PLoS Comput. Biol..

A community effort to create standards for evaluating tumor subclonal reconstruction

Nathan M. Wilson, Ville Mustonen, Salem Malikic, 2020, Nature Biotechnology.

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

Paul C. Boutros, Bradly G. Wouters, Daryl Waggott, 2012, Bioinform..

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

Jun Yu, Chen Hong, Ken Chen, 2020, Nature.

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

Syed Haider, Gerald T. Quon, Paul C. Boutros, 2015, BMC Bioinformatics.

Germline contamination and leakage in whole genome somatic single nucleotide variant detection

Paul C. Boutros, Joshua M. Stuart, J. Christopher Bare, 2017, bioRxiv.

A robust benchmark for germline structural variant detection

Sergey Koren, Adam M. Phillippy, Iman Hajirasouliha, 2019, bioRxiv.

HPCI: A Perl module for writing cluster-portable bioinformatics pipelines

Paul C. Boutros, Anqi Yang, John M. Macdonald, 2018 .

Kronos: a workflow assembler for genome analytics and informatics

Sohrab P. Shah, Ali Bashashati, Paul C. Boutros, 2016, bioRxiv.

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

Gerald T. Quon, Anna Goldenberg, Paul C. Boutros, 2011, Bioinform..

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

Inna Y. Gong, Natalie S. Fox, Paul C. Boutros, 2017, bioRxiv.

Nanocall: An Open Source Basecaller for Oxford Nanopore Sequencing Data

Paul C. Boutros, Jared T. Simpson, Delia Yao, 2016 .

Enhancing Knowledge Discovery from Cancer Genomics Data with Galaxy

Sohrab P. Shah, Paul C. Boutros, Ryan D. Morin, 2016 .

BPG: Seamless, automated and interactive visualization of scientific data

Jianxin Wang, Ying Wu, Natalie S. Fox, 2017, BMC Bioinformatics.

Best Practices for Benchmarking Germline Small Variant Calls in Human Genomes

Birgit Funke, Christopher E. Mason, Paul C. Boutros, 2018 .

A tree-based approach for motif discovery and sequence classification

Rui Yan, Igor Jurisica, Paul C. Boutros, 2011, Bioinform..

Enhancing knowledge discovery from cancer genomics data with Galaxy

Sohrab P. Shah, Paul C. Boutros, Ryan D. Morin, 2016, bioRxiv.

Valection: design optimization for validation and verification studies

Paul C. Boutros, Joshua M. Stuart, Michael Fraser, 2018, BMC Bioinformatics.

Valection: Design Optimization for Validation and Verification Studies

Paul C. Boutros, Michael Fraser, Adam A. Margolin, 2018 .

BPG: Seamless, Automated and Interactive Visualization of Scientific Data

Syed Haider, Ying Wu, Jianxin Wang, 2017 .

ShatterProof: operational detection and quantification of chromothripsis

Pablo H. Hennings-Yeomans, Alexander Wyatt, Colin Collins, 2014, BMC Bioinformatics.

Creating Standards for Evaluating Tumour Subclonal Reconstruction

Nathan M. Wilson, John Chilton, Yuanfang Guan, 2018, bioRxiv.

Fun with Microarrays Part II: Data Analysis

Paul C. Boutros, P. Boutros, 2008 .

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

Hanbo Chen, Paul C. Boutros, P. Boutros, 2011, BMC Bioinformatics.

Subnetwork Integration for Multi-Modal Signatures [R package SIMMS version 1.3.0]

Syed Haider, Paul C. Boutros, 2020 .

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

Paul C. Boutros, Allan B. Okey, P. Boutros, 2005, Briefings Bioinform..

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

Syed Haider, Natalie S. Fox, Paul C. Boutros, 2013, BMC Bioinformatics.

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

Paul C. Boutros, John M. Macdonald, 2016, Source Code for Biology and Medicine.

Abstract 3605: ICGC in the cloud

Lincoln Stein, Brian O'Connor, Khaled El Emam, 2016 .

Pharmacogenomics: Applied Bioinformatics Chapter

Lyle D. Burgoon, Paul C. Boutros, Timothy R. Zacharewski, 2005 .

VennDiagramWeb: a web application for the generation of highly customizable Venn and Euler diagrams

Natalie S. Fox, Paul C. Boutros, Zhiyuan Wang, 2016, BMC Bioinformatics.

Combining accurate tumour genome simulation with crowd-sourcing to benchmark somatic variant detection

Takafumi Yamaguchi, Justin Guinney, Paul C. Boutros, 2015 .

Comparison of Machine Learning and Pattern Discovery Algorithms for the Prediction of Human Single Nucleotide Polymorphisms

Rui Yan, Igor Jurisica, Paul C. Boutros, 2007, 2007 IEEE International Conference on Granular Computing (GRC 2007).

Erratum to: A bedr way of genomic interval processing

Syed Haider, Paul C. Boutros, Clement Fung, 2016, Source Code for Biology and Medicine.

The parameter sensitivity of random forests

Paul C. Boutros, Barbara F. F. Huang, P. Boutros, 2016, BMC Bioinformatics.

Comparison of Machine Learning and Pattern Discovery Algorithms for the Prediction of Human Single Nucleotide Polymorphisms

Rui Yan, Igor Jurisica, Paul C. Boutros, 2007 .

DreamAI: algorithm for the imputation of proteomics data

Thomas Yu, Shrabanti Chowdhury, Jun Zhu, 2020, bioRxiv.

A bedr way of genomic interval processing

Syed Haider, Paul C. Boutros, Clement Fung, 2016, Source Code for Biology and Medicine.

Fast Nonnegative Matrix Factorization and Applications to Pattern Extraction, Deconvolution and Imputation

Paul C. Boutros, Xihui Lin, P. Boutros, 2018, bioRxiv.

NanoStringNormCNV: pre‐processing of NanoString CNV data

Paul C. Boutros, Cindy Q. Yao, Dorota H. Sendorek, 2018, Bioinform..

The Role of Cancer-Testis Antigens as Predictive and Prognostic Markers in Non-Small Cell Lung Cancer

Thomas John, Paul C. Boutros, Nasser Altorki, 2013, PloS one.

Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease

Michael W. Weiner, Robert C. Green, Yen-Jen Oyang, 2016, Alzheimer's & Dementia.

Detecting protein variants by mass spectrometry: a comprehensive study in cancer cell-lines

Paul C. Boutros, Ankit Sinha, Thomas Kislinger, 2017, Genome Medicine.

Fun with Microarrays Part III: Integration and the End of Microarrays as We Know Them

Paul C. Boutros, P. Boutros, 2008 .

Widespread and Functional RNA Circularization in Localized Prostate Cancer

Alain Bergeron, Youri Hoogstrate, Natalie S. Fox, 2019, Cell.

A Comprehensive Assessment of Somatic Mutation Calling in Cancer Genomes

Roland Eils, Pablo H. Hennings-Yeomans, Paul T. Spellman, 2014, bioRxiv.

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

Paul C. Boutros, Mircea Ivan, Francesca M. Buffa, 2014, Nature Communications.

Inferring structural variant cancer cell fraction

Roland Eils, Yuan Ji, Jan Schröder, 2020, Nature Communications.

The Evolutionary Landscape of Localized Prostate Cancers Drives Clinical Aggression

Natalie S. Fox, Paul C. Boutros, Emilie Lalonde, 2018, Cell.

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

Ken Chen, Mark Gerstein, Satoru Miyano, 2018, Nature Genetics.

Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges

Thomas Yu, Justin Guinney, Julio Saez-Rodriguez, 2019, Genome Biology.

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

David Haussler, Justin Guinney, Zechen Chong, 2018, bioRxiv.

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

Igor Jurisica, Paul C. Boutros, Peggy J. Farnham, 2005, Nucleic acids research.

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

Igor Jurisica, Paul C. Boutros, Linda Z. Penn, 2008, Nucleic acids research.

Genomic hallmarks of localized, non-indolent prostate cancer

Alain Bergeron, Colin C. Collins, Mathieu Lupien, 2017, Nature.

LTR: Linear Cross-Platform Integration of Microarray Data

Paul C. Boutros, P. Boutros, 2010, Cancer informatics.

Biomarkers and subtypes of cancer

Paul C. Boutros, Maud H.W. Starmans, M. Starmans, 2015, Aging.

Identification of a microRNA signature associated with risk of distant metastasis in nasopharyngeal carcinoma

Wei Shi, Shao Hui Huang, Brian O'Sullivan, 2014, Oncotarget.

Portraits of genetic intra-tumour heterogeneity and subclonal selection across cancer types

Yuan Ji, Ville Mustonen, Paul T. Spellman, 2018, bioRxiv.

Molecular landmarks of tumor hypoxia across cancer types

Robert Lesurf, Paul C. Boutros, Emilie Lalonde, 2019, Nature Genetics.

Candidate cancer driver mutations in superenhancers and long-range chromatin interaction networks

Parisa Mazrooei, Mathieu Lupien, Paul C. Boutros, 2017, bioRxiv.