PUNS: transcriptomic- and genomic-in silico PCR for enhanced primer design. - Paul C. Boutros; Allan B. Okey (Bioinform., 2004)

Unsupervised pattern recognition: An introduction to the whys and wherefores of clustering microarray data. - Paul C. Boutros; Allan B. Okey (Briefings Bioinform., 2005)

Comparison of Machine Learning and Pattern Discovery Algorithms for the Prediction of Human Single Nucleotide Polymorphisms. - Rui Yan 008; Paul C. Boutros; Igor Jurisica; Linda Z. Penn (GrC, 2007)

Unsupervised detection of genes of influence in lung cancer using biological networks. - Anna Goldenberg; Sara Mostafavi; Gerald T. Quon; Paul C. Boutros; Quaid Morris (Bioinform., 2011)

A tree-based approach for motif discovery and sequence classification. - Rui Yan 008; Paul C. Boutros; Igor Jurisica (Bioinform., 2011)

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R. - Hanbo Chen; Paul C. Boutros (BMC Bioinform., 2011)

NanoStringNorm: an extensible R package for the pre-processing of NanoString mRNA and miRNA data. - Daryl Waggott; Kenneth C. Chu; Shaoming Yin; Bradly G. Wouters; Fei-Fei Liu; Paul C. Boutros (Bioinform., 2012)

Ensemble analyses improve signatures of tumour hypoxia and reveal inter-platform differences. - Natalie S. Fox; Maud H. W. Starmans; Syed Haider; Philippe Lambin; Paul C. Boutros (BMC Bioinform., 2014)

ShatterProof: operational detection and quantification of chromothripsis. - Shaylan K. Govind; Amin Zia; Pablo H. Hennings-Yeomans; John D. Watson; Michael Fraser; Catalina V. Anghel; Alexander Wyatt; Theodorus van der Kwast; Colin C. Collins; John D. McPherson; Robert G. Bristow; Paul C. Boutros (BMC Bioinform., 2014)

ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles. - Catalina V. Anghel; Gerald T. Quon; Syed Haider; Francis Nguyen; Amit G. Deshwar; Quaid Morris; Paul C. Boutros (BMC Bioinform., 2015)

The parameter sensitivity of random forests. - Barbara F. F. Huang; Paul C. Boutros (BMC Bioinform., 2016)

VennDiagramWeb: a web application for the generation of highly customizable Venn and Euler diagrams. - Felix Lam; Christopher M. Lalansingh; Holly E. Babaran; Zhiyuan Wang; Stephenie D. Prokopec; Natalie S. Fox; Paul C. Boutros (BMC Bioinform., 2016)

BAMQL: a query language for extracting reads from BAM files. - Andre P. Masella; Christopher M. Lalansingh; Pragash Sivasundaram; Michael Fraser; Robert G. Bristow; Paul C. Boutros (BMC Bioinform., 2016)

A Crowdsourcing Approach to Developing and Assessing Prediction Algorithms for AML Prognosis. - David Noren; Byron Long; Raquel Norel; Kahn Rhrissorrakrai; Kenneth R. Hess; Chenyue W. Hu; Alex Bisberg; André Schultz; Erik Engquist; Li Liu 035; Xihui Lin; Gregory M. Chen; et al. (PLoS Comput. Biol., 2016)

A bedr way of genomic interval processing. - Syed Haider; Daryl Waggott; Emilie Lalonde; Clement Fung; Fei-Fei Liu; Paul C. Boutros (Source Code Biol. Medicine, 2016)

Log: : ProgramInfo: A Perl module to collect and log data for bioinformatics pipelines. - John M. Macdonald; Paul C. Boutros (Source Code Biol. Medicine, 2016)

Nanocall: an open source basecaller for Oxford Nanopore sequencing data. - Matei David; L. J. Dursi; Delia Yao; Paul C. Boutros; Jared T. Simpson (Bioinform., 2017)

Comparison of pre-processing methods for Infinium HumanMethylation450 BeadChip array. - Yu-Jia Shiah; Michael Fraser; Robert G. Bristow; Paul C. Boutros (Bioinform., 2017)

Erratum to: A bedr way of genomic interval processing. - Syed Haider; Daryl Waggott; Emilie Lalonde; Clement Fung; Fei-Fei Liu; Paul C. Boutros (Source Code Biol. Medicine, 2017)

NanoStringNormCNV: pre-processing of NanoString CNV data. - Dorota H. Sendorek; Emilie Lalonde; Cindy Q. Yao; Veronica Y. Sabelnykova; Robert G. Bristow; Paul C. Boutros (Bioinform., 2018)

Valection: design optimization for validation and verification studies. - Christopher I Cooper; Delia Yao; Dorota H. Sendorek; Takafumi N. Yamaguchi; Christine P'ng; Kathleen E. Houlahan; Cristian Caloian; Michael Fraser; Kyle Ellrott; Adam A. Margolin; Robert G. Bristow; Joshua M. Stuart; et al. (BMC Bioinform., 2018)

A comparative study of survival models for breast cancer prognostication revisited: the benefits of multi-gene models. - Michal R. Grzadkowski; Dorota H. Sendorek; Christine P'ng; Vincent Huang 003; Paul C. Boutros (BMC Bioinform., 2018)

Germline contamination and leakage in whole genome somatic single nucleotide variant detection. - Dorota H. Sendorek; Cristian Caloian; Kyle Ellrott; J. Christopher Bare; Takafumi N. Yamaguchi; Adam D. Ewing; Kathleen E. Houlahan; Thea C. Norman; Adam A. Margolin; Joshua M. Stuart; Paul C. Boutros (BMC Bioinform., 2018)

BPG: Seamless, automated and interactive visualization of scientific data. - Christine P'ng; Jeffrey Green; Lauren C. Chong; Daryl Waggott; Stephenie D. Prokopec; Mehrdad Shamsi; Francis Nguyen; Denise Y. F. Mak; Felix Lam; Marco A. Albuquerque; Ying Wu 012; Esther H. Jung; et al. (BMC Bioinform., 2019)

Optimization and expansion of non-negative matrix factorization. - Xihui Lin; Paul C. Boutros (BMC Bioinform., 2020)

The evolutionary history of 2,658 cancers. - Moritz Gerstung; Clemency Jolly; Ignaty Leshchiner; Stefan C. Dentro; Santiago Gonzalez; Thomas J. Mitchell; Yulia Rubanova; Pavana Anur; Kaixian Yu; Maxime Tarabichi; Amit G. Deshwar; Jeff Wintersinger; et al. (Nat., 2020)

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. - Esther Rheinbay; Morten Muhlig Nielsen; Federico Abascal; Jeremiah Wala; Ofer Shapira; Grace Tiao; Henrik Hornshøj; Julian M. Hess; Randi Istrup Juul; Ziao Lin; Lars Feuerbach; Radhakrishnan Sabarinathan; et al. (Nat., 2020)

Evaluation of software impact designed for biomedical research: Are we measuring what's meaningful? - Awan Afiaz; Andrey Ivanov; John Chamberlin; David Hanauer; Candace Savonen; Mary J. Goldman; Martin Morgan; Michael Reich; Alexander Getka; Aaron Holmes; Sarthak Pati; Dan Knight; et al. (CoRR, 2023)

AI Competitions and Benchmarks: The life cycle of challenges and benchmarks. - Gustavo Stolovitzky; Julio Saez-Rodriguez; Julie Bletz; Jacob Albrecht; Gaia Andreoletti; James C. Costello; Paul C. Boutros (CoRR, 2023)

A digital, decentralized trial of exercise therapy in patients with cancer. - Whitney P. Underwood; Meghan G. Michalski; Catherine P. Lee; Gina A. Fickera; Su S. Chun; Stefan E. Eng; Lydia Y. Liu; Brandon L. Tsai; Chaya S. Moskowitz; Jessica A. Lavery; Kimberly J. Van Zee; Ginger J. Gardner; et al. (npj Digit. Medicine, 2024)

PipeVal: light-weight extensible tool for file validation. - Yash Patel; Arpi Beshlikyan; Madison Jordan; Gina Kim; Aaron Holmes; Takafumi N. Yamaguchi; Paul C. Boutros (Bioinform., 2024)

NFTest: automated testing of Nextflow pipelines. - Yash Patel; Chenghao Zhu; Takafumi N. Yamaguchi; Yuan Zhe Bugh; Mao Tian; Aaron Holmes; Sorel T. Fitz-Gibbon; Paul C. Boutros (Bioinform., 2024)

Bridge2AI: Building A Cross-disciplinary Curriculum Towards AI-Enhanced Biomedical and Clinical Care. - John Rincon; Alexander Russell Pelletier; Destiny Gilliland; Wei Wang 010; Ding Wang; Simha Sankar Baradwaj; Lori Scott-Sheldon; Samson Gebreab; William Hersh; Parisa Rashidi; Sally Baxter; Wade Schulz; et al. (CoRR, 2025)