Paul C. Boutros

According to our database, Paul C. Boutros authored at least 31 papers between 2004 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

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., February, 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., February, 2024

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

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, Paul C. Boutros, Spyridon Bakas, J. Gregory Caporaso, Guilherme Del Fiol, Harry Hochheiser, Brian Haas, Patrick D. Schloss, James A. Eddy, Jake Albrecht, Andrey Fedorov, Levi Waldron, Ava M. Hoffman, Richard L. Bradshaw, Jeffrey T. Leek, Carrie Wright

CoRR, 2023

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, Tobias Madsen, Jaegil Kim, Loris Mularoni, Shimin Shuai, Andrés Lanzós, Carl Herrmann, Yosef E. Maruvka, Ciyue Shen, Samirkumar B. Amin, Pratiti Bandopadhayay, Johanna Bertl, Keith A. Boroevich, John Busanovich, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu Chan, David Craft, Priyanka Dhingra, Klev Diamanti, Nuno A. Fonseca, Abel Gonzalez-Perez, Qianyun Guo, Mark P. Hamilton, Nicholas J. Haradhvala, Chen Hong, Keren Isaev, Todd A. Johnson, Malene Juul, André Kahles, Abdullah Kahraman, Youngwook Kim, Jan Komorowski, Kiran Kumar, Sushant Kumar, Donghoon Lee, Kjong-Van Lehmann, Yilong Li, Eric Minwei Liu, Lucas Lochovsky, Keunchil Park, Oriol Pich, Nicola D. Roberts, Gordon Saksena, Steven E. Schumacher, Nikos Sidiropoulos, Lina Sieverling, Nasa Sinnott-Armstrong, Chip Stewart, David Tamborero, Jose M. C. Tubio, Husen M. Umer, Liis Uusküla-Reimand, Claes Wadelius, Lina Wadi, Xiaotong Yao, Cheng-Zhong Zhang, Jing Zhang, James E. Haber, Asger Hobolth, Marcin Imielinski, Manolis Kellis, Michael S. Lawrence, Christian von Mering, Hidewaki Nakagawa, Benjamin J. Raphael, Mark A. Rubin, Chris Sander, Lincoln D. Stein, Joshua M. Stuart, Tatsuhiko Tsunoda, David A. Wheeler, Rory Johnson, Jüri Reimand, Mark Gerstein, Ekta Khurana, Peter J. Campbell, Núria López-Bigas, Gary D. Bader, Jonathan Barenboim, Rameen Beroukhim, Søren Brunak, Ken Chen, Jung Kyoon Choi, Jordi Deu-Pons, J. Lynn Fink, Joan Frigola, Carlo Gambacorti Passerini, Dale W. Garsed, Gad Getz, Ivo Glynne Gut, David Haan, Arif Ozgun Harmanci, Mohamed Helmy, Ermin Hodzic, José M. G. Izarzugaza, Jong K. Kim, Jan O. Korbel, Erik Larsson, Shantao Li, Xiaotong Li, Shaoke Lou, Kathleen Marchal, Iñigo Martincorena, Alexander Martínez-Fundichely, Patrick D. McGillivray, William Meyerson, Ferran Muiños, Marta Paczkowska, Kiejung Park, Jakob Skou Pedersen, Tirso Pons, Sergio Pulido-Tamayo, Iker Reyes-Salazar, Matthew A. Reyna, Carlota Rubio-Perez, Süleyman Cenk Sahinalp, Leonidas Salichos, Mark Shackleton, Raunak Shrestha, Alfonso Valencia, Miguel Vazquez, Lieven P. C. Verbeke, Jiayin Wang, Jonathan Warrell, Sebastian M. Waszak, Joachim Weischenfeldt, Guanming Wu, Jun Yu, Xuanping Zhang, Yan Zhang, Zhongming Zhao, Lihua Zou, Kadir C. Akdemir, Eva G. Alvarez, Adrian Baez-Ortega, Paul C. Boutros, David D. L. Bowtell, Benedikt Brors, Kathleen H. Burns, Kin Chan, Isidro Cortés-Ciriano, Ana Dueso-Barroso, Andrew J. Dunford, Paul A. Edwards, Xavier Estivill, Dariush Etemadmoghadam, Milana Frenkel-Morgenstern, Dmitry A. Gordenin, Barbara Hutter, David T. W. Jones, Young Seok Ju, Marat D. Kazanov, Leszek J. Klimczak, Youngil Koh, Eunjung Alice Lee, Jake June-Koo Lee, Andy G. Lynch, Geoff MacIntyre, Florian Markowetz, Matthew Meyerson, Satoru Miyano, Fabio C. P. Navarro, Stephan Ossowski, Peter J. Park, John V. Pearson, Montserrat Puiggròs, Karsten Rippe, Steven A. Roberts, Bernardo Rodriguez-Martin, Ralph Scully, David Torrents, Izar Villasante, Nicola Waddell, Jeremiah A. Wala, Lixing Yang, Sung-Soo Yoon, Jorge Zamora

Nat., 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, Kortine Kleinheinz, Ignacio Vázquez-García, Kerstin Haase, Lara Jerman, Subhajit Sengupta, Geoff MacIntyre, Salem Malikic, Nilgun Donmez, Dimitri G. Livitz, Marek Cmero, Jonas Demeulemeester, Steven E. Schumacher, Yu Fan, Xiaotong Yao, Juhee Lee, Matthias Schlesner, Paul C. Boutros, David D. L. Bowtell, Hongtu Zhu, Gad Getz, Marcin Imielinski, Rameen Beroukhim, Süleyman Cenk Sahinalp, Yuan Ji, Martin Peifer, Florian Markowetz, Ville Mustonen, Ke Yuan, Wenyi Wang, Quaid D. Morris, David J. Adams, Peter J. Campbell, Shaolong Cao, Elizabeth L. Christie, Yupeng Cun, Kevin J. Dawson, Ruben M. Drews, Roland Eils, Matthew Fittall, Dale W. Garsed, Gavin Ha, Henry Lee-Six, Iñigo Martincorena, Layla Oesper, Myron Peto, Benjamin J. Raphael, Daniel T. Rosebrock, Adriana Salcedo, Ruian Shi, Seung Jun Shin, Oliver Spiro, Lincoln D. Stein, Shankar Vembu, David A. Wheeler, Tsun-Po Yang, Paul T. Spellman, David C. Wedge, Peter Van Loo

Nat., 2020

Optimization and expansion of non-negative matrix factorization.

Xihui Lin, Paul C. Boutros

BMC Bioinform., 2020

2019

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, Esther H. Jung, Maud H. W. Starmans, Michelle A. Chan-Seng-Yue, Cindy Q. Yao, Bianca Liang, Emilie Lalonde, Syed Haider, Nicole A. Simone, Dorota H. Sendorek, Kenneth C. Chu, Nathalie C. Moon, Natalie S. Fox, Michal R. Grzadkowski, Nicholas J. Harding, Clement Fung, Amanda R. Murdoch, Kathleen E. Houlahan, Jianxin Wang, David R. Garcia, Richard de Borja, Ren X. Sun, Xihui Lin, Gregory M. Chen, Aileen Lu, Yu-Jia Shiah, Amin Zia, Ryan Kearns, Paul C. Boutros

BMC Bioinform., 2019

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

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, Paul C. Boutros

BMC 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, Paul C. Boutros

BMC Bioinform., 2018

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

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

Comparison of pre-processing methods for Infinium HumanMethylation450 BeadChip array.

Yu-Jia Shiah, Michael Fraser, Robert G. Bristow, Paul C. Boutros

Bioinform., 2017

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

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

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

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, Xihui Lin, Gregory M. Chen, Honglei Xie, Geoffrey A. M. Hunter, Paul C. Boutros, Oleg A. Stepanov, DREAM 9 AML-OPC Consortium, Thea Norman, Stephen H. Friend, Gustavo Stolovitzky, Steven M. Kornblau, Amina A. Qutub

PLoS Comput. Biol., 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

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

The parameter sensitivity of random forests.

Barbara F. F. Huang, Paul C. Boutros

BMC Bioinform., 2016

2015

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

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

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

2012

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

2011

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

Hanbo Chen, Paul C. Boutros

BMC Bioinform., 2011

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

Rui Yan, Paul C. Boutros, Igor Jurisica

Bioinform., 2011

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

2007

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

Rui Yan, Paul C. Boutros, Igor Jurisica, Linda Z. Penn

Proceedings of the 2007 IEEE International Conference on Granular Computing, 2007

2005

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

Paul C. Boutros, Allan B. Okey

Briefings Bioinform., 2005

2004

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

Paul C. Boutros, Allan B. Okey

Bioinform., 2004