Paul C. Boutros

Publication Activity (10 Years)

Years Active: 2004-2024
Publications (10 Years): 22

Top Topics

Scientific Data

Matrix Factorization

Interactive Visualization

Top Venues

Source Code Biol. Medicine

Publications

Yash Patel, Chenghao Zhu, Takafumi N. Yamaguchi, Yuan Zhe Bugh, Mao Tian, Aaron Holmes, Sorel T. Fitz-Gibbon, Paul C. Boutros
NFTest: automated testing of Nextflow pipelines. Bioinform. 40 (2) (2024)
Yash Patel, Arpi Beshlikyan, Madison Jordan, Gina Kim, Aaron Holmes, Takafumi N. Yamaguchi, Paul C. Boutros
PipeVal: light-weight extensible tool for file validation. Bioinform. 40 (2) (2024)
Gustavo Stolovitzky, Julio Saez-Rodriguez, Julie Bletz, Jacob Albrecht, Gaia Andreoletti, James C. Costello, Paul C. Boutros
AI Competitions and Benchmarks: The life cycle of challenges and benchmarks. CoRR (2023)
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
Evaluation of software impact designed for biomedical research: Are we measuring what's meaningful? CoRR (2023)
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 G. Gut, David Haan, Arif O. 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
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nat. 578 (7793) (2020)
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
The evolutionary history of 2,658 cancers. Nat. 578 (7793) (2020)
Xihui Lin, Paul C. Boutros
Optimization and expansion of non-negative matrix factorization. BMC Bioinform. 21 (1) (2020)
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
BPG: Seamless, automated and interactive visualization of scientific data. BMC Bioinform. 20 (1) (2019)
Dorota H. Sendorek, Emilie Lalonde, Cindy Q. Yao, Veronica Y. Sabelnykova, Robert G. Bristow, Paul C. Boutros
NanoStringNormCNV: pre-processing of NanoString CNV data. Bioinform. 34 (6) (2018)
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
Germline contamination and leakage in whole genome somatic single nucleotide variant detection. BMC Bioinform. 19 (1) (2018)
Michal R. Grzadkowski, Dorota H. Sendorek, Christine P'ng, Vincent Huang, Paul C. Boutros
A comparative study of survival models for breast cancer prognostication revisited: the benefits of multi-gene models. BMC Bioinform. 19 (1) (2018)
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
Valection: design optimization for validation and verification studies. BMC Bioinform. 19 (1) (2018)
Syed Haider, Daryl Waggott, Emilie Lalonde, Clement Fung, Fei-Fei Liu, Paul C. Boutros
Erratum to: A bedr way of genomic interval processing. Source Code Biol. Medicine 12 (1) (2017)
Yu-Jia Shiah, Michael Fraser, Robert G. Bristow, Paul C. Boutros
Comparison of pre-processing methods for Infinium HumanMethylation450 BeadChip array. Bioinform. 33 (20) (2017)
Matei David, L. J. Dursi, Delia Yao, Paul C. Boutros, Jared T. Simpson
Nanocall: an open source basecaller for Oxford Nanopore sequencing data. Bioinform. 33 (1) (2017)
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
A Crowdsourcing Approach to Developing and Assessing Prediction Algorithms for AML Prognosis. PLoS Comput. Biol. 12 (6) (2016)
Barbara F. F. Huang, Paul C. Boutros
The parameter sensitivity of random forests. BMC Bioinform. 17 (2016)
John M. Macdonald, Paul C. Boutros
Log: : ProgramInfo: A Perl module to collect and log data for bioinformatics pipelines. Source Code Biol. Medicine 11 (1) (2016)
Andre P. Masella, Christopher M. Lalansingh, Pragash Sivasundaram, Michael Fraser, Robert G. Bristow, Paul C. Boutros
BAMQL: a query language for extracting reads from BAM files. BMC Bioinform. 17 (2016)
Felix Lam, Christopher M. Lalansingh, Holly E. Babaran, Zhiyuan Wang, Stephenie D. Prokopec, Natalie S. Fox, Paul C. Boutros
VennDiagramWeb: a web application for the generation of highly customizable Venn and Euler diagrams. BMC Bioinform. 17 (2016)
Syed Haider, Daryl Waggott, Emilie Lalonde, Clement Fung, Fei-Fei Liu, Paul C. Boutros
A bedr way of genomic interval processing. Source Code Biol. Medicine 11 (1) (2016)
Catalina V. Anghel, Gerald T. Quon, Syed Haider, Francis Nguyen, Amit G. Deshwar, Quaid Morris, Paul C. Boutros
ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles. BMC Bioinform. 16 (2015)
Natalie S. Fox, Maud H. W. Starmans, Syed Haider, Philippe Lambin, Paul C. Boutros
Ensemble analyses improve signatures of tumour hypoxia and reveal inter-platform differences. BMC Bioinform. 15 (2014)
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
ShatterProof: operational detection and quantification of chromothripsis. BMC Bioinform. 15 (2014)
Daryl Waggott, Kenneth C. Chu, Shaoming Yin, Bradly G. Wouters, Fei-Fei Liu, Paul C. Boutros
NanoStringNorm: an extensible R package for the pre-processing of NanoString mRNA and miRNA data. Bioinform. 28 (11) (2012)
Hanbo Chen, Paul C. Boutros
VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R. BMC Bioinform. 12 (2011)
Anna Goldenberg, Sara Mostafavi, Gerald T. Quon, Paul C. Boutros, Quaid Morris
Unsupervised detection of genes of influence in lung cancer using biological networks. Bioinform. 27 (22) (2011)
Rui Yan, Paul C. Boutros, Igor Jurisica
A tree-based approach for motif discovery and sequence classification. Bioinform. 27 (15) (2011)
Rui Yan, Paul C. Boutros, Igor Jurisica, Linda Z. Penn
Comparison of Machine Learning and Pattern Discovery Algorithms for the Prediction of Human Single Nucleotide Polymorphisms. GrC (2007)
Paul C. Boutros, Allan B. Okey
Unsupervised pattern recognition: An introduction to the whys and wherefores of clustering microarray data. Briefings Bioinform. 6 (4) (2005)
Paul C. Boutros, Allan B. Okey
PUNS: transcriptomic- and genomic-in silico PCR for enhanced primer design. Bioinform. 20 (15) (2004)