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ORCIDBibTeX records: Joshua M. Stuart
@article{DBLP:journals/ploscb/UzunangelovWS21,
author = {Vladislav Uzunangelov and
Christopher K. Wong and
Joshua M. Stuart},
title = {Accurate cancer phenotype prediction with AKLIMATE, a stacked kernel
learner integrating multimodal genomic data and pathway knowledge},
journal = {PLoS Comput. Biol.},
volume = {17},
number = {4},
year = {2021},
url = {https://doi.org/10.1371/journal.pcbi.1008878},
doi = {10.1371/JOURNAL.PCBI.1008878},
timestamp = {Sun, 15 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/UzunangelovWS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nature/RheinbayNAWSTHH20,
author = {Esther Rheinbay and
Morten Muhlig Nielsen and
Federico Abascal and
Jeremiah Wala and
Ofer Shapira and
Grace Tiao and
Henrik Hornsh{\o}j and
Julian M. Hess and
Randi Istrup Juul and
Ziao Lin and
Lars Feuerbach and
Radhakrishnan Sabarinathan and
Tobias Madsen and
Jaegil Kim and
Loris Mularoni and
Shimin Shuai and
Andr{\'{e}}s Lanz{\'{o}}s and
Carl Herrmann and
Yosef E. Maruvka and
Ciyue Shen and
Samirkumar B. Amin and
Pratiti Bandopadhayay and
Johanna Bertl and
Keith A. Boroevich and
John Busanovich and
Joana Carlevaro{-}Fita and
Dimple Chakravarty and
Calvin Wing Yiu Chan and
David Craft and
Priyanka Dhingra and
Klev Diamanti and
Nuno A. Fonseca and
Abel Gonzalez{-}Perez and
Qianyun Guo and
Mark P. Hamilton and
Nicholas J. Haradhvala and
Chen Hong and
Keren Isaev and
Todd A. Johnson and
Malene Juul and
Andr{\'{e}} Kahles and
Abdullah Kahraman and
Youngwook Kim and
Jan Komorowski and
Kiran Kumar and
Sushant Kumar and
Donghoon Lee and
Kjong{-}Van Lehmann and
Yilong Li and
Eric Minwei Liu and
Lucas Lochovsky and
Keunchil Park and
Oriol Pich and
Nicola D. Roberts and
Gordon Saksena and
Steven E. Schumacher and
Nikos Sidiropoulos and
Lina Sieverling and
Nasa Sinnott{-}Armstrong and
Chip Stewart and
David Tamborero and
Jose M. C. Tubio and
Husen M. Umer and
Liis Uusk{\"{u}}la{-}Reimand and
Claes Wadelius and
Lina Wadi and
Xiaotong Yao and
Cheng{-}Zhong Zhang and
Jing Zhang and
James E. Haber and
Asger Hobolth and
Marcin Imielinski and
Manolis Kellis and
Michael S. Lawrence and
Christian von Mering and
Hidewaki Nakagawa and
Benjamin J. Raphael and
Mark A. Rubin and
Chris Sander and
Lincoln D. Stein and
Joshua M. Stuart and
Tatsuhiko Tsunoda and
David A. Wheeler and
Rory Johnson and
J{\"{u}}ri Reimand and
Mark Gerstein and
Ekta Khurana and
Peter J. Campbell and
N{\'{u}}ria L{\'{o}}pez{-}Bigas and
Gary D. Bader and
Jonathan Barenboim and
Rameen Beroukhim and
S{\o}ren Brunak and
Ken Chen and
Jung Kyoon Choi and
Jordi Deu{-}Pons and
J. Lynn Fink and
Joan Frigola and
Carlo Gambacorti Passerini and
Dale W. Garsed and
Gad Getz and
Ivo Glynne Gut and
David Haan and
Arif Ozgun Harmanci and
Mohamed Helmy and
Ermin Hodzic and
Jos{\'{e}} M. G. Izarzugaza and
Jong K. Kim and
Jan O. Korbel and
Erik Larsson and
Shantao Li and
Xiaotong Li and
Shaoke Lou and
Kathleen Marchal and
I{\~{n}}igo Martincorena and
Alexander Mart{\'{\i}}nez{-}Fundichely and
Patrick D. McGillivray and
William Meyerson and
Ferran Mui{\~{n}}os and
Marta Paczkowska and
Kiejung Park and
Jakob Skou Pedersen and
Tirso Pons and
Sergio Pulido{-}Tamayo and
Iker Reyes{-}Salazar and
Matthew A. Reyna and
Carlota Rubio{-}Perez and
S{\"{u}}leyman Cenk Sahinalp and
Leonidas Salichos and
Mark Shackleton and
Raunak Shrestha and
Alfonso Valencia and
Miguel Vazquez and
Lieven P. C. Verbeke and
Jiayin Wang and
Jonathan Warrell and
Sebastian M. Waszak and
Joachim Weischenfeldt and
Guanming Wu and
Jun Yu and
Xuanping Zhang and
Yan Zhang and
Zhongming Zhao and
Lihua Zou and
Kadir C. Akdemir and
Eva G. Alvarez and
Adrian Baez{-}Ortega and
Paul C. Boutros and
David D. L. Bowtell and
Benedikt Brors and
Kathleen H. Burns and
Kin Chan and
Isidro Cort{\'{e}}s{-}Ciriano and
Ana Dueso{-}Barroso and
Andrew J. Dunford and
Paul A. Edwards and
Xavier Estivill and
Dariush Etemadmoghadam and
Milana Frenkel{-}Morgenstern and
Dmitry A. Gordenin and
Barbara Hutter and
David T. W. Jones and
Young Seok Ju and
Marat D. Kazanov and
Leszek J. Klimczak and
Youngil Koh and
Eunjung Alice Lee and
Jake June{-}Koo Lee and
Andy G. Lynch and
Geoff MacIntyre and
Florian Markowetz and
Matthew Meyerson and
Satoru Miyano and
Fabio C. P. Navarro and
Stephan Ossowski and
Peter J. Park and
John V. Pearson and
Montserrat Puiggr{\`{o}}s and
Karsten Rippe and
Steven A. Roberts and
Bernardo Rodriguez{-}Martin and
Ralph Scully and
David Torrents and
Izar Villasante and
Nicola Waddell and
Jeremiah A. Wala and
Lixing Yang and
Sung{-}Soo Yoon and
Jorge Zamora},
title = {Analyses of non-coding somatic drivers in 2,658 cancer whole genomes},
journal = {Nat.},
volume = {578},
number = {7793},
pages = {102--111},
year = {2020},
url = {https://doi.org/10.1038/s41586-020-1965-x},
doi = {10.1038/S41586-020-1965-X},
timestamp = {Thu, 11 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nature/RheinbayNAWSTHH20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/HaanTFAWWS20,
author = {David Haan and
Ruikang Tao and
Verena Friedl and
Ioannis N. Anastopoulos and
Christopher K. Wong and
Alana S. Weinstein and
Joshua M. Stuart},
title = {Using Transcriptional Signatures to Find Cancer Drivers with {LURE}},
booktitle = {Pacific Symposium on Biocomputing 2020, Fairmont Orchid, Hawaii, USA,
January 3-7, 2020},
pages = {343--354},
year = {2020},
url = {https://psb.stanford.edu/psb-online/proceedings/psb20/Hann.pdf},
timestamp = {Fri, 13 Aug 2021 16:31:26 +0200},
biburl = {https://dblp.org/rec/conf/psb/HaanTFAWWS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/GraimFHS19,
author = {Kiley Graim and
Verena Friedl and
Kathleen E. Houlahan and
Joshua M. Stuart},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Marylyn D. Ritchie and
Teri E. Klein},
title = {{PLATYPUS:} {A} Multiple-View Learning Predictive Framework for Cancer
Drug Sensitivity Prediction},
booktitle = {Biocomputing 2019: Proceedings of the Pacific Symposium, The Big Island
of Hawaii, Hawaii, USA, January 3-7, 2019},
pages = {136--147},
year = {2019},
url = {http://psb.stanford.edu/psb-online/proceedings/psb19/graim.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/GraimFHS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SendorekCEBYEHN18,
author = {Dorota H. Sendorek and
Cristian Caloian and
Kyle Ellrott and
J. Christopher Bare and
Takafumi N. Yamaguchi and
Adam D. Ewing and
Kathleen E. Houlahan and
Thea C. Norman and
Adam A. Margolin and
Joshua M. Stuart and
Paul C. Boutros},
title = {Germline contamination and leakage in whole genome somatic single
nucleotide variant detection},
journal = {{BMC} Bioinform.},
volume = {19},
number = {1},
pages = {28:1--28:9},
year = {2018},
url = {https://doi.org/10.1186/s12859-018-2046-0},
doi = {10.1186/S12859-018-2046-0},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/SendorekCEBYEHN18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CooperYSYPHCFEM18,
author = {Christopher I Cooper and
Delia Yao and
Dorota H. Sendorek and
Takafumi N. Yamaguchi and
Christine P'ng and
Kathleen E. Houlahan and
Cristian Caloian and
Michael Fraser and
Kyle Ellrott and
Adam A. Margolin and
Robert G. Bristow and
Joshua M. Stuart and
Paul C. Boutros},
title = {Valection: design optimization for validation and verification studies},
journal = {{BMC} Bioinform.},
volume = {19},
number = {1},
pages = {339:1--339:11},
year = {2018},
url = {https://doi.org/10.1186/s12859-018-2391-z},
doi = {10.1186/S12859-018-2391-Z},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/CooperYSYPHCFEM18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/CorderoS17,
author = {Pablo Cordero and
Joshua M. Stuart},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Marylyn D. Ritchie and
Teri E. Klein},
title = {Tracing Co-Regulatory Network Dynamics in Noisy, Single-Cell Transcriptome
Trajectories},
booktitle = {Biocomputing 2017: Proceedings of the Pacific Symposium, Kohala Coast,
Hawaii, USA, January 3-7, 2017},
pages = {576--587},
year = {2017},
url = {http://psb.stanford.edu/psb-online/proceedings/psb17/cordero.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/CorderoS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/SokolovCPBS16,
author = {Artem Sokolov and
Daniel E. Carlin and
Evan O. Paull and
Robert Baertsch and
Joshua M. Stuart},
title = {Pathway-Based Genomics Prediction using Generalized Elastic Net},
journal = {PLoS Comput. Biol.},
volume = {12},
number = {3},
year = {2016},
url = {https://doi.org/10.1371/journal.pcbi.1004790},
doi = {10.1371/JOURNAL.PCBI.1004790},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/SokolovCPBS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/SokolovPS16,
author = {Artem Sokolov and
Evan O. Paull and
Joshua M. Stuart},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Teri E. Klein and
Marylyn D. Ritchie},
title = {One-Class Detection of Cell States in Tumor Subtypes},
booktitle = {Biocomputing 2016: Proceedings of the Pacific Symposium, Kohala Coast,
Hawaii, USA, January 4-8, 2016},
pages = {405--416},
year = {2016},
url = {http://psb.stanford.edu/psb-online/proceedings/psb16/sokolov.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/SokolovPS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jamia/PatenDDFGGGKMMM15,
author = {Benedict Paten and
Mark Diekhans and
Brian J. Druker and
Stephen H. Friend and
Justin Guinney and
Nadine Gassner and
Mitchell Guttman and
W. James Kent and
Patrick Mantey and
Adam A. Margolin and
Matt Massie and
Adam M. Novak and
Frank A. Nothaft and
Lior Pachter and
David A. Patterson and
Maciej Smuga{-}Otto and
Joshua M. Stuart and
Laura J. van't Veer and
Barbara J. Wold and
David Haussler},
title = {The {NIH} {BD2K} center for big data in translational genomics},
journal = {J. Am. Medical Informatics Assoc.},
volume = {22},
number = {6},
pages = {1143--1147},
year = {2015},
url = {https://doi.org/10.1093/jamia/ocv047},
doi = {10.1093/JAMIA/OCV047},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jamia/PatenDDFGGGKMMM15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/BrunakVMRRS15,
author = {S{\o}ren Brunak and
Francisco M. de la Vega and
Adam A. Margolin and
Benjamin J. Raphael and
Gunnar R{\"{a}}tsch and
Joshua M. Stuart},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Teri E. Klein and
Marylyn D. Ritchie},
title = {Session Introduction},
booktitle = {Biocomputing 2015: Proceedings of the Pacific Symposium, Kohala Coast,
Hawaii, USA, January 4-8, 2015},
pages = {8--9},
year = {2015},
url = {http://psb.stanford.edu/psb-online/proceedings/psb15/intro-panomics.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/BrunakVMRRS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/BrunakVRS14,
author = {S{\o}ren Brunak and
Francisco M. de la Vega and
Gunnar R{\"{a}}tsch and
Joshua M. Stuart},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Teri E. Klein and
Marylyn D. Ritchie},
title = {Session Introduction},
booktitle = {Biocomputing 2014: Proceedings of the Pacific Symposium, Kohala Coast,
Hawaii, USA, January 3-7, 2014},
pages = {1--2},
year = {2014},
url = {http://psb.stanford.edu/psb-online/proceedings/psb14/intro-cp.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/BrunakVRS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PaullCNSHS13,
author = {Evan O. Paull and
Daniel E. Carlin and
Mario Niepel and
Peter K. Sorger and
David Haussler and
Joshua M. Stuart},
title = {Discovering causal pathways linking genomic events to transcriptional
states using Tied Diffusion Through Interacting Events (TieDIE)},
journal = {Bioinform.},
volume = {29},
number = {21},
pages = {2757--2764},
year = {2013},
url = {https://doi.org/10.1093/bioinformatics/btt471},
doi = {10.1093/BIOINFORMATICS/BTT471},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PaullCNSHS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/GoldmanCSECDMWSHZ13,
author = {Mary Goldman and
Brian Craft and
Teresa Swatloski and
Kyle Ellrott and
Melissa S. Cline and
Mark Diekhans and
Singer Ma and
Chris Wilks and
Joshua M. Stuart and
David Haussler and
Jingchun Zhu},
title = {The {UCSC} Cancer Genomics Browser: update 2013},
journal = {Nucleic Acids Res.},
volume = {41},
number = {Database-Issue},
pages = {949--954},
year = {2013},
url = {https://doi.org/10.1093/nar/gks1008},
doi = {10.1093/NAR/GKS1008},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/GoldmanCSECDMWSHZ13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/WongVNSBHS13,
author = {Christopher K. Wong and
Charles J. Vaske and
Sam Ng and
J. Zachary Sanborn and
Stephen C. Benz and
David Haussler and
Joshua M. Stuart},
title = {The {UCSC} Interaction Browser: multidimensional data views in pathway
context},
journal = {Nucleic Acids Res.},
volume = {41},
number = {Webserver-Issue},
pages = {218--224},
year = {2013},
url = {https://doi.org/10.1093/nar/gkt473},
doi = {10.1093/NAR/GKT473},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/WongVNSBHS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/KarchinOSIB13,
author = {Rachel Karchin and
Michael F. Ochs and
Joshua M. Stuart and
Trey Ideker and
Joel S. Bader},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Tiffany Murray and
Teri E. Klein},
title = {Session Introduction},
booktitle = {Biocomputing 2013: Proceedings of the Pacific Symposium, Kohala Coast,
Hawaii, USA, January 3-7, 2013},
pages = {103--110},
publisher = {World Scientific Publishing},
year = {2013},
url = {http://psb.stanford.edu/psb-online/proceedings/psb13/intro-ap.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/KarchinOSIB13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NgCSGGLBHS12,
author = {Sam Ng and
Eric A. Collisson and
Artem Sokolov and
Theodore Goldstein and
Abel Gonzalez{-}Perez and
N{\'{u}}ria L{\'{o}}pez{-}Bigas and
Christopher Benz and
David Haussler and
Joshua M. Stuart},
title = {{PARADIGM-SHIFT} predicts the function of mutations in multiple cancers
using pathway impact analysis},
journal = {Bioinform.},
volume = {28},
number = {18},
pages = {640--646},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/bts402},
doi = {10.1093/BIOINFORMATICS/BTS402},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/NgCSGGLBHS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/KarchinOSB12,
author = {Rachel Karchin and
Michael F. Ochs and
Joshua M. Stuart and
Joel S. Bader},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Tiffany Murray and
Teri E. Klein},
title = {Session Introduction},
booktitle = {Biocomputing 2012: Proceedings of the Pacific Symposium, Kohala Coast,
Hawaii, USA, January 3-7, 2012},
pages = {1--6},
publisher = {World Scientific Publishing},
year = {2012},
url = {http://psb.stanford.edu/psb-online/proceedings/psb12/intro-pathway.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/KarchinOSB12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SanbornBCSKMVGSKKKSHZ11,
author = {J. Zachary Sanborn and
Stephen C. Benz and
Brian Craft and
Christopher Szeto and
Kord M. Kober and
Laurence R. Meyer and
Charles J. Vaske and
Mary Goldman and
Kayla E. Smith and
Robert M. Kuhn and
Donna Karolchik and
W. James Kent and
Joshua M. Stuart and
David Haussler and
Jingchun Zhu},
title = {The {UCSC} cancer genomics browser: update 2011},
journal = {Nucleic Acids Res.},
volume = {39},
number = {Database-Issue},
pages = {951--959},
year = {2011},
url = {https://doi.org/10.1093/nar/gkq1113},
doi = {10.1093/NAR/GKQ1113},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/SanbornBCSKMVGSKKKSHZ11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/VaskeBSESZHS10,
author = {Charles J. Vaske and
Stephen C. Benz and
J. Zachary Sanborn and
Dent Earl and
Christopher Szeto and
Jingchun Zhu and
David Haussler and
Joshua M. Stuart},
title = {Inference of patient-specific pathway activities from multi-dimensional
cancer genomics data using {PARADIGM}},
journal = {Bioinform.},
volume = {26},
number = {12},
pages = {237--245},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btq182},
doi = {10.1093/BIOINFORMATICS/BTQ182},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/VaskeBSESZHS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KoevaFS09,
author = {Martina Koeva and
E. Camilla Forsberg and
Joshua M. Stuart},
title = {Core stemness mechanisms revealed through homology},
journal = {{BMC} Bioinform.},
volume = {10},
number = {{S-13}},
pages = {0},
year = {2009},
url = {http://www.biomedcentral.com/1471-2105/10/S13/O4},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/KoevaFS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/VaskeHLFYLS09,
author = {Charles J. Vaske and
Carrie House and
Truong Luu and
Bryan Frank and
Chen{-}Hsiang Yeang and
Norman H. Lee and
Joshua M. Stuart},
title = {A Factor Graph Nested Effects Model To Identify Networks from Genetic
Perturbations},
journal = {PLoS Comput. Biol.},
volume = {5},
number = {1},
year = {2009},
url = {https://doi.org/10.1371/journal.pcbi.1000274},
doi = {10.1371/JOURNAL.PCBI.1000274},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/VaskeHLFYLS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/KanabarVYYS09,
author = {Pinal N. Kanabar and
Charles J. Vaske and
Chen{-}Hsiang Yeang and
Fitnat H. Yildiz and
Joshua M. Stuart},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Tiffany Murray and
Teri E. Klein},
title = {Inferring Disease-Related Pathways Using {A} Probabilistic Epistasis
Model},
booktitle = {Biocomputing 2009: Proceedings of the Pacific Symposium, Kohala Coast,
Hawaii, USA, 5-9 January 2009},
pages = {480--491},
year = {2009},
url = {http://psb.stanford.edu/psb-online/proceedings/psb09/kanabar.pdf},
timestamp = {Thu, 01 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/psb/KanabarVYYS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WeirauchWBS08,
author = {Matthew T. Weirauch and
Christopher K. Wong and
Alexandra B. Byrne and
Joshua M. Stuart},
title = {Information-based methods for predicting gene function from systematic
gene knock-downs},
journal = {{BMC} Bioinform.},
volume = {9},
year = {2008},
url = {https://doi.org/10.1186/1471-2105-9-463},
doi = {10.1186/1471-2105-9-463},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/WeirauchWBS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SalomonisHZVLDDSCP07,
author = {Nathan Salomonis and
Kristina Hanspers and
Alexander C. Zambon and
Karen Vranizan and
Steven C. Lawlor and
Kam D. Dahlquist and
Scott Doniger and
Joshua M. Stuart and
Bruce R. Conklin and
Alexander R. Pico},
title = {GenMAPP 2: new features and resources for pathway analysis},
journal = {{BMC} Bioinform.},
volume = {8},
year = {2007},
url = {https://doi.org/10.1186/1471-2105-8-217},
doi = {10.1186/1471-2105-8-217},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/SalomonisHZVLDDSCP07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/ChenWPZS07,
author = {Chunnuan Chen and
Matthew T. Weirauch and
Corey Powell and
Alexander C. Zambon and
Joshua M. Stuart},
title = {A search engine to identify pathway genes from expression data on
multiple organisms},
journal = {{BMC} Syst. Biol.},
volume = {1},
pages = {20},
year = {2007},
url = {https://doi.org/10.1186/1752-0509-1-20},
doi = {10.1186/1752-0509-1-20},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcsb/ChenWPZS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/HuNYCKMLKSD07,
author = {Zhenjun Hu and
David M. Ng and
Takuji Yamada and
Chunnuan Chen and
Shuichi Kawashima and
Joe Mellor and
Bolan Linghu and
Minoru Kanehisa and
Joshua M. Stuart and
Charles DeLisi},
title = {VisANT 3.0: new modules for pathway visualization, editing, prediction
and construction},
journal = {Nucleic Acids Res.},
volume = {35},
number = {Web-Server-Issue},
pages = {625--632},
year = {2007},
url = {https://doi.org/10.1093/nar/gkm295},
doi = {10.1093/NAR/GKM295},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/HuNYCKMLKSD07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/NgWS07,
author = {David M. Ng and
Marcos H. Woehrmann and
Joshua M. Stuart},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Tiffany Murray and
Teri E. Klein},
title = {Recommending Pathway Genes Using a Compendium of Clustering Solutions},
booktitle = {Biocomputing 2007, Proceedings of the Pacific Symposium, Maui, Hawaii,
USA, 3-7 January 2007},
pages = {379--390},
publisher = {World Scientific},
year = {2007},
url = {http://psb.stanford.edu/psb-online/proceedings/psb07/ng.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/NgWS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/csb/PowellS05,
author = {Corey Powell and
Joshua M. Stuart},
title = {A Novel Quartet-Based Method for Phylogenetic Inference},
booktitle = {Fourth International {IEEE} Computer Society Computational Systems
Bioinformatics Conference Workshops {\&} Poster Abstracts, {CSB}
2005 Workshops, Stanford, CA, USA, August 8-11, 2005},
pages = {59--60},
publisher = {{IEEE} Computer Society},
year = {2005},
url = {https://doi.org/10.1109/CSBW.2005.12},
doi = {10.1109/CSBW.2005.12},
timestamp = {Thu, 23 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/csb/PowellS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/csb/PowellS05a,
author = {Corey Powell and
Joshua M. Stuart},
title = {Biological Pathway Prediction from Multiple Data Sources Using Iterative
Bayesian Updating},
booktitle = {Fourth International {IEEE} Computer Society Computational Systems
Bioinformatics Conference Workshops {\&} Poster Abstracts, {CSB}
2005 Workshops, Stanford, CA, USA, August 8-11, 2005},
pages = {159--160},
publisher = {{IEEE} Computer Society},
year = {2005},
url = {https://doi.org/10.1109/CSBW.2005.30},
doi = {10.1109/CSBW.2005.30},
timestamp = {Thu, 23 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/csb/PowellS05a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/csb/WeirauchS05,
author = {Matthew T. Weirauch and
Joshua M. Stuart},
title = {Discovering Functional Transcription Factor Binding from Superimposed
Gene Networks},
booktitle = {Fourth International {IEEE} Computer Society Computational Systems
Bioinformatics Conference Workshops {\&} Poster Abstracts, {CSB}
2005 Workshops, Stanford, CA, USA, August 8-11, 2005},
pages = {178--179},
publisher = {{IEEE} Computer Society},
year = {2005},
url = {https://doi.org/10.1109/CSBW.2005.53},
doi = {10.1109/CSBW.2005.53},
timestamp = {Thu, 23 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/csb/WeirauchS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/HewettORESAK03,
author = {Micheal Hewett and
Diane E. Oliver and
Daniel L. Rubin and
Katrina L. Easton and
Joshua M. Stuart and
Russ B. Altman and
Teri E. Klein},
title = {PharmGKB: the Pharmacogenetics Knowledge Base},
journal = {Nucleic Acids Res.},
volume = {30},
number = {1},
pages = {163--165},
year = {2002},
url = {https://doi.org/10.1093/nar/30.1.163},
doi = {10.1093/NAR/30.1.163},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/HewettORESAK03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/OliverRSHKA02,
author = {Diane E. Oliver and
Daniel L. Rubin and
Joshua M. Stuart and
Micheal Hewett and
Teri E. Klein and
Russ B. Altman},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Teri E. Klein},
title = {Ontology Development for a Pharmacogenetics Knowledge Base},
booktitle = {Proceedings of the 7th Pacific Symposium on Biocomputing, {PSB} 2002,
Lihue, Hawaii, USA, January 3-7, 2002},
pages = {65--76},
year = {2002},
url = {http://psb.stanford.edu/psb-online/proceedings/psb02/oliver.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/OliverRSHKA02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/RaychaudhuriSLSA00,
author = {Soumya Raychaudhuri and
Joshua M. Stuart and
Xuemin Liu and
Peter M. Small and
Russ B. Altman},
editor = {Philip E. Bourne and
Michael Gribskov and
Russ B. Altman and
Nancy Jensen and
Debra A. Hope and
Thomas Lengauer and
Julie C. Mitchell and
Eric D. Scheeff and
Chris Smith and
Shawn Strande and
Helge Weissig},
title = {Pattern Recognition of Genomic Features with Microarrays: Site Typing
of Mycobacterium Tuberculosis Strains},
booktitle = {Proceedings of the Eighth International Conference on Intelligent
Systems for Molecular Biology, August 19-23, 2000, La Jolla / San
Diego, CA, {USA}},
pages = {286--295},
publisher = {{AAAI}},
year = {2000},
url = {http://www.aaai.org/Library/ISMB/2000/ismb00-030.php},
timestamp = {Thu, 13 Dec 2012 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/RaychaudhuriSLSA00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icml/StuartB98,
author = {Joshua M. Stuart and
Elizabeth Bradley},
editor = {Jude W. Shavlik},
title = {Learning the Grammar of Dance},
booktitle = {Proceedings of the Fifteenth International Conference on Machine Learning
{(ICML} 1998), Madison, Wisconsin, USA, July 24-27, 1998},
pages = {547--555},
publisher = {Morgan Kaufmann},
year = {1998},
timestamp = {Thu, 30 Jun 2011 10:34:12 +0200},
biburl = {https://dblp.org/rec/conf/icml/StuartB98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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