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ORCIDBibTeX records: Scott Christley
@article{DBLP:journals/corr/abs-2204-10382,
author = {Chase Cockrell and
Scott Christley and
Gary An},
title = {Facilitating automated conversion of scientific knowledge into scientific
simulation models with the Machine Assisted Generation, Calibration,
and Comparison {(MAGCC)} Framework},
journal = {CoRR},
volume = {abs/2204.10382},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2204.10382},
doi = {10.48550/ARXIV.2204.10382},
eprinttype = {arXiv},
eprint = {2204.10382},
timestamp = {Mon, 25 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2204-10382.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/natmi/PavlovicSMKKVWB21,
author = {Milena Pavlovic and
Lonneke Scheffer and
Keshav Motwani and
Chakravarthi Kanduri and
Radmila Kompova and
Nikolay Vazov and
Knut Waagan and
Fabian L. M. Bernal and
Alexandre Almeida Costa and
Brian Corrie and
Rahmad Akbar and
Ghadi S. Al Hajj and
Gabriel Balaban and
Todd M. Brusko and
Maria Chernigovskaya and
Scott Christley and
Lindsay G. Cowell and
Robert Frank and
Ivar Grytten and
Sveinung Gundersen and
Ingrid Hob{\ae}k Haff and
Eivind Hovig and
Ping{-}Han Hsieh and
G{\"{u}}nter Klambauer and
Marieke L. Kuijjer and
Christin Lund{-}Andersen and
Antonio Martini and
Thomas Minotto and
Johan Pensar and
Knut D. Rand and
Enrico Riccardi and
Philippe A. Robert and
Artur Rocha and
Andrei Slabodkin and
Igor Snapkov and
Ludvig M. Sollid and
Dmytro Titov and
C{\'{e}}dric R. Weber and
Michael Widrich and
Gur Yaari and
Victor Greiff and
Geir Kjetil Sandve},
title = {The immuneML ecosystem for machine learning analysis of adaptive immune
receptor repertoires},
journal = {Nat. Mach. Intell.},
volume = {3},
number = {11},
pages = {936--944},
year = {2021},
url = {https://doi.org/10.1038/s42256-021-00413-z},
doi = {10.1038/S42256-021-00413-Z},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/natmi/PavlovicSMKKVWB21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2103-10472,
author = {Jared Ostmeyer and
Scott Christley and
Lindsay G. Cowell},
title = {Dynamic Kernel Matching for Non-conforming Data: {A} Case Study of
T-cell Receptor Datasets},
journal = {CoRR},
volume = {abs/2103.10472},
year = {2021},
url = {https://arxiv.org/abs/2103.10472},
eprinttype = {arXiv},
eprint = {2103.10472},
timestamp = {Wed, 24 Mar 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2103-10472.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/fdata/ChristleyABBBBJ20,
author = {Scott Christley and
Ademar Aguiar and
George Blanck and
Felix Breden and
Syed Ahmad Chan Bukhari and
Christian E. Busse and
Jerome Jaglale and
Srilakshmy L. Harikrishnan and
Uri Laserson and
Bjoern Peters and
Artur Rocha and
Chaim A. Schramm and
Sarah Taylor and
Jason A. Vander Heiden and
Bojan Zimonja and
Corey T. Watson and
Brian Corrie and
Lindsay G. Cowell},
title = {The {ADC} {API:} {A} Web {API} for the Programmatic Query of the {AIRR}
Data Commons},
journal = {Frontiers Big Data},
volume = {3},
pages = {22},
year = {2020},
url = {https://doi.org/10.3389/fdata.2020.00022},
doi = {10.3389/FDATA.2020.00022},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/fdata/ChristleyABBBBJ20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/OstmeyerCRTGMC17,
author = {Jared Ostmeyer and
Scott Christley and
William Rounds and
Inimary T. Toby and
Benjamin M. Greenberg and
Nancy Monson and
Lindsay G. Cowell},
title = {Statistical classifiers for diagnosing disease from immune repertoires:
a case study using multiple sclerosis},
journal = {{BMC} Bioinform.},
volume = {18},
number = {1},
pages = {401:1--401:10},
year = {2017},
url = {https://doi.org/10.1186/s12859-017-1814-6},
doi = {10.1186/S12859-017-1814-6},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/OstmeyerCRTGMC17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChristleyLTFMRR17,
author = {Scott Christley and
Mikhail K. Levin and
Inimary T. Toby and
John M. Fonner and
Nancy Monson and
William Rounds and
Florian Rubelt and
Walter Scarborough and
Richard H. Scheuermann and
Lindsay G. Cowell},
title = {VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing
data},
journal = {{BMC} Bioinform.},
volume = {18},
number = {1},
pages = {448:1--448:5},
year = {2017},
url = {https://doi.org/10.1186/s12859-017-1853-z},
doi = {10.1186/S12859-017-1853-Z},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ChristleyLTFMRR17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/TobyLSCBBBCFGHM16,
author = {Inimary T. Toby and
Mikhail K. Levin and
Edward Salinas and
Scott Christley and
Sanchita Bhattacharya and
Felix Breden and
Adam Buntzman and
Brian Corrie and
John M. Fonner and
Namita T. Gupta and
Uri Hershberg and
Nishanth Marthandan and
Aaron M. Rosenfeld and
William Rounds and
Florian Rubelt and
Walter Scarborough and
Jamie K. Scott and
Mohamed Uduman and
Jason A. Vander Heiden and
Richard H. Scheuermann and
Nancy Monson and
Steven H. Kleinstein and
Lindsay G. Cowell},
title = {{VDJML:} a file format with tools for capturing the results of inferring
immune receptor rearrangements},
journal = {{BMC} Bioinform.},
volume = {17},
number = {{S-13}},
pages = {333},
year = {2016},
url = {https://doi.org/10.1186/s12859-016-1214-3},
doi = {10.1186/S12859-016-1214-3},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/TobyLSCBBBCFGHM16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/computation/ChristleyCA15,
author = {Scott Christley and
Chase Cockrell and
Gary An},
title = {Computational Studies of the Intestinal Host-Microbiota Interactome},
journal = {Comput.},
volume = {3},
number = {1},
pages = {2--28},
year = {2015},
url = {https://doi.org/10.3390/computation3010002},
doi = {10.3390/COMPUTATION3010002},
timestamp = {Thu, 01 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/computation/ChristleyCA15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/ZhengCCBXCN14,
author = {Zhenzhen Zheng and
Scott Christley and
William T. Chiu and
Ira L. Blitz and
Xiaohui Xie and
Ken W. Y. Cho and
Qing Nie},
title = {Inference of the Xenopus tropicalis embryonic regulatory network and
spatial gene expression patterns},
journal = {{BMC} Syst. Biol.},
volume = {8},
pages = {3},
year = {2014},
url = {https://doi.org/10.1186/1752-0509-8-3},
doi = {10.1186/1752-0509-8-3},
timestamp = {Tue, 05 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/ZhengCCBXCN14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/CockrellCA14,
author = {Chase Cockrell and
Scott Christley and
Gary An},
title = {Investigation of Inflammation and Tissue Patterning in the Gut Using
a Spatially Explicit General-Purpose Model of Enteric Tissue (SEGMEnT)},
journal = {PLoS Comput. Biol.},
volume = {10},
number = {3},
year = {2014},
url = {https://doi.org/10.1371/journal.pcbi.1003507},
doi = {10.1371/JOURNAL.PCBI.1003507},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/CockrellCA14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/springsim/CockrellCACW13,
author = {Chase Cockrell and
Scott Christley and
Gary An and
Eugene Chang and
Marc Ward},
editor = {Levent Yilmaz and
Tuncer I. {\"{O}}ren and
Greg Madey and
Maarten Sierhuis and
Yu Zhang},
title = {Examining the dynamics of epithelial metaplasia and pouchitis in an
ileal pouch with a spatially-explicit computational multi-scale gut
model {(MSGM)}},
booktitle = {Proceedings of the Agent-Directed Simulation Symposium, part of the
2013 Spring Simulation Multiconference, SpringSim '13, San Diego,
CA, USA, April 07 - 10, 2013},
pages = {4},
publisher = {{SCS/ACM}},
year = {2013},
url = {http://dl.acm.org/citation.cfm?id=2499596},
timestamp = {Fri, 20 Sep 2013 07:56:35 +0200},
biburl = {https://dblp.org/rec/conf/springsim/CockrellCACW13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cmot/ChristleyA12,
author = {Scott Christley and
Gary An},
title = {A proposal for augmenting biological model construction with a semi-intelligent
computational modeling assistant},
journal = {Comput. Math. Organ. Theory},
volume = {18},
number = {4},
pages = {380--403},
year = {2012},
url = {https://doi.org/10.1007/s10588-011-9101-y},
doi = {10.1007/S10588-011-9101-Y},
timestamp = {Thu, 04 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cmot/ChristleyA12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KennedyUCCM11,
author = {Ryan C. Kennedy and
Maria F. Unger and
Scott Christley and
Frank H. Collins and
Gregory R. Madey},
title = {An automated homology-based approach for identifying transposable
elements},
journal = {{BMC} Bioinform.},
volume = {12},
pages = {130},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-130},
doi = {10.1186/1471-2105-12-130},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/KennedyUCCM11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/springsim/ChristleyA11,
author = {Scott Christley and
Gary An},
editor = {Levent Yilmaz and
Tuncer I. {\"{O}}ren},
title = {A proposed method for dynamic knowledge representation via agent-directed
composition from biomedical and simulation ontologies: an example
using gut mucus layer dynamics},
booktitle = {2011 Spring Simulation Multi-conference, SpringSim '11, Boston, MA,
USA, April 03-07, 2011. Volume 1: Proceedings of the 2011 Workshop
on Agent-Directed Simulation {(ADS)}},
pages = {37--44},
publisher = {{SCS/ACM}},
year = {2011},
url = {http://dl.acm.org/citation.cfm?id=2048360},
timestamp = {Thu, 01 Dec 2011 15:40:11 +0100},
biburl = {https://dblp.org/rec/conf/springsim/ChristleyA11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/DailyRCXB10,
author = {Kenny Daily and
Paul Rigor and
Scott Christley and
Xiaohui Xie and
Pierre Baldi},
title = {Data structures and compression algorithms for high-throughput sequencing
technologies},
journal = {{BMC} Bioinform.},
volume = {11},
pages = {514},
year = {2010},
url = {https://doi.org/10.1186/1471-2105-11-514},
doi = {10.1186/1471-2105-11-514},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/DailyRCXB10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/WangCMX10,
author = {Yuanfeng Wang and
Scott Christley and
Eric Mjolsness and
Xiaohui Xie},
title = {Parameter inference for discretely observed stochastic kinetic models
using stochastic gradient descent},
journal = {{BMC} Syst. Biol.},
volume = {4},
pages = {99},
year = {2010},
url = {https://doi.org/10.1186/1752-0509-4-99},
doi = {10.1186/1752-0509-4-99},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcsb/WangCMX10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/ChristleyLDN10,
author = {Scott Christley and
Briana Lee and
Xing Dai and
Qing Nie},
title = {Integrative multicellular biological modeling: a case study of 3D
epidermal development using {GPU} algorithms},
journal = {{BMC} Syst. Biol.},
volume = {4},
pages = {107},
year = {2010},
url = {https://doi.org/10.1186/1752-0509-4-107},
doi = {10.1186/1752-0509-4-107},
timestamp = {Tue, 05 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/ChristleyLDN10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChristleyLLX09,
author = {Scott Christley and
Yiming Lu and
Chen Li and
Xiaohui Xie},
title = {Human genomes as email attachments},
journal = {Bioinform.},
volume = {25},
number = {2},
pages = {274--275},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btn582},
doi = {10.1093/BIOINFORMATICS/BTN582},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChristleyLLX09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/LawsonAABBBCCCDHHKLMMMMRSSTBGKLC09,
author = {Daniel Lawson and
Peter Arensburger and
Peter Atkinson and
Nora J. Besansky and
Robert V. Bruggner and
Ryan Butler and
Kathryn S. Campbell and
George K. Christophides and
Scott Christley and
Emmanuel Dialynas and
Martin Hammond and
Catherine A. Hill and
Nathan Konopinski and
Neil F. Lobo and
Robert M. MacCallum and
Gregory R. Madey and
Karine Megy and
Jason Meyer and
Seth Redmond and
David W. Severson and
Eric O. Stinson and
Pantelis Topalis and
Ewan Birney and
William M. Gelbart and
Fotis C. Kafatos and
Christos Louis and
Frank H. Collins},
title = {VectorBase: a data resource for invertebrate vector genomics},
journal = {Nucleic Acids Res.},
volume = {37},
number = {Database-Issue},
pages = {583--587},
year = {2009},
url = {https://doi.org/10.1093/nar/gkn857},
doi = {10.1093/NAR/GKN857},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/LawsonAABBBCCCDHHKLMMMMRSSTBGKLC09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChristleyLM08,
author = {Scott Christley and
Neil F. Lobo and
Gregory R. Madey},
title = {Multiple organism algorithm for finding ultraconserved elements},
journal = {{BMC} Bioinform.},
volume = {9},
year = {2008},
url = {https://doi.org/10.1186/1471-2105-9-15},
doi = {10.1186/1471-2105-9-15},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ChristleyLM08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cas/ChristleyZNA07,
author = {Scott Christley and
Xuelian Zhu and
Stuart A. Newman and
Mark S. Alber},
title = {Multiscale Agent-based Simulation for Chondrogenic Pattern Formation
\emph{in Vitro}},
journal = {Cybern. Syst.},
volume = {38},
number = {7},
pages = {707--727},
year = {2007},
url = {https://doi.org/10.1080/01969720701534125},
doi = {10.1080/01969720701534125},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cas/ChristleyZNA07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/LawsonAABBBCCCDEHHKLMMMRRSSTZBGKLC07,
author = {Daniel Lawson and
Peter Arensburger and
Peter Atkinson and
Nora J. Besansky and
Robert V. Bruggner and
Ryan Butler and
Kathryn S. Campbell and
George K. Christophides and
Scott Christley and
Emmanuel Dialynas and
David B. Emmert and
Martin Hammond and
Catherine A. Hill and
Ryan C. Kennedy and
Neil F. Lobo and
Robert M. MacCallum and
Gregory R. Madey and
Karine Megy and
Seth Redmond and
Susan Russo and
David W. Severson and
Eric O. Stinson and
Pantelis Topalis and
Evgeni M. Zdobnov and
Ewan Birney and
William M. Gelbart and
Fotis C. Kafatos and
Christos Louis and
Frank H. Collins},
title = {VectorBase: a home for invertebrate vectors of human pathogens},
journal = {Nucleic Acids Res.},
volume = {35},
number = {Database-Issue},
pages = {503--505},
year = {2007},
url = {https://doi.org/10.1093/nar/gkl960},
doi = {10.1093/NAR/GKL960},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/LawsonAABBBCCCDEHHKLMMMRRSSTZBGKLC07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/ChristleyAN07,
author = {Scott Christley and
Mark S. Alber and
Stuart A. Newman},
title = {Patterns of Mesenchymal Condensation in a Multiscale, Discrete Stochastic
Model},
journal = {PLoS Comput. Biol.},
volume = {3},
number = {4},
year = {2007},
url = {https://doi.org/10.1371/journal.pcbi.0030076},
doi = {10.1371/JOURNAL.PCBI.0030076},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/ChristleyAN07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/hicss/ChristleyM07,
author = {Scott Christley and
Gregory R. Madey},
title = {Analysis of Activity in the Open Source Software Development Community},
booktitle = {40th Hawaii International International Conference on Systems Science
{(HICSS-40} 2007), {CD-ROM} / Abstracts Proceedings, 3-6 January 2007,
Waikoloa, Big Island, HI, {USA}},
pages = {166},
publisher = {{IEEE} Computer Society},
year = {2007},
url = {https://doi.org/10.1109/HICSS.2007.74},
doi = {10.1109/HICSS.2007.74},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/hicss/ChristleyM07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/hicss/XuGCM05,
author = {Jin Xu and
Yongqin Gao and
Scott Christley and
Gregory R. Madey},
title = {A Topological Analysis of the Open Souce Software Development Community},
booktitle = {38th Hawaii International Conference on System Sciences {(HICSS-38}
2005), {CD-ROM} / Abstracts Proceedings, 3-6 January 2005, Big Island,
HI, {USA}},
publisher = {{IEEE} Computer Society},
year = {2005},
url = {https://doi.org/10.1109/HICSS.2005.57},
doi = {10.1109/HICSS.2005.57},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/hicss/XuGCM05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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