BibTeX records: Gary An

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@article{DBLP:journals/ploscb/ShinAC24,
  author       = {Bryan Shin and
                  Gary An and
                  Chase Cockrell},
  title        = {Examining B-cell dynamics and responsiveness in different inflammatory
                  milieus using an agent-based model},
  journal      = {PLoS Comput. Biol.},
  volume       = {20},
  number       = {1},
  year         = {2024},
  url          = {https://doi.org/10.1371/journal.pcbi.1011776},
  doi          = {10.1371/JOURNAL.PCBI.1011776},
  timestamp    = {Sat, 16 Mar 2024 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/ploscb/ShinAC24.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2303-09056,
  author       = {Gary An and
                  Chase Cockrell},
  title        = {Generating synthetic multi-dimensional molecular-mediator time series
                  data for artificial intelligence-based disease trajectory forecasting
                  and drug development digital twins: Considerations},
  journal      = {CoRR},
  volume       = {abs/2303.09056},
  year         = {2023},
  url          = {https://doi.org/10.48550/arXiv.2303.09056},
  doi          = {10.48550/ARXIV.2303.09056},
  eprinttype    = {arXiv},
  eprint       = {2303.09056},
  timestamp    = {Mon, 20 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2303-09056.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/npjdm/LaubenbacherNHA22,
  author       = {Reinhard C. Laubenbacher and
                  Anna Niarakis and
                  Tom{\'{a}}s Helikar and
                  Gary An and
                  B. Shapiro and
                  Rahuman S. Malik{-}Sheriff and
                  T. J. Sego and
                  Adam C. Knapp and
                  Paul Macklin and
                  James A. Glazier},
  title        = {Building digital twins of the human immune system: toward a roadmap},
  journal      = {npj Digit. Medicine},
  volume       = {5},
  year         = {2022},
  url          = {https://doi.org/10.1038/s41746-022-00610-z},
  doi          = {10.1038/S41746-022-00610-Z},
  timestamp    = {Mon, 01 May 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/npjdm/LaubenbacherNHA22.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@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/simulation/CockrellOCA21,
  author       = {Chase Cockrell and
                  Jonathan Ozik and
                  Nick Collier and
                  Gary An},
  title        = {Nested active learning for efficient model contextualization and parameterization:
                  pathway to generating simulated populations using multi-scale computational
                  models},
  journal      = {Simul.},
  volume       = {97},
  number       = {4},
  year         = {2021},
  url          = {https://doi.org/10.1177/0037549720975075},
  doi          = {10.1177/0037549720975075},
  timestamp    = {Mon, 03 May 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/simulation/CockrellOCA21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/PetersenYGCSAF19,
  author       = {Brenden K. Petersen and
                  Jiachen Yang and
                  Will S. Grathwohl and
                  Chase Cockrell and
                  Claudio Santiago and
                  Gary An and
                  Daniel M. Faissol},
  title        = {Deep Reinforcement Learning and Simulation as a Path Toward Precision
                  Medicine},
  journal      = {J. Comput. Biol.},
  volume       = {26},
  number       = {6},
  pages        = {597--604},
  year         = {2019},
  url          = {https://doi.org/10.1089/cmb.2018.0168},
  doi          = {10.1089/CMB.2018.0168},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jcb/PetersenYGCSAF19.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/OzikCWMCFGHAM18,
  author       = {Jonathan Ozik and
                  Nicholson T. Collier and
                  Justin M. Wozniak and
                  Charles M. Macal and
                  Chase Cockrell and
                  Samuel H. Friedman and
                  Ahmadreza Ghaffarizadeh and
                  Randy W. Heiland and
                  Gary An and
                  Paul Macklin},
  title        = {High-throughput cancer hypothesis testing with an integrated PhysiCell-EMEWS
                  workflow},
  journal      = {{BMC} Bioinform.},
  volume       = {19-S},
  number       = {18},
  pages        = {81--97},
  year         = {2018},
  url          = {https://doi.org/10.1186/s12859-018-2510-x},
  doi          = {10.1186/S12859-018-2510-X},
  timestamp    = {Sun, 15 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bmcbi/OzikCWMCFGHAM18.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/CockrellA18,
  author       = {Chase Cockrell and
                  Gary An},
  title        = {Examining the controllability of sepsis using genetic algorithms on
                  an agent-based model of systemic inflammation},
  journal      = {PLoS Comput. Biol.},
  volume       = {14},
  number       = {2},
  year         = {2018},
  url          = {https://doi.org/10.1371/journal.pcbi.1005876},
  doi          = {10.1371/JOURNAL.PCBI.1005876},
  timestamp    = {Sat, 25 Dec 2021 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/ploscb/CockrellA18.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcss/OzikCWMA18,
  author       = {Jonathan Ozik and
                  Nicholson T. Collier and
                  Justin M. Wozniak and
                  Charles M. Macal and
                  Gary An},
  title        = {Extreme-Scale Dynamic Exploration of a Distributed Agent-Based Model
                  With the {EMEWS} Framework},
  journal      = {{IEEE} Trans. Comput. Soc. Syst.},
  volume       = {5},
  number       = {3},
  pages        = {884--895},
  year         = {2018},
  url          = {https://doi.org/10.1109/TCSS.2018.2859189},
  doi          = {10.1109/TCSS.2018.2859189},
  timestamp    = {Mon, 08 Jun 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/tcss/OzikCWMA18.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1802-10440,
  author       = {Brenden K. Petersen and
                  Jiachen Yang and
                  Will S. Grathwohl and
                  Chase Cockrell and
                  Claudio Santiago and
                  Gary An and
                  Daniel M. Faissol},
  title        = {Precision medicine as a control problem: Using simulation and deep
                  reinforcement learning to discover adaptive, personalized multi-cytokine
                  therapy for sepsis},
  journal      = {CoRR},
  volume       = {abs/1802.10440},
  year         = {2018},
  url          = {http://arxiv.org/abs/1802.10440},
  eprinttype    = {arXiv},
  eprint       = {1802.10440},
  timestamp    = {Mon, 13 Aug 2018 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-1802-10440.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/ploscb/ZiraldoSAKHSBAM15,
  author       = {Cordelia Ziraldo and
                  Alexey Solovyev and
                  Ana Allegretti and
                  Shilpa Krishnan and
                  M. Kristi Henzel and
                  Gwendolyn A. Sowa and
                  David M. Brienza and
                  Gary An and
                  Qi Mi and
                  Yoram Vodovotz},
  title        = {A Computational, Tissue-Realistic Model of Pressure Ulcer Formation
                  in Individuals with Spinal Cord Injury},
  journal      = {PLoS Comput. Biol.},
  volume       = {11},
  number       = {6},
  year         = {2015},
  url          = {https://doi.org/10.1371/journal.pcbi.1004309},
  doi          = {10.1371/JOURNAL.PCBI.1004309},
  timestamp    = {Tue, 11 Jan 2022 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/ploscb/ZiraldoSAKHSBAM15.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}
}
@article{DBLP:journals/jcphy/ScheffMFACDDLVA13,
  author       = {Jeremy D. Scheff and
                  Panteleimon D. Mavroudis and
                  Panagiota T. Foteinou and
                  Gary An and
                  Steve E. Calvano and
                  John Doyle and
                  Thomas E. Dick and
                  Stephen F. Lowry and
                  Yoram Vodovotz and
                  Ioannis P. Androulakis},
  title        = {A multiscale modeling approach to inflammation: {A} case study in
                  human endotoxemia},
  journal      = {J. Comput. Phys.},
  volume       = {244},
  pages        = {279--289},
  year         = {2013},
  url          = {https://doi.org/10.1016/j.jcp.2012.09.024},
  doi          = {10.1016/J.JCP.2012.09.024},
  timestamp    = {Wed, 19 Feb 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/jcphy/ScheffMFACDDLVA13.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/simulation/AlbertsKDA12,
  author       = {Samuel Alberts and
                  Michael K. Keenan and
                  Roshan M. D'Souza and
                  Gary An},
  title        = {Data-parallel techniques for simulating a mega-scale agent-based model
                  of systemic inflammatory response syndrome on graphics processing
                  units},
  journal      = {Simul.},
  volume       = {88},
  number       = {8},
  pages        = {895--907},
  year         = {2012},
  url          = {https://doi.org/10.1177/0037549711425180},
  doi          = {10.1177/0037549711425180},
  timestamp    = {Mon, 08 Jun 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/simulation/AlbertsKDA12.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/ijats/SolovyevMZDZAVM10,
  author       = {Alexey Solovyev and
                  Maxim Mikheev and
                  Leming Zhou and
                  Joyeeta Dutta{-}Moscato and
                  Cordelia Ziraldo and
                  Gary An and
                  Yoram Vodovotz and
                  Qi Mi},
  title        = {{SPARK:} {A} Framework for Multi-Scale Agent-Based Biomedical Modeling},
  journal      = {Int. J. Agent Technol. Syst.},
  volume       = {2},
  number       = {3},
  pages        = {18--30},
  year         = {2010},
  url          = {https://doi.org/10.4018/jats.2010070102},
  doi          = {10.4018/JATS.2010070102},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ijats/SolovyevMZDZAVM10.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/lrec/ApostolovaNATL10,
  author       = {Emilia Apostolova and
                  Sean Neilan and
                  Gary An and
                  Noriko Tomuro and
                  Steven L. Lytinen},
  editor       = {Nicoletta Calzolari and
                  Khalid Choukri and
                  Bente Maegaard and
                  Joseph Mariani and
                  Jan Odijk and
                  Stelios Piperidis and
                  Mike Rosner and
                  Daniel Tapias},
  title        = {Djangology: {A} Light-weight Web-based Tool for Distributed Collaborative
                  Text Annotation},
  booktitle    = {Proceedings of the International Conference on Language Resources
                  and Evaluation, {LREC} 2010, 17-23 May 2010, Valletta, Malta},
  publisher    = {European Language Resources Association},
  year         = {2010},
  url          = {http://www.lrec-conf.org/proceedings/lrec2010/summaries/543.html},
  timestamp    = {Mon, 19 Aug 2019 15:22:48 +0200},
  biburl       = {https://dblp.org/rec/conf/lrec/ApostolovaNATL10.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/springsim/SolovyevMZDZAVM10,
  author       = {Alexey Solovyev and
                  Maxim Mikheev and
                  Leming Zhou and
                  Joyeeta Dutta{-}Moscato and
                  Cordelia Ziraldo and
                  Gary An and
                  Yoram Vodovotz and
                  Qi Mi},
  editor       = {Robert M. McGraw and
                  Eric S. Imsand and
                  Michael J. Chinni},
  title        = {{SPARK:} a framework for multi-scale agent-based biomedical modeling},
  booktitle    = {Proceedings of the 2010 Spring Simulation Multiconference, SpringSim
                  2010, Orlando, Florida, USA, April 11-15, 2010},
  pages        = {3},
  publisher    = {{SCS/ACM}},
  year         = {2010},
  url          = {https://doi.org/10.1145/1878537.1878541},
  doi          = {10.1145/1878537.1878541},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/springsim/SolovyevMZDZAVM10.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/TegnerCAACCGOSTV09,
  author       = {Jesper Tegn{\'{e}}r and
                  Albert Compte and
                  Charles Auffray and
                  Gary An and
                  Gunnar Cedersund and
                  Gilles Clermont and
                  Boris S. Gutkin and
                  Zolt{\'{a}}n N. Oltvai and
                  Klaas Enno Stephan and
                  Randy Thomas and
                  Pablo Villoslada},
  title        = {Computational disease modeling - fact or fiction?},
  journal      = {{BMC} Syst. Biol.},
  volume       = {3},
  pages        = {56},
  year         = {2009},
  url          = {https://doi.org/10.1186/1752-0509-3-56},
  doi          = {10.1186/1752-0509-3-56},
  timestamp    = {Tue, 05 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bmcsb/TegnerCAACCGOSTV09.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/VodovotzCBCA08,
  author       = {Yoram Vodovotz and
                  M{\'{a}}rie Csete and
                  John Bartels and
                  Steven Chang and
                  Gary An},
  title        = {Translational Systems Biology of Inflammation},
  journal      = {PLoS Comput. Biol.},
  volume       = {4},
  number       = {4},
  year         = {2008},
  url          = {https://doi.org/10.1371/journal.pcbi.1000014},
  doi          = {10.1371/JOURNAL.PCBI.1000014},
  timestamp    = {Thu, 10 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/VodovotzCBCA08.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/springsim/WakelandMA07,
  author       = {Wayne W. Wakeland and
                  Louis M. Macovsky and
                  Gary An},
  editor       = {Maurice J. Ades},
  title        = {A hybrid simulation model for studying acute inflammatory response},
  booktitle    = {Proceedings of the 2007 Spring Simulation Multiconference, SpringSim
                  2007, Norfolk, Virginia, USA, March 25-29, 2007, Volume 2},
  pages        = {39--46},
  publisher    = {{SCS/ACM}},
  year         = {2007},
  url          = {http://dl.acm.org/citation.cfm?id=1404680.1404686},
  timestamp    = {Mon, 10 Dec 2012 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/springsim/WakelandMA07.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
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