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ORCIDBibTeX records: James R. Faeder
@article{DBLP:journals/nar/ShaikhSVMWAAAAB22,
author = {Bilal Shaikh and
Lucian P. Smith and
Dan Vasilescu and
Gnaneswara Marupilla and
Michael Wilson and
Eran Agmon and
Henry Agnew and
Steven S. Andrews and
Azraf Anwar and
Moritz E. Beber and
Frank T. Bergmann and
David Brooks and
Lutz Brusch and
Laurence Calzone and
Kiri Choi and
Joshua Cooper and
John Detloff and
Brian Drawert and
Michel Dumontier and
G. Bard Ermentrout and
James R. Faeder and
Andrew P. Freiburger and
Fabian Fr{\"{o}}hlich and
Akira Funahashi and
Alan Garny and
John H. Gennari and
Padraig Gleeson and
Anne Goelzer and
Zachary B. Haiman and
Jan Hasenauer and
Joseph L. Hellerstein and
Henning Hermjakob and
Stefan Hoops and
Jon C. Ison and
Diego Jahn and
Henry V. Jakubowski and
Ryann Jordan and
Mat{\'{u}}s Kalas and
Matthias K{\"{o}}nig and
Wolfram Liebermeister and
Rahuman S. Malik{-}Sheriff and
Synchon Mandal and
Robert A. McDougal and
J. Kyle Medley and
Pedro Mendes and
Robert M{\"{u}}ller and
Chris J. Myers and
Aur{\'{e}}lien Naldi and
Tung V. N. Nguyen and
David P. Nickerson and
Brett G. Olivier and
Drashti Patoliya and
Lo{\"{\i}}c Paulev{\'{e}} and
Linda R. Petzold and
Ankita Priya and
Anand K. Rampadarath and
Johann M. Rohwer and
Ali Sinan Saglam and
Dilawar Singh and
Ankur Sinha and
Jacky L. Snoep and
Hugh Sorby and
Ryan K. Spangler and
J{\"{o}}rn Starru{\ss} and
Payton J. Thomas and
David D. van Niekerk and
Daniel Weindl and
Fengkai Zhang and
Anna Zhukova and
Arthur P. Goldberg and
James C. Schaff and
Michael L. Blinov and
Herbert M. Sauro and
Ion I. Moraru and
Jonathan R. Karr},
title = {BioSimulators: a central registry of simulation engines and services
for recommending specific tools},
journal = {Nucleic Acids Res.},
volume = {50},
number = {{W1}},
pages = {108--114},
year = {2022},
url = {https://doi.org/10.1093/nar/gkac331},
doi = {10.1093/NAR/GKAC331},
timestamp = {Mon, 08 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/ShaikhSVMWAAAAB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2203-06732,
author = {Bilal Shaikh and
Lucian P. Smith and
Dan Vasilescu and
Gnaneswara Marupilla and
Michael Wilson and
Eran Agmon and
Henry Agnew and
Steven S. Andrews and
Azraf Anwar and
Moritz E. Beber and
Frank T. Bergmann and
David Brooks and
Lutz Brusch and
Laurence Calzone and
Kiri Choi and
Joshua Cooper and
John Detloff and
Brian Drawert and
Michel Dumontier and
G. Bard Ermentrout and
James R. Faeder and
Andrew P. Freiburger and
Fabian Fr{\"{o}}hlich and
Akira Funahashi and
Alan Garny and
John H. Gennari and
Padraig Gleeson and
Anne Goelzer and
Zachary B. Haiman and
Joseph L. Hellerstein and
Stefan Hoops and
Jon C. Ison and
Diego Jahn and
Henry V. Jakubowski and
Ryann Jordan and
Mat{\'{u}}s Kalas and
Matthias K{\"{o}}nig and
Wolfram Liebermeister and
Synchon Mandal and
Robert A. McDougal and
J. Kyle Medley and
Pedro Mendes and
Robert M{\"{u}}ller and
Chris J. Myers and
Aur{\'{e}}lien Naldi and
Tung V. N. Nguyen and
David P. Nickerson and
Brett G. Olivier and
Drashti Patoliya and
Lo{\"{\i}}c Paulev{\'{e}} and
Linda R. Petzold and
Ankita Priya and
Anand K. Rampadarath and
Johann M. Rohwer and
Ali Sinan Saglam and
Dilawar Singh and
Ankur Sinha and
Jacky L. Snoep and
Hugh Sorby and
Ryan K. Spangler and
J{\"{o}}rn Starru{\ss} and
Payton J. Thomas and
David D. van Niekerk and
Daniel Weindl and
Fengkai Zhang and
Anna Zhukova and
Arthur P. Goldberg and
Michael L. Blinov and
Herbert M. Sauro and
Ion I. Moraru and
Jonathan R. Karr},
title = {BioSimulators: a central registry of simulation engines and services
for recommending specific tools},
journal = {CoRR},
volume = {abs/2203.06732},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2203.06732},
doi = {10.48550/ARXIV.2203.06732},
eprinttype = {arXiv},
eprint = {2203.06732},
timestamp = {Mon, 08 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2203-06732.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/SchmuckerFFFSS21,
author = {Robin Schmucker and
Gabriele Farina and
James R. Faeder and
Fabian Fr{\"{o}}hlich and
Ali Sinan Saglam and
Tuomas Sandholm},
title = {Combination treatment optimization using a pan-cancer pathway model},
journal = {PLoS Comput. Biol.},
volume = {17},
number = {12},
year = {2021},
url = {https://doi.org/10.1371/journal.pcbi.1009689},
doi = {10.1371/JOURNAL.PCBI.1009689},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/SchmuckerFFFSS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jib/ZhangSBFHTKRDHF20,
author = {Fengkai Zhang and
Lucian P. Smith and
Michael L. Blinov and
James R. Faeder and
William S. Hlavacek and
Jos{\'{e}} Juan Tapia and
Sarah M. Keating and
Nicolas Rodriguez and
Andreas Dr{\"{a}}ger and
Leonard A. Harris and
Andrew Finney and
Bin Hu and
Michael Hucka and
Martin Meier{-}Schellersheim},
title = {Systems biology markup language {(SBML)} level 3 package: multistate,
multicomponent and multicompartment species, version 1, release 2},
journal = {J. Integr. Bioinform.},
volume = {17},
number = {2-3},
year = {2020},
url = {https://doi.org/10.1515/jib-2020-0015},
doi = {10.1515/JIB-2020-0015},
timestamp = {Thu, 03 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jib/ZhangSBFHTKRDHF20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/GuptaLF20,
author = {Sanjana Gupta and
Robin E. C. Lee and
James R. Faeder},
title = {Parallel Tempering with Lasso for model reduction in systems biology},
journal = {PLoS Comput. Biol.},
volume = {16},
number = {3},
year = {2020},
url = {https://doi.org/10.1371/journal.pcbi.1007669},
doi = {10.1371/JOURNAL.PCBI.1007669},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/GuptaLF20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/pdp/GuptaHHLF18,
author = {Sanjana Gupta and
Liam Hainsworth and
Justin S. Hogg and
Robin Lee and
James R. Faeder},
editor = {Ivan Merelli and
Pietro Li{\`{o}} and
Igor V. Kotenko},
title = {Evaluation of Parallel Tempering to Accelerate Bayesian Parameter
Estimation in Systems Biology},
booktitle = {26th Euromicro International Conference on Parallel, Distributed and
Network-based Processing, {PDP} 2018, Cambridge, United Kingdom, March
21-23, 2018},
pages = {690--697},
publisher = {{IEEE} Computer Society},
year = {2018},
url = {https://doi.org/10.1109/PDP2018.2018.00114},
doi = {10.1109/PDP2018.2018.00114},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/pdp/GuptaHHLF18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/SekarTF17,
author = {John A. P. Sekar and
Jos{\'{e}} Juan Tapia and
James R. Faeder},
title = {Automated visualization of rule-based models},
journal = {PLoS Comput. Biol.},
volume = {13},
number = {11},
year = {2017},
url = {https://doi.org/10.1371/journal.pcbi.1005857},
doi = {10.1371/JOURNAL.PCBI.1005857},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/SekarTF17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HarrisHTSGKABSF16,
author = {Leonard A. Harris and
Justin S. Hogg and
Jos{\'{e}} Juan Tapia and
John A. P. Sekar and
Sanjana Gupta and
Ilya Korsunsky and
Arshi Arora and
Dipak Barua and
Robert P. Sheehan and
James R. Faeder},
title = {BioNetGen 2.2: advances in rule-based modeling},
journal = {Bioinform.},
volume = {32},
number = {21},
pages = {3366--3368},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btw469},
doi = {10.1093/BIOINFORMATICS/BTW469},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HarrisHTSGKABSF16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/DonovanTSFMDZ16,
author = {Rory M. Donovan and
Jos{\'{e}} Juan Tapia and
Devin P. Sullivan and
James R. Faeder and
Robert F. Murphy and
Markus Dittrich and
Daniel M. Zuckerman},
title = {Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology
Models Using a Weighted Ensemble of Trajectories},
journal = {PLoS Comput. Biol.},
volume = {12},
number = {2},
year = {2016},
url = {https://doi.org/10.1371/journal.pcbi.1004611},
doi = {10.1371/JOURNAL.PCBI.1004611},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/DonovanTSFMDZ16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/LiuF16,
author = {Bing Liu and
James R. Faeder},
editor = {Tianhai Tian and
Qinghua Jiang and
Yunlong Liu and
Kevin Burrage and
Jiangning Song and
Yadong Wang and
Xiaohua Hu and
Shinichi Morishita and
Qian Zhu and
Guohua Wang},
title = {Parameter estimation of rule-based models using statistical model
checking},
booktitle = {{IEEE} International Conference on Bioinformatics and Biomedicine,
{BIBM} 2016, Shenzhen, China, December 15-18, 2016},
pages = {1453--1459},
publisher = {{IEEE} Computer Society},
year = {2016},
url = {https://doi.org/10.1109/BIBM.2016.7822738},
doi = {10.1109/BIBM.2016.7822738},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bibm/LiuF16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/SekarHF16,
author = {John A. P. Sekar and
Justin S. Hogg and
James R. Faeder},
editor = {Tianhai Tian and
Qinghua Jiang and
Yunlong Liu and
Kevin Burrage and
Jiangning Song and
Yadong Wang and
Xiaohua Hu and
Shinichi Morishita and
Qian Zhu and
Guohua Wang},
title = {Energy-based modeling in BioNetGen},
booktitle = {{IEEE} International Conference on Bioinformatics and Biomedicine,
{BIBM} 2016, Shenzhen, China, December 15-18, 2016},
pages = {1460--1467},
publisher = {{IEEE} Computer Society},
year = {2016},
url = {https://doi.org/10.1109/BIBM.2016.7822739},
doi = {10.1109/BIBM.2016.7822739},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bibm/SekarHF16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cmsb/WangMLFLC16,
author = {Qinsi Wang and
Natasa Miskov{-}Zivanov and
Bing Liu and
James R. Faeder and
Michael Lotze and
Edmund M. Clarke},
editor = {Ezio Bartocci and
Pietro Li{\`{o}} and
Nicola Paoletti},
title = {Formal Modeling and Analysis of Pancreatic Cancer Microenvironment},
booktitle = {Computational Methods in Systems Biology - 14th International Conference,
{CMSB} 2016, Cambridge, UK, September 21-23, 2016, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {9859},
pages = {289--305},
publisher = {Springer},
year = {2016},
url = {https://doi.org/10.1007/978-3-319-45177-0\_18},
doi = {10.1007/978-3-319-45177-0\_18},
timestamp = {Sun, 02 Jun 2019 21:13:15 +0200},
biburl = {https://dblp.org/rec/conf/cmsb/WangMLFLC16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/hldvt/Miskov-ZivanovZ16,
author = {Natasa Miskov{-}Zivanov and
Paolo Zuliani and
Qinsi Wang and
Edmund M. Clarke and
James R. Faeder},
title = {High-level modeling and verification of cellular signaling},
booktitle = {{IEEE} International High Level Design Validation and Test Workshop,
{HLDVT} 2016, Santa Cruz, CA, USA, October 7-8, 2016},
pages = {162--169},
publisher = {{IEEE}},
year = {2016},
url = {https://doi.org/10.1109/HLDVT.2016.7748271},
doi = {10.1109/HLDVT.2016.7748271},
timestamp = {Thu, 23 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/hldvt/Miskov-ZivanovZ16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/glvlsi/SullivanAMTFDC15,
author = {Devin P. Sullivan and
Rohan Arepally and
Robert F. Murphy and
Jos{\'{e}} Juan Tapia and
James R. Faeder and
Markus Dittrich and
Jacob Czech},
editor = {Alex K. Jones and
Hai (Helen) Li and
Ayse K. Coskun and
Martin Margala},
title = {Design Automation for Biological Models: {A} Pipeline that Incorporates
Spatial and Molecular Complexity},
booktitle = {Proceedings of the 25th edition on Great Lakes Symposium on VLSI,
{GLVLSI} 2015, Pittsburgh, PA, USA, May 20 - 22, 2015},
pages = {321--323},
publisher = {{ACM}},
year = {2015},
url = {https://doi.org/10.1145/2742060.2743763},
doi = {10.1145/2742060.2743763},
timestamp = {Tue, 23 Jul 2019 15:03:09 +0200},
biburl = {https://dblp.org/rec/conf/glvlsi/SullivanAMTFDC15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WenskovitchHTFM14,
author = {John E. Wenskovitch and
Leonard A. Harris and
Jos{\'{e}} Juan Tapia and
James R. Faeder and
G. Elisabeta Marai},
title = {{MOSBIE:} a tool for comparison and analysis of rule-based biochemical
models},
journal = {{BMC} Bioinform.},
volume = {15},
pages = {316},
year = {2014},
url = {https://doi.org/10.1186/1471-2105-15-316},
doi = {10.1186/1471-2105-15-316},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/WenskovitchHTFM14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/HoggHSNF14,
author = {Justin S. Hogg and
Leonard A. Harris and
Lori J. Stover and
Niketh S. Nair and
James R. Faeder},
title = {Exact Hybrid Particle/Population Simulation of Rule-Based Models of
Biochemical Systems},
journal = {PLoS Comput. Biol.},
volume = {10},
number = {4},
year = {2014},
url = {https://doi.org/10.1371/journal.pcbi.1003544},
doi = {10.1371/JOURNAL.PCBI.1003544},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/HoggHSNF14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:reference/cn/BartolDF14,
author = {Thomas M. Bartol and
Markus Dittrich and
James R. Faeder},
editor = {Dieter Jaeger and
Ranu Jung},
title = {MCell},
booktitle = {Encyclopedia of Computational Neuroscience},
publisher = {Springer},
year = {2014},
url = {https://doi.org/10.1007/978-1-4614-7320-6\_256-1},
doi = {10.1007/978-1-4614-7320-6\_256-1},
timestamp = {Wed, 12 Jul 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/reference/cn/BartolDF14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/TapiaF13,
author = {Jos{\'{e}} Juan Tapia and
James R. Faeder},
editor = {Jing Gao},
title = {The Atomizer: Extracting Implicit Molecular Structure from Reaction
Network Models},
booktitle = {{ACM} Conference on Bioinformatics, Computational Biology and Biomedical
Informatics. {ACM-BCB} 2013, Washington, DC, USA, September 22-25,
2013},
pages = {726},
publisher = {{ACM}},
year = {2013},
url = {https://doi.org/10.1145/2506583.2512389},
doi = {10.1145/2506583.2512389},
timestamp = {Tue, 06 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bcb/TapiaF13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/Miskov-ZivanovZCF13,
author = {Natasa Miskov{-}Zivanov and
Paolo Zuliani and
Edmund M. Clarke and
James R. Faeder},
editor = {Jing Gao},
title = {Studies of biological networks with statistical model checking: application
to immune system cells},
booktitle = {{ACM} Conference on Bioinformatics, Computational Biology and Biomedical
Informatics. {ACM-BCB} 2013, Washington, DC, USA, September 22-25,
2013},
pages = {728},
publisher = {{ACM}},
year = {2013},
url = {https://doi.org/10.1145/2506583.2512390},
doi = {10.1145/2506583.2512390},
timestamp = {Tue, 06 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bcb/Miskov-ZivanovZCF13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/dac/Miskov-ZivanovMF13,
author = {Natasa Miskov{-}Zivanov and
Diana Marculescu and
James R. Faeder},
title = {Dynamic behavior of cell signaling networks: model design and analysis
automation},
booktitle = {The 50th Annual Design Automation Conference 2013, {DAC} '13, Austin,
TX, USA, May 29 - June 07, 2013},
pages = {8:1--8:6},
publisher = {{ACM}},
year = {2013},
url = {https://doi.org/10.1145/2463209.2488743},
doi = {10.1145/2463209.2488743},
timestamp = {Tue, 06 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/dac/Miskov-ZivanovMF13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SmithXSFM12,
author = {Adam M. Smith and
Wen Xu and
Yao Sun and
James R. Faeder and
G. Elisabeta Marai},
title = {RuleBender: integrated modeling, simulation and visualization for
rule-based intracellular biochemistry},
journal = {{BMC} Bioinform.},
volume = {13},
number = {{S-8}},
pages = {S3},
year = {2012},
url = {https://doi.org/10.1186/1471-2105-13-S8-S3},
doi = {10.1186/1471-2105-13-S8-S3},
timestamp = {Thu, 24 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SmithXSFM12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cdc/TapiaFM12,
author = {Jos{\'{e}} Juan Tapia and
James R. Faeder and
Brian Munsky},
title = {Adaptive coarse-graining for transient and quasi-equilibrium analyses
of stochastic gene regulation},
booktitle = {Proceedings of the 51th {IEEE} Conference on Decision and Control,
{CDC} 2012, December 10-13, 2012, Maui, HI, {USA}},
pages = {5361--5366},
publisher = {{IEEE}},
year = {2012},
url = {https://doi.org/10.1109/CDC.2012.6425828},
doi = {10.1109/CDC.2012.6425828},
timestamp = {Fri, 04 Mar 2022 13:28:47 +0100},
biburl = {https://dblp.org/rec/conf/cdc/TapiaFM12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iccad/Miskov-ZivanovFMS12,
author = {Natasa Miskov{-}Zivanov and
James R. Faeder and
Chris J. Myers and
Herbert M. Sauro},
editor = {Alan J. Hu},
title = {Modeling and design automation of biological circuits and systems},
booktitle = {2012 {IEEE/ACM} International Conference on Computer-Aided Design,
{ICCAD} 2012, San Jose, CA, USA, November 5-8, 2012},
pages = {291--293},
publisher = {{ACM}},
year = {2012},
url = {https://doi.org/10.1145/2429384.2429444},
doi = {10.1145/2429384.2429444},
timestamp = {Mon, 09 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/iccad/Miskov-ZivanovFMS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/XuSFM11,
author = {Wen Xu and
Adam M. Smith and
James R. Faeder and
G. Elisabeta Marai},
title = {RuleBender: a visual interface for rule-based modeling},
journal = {Bioinform.},
volume = {27},
number = {12},
pages = {1721--1722},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr197},
doi = {10.1093/BIOINFORMATICS/BTR197},
timestamp = {Mon, 17 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/XuSFM11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/Miskov-ZivanovBKVMF11,
author = {Natasa Miskov{-}Zivanov and
Andrew Bresticker and
Deepa Krishnaswamy and
Sreesan Venkatakrishnan and
Diana Marculescu and
James R. Faeder},
editor = {Robert Grossman and
Andrey Rzhetsky and
Sun Kim and
Wei Wang},
title = {Emulation of biological networks in reconfigurable hardware},
booktitle = {{ACM} International Conference on Bioinformatics, Computational Biology
and Biomedicine, BCB' 11, Chicago, IL, {USA} - July 31 - August 03,
2011},
pages = {536--540},
publisher = {{ACM}},
year = {2011},
url = {https://doi.org/10.1145/2147805.2147893},
doi = {10.1145/2147805.2147893},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bcb/Miskov-ZivanovBKVMF11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bicob/GongWZFL11,
author = {Haijun Gong and
Qinsi Wang and
Paolo Zuliani and
James R. Faeder and
Michael Lotze},
editor = {Hisham Al{-}Mubaid},
title = {Symbolic Model Checking of Signaling Pathways in Pancreatic Cancer},
booktitle = {Proceedings of the {ISCA} 3rd International Conference on Bioinformatics
and Computational Biology, BICoB-2011, March 23-25, 2011, Holiday
Inn Downtown-Superdome, New Orleans, Louisiana, {USA}},
pages = {245},
publisher = {{ISCA}},
year = {2011},
timestamp = {Mon, 14 Nov 2011 12:10:34 +0100},
biburl = {https://dblp.org/rec/conf/bicob/GongWZFL11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/biovis/SmithXSFM11,
author = {Adam M. Smith and
Wen Xu and
Yao Sun and
James R. Faeder and
G. Elisabeta Marai},
editor = {Jessie Kennedy and
Jos B. T. M. Roerdink},
title = {RuleBender: Integrated visualization for biochemical rule-based modeling},
booktitle = {2011 {IEEE} Symposium on Biological Data Visualization, BioVis 2011,
Providence, RI, USA, October 23-24, 2011},
pages = {103--110},
publisher = {{IEEE} Computer Society},
year = {2011},
url = {https://doi.org/10.1109/BioVis.2011.6094054},
doi = {10.1109/BIOVIS.2011.6094054},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/biovis/SmithXSFM11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/embc/Miskov-ZivanovB11,
author = {Natasa Miskov{-}Zivanov and
Andrew Bresticker and
Deepa Krishnaswamy and
Sreesan Venkatakrishnan and
Prashant Kashinkunti and
Diana Marculescu and
James R. Faeder},
title = {Regulatory network analysis acceleration with reconfigurable hardware},
booktitle = {33rd Annual International Conference of the {IEEE} Engineering in
Medicine and Biology Society, {EMBC} 2011, Boston, MA, USA, August
30 - Sept. 3, 2011},
pages = {149--152},
publisher = {{IEEE}},
year = {2011},
url = {https://doi.org/10.1109/IEMBS.2011.6089916},
doi = {10.1109/IEMBS.2011.6089916},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/embc/Miskov-ZivanovB11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GongZKFC10,
author = {Haijun Gong and
Paolo Zuliani and
Anvesh Komuravelli and
James R. Faeder and
Edmund M. Clarke},
title = {Analysis and verification of the {HMGB1} signaling pathway},
journal = {{BMC} Bioinform.},
volume = {11},
number = {{S-7}},
pages = {S10},
year = {2010},
url = {https://doi.org/10.1186/1471-2105-11-S7-S10},
doi = {10.1186/1471-2105-11-S7-S10},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/GongZKFC10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/anb/GongZKFC10,
author = {Haijun Gong and
Paolo Zuliani and
Anvesh Komuravelli and
James R. Faeder and
Edmund M. Clarke},
editor = {Katsuhisa Horimoto and
Masahiko Nakatsui and
Nikolaj Popov},
title = {Computational Modeling and Verification of Signaling Pathways in Cancer},
booktitle = {Algebraic and Numeric Biology - 4th International Conference, {ANB}
2010, Hagenberg, Austria, July 31- August 2, 2010, Revised Selected
Papers},
series = {Lecture Notes in Computer Science},
volume = {6479},
pages = {117--135},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-3-642-28067-2\_7},
doi = {10.1007/978-3-642-28067-2\_7},
timestamp = {Sat, 19 Oct 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/anb/GongZKFC10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ColvinMFHHP09,
author = {Joshua Colvin and
Michael I. Monine and
James R. Faeder and
William S. Hlavacek and
Daniel D. Von Hoff and
Richard G. Posner},
title = {Simulation of large-scale rule-based models},
journal = {Bioinform.},
volume = {25},
number = {7},
pages = {910--917},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp066},
doi = {10.1093/BIOINFORMATICS/BTP066},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ColvinMFHHP09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuFFPH09,
author = {Bin Hu and
G. Matthew Fricke and
James R. Faeder and
Richard G. Posner and
William S. Hlavacek},
title = {GetBonNie for building, analyzing and sharing rule-based models},
journal = {Bioinform.},
volume = {25},
number = {11},
pages = {1457--1460},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp173},
doi = {10.1093/BIOINFORMATICS/BTP173},
timestamp = {Wed, 19 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HuFFPH09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/BaruaFH09,
author = {Dipak Barua and
James R. Faeder and
Jason M. Haugh},
title = {A Bipolar Clamp Mechanism for Activation of Jak-Family Protein Tyrosine
Kinases},
journal = {PLoS Comput. Biol.},
volume = {5},
number = {4},
year = {2009},
url = {https://doi.org/10.1371/journal.pcbi.1000364},
doi = {10.1371/JOURNAL.PCBI.1000364},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/BaruaFH09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wsc/HarrisHF09,
author = {Leonard A. Harris and
Justin S. Hogg and
James R. Faeder},
editor = {Ann Dunkin and
Ricki G. Ingalls and
Enver Y{\"{u}}cesan and
Manuel D. Rossetti and
Ray Hill and
Bj{\"{o}}rn Johansson},
title = {Compartmental Rule-based Modeling of Biochemical Systems},
booktitle = {Proceedings of the 2009 Winter Simulation Conference, {WSC} 2009,
Hilton Austin Hotel, Austin, TX, USA, December 13-16, 2009},
pages = {908--919},
publisher = {{IEEE}},
year = {2009},
url = {https://doi.org/10.1109/WSC.2009.5429719},
doi = {10.1109/WSC.2009.5429719},
timestamp = {Thu, 10 Jun 2021 22:18:58 +0200},
biburl = {https://dblp.org/rec/conf/wsc/HarrisHF09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cmsb/ClarkeFLHJL08,
author = {Edmund M. Clarke and
James R. Faeder and
Christopher James Langmead and
Leonard A. Harris and
Sumit Kumar Jha and
Axel Legay},
editor = {Monika Heiner and
Adelinde M. Uhrmacher},
title = {Statistical Model Checking in BioLab: Applications to the Automated
Analysis of T-Cell Receptor Signaling Pathway},
booktitle = {Computational Methods in Systems Biology, 6th International Conference,
{CMSB} 2008, Rostock, Germany, October 12-15, 2008. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5307},
pages = {231--250},
publisher = {Springer},
year = {2008},
url = {https://doi.org/10.1007/978-3-540-88562-7\_18},
doi = {10.1007/978-3-540-88562-7\_18},
timestamp = {Wed, 19 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cmsb/ClarkeFLHJL08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MuWUUFH07,
author = {Fangping Mu and
Robert F. Williams and
Clifford J. Unkefer and
Pat J. Unkefer and
James R. Faeder and
William S. Hlavacek},
title = {Carbon-fate maps for metabolic reactions},
journal = {Bioinform.},
volume = {23},
number = {23},
pages = {3193--3199},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btm498},
doi = {10.1093/BIOINFORMATICS/BTM498},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MuWUUFH07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcsb/BlinovYFH06,
author = {Michael L. Blinov and
Jin Yang and
James R. Faeder and
William S. Hlavacek},
title = {Graph Theory for Rule-Based Modeling of Biochemical Networks},
journal = {Trans. Comp. Sys. Biology},
volume = {7},
pages = {89--106},
year = {2006},
url = {https://doi.org/10.1007/11905455\_5},
doi = {10.1007/11905455\_5},
timestamp = {Wed, 06 Jan 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcsb/BlinovYFH06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/complexity/FaederBGH05,
author = {James R. Faeder and
Michael L. Blinov and
Byron Goldstein and
William S. Hlavacek},
title = {Rule-based modeling of biochemical networks},
journal = {Complex.},
volume = {10},
number = {4},
pages = {22--41},
year = {2005},
url = {https://doi.org/10.1002/cplx.20074},
doi = {10.1002/CPLX.20074},
timestamp = {Thu, 24 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/complexity/FaederBGH05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/sac/FaederBH05,
author = {James R. Faeder and
Michael L. Blinov and
William S. Hlavacek},
editor = {Hisham Haddad and
Lorie M. Liebrock and
Andrea Omicini and
Roger L. Wainwright},
title = {Graphical rule-based representation of signal-transduction networks},
booktitle = {Proceedings of the 2005 {ACM} Symposium on Applied Computing (SAC),
Santa Fe, New Mexico, USA, March 13-17, 2005},
pages = {133--140},
publisher = {{ACM}},
year = {2005},
url = {https://doi.org/10.1145/1066677.1066712},
doi = {10.1145/1066677.1066712},
timestamp = {Fri, 27 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/sac/FaederBH05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BlinovFGH04,
author = {Michael L. Blinov and
James R. Faeder and
Byron Goldstein and
William S. Hlavacek},
title = {BioNetGen: software for rule-based modeling of signal transduction
based on the interactions of molecular domains},
journal = {Bioinform.},
volume = {20},
number = {17},
pages = {3289--3291},
year = {2004},
url = {https://doi.org/10.1093/bioinformatics/bth378},
doi = {10.1093/BIOINFORMATICS/BTH378},
timestamp = {Fri, 27 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BlinovFGH04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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