Publications
2018
T. Neupane, Z. Zhang, C. Madsen, H. Zheng, and C. J. Myers, “Approximation Techniques for Stochastic Analysis of Biological Systems,” in Automated Reasoning for Systems Biology and Medicine, P. Liò and P. Zuliani, Ed., Springer, 2018 (submitted).
[Bibtex]
@incollection{Neupane2018,
Author = {Thakur Neupane and
Zhen Zhang and
Curtis Madsen and
Hao Zheng and
Chris J. Myers},
Series={Computational Biology},
Editor={Pietro Li\`{o} and
Paolo Zuliani},
Publisher={Springer},
Title = {Approximation Techniques for Stochastic Analysis of Biological Systems},
Booktitle = {Automated Reasoning for Systems Biology and Medicine},
Year = {2018}
}
C. Madsen, P. Vaidyanathan, S. Sadraddini, C. Vasile, N. A. DeLateur, R. Weiss, D. Densmore, and C. Belta, “Metrics for Signal Temporal Logic Formulae,” IEEE Conference on Decision and Control (CDC), 2018 (accepted).
[Bibtex]
@inproceedings{Madsen2018,
Author = {Curtis Madsen and
Prashant Vaidyanathan and
Sadra Sadraddini and
Cristian-Ioan Vasile and
Nicholas A. DeLateur and
Ron Weiss and
Douglas Densmore and
Calin Belta},
Title = {Metrics for Signal Temporal Logic Formulae},
Booktitle = {IEEE Conference on Decision and Control (CDC)},
Year = {2018}
}
![[DOI]](/ckmadsen/files/2016/03/external.png){kind=small}
L. Watanabe, T. Nguyen, M. Zhang, Z. Zundel, Z. Zhang, C. Madsen, N. Roehner, and C. J. Myers, “iBioSim 3: A Tool for Model-Based Genetic Circuit Design,” ACS Synthetic Biology, 2018.
[Bibtex]
@article{Watanabe2018,
author = {Leandro Watanabe and
Tramy Nguyen and
Michael Zhang and
Zach Zundel and
Curtis Madsen and
Nicholas Roehner and
Chris J. Myers},
title = {i{B}io{S}im 3: A Tool for Model-Based Genetic Circuit Design},
journal = {ACS Synthetic Biology},
year = {2018},
doi = {10.1021/acssynbio.8b00078}
}
R. S. Cox III, C. Madsen, J. A. McLaughlin, T. Nguyen, N. Roehner, B. Bartley, S. Bhatia, M. Bissell, K. Clancy, T. Gorochowski, R. Grünberg, A. Luna, N. Le Novère, M. R. Pocock, H. M. Sauro, J. T. Sexton, G. Stan, J. J. Tabor, C. Voigt, Z. Zundel, C. J. Myers, J. Beal, and A. Wipat, “Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0,” Journal of Integrative Bioinformatics, 2018.
[Bibtex]
@article{Cox2018,
author = {Robert Sidney Cox III and
Curtis Madsen and
James Alastair McLaughlin and
Tramy Nguyen and
Nicholas Roehner and
Bryan Bartley and
Swapnil Bhatia and
Michael Bissell and
Kevin Clancy and
Thomas Gorochowski and
Raik Gr{\"{u}}nberg and
Augustin Luna and
Nicolas Le Nov\`{e}re and
Matthew R. Pocock and
Herbert M. Sauro and
John T. Sexton and
Guy-Bart Stan and
Jeffery J. Tabor and
Chris Voigt and
Zach Zundel and
Chris J. Myers and
Jacob Beal and
Anil Wipat},
title = {Synthetic Biology Open Language Visual {(SBOL Visual)} Version 2.0},
journal = {J. Integrative Bioinformatics},
year = {2018}
}
R. S. Cox III, C. Madsen, J. A. McLaughlin, T. Nguyen, N. Roehner, B. Bartley, J. Beal, M. Bissell, K. Choi, K. Clancy, R. Grünberg, C. Macklin, G. Misirli, E. Oberortner, M. R. Pocock, M. Samineni, M. Zhang, Z. Zhang, Z. Zundel, J. H. Gennari, C. J. Myers, H. M. Sauro, and A. Wipat, “Synthetic Biology Open Language (SBOL) Version 2.2.0,” Journal of Integrative Bioinformatics, 2018.
[Bibtex]
@article{Cox2018,
author = {Robert Sidney Cox III and
Curtis Madsen and
James Alastair McLaughlin and
Tramy Nguyen and
Nicholas Roehner and
Bryan Bartley and
Jacob Beal and
Michael Bissell and
Kiri Choi and
Kevin Clancy and
Raik Gr{\"{u}}nberg and
Chris Macklin and
Goksel Misirli and
Ernst Oberortner and
Matthew R. Pocock and
Meher Samineni and
Michael Zhang and
Zhen Zhang and
Zach Zundel and
John H. Gennari and
Chris J. Myers and
Herbert M. Sauro and
Anil Wipat},
title = {Synthetic Biology Open Language {(SBOL)} Version 2.2.0},
journal = {J. Integrative Bioinformatics},
year = {2018}
}
2017
R. S. Cox III, C. Madsen, J. A. McLaughlin, T. Nguyen, N. Roehner, A. Wipat, B. Bartley, J. Beal, S. Bhatia, M. Bissell, K. Clancy, T. Gorochowski, R. Grünberg, A. Luna, C. J. Myers, N. Le Novère, M. R. Pocock, H. M. Sauro, J. T. Sexton, G. Stan, J. J. Tabor, C. Voigt, and Z. Zundel, “Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0,” BBF RFC #115, 2017.
[Bibtex]
@techreport{Cox2017,
author = {Robert Sidney Cox III and
Curtis Madsen and
James Alastair McLaughlin and
Tramy Nguyen and
Nicholas Roehner and
Anil Wipat and
Bryan Bartley and
Jacob Beal and
Swapnil Bhatia and
Mike Bissell and
Kevin Clancy and
Thomas Gorochowski and
Raik Gr{\"{u}}nberg and
Augustin Luna and
Chris J. Myers and
Nicolas Le Nov\`{e}re and
Matthew R. Pocock and
Herbert M. Sauro and
John T. Sexton and
Guy-Bart Stan and
Jeffrey J. Tabor and
Chris Voigt and
Zach Zundel},
Title = {{S}ynthetic {B}iology {O}pen {L}anguage {V}isual ({SBOL} {V}isual) {V}ersion 2.0},
Keywords = {SBOL},
Year = {2017},
Number = {BBF RFC #115}
}
}
R. S. Cox III, C. Madsen, J. A. McLaughlin, T. Nguyen, N. Roehner, A. Wipat, J. Beal, K. Clancy, R. Grünberg, C. Macklin, M. Bissell, G. Misirli, E. Oberortner, M. R. Pocock, Z. Zhang, C. Myers, M. Zhang, M. Samineni, Z. Zundel, B. Bartley, K. Choi, J. H. Gennari, and H. M. Sauro, “Synthetic Biology Open Language (SBOL) Version 2.2.0,” BBF RFC #114, 2017.
[Bibtex]
@techreport{Cox2017,
author = {Robert Sidney Cox III and
Curtis Madsen and
James Alastair McLaughlin and
Tramy Nguyen and
Nicholas Roehner and
Anil Wipat and
Jacob Beal and
Kevin Clancy and
Raik Gr{\"{u}}nberg and
Chris Macklin and
Michael Bissell and
Goksel Misirli and
Ernst Oberortner and
Matthew R. Pocock and
Zhen Zhang and
Chris Myers and
Michael Zhang and
Meher Samineni and
Zach Zundel and
Bryan Bartley and
Kiri Choi and
John H. Gennari and
Herbert M. Sauro},
Title = {{S}ynthetic {B}iology {O}pen {L}anguage ({SBOL}) {V}ersion 2.2.0},
Keywords = {SBOL},
Year = {2017},
Number = {BBF RFC #114}
}
}
E. Appleton, D. Densmore, C. Madsen, and N. Roehner, “Needs and Opportunities in Bio-Design Automation: Four Areas for Focus,” Current Opinion in Chemical Biology, vol. 40, pp. 111-118, 2017.
[Bibtex]
@article{Appleton2017,
author = {Evan Appleton and
Douglas Densmore and
Curtis Madsen and
Nicholas Roehner},
title = "Needs and opportunities in bio-design automation: four areas for focus",
journal = "Current Opinion in Chemical Biology",
volume = "40",
number = "Supplement C",
pages = "111 - 118",
year = "2017",
note = "Synthetic Biology Synthetic Biomolecules",
issn = "1367-5931",
doi = "https://doi.org/10.1016/j.cbpa.2017.08.005",
url = "http://www.sciencedirect.com/science/article/pii/S1367593117300753"
}
P. G. Jayathilake, P. Gupta, B. Li, C. Madsen, O. Oyebamiji, R. González-Cabaleiro, S. Rushton, B. Bridgens, D. Swailes, B. Allen, A.S. McGough, P. Zuliani, I. D. Ofiteru, D. Wilkinson, J. Chen, and T. Curtis, “A Mechanistic Individual-Based Model of Microbial Communities,” PLOS One, vol. 12(8), pp. 1-26, 2017.
[Bibtex]
@article{Jayathilake2017,
author = {Pahala Gedara Jayathilake and
Prashant Gupta and
Bowen Li and
Curtis Madsen and
Oluwole Oyebamiji and
Rebeca Gonz\'{a}lez-Cabaleiro and
Steve Rushton and
Ben Bridgens and
David Swailes and
Ben Allen and
A. Stephen McGough and
Paolo Zuliani and
Irina Dana Ofiteru and
Darren Wilkinson and
Jinju Chen and
Tom Curtis},
journal = {PLOS ONE},
publisher = {Public Library of Science},
title = {A mechanistic Individual-based Model of microbial communities},
year = {2017},
month = {08},
volume = {12},
url = {https://doi.org/10.1371/journal.pone.0181965},
pages = {1-26},
number = {8},
doi = {10.1371/journal.pone.0181965}
}
C. Myers, J. Beal, T. Gorochowski, H. Kuwahara, C. Madsen, J. A. McLaughlin, G. Misirli, T. Nguyen, E. Oberortner, M. Samineni, A. Wipat, M. Zhang, and Z. Zundel, “A Standard-Enabled Workflow for Synthetic Biology,” Biochemical Society Transactions, vol. 45(3), pp. 793-803, 2017.
[Bibtex]
@article{Myers2017,
author = {Chris Myers and
Jacob Beal and
Thomas Gorochowski and
Hiroyuki Kuwahara and
Curtis Madsen and
James Alastair McLaughlin and
Goksel Misirli and
Tramy Nguyen and
Ernst Oberortner and
Meher Samineni and
Anil Wipat and
Michael Zhang and
Zach Zundel},
title = {A standard-enabled workflow for synthetic biology},
volume = {45},
number = {3},
pages = {793--803},
year = {2017},
doi = {10.1042/BST20160347},
publisher = {Portland Press Limited},
issn = {0300-5127},
URL = {http://www.biochemsoctrans.org/content/45/3/793},
eprint = {http://www.biochemsoctrans.org/content/45/3/793.full.pdf},
journal = {Biochemical Society Transactions}
}
G. Misirli, C. Madsen, I. S. de Murieta, M. Bultelle, K. Flanagan, M. Pocock, J. Hallinan, J. A. McLaughlin, J. Clark-Casey, M. Lyne, G. Micklem, G. Stan, R. Kitney, and A. Wipat, “Constructing Synthetic Biology Workflows in the Cloud,” IET Engineering Biology, vol. 1(1), pp. 61-65, 2017.
[Bibtex]
@article{Misirli2017,
author = {Goksel Misirli and
Curtis Madsen and
I\~{n}aki Sainz de Murieta and
Matthieu Bultelle and
Keith Flanagan and
Matthew Pocock and
Jennifer Hallinan and
James Alastair McLaughlin and
Justin Clark-Casey and
Mike Lyne and
Gos Micklem and
Guy-Bart Stan and
Richard Kitney and
Anil Wipat},
journal={Engineering Biology},
title={Constructing synthetic biology workflows in the cloud},
year={2017},
volume={1},
number={1},
pages={61-65},
keywords={bioinformatics;cloud computing;Cloud-based system;Protocol for Linking External Nodes;bioinformatics;computational workflows;synthetic biology},
doi={10.1049/enb.2017.0001}
}
E. Appleton, C. Madsen, N. Roehner, and D. Densmore, “Design Automation in Synthetic Biology,” Cold Spring Harbor Perspectives in Biology, 2017.
[Bibtex]
@article{Appleton2017,
author = {Evan Appleton and
Curtis Madsen and
Nicholas Roehner and
Douglas Densmore},
title = {Design Automation in Synthetic Biology},
year = {2017},
doi = {10.1101/cshperspect.a023978},
journal = {Cold Spring Harbor Perspectives in Biology}
}
2016
J. Beal, R. S. Cox III, R. Grünberg, J. McLaughlin, T. Nguyen, B. Bartley, M. Bissell, K. Choi, K. Clancy, C. Macklin, C. Madsen, G. Misirli, E. Oberortner, M. R. Pocock, N. Roehner, M. Samineni, M. Zhang, Z. Zhang, Z. Zundel, J. H. Gennari, C. J. Myers, H. M. Sauro, and A. Wipat, “Synthetic Biology Open Language (SBOL) Version 2.1.0,” Journal of Integrative Bioinformatics, vol. 13(3), 2016.
[Bibtex]
@article{Beal2016,
author = {Jacob Beal and
Robert Sidney Cox III and
Raik Gr{\"{u}}nberg and
James McLaughlin and
Tramy Nguyen and
Bryan Bartley and
Michael Bissell and
Kiri Choi and
Kevin Clancy and
Chris Macklin and
Curtis Madsen and
Goksel Misirli and
Ernst Oberortner and
Matthew R. Pocock and
Nicholas Roehner and
Meher Samineni and
Michael Zhang and
Zhen Zhang and
Zach Zundel and
John H. Gennari and
Chris J. Myers and
Herbert M. Sauro and
Anil Wipat},
title = {Synthetic Biology Open Language {(SBOL)} Version 2.1.0},
journal = {J. Integrative Bioinformatics},
volume = {13},
number = {3},
year = {2016},
url = {https://doi.org/10.2390/biecoll-jib-2016-291},
doi = {10.2390/biecoll-jib-2016-291}
}
J. Beal, R. S. Cox III; R. Grünberg, J. McLaughlin, T. Nguyen, C. Macklin, M. Bissell, C. Madsen, N. Roehner, E. Oberortner, G. Misirli, K. Clancy, M. R. Pocock, Z. Zhang, C. J. Myers, M. Zhang, M. Samineni, Z. Zundel, B. Bartley, K. Choi, J. H. Gennari, and H. M. Sauro, “Synthetic Biology Open Language (SBOL) Version 2.1.0,” BBF RFC #112, 2016.
[Bibtex]
@techreport{Beal2016,
author = {Jacob Beal and
Robert Sidney Cox III and
Raik Gr\"{u}nberg and
James Alastair McLaughlin and
Tramy Nguyen and
Chris Macklin and
Michael Bissell and
Curtis Madsen and
Nicholas Roehner and
Ernst Oberortner and
Goksel Misirli and
Kevin Clancy and
Matthew R. Pocock and
Zhen Zhang and
Chris J. Myers and
Michael Zhang and
Meher Samineni and
Zach Zundel and
Bryan Bartley and
Kiri Choi and
John H. Gennari and
Herbert M. Sauro},
Title = {{S}ynthetic {B}iology {O}pen {L}anguage ({SBOL}) {V}ersion 2.1.0},
Keywords = {SBOL},
Year = {2016},
Number = {BBF RFC #112},
doi = {1721.1/105278}
}
}
C. Madsen, J. A. McLaughlin, G. Misirli, M. Pocock, K. Flanagan, J. Hallinan, and A. Wipat, “The SBOL Stack: A Platform for Storing, Publishing, and Sharing Synthetic Biology Designs,” ACS Synthetic Biology, 2016.
[Bibtex]
@article{Madsen2016,
author = {Curtis Madsen and
James Alastair McLaughlin and
Goksel Misirli and
Matthew Pocock and
Keith Flanagan and
Jennifer Hallinan and
Anil Wipat},
title = {The {SBOL} Stack: A Platform for Storing, Publishing, and Sharing Synthetic Biology Designs},
journal = {ACS Synthetic Biology},
year = {2016},
doi = {10.1021/acssynbio.5b00210},
URL = {http://dx.doi.org/10.1021/acssynbio.5b00210},
eprint = {http://dx.doi.org/10.1021/acssynbio.5b00210}
}
N. Roehner, J. Beal, K. Clancy, B. Bartley, G. Misirli, R. Grünberg, E. Oberortner, M. Pocock, M. Bissell, C. Madsen, T. Nguyen, Z. Zhang, Z. Zundel, J. H. Gennari, A. Wipat, H. M. Sauro, and C. J. Myers, “Sharing Structure and Function in Biological Design with SBOL 2.0,” ACS Synthetic Biology, 2016.
[Bibtex]
@article{Roehner2016,
author = {Roehner, Nicholas and
Beal, Jacob and
Clancy, Kevin and
Bartley, Bryan and
Misirli, Goksel and
Gr\"{u}nberg, Raik and
Oberortner, Ernst and
Pocock, Matthew and
Bissell, Michael and
Madsen, Curtis and
Nguyen, Tramy and
Zhang, Zhen and
Zundel, Zach and
Gennari, John H. and
Wipat, Anil and
Sauro, Herbert M. and
Myers, Chris J.},
title = {Sharing Structure and Function in Biological Design with {SBOL} 2.0},
journal = {ACS Synthetic Biology},
year = {2016},
doi = {10.1021/acssynbio.5b00215},
URL = {http://dx.doi.org/10.1021/acssynbio.5b00215},
eprint = {http://dx.doi.org/10.1021/acssynbio.5b00215}
}
J. A. McLaughlin, M. Pocock, G. Misirli, C. Madsen, and A. Wipat, “VisBOL: Web-Based Tools for Synthetic Biology Design Visualization,” ACS Synthetic Biology, 2016.
[Bibtex]
@article{McLaughlin2016,
author = {James Alastair McLaughlin and
Matthew Pocock and
Goksel Misirli and
Curtis Madsen and
Anil Wipat},
title = {{VisBOL}: Web-Based Tools for Synthetic Biology Design Visualization},
journal = {ACS Synthetic Biology},
year = {2016},
doi = {10.1021/acssynbio.5b00244},
URL = {http://dx.doi.org/10.1021/acssynbio.5b00244},
eprint = {http://dx.doi.org/10.1021/acssynbio.5b00244}
}
H. Fellermann, O. Markovitch, O. Gilfellon, C. Madsen, and A. Phillips, “Toward Programmable Biology,” ACS Synthetic Biology, 2016.
[Bibtex]
@article{Fellermann2016,
author = {Harold Fellermann and
Omer Markovitch and
Owen Gilfellon and
Curtis Madsen and
Andrew Phillips},
title = {Toward Programmable Biology},
journal = {ACS Synthetic Biology},
year = {2016},
doi = {10.1021/acssynbio.6b00213},
URL = {http://dx.doi.org/10.1021/acssynbio.6b00213},
eprint = {http://dx.doi.org/10.1021/acssynbio.6b00213}
}
G. Misirli, M. Cavaliere, W. Waites, M. Pocock, C. Madsen, O. Gilfellon, R. Honorato-Zimmer, P. Zuliani, V. Danos, and A. Wipat, “Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualisation,” Bioinformatics, vol. 32, iss. 6, pp. 908-917, 2016.
[Bibtex]
@article{Misirli2016,
author = {Misirli, Goksel and
Cavaliere, Matteo and
Waites, William and
Pocock, Matthew and
Madsen, Curtis and
Gilfellon, Owen and
Honorato-Zimmer, Ricardo and
Zuliani, Paolo and
Danos, Vincent and
Wipat, Anil},
title = {Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualisation},
volume = {32},
number = {6},
year = {2016},
pages = {908-917},
doi = {10.1093/bioinformatics/btv660},
URL = {http://bioinformatics.oxfordjournals.org/content/early/2015/11/11/bioinformatics.btv660.abstract},
eprint = {http://bioinformatics.oxfordjournals.org/content/early/2015/11/11/bioinformatics.btv660.full.pdf+html},
journal = {Bioinformatics}
}
2015
C. Madsen, F. Shmarov, and P. Zuliani, “BioPSy: An SMT-based Tool for Guaranteed Parameter Set Synthesis of Biological Models,” Computational Methods in Systems Biology (CMSB), p. 182–194, 2015.
[Bibtex]
@inproceedings{Madsen2015,
Author = {Curtis Madsen and
Fedor Shmarov and
Paolo Zuliani},
Title = {BioPSy: An SMT-based Tool for Guaranteed Parameter Set Synthesis of Biological Models},
Booktitle = {Computational Methods in Systems Biology (CMSB)},
Pages = {182--194},
Year = {2015},
url = {http://dx.doi.org/10.1007/978-3-319-23401-4_16},
doi = {10.1007/978-3-319-23401-4_16}
}
B. Bartley, J. Beal, K. Clancy, G. Misirli, N. Roehner, E. Oberortner, M. R. Pocock, M. Bissell, C. Madsen, T. Nguyen, Z. Zhang, J. H. Gennari, C. J. Myers, A. Wipat, and H. M. Sauro, “Synthetic Biology Open Language (SBOL) Version 2.0.0,” Journal of Integrative Bioinformatics, vol. 12(2), 2015.
[Bibtex]
@article{Bartley2015,
author = {Bryan Bartley and
Jacob Beal and
Kevin Clancy and
Goksel Misirli and
Nicholas Roehner and
Ernst Oberortner and
Matthew R. Pocock and
Michael Bissell and
Curtis Madsen and
Tramy Nguyen and
Zhen Zhang and
John H. Gennari and
Chris J. Myers and
Anil Wipat and
Herbert M. Sauro},
title = {Synthetic Biology Open Language {(SBOL)} Version 2.0.0},
journal = {J. Integrative Bioinformatics},
volume = {12},
number = {2},
year = {2015},
url = {https://doi.org/10.2390/biecoll-jib-2015-272},
doi = {10.2390/biecoll-jib-2015-272}
}
B. Bartley, J. Beal, K. Clancy, G. Misirli, N. Roehner, H. M. Sauro, E. Oberortner, C. Madsen, M. R. Pocock, A. Wipat, T. Nguyen, Z. Zhang, C. J. Myers, J. H. Gennari, and M. Bissell, “Synthetic Biology Open Language (SBOL) Version 2.0.0,” BBF RFC #108, 2015.
[Bibtex]
@techreport{Bartley2015,
Author = {Bartley, Bryan and
Beal, Jacob and
Clancy, Kevin and
Misirli, Goksel and
Roehner, Nicholas and
Sauro, Herbert M. and
Oberortner, Ernst and
Madsen, Curtis and
Pocock, Matthew R. and
Wipat, Anil and
Nguyen, Tramy and
Zhang, Zhen and
Myers, Chris J. and
Gennari, John H. and
Bissell, Michael},
Title = {{S}ynthetic {B}iology {O}pen {L}anguage ({SBOL}) {V}ersion 2.0.0},
Keywords = {SBOL},
Year = {2015},
Number = {BBF RFC #108},
doi = {1721.1/98369}
}
C. Madsen, C. J. Myers, N. Roehner, C. Winstead, and Z. Zhang, “Efficient analysis methods in synthetic biology,” in Computational methods in synthetic biology, M. A. Marchisio, Ed., Springer New York, 2015, vol. 1244, pp. 217-257.
[Bibtex]
@incollection{Madsen2015,
year={2015},
isbn={978-1-4939-1877-5},
booktitle={Computational Methods in Synthetic Biology},
volume={1244},
series={Methods in Molecular Biology},
editor={Mario Andrea Marchisio},
doi={10.1007/978-1-4939-1878-2_11},
title={Efficient Analysis Methods in Synthetic Biology},
url={http://dx.doi.org/10.1007/978-1-4939-1878-2_11},
publisher={Springer New York},
keywords={Design space exploration;
Synthetic genetic circuits;
Stochastic model checking;
Stochastic simulation;
Synthetic biology},
author = {Curtis Madsen and
Chris J. Myers and
Nicholas Roehner and
Chris Winstead and
Zhen Zhang},
pages={217-257}
}
2014
C. Madsen, Z. Zhang, N. Roehner, C. Winstead, and C. J. Myers, “Stochastic model checking of genetic circuits,” J. emerg. technol. comput. syst., vol. 11, iss. 3, p. 23:1–23:21, 2014.
[Bibtex]
@article{Madsen2014,
author = {Curtis Madsen and
Zhen Zhang and
Nicholas Roehner and
Chris Winstead and
Chris J. Myers},
title = {Stochastic Model Checking of Genetic Circuits},
journal = {J. Emerg. Technol. Comput. Syst.},
volume = {11},
number = {3},
month = dec,
year = {2014},
issn = {1550-4832},
pages = {23:1--23:21},
articleno = {23},
numpages = {21},
url = {http://doi.acm.org/10.1145/2644817},
doi = {10.1145/2644817},
acmid = {2644817},
publisher = {ACM},
address = {New York, NY, USA},
keywords = {Markov chain analysis,
Stochastic model checking,
continuous stochastic logic,
design space exploration,
synthetic genetic circuits},
}
N. Roehner, E. Oberortner, M. Pocock, J. Beal, K. Clancy, C. Madsen, G. Misirli, A. Wipat, H. Sauro, and C. J. Myers, “Proposed data model for the next version of the synthetic biology open language,” ACS Synthetic Biology, 2014.
[Bibtex]
@article{Roehner2014,
author = {Roehner, Nicholas and
Oberortner, Ernst and
Pocock, Matthew and
Beal, Jacob and
Clancy, Kevin and
Madsen, Curtis and
Misirli, Goksel and
Wipat, Anil and
Sauro, Herbert and
Myers, Chris J.},
title = {Proposed Data Model for the Next Version
of the Synthetic Biology Open Language},
journal = {{ACS} {S}ynthetic {B}iology},
year = 2014,
doi = {10.1021/sb500176h},
URL = {http://pubs.acs.org/doi/abs/10.1021/sb500176h},
eprint = {http://pubs.acs.org/doi/pdf/10.1021/sb500176h}
}
2012
M. Galdzicki, M. L. Wilson, C. A. Rodriguez, M. R. Pocock, E. Oberortner, L. Adam, A. Adler, C. J. Anderson, J. Beal, Y. Cai, D. Chandran, D. Densmore, O. A. Drory, D. Endy, J. H. Gennari, R. Grünberg, T. S. Ham, N. J. Hillson, J. D. Johnson, A. Kuchinsky, M. W. Lux, C. Madsen, G. Misirli, C. J. Myers, C. Olguin, J. Peccoud, H. Plahar, D. Platt, N. Roehner, E. Sirin, T. F. Smith, G. Stan, A. Villalobos, A. Wipat, and H. M. Sauro, “Synthetic Biology Open Language (SBOL) Version 1.1.0,” BBF RFC #87, 2012.
[Bibtex]
@techreport{Galdzicki2012,
Author = {Galdzicki, Michal and
Wilson, Mandy L. and
Rodriguez, Cesar A. and
Pocock, Matthew R. and
Oberortner, Ernst and
Adam, Laura and
Adler, Aaron and
Anderson, J. Christopher and
Beal, Jacob and
Cai, Yizhi and
Chandran, Deepak and
Densmore, Douglas and
Drory, Omri A. and
Endy, Drew and
Gennari, John H. and
Gr\"{u}nberg, Raik and
Ham, Timothy S. and
Hillson, Nathan J. and
Johnson, Jeffrey D. and
Kuchinsky, Allan and
Lux, Matthew W. and
Madsen, Curtis and
Misirli, Goksel and
Myers, Chris J. and
Olguin, Carlos and
Peccoud, Jean and
Plahar, Hector and
Platt, Darren and
Roehner, Nicholas and
Sirin, Evren and
Smith, Trevor F. and
Stan, Guy-Bart and
Villalobos, Alan and
Wipat, Anil and
Sauro, Herbert M.},
Title = {{S}ynthetic {B}iology {O}pen {L}anguage ({SBOL}) {V}ersion 1.1.0},
Keywords = {SBOL},
Year = {2012},
Number = {BBF RFC #87},
doi = {1721.1/73909}
}
C. Madsen, C. J. Myers, T. Patterson, N. Roehner, J. T. Stevens, and C. Winstead, “Design and test of genetic circuits using iBioSim,” IEEE Design & Test of Computers, vol. 29, iss. 3, pp. 32-39, 2012.
[Bibtex]
@article{Madsen2012,
author = {Curtis Madsen and
Chris J. Myers and
Tyler Patterson and
Nicholas Roehner and
Jason T. Stevens and
Chris Winstead},
title = {Design and Test of Genetic Circuits Using {iBioSim}},
journal = {{IEEE Design {\&} Test of Computers}},
volume = {29},
number = {3},
year = {2012},
pages = {32-39},
doi = {10.1109/MDT.2012.2187875},
ee = {http://dx.doi.org/10.1109/MDT.2012.2187875}
}
C. Madsen, C. J. Myers, N. Roehner, C. Winstead, and Z. Zhang, “Utilizing stochastic model checking to analyze genetic circuits.,” in IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2012, pp. 379-386 (Best Student Paper).
[Bibtex]
@inproceedings{Madsen2012,
author = {Madsen, Curtis and
Myers, Chris J. and
Roehner, Nicholas and
Winstead, Chris and
Zhang, Zhen},
booktitle = {{IEEE Symposium on Computational Intelligence
in Bioinformatics and Computational Biology (CIBCB)}},
ee = {http://dx.doi.org/10.1109/CIBCB.2012.6217255},
interhash = {613357012415bdba0883eee6fe183ff6},
intrahash = {c5c868dd08b7df5ea2241fbee03a618a},
isbn = {978-1-4673-1190-8},
keywords = {dblp},
pages = {379-386},
timestamp = {2012-06-20T00:00:00.000+0200},
title = {Utilizing stochastic model checking to analyze genetic circuits.},
url = {http://dblp.uni-trier.de/db/conf/cibcb/cibcb2012.html#MadsenMRWZ12},
year = 2012,
doi = {10.1109/CIBCB.2012.6217255},
note = {(best student paper)}
}
2011
M. Galdzicki, M. L. Wilson, C. A. Rodriguez, L. Adam, A. Adler, C. J. Anderson, J. Beal, D. Chandran, D. Densmore, O. A. Drory, D. Endy, J. H. Gennari, R. Grünberg, T. S. Ham, A. Kuchinsky, M. W. Lux, C. Madsen, G. Misirli, C. J. Myers, J. Peccoud, H. Plahar, M. R. Pocock, N. Roehner, T. F. Smith, G. Stan, A. Villalobos, A. Wipat, and H. M. Sauro, “Synthetic Biology Open Language (SBOL) Version 1.0.0,” BBF RFC #84, 2011.
[Bibtex]
@techreport{Galdzicki2011,
Author = {Galdzicki, Michal and
Wilson, Mandy L. and
Rodriguez, Cesar A. and
Adam, Laura and
Adler, Aaron and
Anderson, J. Christopher and
Beal, Jacob and
Chandran, Deepak and
Densmore, Douglas and
Drory, Omri A. and
Endy, Drew and
Gennari, John H. and
Gr\"{u}nberg, Raik and
Ham, Timothy S. and
Kuchinsky, Allan and
Lux, Matthew W. and
Madsen, Curtis and
Misirli, Goksel and
Myers, Chris J. and
Peccoud, Jean and
Plahar, Hector and
Pocock, Matthew R. and
Roehner, Nicholas and
Smith, Trevor F. and
Stan, Guy-Bart and
Villalobos, Alan and
Wipat, Anil and
Sauro, Herbert M.},
Title = {{S}ynthetic {B}iology {O}pen {L}anguage ({SBOL}) {V}ersion 1.0.0},
Keywords = {SBOL},
Year = {2011},
Number = {BBF RFC #84},
doi = {1721.1/66172}
}
2010
H. Kuwahara, C. Madsen, I. Mura, C. J. Myers, A. Tejeda, and C. Winstead, “Efficient stochastic simulation to analyze targeted properties of biological systems,” in Stochastic control, C. J. Myers, Ed., Sciyo, 2010, pp. 505-532.
[Bibtex]
@incollection{Kuwahara2010,
author = {Hiroyuki Kuwahara and
Curtis Madsen and
Ivan Mura and
Chris J. Myers and
Abiezer Tejeda and
Chris Winstead},
title = {Efficient stochastic simulation
to analyze targeted properties of biological systems},
booktitle = {Stochastic Control},
editor = {Chris J. Myers},
publisher = {Sciyo},
pages = {505--532},
year = 2010
}
C. Winstead, C. Madsen, and C. J. Myers, “iSSA: An incremental stochastic simulation algorithm for genetic circuits,” in International Symposium on Circuits and Systems (ISCAS), 2010, pp. 553-556.
[Bibtex]
@inproceedings{Winstead2010,
author = {Chris Winstead and
Curtis Madsen and
Chris J. Myers},
title = {{iSSA}: {A}n incremental stochastic simulation algorithm for
genetic circuits},
booktitle = {{International Symposium on Circuits and Systems (ISCAS)}},
year = {2010},
pages = {553-556},
doi = {10.1109/ISCAS.2010.5537539},
ee = {http://dx.doi.org/10.1109/ISCAS.2010.5537539}
}
2009
C. J. Myers, N. A. Barker, H. Kuwahara, K. R. Jones, C. Madsen, and N. D. Nguyen, “Genetic design automation,” in International Conference on Computer-Aided Design (ICCAD), 2009, pp. 713-716.
[Bibtex]
@inproceedings{Myers2009,
author = {Chris J. Myers and
Nathan A. Barker and
Hiroyuki Kuwahara and
Kevin R. Jones and
Curtis Madsen and
Nam-Phuong D. Nguyen},
title = {Genetic design automation},
booktitle = {{International Conference on Computer-Aided Design (ICCAD)}},
year = {2009},
pages = {713-716},
ee = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5361217},
doi = {10.1145/1687399.1687531}
}
C. J. Myers, N. A. Barker, K. R. Jones, H. Kuwahara, C. Madsen, and N. D. Nguyen, “iBioSim: a tool for the analysis and design of genetic circuits,” Bioinformatics, vol. 25, iss. 21, pp. 2848-2849, 2009.
[Bibtex]
@article{Myers2009,
author = {Chris J. Myers and
Nathan A. Barker and
Kevin R. Jones and
Hiroyuki Kuwahara and
Curtis Madsen and
Nam-Phuong D. Nguyen},
title = {{iBioSim}: a tool for the analysis and design of genetic circuits},
journal = {Bioinformatics},
volume = {25},
number = {21},
year = {2009},
pages = {2848-2849},
doi = {10.1093/bioinformatics/btp457},
ee = {http://dx.doi.org/10.1093/bioinformatics/btp457}
}
