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]

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]

[DOI]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]

[DOI]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]

[DOI]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]

2017

[DOI]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]

[DOI]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]

[DOI]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]

[DOI]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]

[DOI]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]

[DOI]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]

[DOI]E. Appleton, C. Madsen, N. Roehner, and D. Densmore, “Design Automation in Synthetic Biology,” Cold Spring Harbor Perspectives in Biology, 2017.
[Bibtex]

2016

[DOI] 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]

[DOI] 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]

[DOI] 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]

[DOI] 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]

[DOI] 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]

[DOI] H. Fellermann, O. Markovitch, O. Gilfellon, C. Madsen, and A. Phillips, “Toward Programmable Biology,” ACS Synthetic Biology, 2016.
[Bibtex]

[DOI] 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]

2015

[DOI] 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]

[DOI] 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]

[DOI] 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]

[DOI] 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]

2014

[DOI] 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]

[DOI] 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]

2012

[DOI] 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]

[DOI] 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]

[DOI] 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]

2011

[DOI] 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]

2010

[DOI] 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]

[DOI] 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]

2009

[DOI] 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]

[DOI] 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]