Supported by the National Science Foundation (NSF QSB award 0331270, NSF CCF award 0737644, NSF CCF award 0916042, NSF CCF award 1218095, NSF CCF award 1748200), Professor Myers and his colleagues have been developing methods for the modeling, analysis, and design of genetic circuits. In these projects, Professor Myers and his colleagues developed, among other things, a method to learn genetic circuit models from time series experimental data, efficient abstraction-based stochastic analysis methods, and methods for genetic circuit design. This research has been implemented within the freely available software tools SBOLDesigner, iBioSim, and SynBioHub. Under NSF DBI award 1356041, Professor Myers his colleagues at the University of Washington (Professors Herbert Sauro and John Gennari) are developing infrastructure to support the synthetic biology open language (SBOL).

Faculty:

• Chris J. Myers, Professor, University of Utah
• Herbert Sauro, Professor, University of Washington
• John Gennari, Professor, University of Washington
• Chris Winstead, Associate Professor, Utah State University

Students:

• Sam Bridge
• Pedro Fontanarrosa
• Jet Mante
• James Scholz
• Eric Yu
• Zach Zundel

Alumni:

• Nathan Barker (PhD), Southern Utah University, Cedar City, UT.
• Scott Glass (BS), University of Utah, UT.
• Kevin Jones (BS), Aberdeen Proving Ground, Philadelphia, PA.
• Hiroyuki Kuwahara (PhD) , Carnegie Mellon University, Pittsburgh, PA.
• Curtis Madsen (PhD), Newcastle University, Newcastle, UK.
• Nam Nguyen (MS), PhD student at University of Texas in Austin.
• Tramy Nguyen (PhD), BBN/Raytheon, Boston, MA.
• Tyler Patterson (BS), DataStax, Salt Lake City, UT.
• Nicholas Roehner (PhD), Boston University, Boston, MA.
• Meher Samineni (MS)
• Jason Stevens (BS), PhD student at the University of Washington, Seattle, WA.
• Michael Zhang (MS), Google, Sunnyvale, CA.
• Zhen Zhang, Assistant Professor, Utah State University, Logan, UT.

Software:

• iBioSim

Books:

• Chris J. Myers, Engineering Genetic Circuits, Chapman & Hall/CRC Press, July, 2009.

Book Chapters:

• T. Neupane, Z. Zhang, C. Madsen, H. Zheng, and C. Myers, Approximation techniques for stochastic analysis of biological systems, in Automated Reasoning for Systems Biology and Medicine, pages 327-348, 2019.
• C. Myers, K. Clancy, G. Misirli, E. Oberortner, M. Pocock, J. Quinn, N. Roehner, and H. Sauro, The Synthetic Biology Open Language, in Computational Methods in Synthetic Biology, Methods in Molecular Biology, Volume 1244, pages 323-336, 2015.
• C. Madsen, C. Myers, N. Roehner, C. Winstead, and Z. Zhang, Efficient Analysis Methods in Synthetic Biology, in Computational Methods in Synthetic Biology, Methods in Molecular Biology, Volume 1244, pages 217-257, 2015.
• C. Myers, Platforms for Genetic Design Automation, in Methods in Microbiology 2013: Microbial Synthetic Biology, November, 2013.
• H. Kuwahara, C. Madsen, I. Mura, C. Myers, A. Tejeda, and C. Winstead, Efficient stochastic simulation to analyze targeted properties of biological systems in Stochastic Control, Sciyo, pages 505-532, August, 2010.
• H. Kuwahara and C. J. Myers, Abstraction methods for analysis of gene regulatory networks in Computational Methods in Gene Regulatory Networks, IGI Global, pages 352-385, 2010.

PhD Dissertations:

• Leandro Watanabe, Scalable and Reproducible Modeling and Simulation for Heterogeneous Populations, PhD Dissertation, University of Utah, May 2019
• Nicholas Roehner, Technology Mapping of Genetic Circuits Designs , PhD Dissertation, University of Utah, December, 2014.
• Curtis K. Madsen, Stochastic Analysis of Synthetic Genetic Circuits , PhD Dissertation, University of Utah, August, 2013.
• Hiroyuki Kuwahara, Model Abstraction and Temporal Behavior Analysis of Genetic Regulatory Networks , PhD Dissertation, University of Utah, December, 2007.
• Nathan Barker, Learning Genetic Regulatory Network Connectivity from Time Series Data , PhD Dissertation, University of Utah, December, 2007.

Master’s Theses:

• Nam Nguyen, Design and Analysis of Genetic Circuits , MS Thesis, University of Utah, August, 2008.

Bachelor’s Theses:

• Z. Zundel, Improving Authentication and Authorization on SynBioHub, BS Thesis, University of Utah, December 2019
• M. Zhang, SBOLDesigner: A Hierarchical Genetic Design Editor, BS Thesis, University of Utah, April 2018
• M. Samineni, Software Compliance Testing for the Synthetic Biology Open Language, BS Thesis, University of Utah, August 2017
• L. Watanabe, Hierarchical Stochastic Simulation of Genetic Circuits, BS Thesis, University of Utah, May, 2014.
• T. Patterson, Modeling and Visualization of Synthetic Genetic Circuits, BS Thesis, University of Utah, May, 2011.
• C. Madsen, Representing Genetic Networks as Labeled Hybrid Petri Nets for State Space Exploration and Markov Chain Analysis, BS Thesis, University of Utah, June, 2009.

Journal Publications:

• L. Watanabe, J. Barhak, and C. Myers, Toward reproducible disease models using the Systems Biology Markup Language, in Simulation, September 6, 2018.
• 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, in ACS Synthetic Biology, June 26, 2018.
• G. Mısırlı, T. Nguyen, J. A. McLaughlin, P. Vaidyanathan, T. Jones, D. Densmore, C. J. Myers, and A. Wipat, A computational workflow for the automated generation of models of genetic designs, in ACS Synthetic Biology, May 21, 2018.
• F. Schreiber, G. Bader, P. Gleeson, M. Golebiewski, M. Hucka, S. Keating, N. Le Novère, C. Myers, D. Nickerson, B. Sommer, and D. Waltemath, Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017, in Journal of Integrative Bioinformatics, Mar 29, 2018.
• R. Cox, C. Madsen, J. McLaughlin, T. Nguyen, N. Roehner, B. Bartley, J. Beal, M. Bissell, K. Choi, K. Clancy, R. Grünberg, C. Macklin, G. Misirli, E. Oberortner, M. Pocock, M. Samineni, M. Zhang, Z. Zhang, Z. Zundel, J. Gennari, C. Myers, H. Sauro, A. Wipat. Synthetic Biology Open Language (SBOL) Version 2.2.0, in Journal of Integrative Bioinformatics, 15(1), April 2, 2018.
• R. Cox, C. Madsen, J. McLaughlin, T. Nguyen, N. Roehner, B. Bartley, S. Bhatia, M. Bissell, K. Clancy, T. Gorochowski, R. Grünberg, A. Luna, N. Le, M. Pocock, H. Sauro, J. Sexton, G. Stan, J. Tabor, C. Voigt, Z. Zundel, C. Myers, J. Beal, A. Wipat. Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0, in Journal of Integrative Bioinformatics, 15(1), April 2, 2018.
• J. McLaughlin, C. Myers, Z. Zundel, G. Misirli, M. Zhang, I. Ofiteru, A. Moreno, and A. Wipat, SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology, in ACS Synthetic Biology, 7 (2): pp 682–688, 2018.
• M. Zhang, J. McLaughlin, A. Wipat, and C. Myers, SBOLDesigner 2: An Intuitive Tool for Structural Genetic Design, in ACS Synthetic Biology, 6(7): 1150-1160, July 21, 2017.
• Z. Zundel, M. Samineni, Z. Zhang, and C. Myers, A validator and Converter for the Synthetic Biology Open Language, ACS Synthetic Biology, 6(7):1161–1168, July 21, 2017.
• C. Myers, J. Beal, T. Gorochowski, H. Kuwahara, C. Madsen, J. McLaughlin, G. Misirli, T. Nguyen, E. Oberortner, M. Samineni, A. Wipat, M. Zhang, and Z. Zundel, A Standard-Enabled Workflow for Synthetic Biology, in Biochemical Society Transactions, 45: 793-803, June 15, 2017.
• H. Kuwahara, X. Cui, R. Umarov, R. Gruenberg, C. Myers, and X. Gao, SBOLme: a Repository of SBOL Parts for Metabolic Engineering, ACS Synthetic Biology, 2017.
• J. Beal, R. Cox, R. Grunberg, J. McLaughlin, T. Nguyen, B. Bartley, M. Bissell, K. Choi, K. Clancy, C. Macklin, C. Madsen, G. Misirli, E. Oberortner, M. Pocock, N. Roehner, M. Samineni, M. Zhang, Z. Zhang, Z. Zundel, J. Gennari, C. Myers, H. Sauro, A. Wipat. Synthetic Biology Open Language (SBOL) Version 2.1.0, Journal of Integrative Bioinformatics, 13(3):291, 2016.
• F. Schreiber, G. Bader, P. Gleeson, M. Golebiewski, M. Hucka, B. Kornmeier, N. Le Novere, C. Myers, D. Nickerson, B. Sommer, and D. Waltemath. Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016, Journal of Integrative Bioinformatics, 13(3):289, 2016.
• D. Waltemath, J.. Karr, F. Bergmann, V. Chelliah, M. Hucka, M. Krantz, W. Liebermeister, P. Mendes, C. Myers, P. Pir, B. Alaybeyoglu, N. Aranganathan, K. Baghalian, A. Bittig, P. Burke, M. Cantarelli, Y. Chew, R. Costa, J. Cursons, T. Czauderna, A. Goldberg, H. Gómez, J. Hahn, T. Hameri, D. Kazakiewicz, I. Kiselev, V. Knight-Schrijver, C. Knüpfer, M. König, D. Lee, A. Lloret-Villas, N. Mandrik, J. Medley, B. Moreau, H. Meshkin, S. Palaniappan, D. Priego-Espinosa, M. Scharm, M. Sharma, K. Smallbone, N. Stanford, J. Song, T. Theile, M. Tokic, N. Tomar, V. Touré, J. Uhlendorf, T. Varusai, L. Watanabe, F. Wendland, M. Wolfien, J. Yurkovich, Y. Zhu, A. Zardilis, A. Zhukova, and F. Schreiber, Toward community standards and software for whole-cell modeling, in IEEE Transactions on Biomedical Engineering, 63(10):2007-2014, 2016.
• L. Watanabe and C. J. Myers, Efficient analysis of SBML models of cellular populations using arrays, in ACS Synthetic Biology, 5(8): 835-841, 2016.
• N. Roehner, J. Beal, K. Clancy, B. Bartley, G. Misirli, R. Grunberg, E. Oberortner, M. Pocock, M. Bissell, C. Madsen, T. Nguyen, M. Zhang, Z. Zhang, Z. Zundel, D. Densmore, J. Gennari, A. Wipat, H. Sauro, and C. Myers, Sharing structure and function in biological design with SBOL 2.0, in ACS Synthetic Biology, 5 (6), pp 498–506, 2016.
• T. Nguyen, N. Roehner, Z. Zundel, and C. Myers, A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language, in ACS Synthetic Biology, 5 (6), pp 479–486, 2016.
• Z. Zhang, T. Nguyen, N. Roehner, G. Misirli, M. Pocock, E. Oberortner, M. Samineni, Z. Zundel, J. Beal, K. Clancy, A. Wipat, C. Myers, libSBOLj 2.0: A Java Library to Support SBOL 2.0, in IEEE Life Sciences Letters, 1 (4), pp 34-37, 2015.
• C. Myers, Computational Synthetic Biology: Progress and the Road Ahead, in IEEE Transactions on Multi-scale Computing Systems, 1(1): 19-32, 2015.
• J. Quinn, R. Cox, A. Adler, J. Beal, S. Bhatia, Y. Cai, J. Chen, K. Clancy, M. Galdzicki, N. Hillson, N. Le Novère, A. Maheshwari, J. Alastair, C. Myers, Umesh P, M. Pocock, C. Rodriguez, L. Soldatova, G.-B. Stan, N. Swainston, A. Wipat, and H. Sauro, SBOL Visual: A Graphical Language for Genetic Designs, in PLOS Biology, 13(12): e1002310, 2015.
• N. Rodriguez, A. Thomas, L. Watanabe, I. Vazirabad, V. Kofia, H. Gómez, F. Mittag, J. Rudolph, F. Wrzodek, E. Netz, A. Diamantikos, J. Eichner, R. Keller, C. Wrzodek, S. Fröhlich, N. Lewis, C. Myers, N. Le Novère B. Palsson, M. Hucka, and A. Dräger, JSBML 1.0: providing a smorgasbord of options to encode systems biology models, in Bioinformatics, 31(20):3383-6, 2015.
• F. Schreiber, G. Bader, M. Golebiewski, M. Hucka, B. Kornmeier, N. Le Novère, C. Myers, D. Nickerson, B. Sommer, D. Waltemath and S. Weise, Specifications of Standards in Systems and Synthetic Biology, Journal of Integrative Bioinformatics, 12(2):258, 2015.
• L. Smith, M. Hucka, S. Hoops, A. Finney, M. Ginkel, C. Myers, I. Moraru and W. Liebermeister, SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3, Journal of Integrative Bioinformatics, 12(2):268, 2015.
• M. Hucka, F. Bergmann, A. Dräger, S. Hoops, S. Keating, N. Le Novère, C. Myers, B. Olivier, S. Sahle, J. Schaff, L. Smith, D. Waltemath and D. Wilkinson. Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions, Journal of Integrative Bioinformatics, 12(2):271, 2015.
• B.Bartley, J.Beal, K.Clancy, G.Misirli, N.Roehner, E.Oberortner, M.Pocock, M.Bissell, C. Madsen, T. Nguyen, Z. Zhang, J. Gennari, C. Myers, A. Wipat and H. Sauro. Synthetic Biology Open Language (SBOL) Version 2.0.0, Journal of Integrative Bioinformatics, 12(2):272, 2015.
• N. Roehner, Z. Zhang, T. Nguyen, C. Myers, Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language, in ACS Synthetic Biology, 4(8), 867-943, August 21, 2015.
• M. Hucka, D. Nickerson, G. Bader, F. Bergmann, J. Cooper, E. Demir, A. Garny, M. Golebiewski, C. Myers, F. Schreiber, D. Waltemath, N. Le Novère, Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative, in Frontiers in Bioengineering and Biotechnology, 3(19), 2015.
• N. Roehner, E Oberortner, M. Pocock, J. Beal, K. Clancy, C. Madsen, G. Misirli, A. Wipat, H. Sauro, C. Myers, A Proposed Data Model for the Next Version of the Synthetic Biology Open Language, in ACS Synthetic Biology, 4(1), 57-71, January 16, 2015.
• C. Myers, H. Sauro, and A. Wipat, Introduction to the Special Issue on Computational Synthetic Biology, in ACM Journal on Emerging Technologies in Computing Systems, 11(3), December, 2014.
• C. Madsen, Z. Zhang, N. Roehner, C. Winstead, and C. Myers, Stochastic Model Checking of Genetic Circuits, in ACM Journal on Emerging Technologies in Computing Systems, 11(3), December, 2014.
• L. Watanabe and C. Myers, Hierarchical Stochastic Simulation Algorithm for SBML Models of Genetic Circuits, in Frontiers in Bioengineering and Biotechnology, 2(55), 2014.
• N. Roehner and C. J. Myers, Directed Acyclic Graph-Based Technology Mapping of Genetic Circuit Models, in ACS Synthetic Biology, 3(8), 543-555, August 15, 2014.
• M. Galdzicki, K. Clancy, E. Oberortner, M. Pocock, J. Quinn, C. Rodriguez, N. Roehner, M. Wilson, L. Adam, J. C. Anderson, B. Bartley, J. Beal, D. Chandran, J. Chen, D. Densmore, D. Endy, R. GruÌĹnberg, J. Hallinan, N. Hillson, J. Johnson, A. Kuchinsky, M. Lux, G. Misirli, J. Peccoud, H. Plahar, E. Sirin, G.-B. Stan, A. Villalobos, A. Wipat, J. Gennari, C. Myers, H. Sauro, SBOL: A community standard for communicating designs in synthetic biology, in Nature Biotechnology, 32(6): 545-550, June, 2014.
• D. Waltemath, F. Bergmann, C. Chaouiya, T. Czauderna, P. Gleeson, C. Goble, M. Golebiewski, M. Hucka, N. Juty, O. Krebs, N. Le Novère, H. Mi, I. Moraru, C. Myers, D. Nickerson, B. Olivier, N. Rodriguez, F. Schreiber, L. Smith, F. Zhang, and E. Bonnet, Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE), in Standards in Genomic Sciences, 9(3), 2014.
• N. Roehner and C. J. Myers, A Methodology to Annotate Systems Biology Markup Language Models with the Synthetic Biology Open Language, in ACS Synthetic Biology, 3(2): 57-66, Feb. 21, 2014.
• J. Stevens and C. Myers, Dynamic Modeling of Cellular Populations within iBioSim, in ACS Synthetic Biology, 2(5): 223-229, November 21, 2012.
• C. Madsen, C. Myers, T. Patterson, N. Roehner, J. Stevens, and C.Winstead, Design and test of genetic circuits using iBioSim,” in IEEE Design and Test, 29(3): 32-39, May/June 2012.
• N. Barker, C. Myers, and H. Kuwahara, Learning genetic regulatory network connectivity from time series data , in IEEE Transactions on Computational Biology and Bioinformatics, 8(1):152-165, Jan-Mar, 2011.
• N. Nguyen, C. Myers, H. Kuwahara, C. Winstead, and J. Keener, Design and analysis of a robust genetic Muller C-element, in Journal of Theoretical Biology, 264(2): 174-187, May, 2010.
• H. Kuwahara, C. Myers, and M. Samoilov, Temperature control of fimbriation circuit switch in uropathogenic escherichia coli: quantitative analysis via automated model abstraction, in PLoS Computational Biology, 6(3): e1000723, March 2010.
• C. Myers, N. Barker, K. Jones, H. Kuwahara, C. Madsen, and N. Nguyen, iBioSim: a tool for the analysis and design of genetic circuits, in Bioinformatics, 25(21): 2848-2849, November 1, 2009.
• H. Kuwahara and C. Myers, Production-passage-time approximation: A new approximation method to accelerate the simulation process of enzymatic reactions, in Journal of Computational Biology, 15(7): 779-792, September, 2008.
• H. Kuwahara, C. Myers, M. Samoilov, N. Barker, and A. Arkin, Automated abstraction methodology for genetic regulatory networks, in Transactions on Computational Systems Biology VI, LNBI 4220, 2006 (Invited Paper).

Conference and Workshop Papers:

• C. Myers, G. Bader, P. Gleeson, M. Golebiewski, M. Hucka, N. Le Novere, D. Nickerson, F. Schreiber, and D. Waltemath, A Brief History of COMBINE, in 2017 Winter Simulation Conference, December, 2017.
• L. Watanabe and C. Myers, Hierarchical stochastic simulation of genetic circuits, in 2014 Symposium on Theory of Modeling and Simulation, April, 2014.

• N. Miskov-Zivanov, J. Faeder, C. Myers, and H. Sauro, Modeling and design automation of biological circuits and systems, in 2012 International Conference on Computer-Aided Design, November, 2012 (invited).
• C. Madsen, C. Myers, N. Roehner, C. Winstead, and Z. Zhang, Utilizing stochastic model checking to analyze genetic circuits, in 2012 Computational Intelligence in Bioinformatics and Computational Biology, May, 2012 (best student paper).
• H. Kuwahara and C. Myers, Erlang-delayed stochastic chemical kinetic formalism for efficient analysis of biological systems with non-elementary reaction effects, in 2011 ACM Conference on Bioinformatics, Computational Biology, & Biomedicine, August, 2011.
• C. Winstead, C. Madsen, and C. Myers, iSSA: an incremental stochastic simulation algorithm for genetic circuits, in 2010 International Conference on Circuits and Systems, May, 2010.
• C. Myers, N. Barker, H. Kuwahara, K. Jones, C. Madsen, and N. Nguyen, Genetic design automation, in 2009 International Conference on Computer-Aided Design, November, 2009 (invited).
• N. Nguyen, N. Barker, H. Kuwahra, C. Madsen, and C. Myers, Synthesis of genetic circuits from graphical specifications, in 2008 Int. Workshop on Logic Synthesis, June, 2008 (invited).
• H. Kuwahara and C. Myers, Production-passage-time approximation: a new approximation method to accelerate the simulation process of enzymatic reactions, in The Elventh Annual International Conference on Research in Computational Molecular Biology, April, 2007.
• N. Nguyen, H. Kuwahara, C. Myers, and J. Keener, The design of a genetic Muller C-element, in The Thirteenth International Symposium on Asynchronous Circuits and Systems, March, 2007 (best paper).
• H. Kuwahara, C. Myers, and M. Samoilov, Abstracted stochastic analysis of type 1 pili expression in E. coli, to appear at The 2006 International Conference on Bioinformatics and Computational Biology, June, 2006.
• N. Barker, C. Myers, and H. Kuwahara, Learning genetic regulatory network connectivity from time series data, to appear at The 19th International Conference on Industrial, Engineering, and Other Applications of Applied Intelligent Systems (IEA/AIE’06), June, 2006.
• H. Kuwahara, C. Myers, N. Barker, M. Samoilov, and A. Arkin, Asynchronous abstraction methodology for genetic regulatory networks, in The Third International Workshop on Computational Methods in Systems Biology, April, 2005.