Formal Verification Research

Zhen Zhang's Research Group at Utah State University

Funded by the National Science Foundation

Github
About
People
Publications

Nice to meet you!

We're a research lab based at Utah State University in Logan, Utah. We use formal methods to verify engineered systems. We're hard at work exploring a handful of topics:

Probabilistic verification of synthetic biology and biochemical reaction networks

STAMINA, a tool for probabilistic state space exploration
RAGTIMER, a tool for rare event verification
Wayfarer, a tool for rare event probability calculation
Exploration of multi-threaded state space exploration
Contributions to a large collection of Stochastic Model Case Studies

Formal verification of Network-on-Chip (NoC)

Probabilistic verification of NoC reliability in Modest
Verification of livelock and deadlock in asynchronous fault-tolerant NoCs

Deep Neural Network (DNN) verification for classification problems

Verapak, a tool for DNN adversarial example verification

Parameter optimization for biosynthetic pathway models

Exploration of resveratrol and curcumin pathway models with stochastic model checking

Stochastic modeling of age-related macular degenerative retinal angiogenesis

Our publications are listed below, and our projects are open-source at Github. Many of our group members also contribute to the FLUENT Verification group, a multi-university collaboration for stochastic system verification.

Meet the Team

Zhen Zhang | Principal Investigator
My primary research interest is in the modeling and verification of concurrent and stochastic systems, ranging from asynchronous systems and distributed protocols to embedded software and biological systems. I am interested in developing theories and algorithms to advance techniques in the area of formal and semi-formal methods, and their applications in system diagnosis and embedded controller and parameter synthesis.

Student Researchers

Beckey Hu | PhD Student
PMC Applications in Synthetic Biology

Josh Jeppson | PhD Student
Contact for the STAMINA tool

Landon Taylor | PhD Student
Chemical Reaction Networks

Mason Davis | MS Student
Neural Network Verification

Nick Waddoups | MS Student
Architecture Verification

Bennett DenBleyker | Undergrad
Neural Network Verification

Cassandra DuBose | Undergrad
Biological Systems

Lukas Keller | Undergrad
Stochastic Metabolic Model Verification

Easton McBeth | Undergrad
Concurrency Modeling in Dafny

Alumni

Jonah Boe, Probabilistic Network-on-Chip
Bryant Israelsen, Chemical Reaction Networks
Riley Roberts, Developer for STAMINA Tool
Thakur Neupane, Stochastic Model Checking
Joshua Smith, Neural Network Verification

Publications

You can download a BibTeX file that contains references to all of these papers.

2008 2011 2012 2014 2015 2016 2017 2018 2019 2020 2021 2022 2023 2025

2025

2025 Modest Models and Tools for Real Stochastic Timed Systems Principles of Verification: Cycling the Probabilistic Landscape : Essays Dedicated to Joost-Pieter Katoen on the Occasion of His 60th Birthday, Part II Carlos E. Budde, Pedro R. D'Argenio, Juan A. Fraire, Arnd Hartmanns, and Zhen Zhang

BibTeX View Paper

@incollection{Budde2025,
	address = {Cham},
	author = {Budde, Carlos E. and D'Argenio, Pedro R. and Fraire, Juan A. and Hartmanns, Arnd and Zhang, Zhen},
	booktitle = {Principles of {{Verification}}: {{Cycling}} the {{Probabilistic Landscape}} : {{Essays Dedicated}} to {{Joost-Pieter Katoen}} on the {{Occasion}} of {{His}} 60th {{Birthday}}, {{Part II}}},
	doi = {10.1007/978-3-031-75775-4_6},
	editor = {Jansen, Nils and Junges, Sebastian and Kaminski, Benjamin Lucien and Matheja, Christoph and Noll, Thomas and Quatmann, Tim and Stoelinga, Mari{\"e}lle and Volk, Matthias},
	isbn = {978-3-031-75775-4},
	langid = {english},
	pages = {115--142},
	publisher = {Springer Nature Switzerland},
	title = {Modest {{Models}} and {{Tools}} for {{Real Stochastic Timed Systems}}},
	urldate = {2024-11-18},
	year = {2025}
}

2025 Tools at the Frontiers of Quantitative Verification TOOLympics Challenge 2023 Roman Andriushchenko, Alexander Bork, Carlos E. Budde, Milan Češka, Kush Grover, Ernst Moritz Hahn, Arnd Hartmanns, Bryant Israelsen, Nils Jansen, Joshua Jeppson, Sebastian Junges, Maximilian A. Köhl, Bettina Könighofer, Jan Křetínský, Tobias Meggendorfer, David Parker, Stefan Pranger, Tim Quatmann, Enno Ruijters, Landon Taylor, Matthias Volk, Maximilian Weininger, and Zhen Zhang

BibTeX View Paper

@inproceedings{Andriushchenko2025,
	address = {Cham},
	author = {Andriushchenko, Roman and Bork, Alexander and Budde, Carlos E. and {\v C}e{\v s}ka, Milan and Grover, Kush and Hahn, Ernst Moritz and Hartmanns, Arnd and Israelsen, Bryant and Jansen, Nils and Jeppson, Joshua and Junges, Sebastian and K{\"o}hl, Maximilian A. and K{\"o}nighofer, Bettina and K{\v r}et{\'i}nsk{\'y}, Jan and Meggendorfer, Tobias and Parker, David and Pranger, Stefan and Quatmann, Tim and Ruijters, Enno and Taylor, Landon and Volk, Matthias and Weininger, Maximilian and Zhang, Zhen},
	booktitle = {{{TOOLympics Challenge}} 2023},
	doi = {10.1007/978-3-031-67695-6_4},
	editor = {Beyer, Dirk and Hartmanns, Arnd and Kordon, Fabrice},
	isbn = {978-3-031-67695-6},
	langid = {english},
	pages = {90--146},
	publisher = {Springer Nature Switzerland},
	title = {Tools at~the~{{Frontiers}} of~{{Quantitative Verification}}},
	year = {2025}
}

2023

2023 Cycle and Commute: Rare-Event Probability Verification for Chemical Reaction Networks Formal Methods in Computer-Aided Design Landon Taylor, Bryant Israelsen, and Zhen Zhang

BibTeX View Paper

@inproceedings{Taylor2023,
	annotation = {Accepted: 2023-10-10T08:19:44Z},
	author = {Taylor, Landon and Israelsen, Bryant and Zhang, Zhen},
	booktitle = {Formal {{Methods}} in {{Computer-Aided Design}}},
	copyright = {http://creativecommons.org/licenses/by/4.0/},
	doi = {10.34727/2023/isbn.978-3-85448-060-0_37},
	isbn = {978-3-85448-060-0},
	langid = {english},
	month = {October},
	pages = {284--293},
	publisher = {TU Wien Academic Press},
	shorttitle = {Cycle and {{Commute}}},
	title = {Cycle and {{Commute}}: {{Rare-Event Probability Verification}} for {{Chemical Reaction Networks}}},
	urldate = {2023-11-08},
	year = {2023}
}

2023 Efficient Trace Generation for Rare-Event Analysis in Chemical Reaction Networks Model Checking Software Bryant Israelsen, Landon Taylor, and Zhen Zhang

BibTeX View Paper

@inproceedings{Israelsen2023,
	address = {Cham},
	author = {Israelsen, Bryant and Taylor, Landon and Zhang, Zhen},
	booktitle = {Model {{Checking Software}}},
	copyright = {All rights reserved},
	doi = {10.1007/978-3-031-32157-3_5},
	editor = {Caltais, Georgiana and Schilling, Christian},
	isbn = {978-3-031-32156-6 978-3-031-32157-3},
	langid = {english},
	month = {May},
	pages = {83--102},
	publisher = {Springer Nature Switzerland},
	title = {Efficient {{Trace Generation}} for {{Rare-Event Analysis}} in {{Chemical Reaction Networks}}},
	urldate = {2023-11-08},
	volume = {13872},
	year = {2023}
}

2023 STAMINA in C++: Modernizing an Infinite-State Probabilistic Model Checker Quantitative Evaluation of Systems Joshua Jeppson, Matthias Volk, Bryant Israelsen, Riley Roberts, Andrew Williams, Lukas Buecherl, Chris J. Myers, Hao Zheng, Chris Winstead, and Zhen Zhang

BibTeX View Paper

@inproceedings{Jeppson2023,
	address = {Cham},
	author = {Jeppson, Joshua and Volk, Matthias and Israelsen, Bryant and Roberts, Riley and Williams, Andrew and Buecherl, Lukas and Myers, Chris J. and Zheng, Hao and Winstead, Chris and Zhang, Zhen},
	booktitle = {Quantitative {{Evaluation}} of {{Systems}}},
	doi = {10.1007/978-3-031-43835-6_7},
	editor = {Jansen, Nils and Tribastone, Mirco},
	isbn = {978-3-031-43835-6},
	langid = {english},
	month = {September},
	pages = {101--109},
	publisher = {Springer Nature Switzerland},
	series = {Lecture {{Notes}} in {{Computer Science}}},
	shorttitle = {{{STAMINA}} in~{{C}}++},
	title = {{{STAMINA}} in~{{C}}++: {{Modernizing}} an~{{Infinite-State Probabilistic Model Checker}}},
	year = {2023}
}

2022

2022 Scaling Up Livelock Verification for Network-on-Chip Routing Algorithms Verification, Model Checking, and Abstract Interpretation Landon Taylor and Zhen Zhang

BibTeX View Paper

@inproceedings{Taylor2022a,
	address = {Cham},
	author = {Taylor, Landon and Zhang, Zhen},
	booktitle = {Verification, {{Model Checking}}, and {{Abstract Interpretation}}},
	copyright = {All rights reserved},
	doi = {10.1007/978-3-030-94583-1_19},
	editor = {Finkbeiner, Bernd and Wies, Thomas},
	isbn = {978-3-030-94582-4 978-3-030-94583-1},
	langid = {english},
	pages = {378--399},
	publisher = {Springer International Publishing},
	title = {Scaling {{Up Livelock Verification}} for {{Network-on-Chip Routing Algorithms}}},
	urldate = {2023-11-08},
	volume = {13182},
	year = {2022}
}

2022 STAMINA 2.0: Improving Scalability of Infinite-State Stochastic Model Checking Verification, Model Checking, and Abstract Interpretation Riley Roberts, Thakur Neupane, Lukas Buecherl, Chris J. Myers, and Zhen Zhang

BibTeX View Paper

@inproceedings{Roberts2022a,
	address = {Cham},
	author = {Roberts, Riley and Neupane, Thakur and Buecherl, Lukas and Myers, Chris J. and Zhang, Zhen},
	booktitle = {Verification, {{Model Checking}}, and {{Abstract Interpretation}}},
	doi = {10.1007/978-3-030-94583-1_16},
	editor = {Finkbeiner, Bernd and Wies, Thomas},
	isbn = {978-3-030-94583-1},
	langid = {english},
	pages = {319--331},
	publisher = {Springer International Publishing},
	series = {Lecture {{Notes}} in {{Computer Science}}},
	shorttitle = {{{STAMINA}} 2.0},
	title = {{{STAMINA}} 2.0: {{Improving Scalability}} of~{{Infinite-State Stochastic Model Checking}}},
	year = {2022}
}

2021

2021 A Computational Metabolic Model for Engineered Production of Resveratrol in Escherichia Coli ACS Synthetic Biology Michael Cotner, Jixun Zhan, and Zhen Zhang

BibTeX View Paper

@article{Cotner2021,
	author = {Cotner, Michael and Zhan, Jixun and Zhang, Zhen},
	doi = {10.1021/acssynbio.1c00163},
	journal = {ACS Synthetic Biology},
	month = {August},
	number = {8},
	pages = {1992--2001},
	publisher = {American Chemical Society},
	title = {A {{Computational Metabolic Model}} for {{Engineered Production}} of {{Resveratrol}} in {{Escherichia}} Coli},
	urldate = {2023-02-22},
	volume = {10},
	year = {2021}
}

2021 On Correctness, Precision, and Performance in Quantitative Verification: QComp 2020 Competition Report Leveraging Applications of Formal Methods, Verification and Validation: Tools and Trends Carlos E. Budde, Arnd Hartmanns, Michaela Klauck, Jan Křetínský, David Parker, Tim Quatmann, Andrea Turrini, and Zhen Zhang

BibTeX View Paper

@incollection{Budde2021,
	address = {Cham},
	author = {Budde, Carlos E. and Hartmanns, Arnd and Klauck, Michaela and K{\v r}et{\'i}nsk{\'y}, Jan and Parker, David and Quatmann, Tim and Turrini, Andrea and Zhang, Zhen},
	booktitle = {Leveraging {{Applications}} of {{Formal Methods}}, {{Verification}} and {{Validation}}: {{Tools}} and {{Trends}}},
	doi = {10.1007/978-3-030-83723-5_15},
	editor = {Margaria, Tiziana and Steffen, Bernhard},
	isbn = {978-3-030-83722-8 978-3-030-83723-5},
	langid = {english},
	pages = {216--241},
	publisher = {Springer International Publishing},
	shorttitle = {On {{Correctness}}, {{Precision}}, and {{Performance}} in {{Quantitative Verification}}},
	title = {On {{Correctness}}, {{Precision}}, and {{Performance}} in {{Quantitative Verification}}: {{QComp}} 2020 {{Competition Report}}},
	urldate = {2022-06-07},
	volume = {12479},
	year = {2021}
}

2021 Probabilistic Verification for Reliability of a Two-by-Two Network-on-Chip System Formal Methods for Industrial Critical Systems Riley Roberts, Benjamin Lewis, Arnd Hartmanns, Prabal Basu, Sanghamitra Roy, Koushik Chakraborty, and Zhen Zhang

BibTeX View Paper

@inproceedings{Roberts2021,
	address = {Cham},
	author = {Roberts, Riley and Lewis, Benjamin and Hartmanns, Arnd and Basu, Prabal and Roy, Sanghamitra and Chakraborty, Koushik and Zhang, Zhen},
	booktitle = {Formal {{Methods}} for {{Industrial Critical Systems}}},
	doi = {10.1007/978-3-030-85248-1_16},
	editor = {Lluch Lafuente, Alberto and Mavridou, Anastasia},
	isbn = {978-3-030-85248-1},
	langid = {english},
	pages = {232--248},
	publisher = {Springer International Publishing},
	series = {Lecture {{Notes}} in {{Computer Science}}},
	title = {Probabilistic {{Verification}} for {{Reliability}} of a {{Two-by-Two Network-on-Chip System}}},
	year = {2021}
}

2021 Refutation-Based Adversarial Robustness Verification of Deep Neural Networks Formal Methods for ML-Enabled Autonomous Systems (FoMLAS) Joshua Smith, Jarom Allan, Viswanathan Swaminathan, and Zhen Zhang

BibTeX View Paper

@inproceedings{Smith2021,
	author = {Smith, Joshua and Allan, Jarom and Swaminathan, Viswanathan and Zhang, Zhen},
	booktitle = {Formal {{Methods}} for {{ML-Enabled Autonomous Systems}} ({{FoMLAS}})},
	month = {July},
	title = {Refutation-Based Adversarial Robustness Verification of Deep Neural Networks},
	url = {https://fomlas2021.wixsite.com/fomlas2021/home},
	year = {2021}
}

2021 Stochastic Hazard Analysis of Genetic Circuits in iBioSim and STAMINA ACS Synthetic Biology Lukas Buecherl, Riley Roberts, Pedro Fontanarrosa, Payton J. Thomas, Jeanet Mante, Zhen Zhang, and Chris J. Myers

BibTeX View Paper

@article{Buecherl2021,
	author = {Buecherl, Lukas and Roberts, Riley and Fontanarrosa, Pedro and Thomas, Payton J. and Mante, Jeanet and Zhang, Zhen and Myers, Chris J.},
	doi = {10.1021/acssynbio.1c00159},
	journal = {ACS Synthetic Biology},
	month = {October},
	number = {10},
	pages = {2532--2540},
	publisher = {American Chemical Society},
	title = {Stochastic {{Hazard Analysis}} of {{Genetic Circuits}} in {{iBioSim}} and {{STAMINA}}},
	urldate = {2023-11-08},
	volume = {10},
	year = {2021}
}

2020

2020 (Abstract) A Computational Model of the Effect of VEGF Production in Wet Age-Related Macular Degeneration on Neovascularization Investigative Ophthalmology & Visual Science Kelsey Bradshaw, Elizabeth Vargis, and Zhen Zang

BibTeX View Paper

@article{Bradshaw2020,
	author = {Bradshaw, Kelsey and Vargis, Elizabeth and Zang, Zhen},
	issn = {1552-5783},
	journal = {Investigative Ophthalmology \& Visual Science},
	month = {June},
	number = {7},
	pages = {5404},
	title = {({{Abstract}}) {{A}} Computational Model of the Effect of {{VEGF}} Production in Wet Age-Related Macular Degeneration on Neovascularization},
	url = {https://iovs.arvojournals.org/article.aspx?articleid=2769952},
	volume = {61},
	year = {2020}
}

2020 (Abstract) Enhanced Microbial Production of Valuable Natural Products through Computational Metabolic Models International Workshop on Bio-Design Automation (IWBDA) Michael Cotner, Zhen Zhang, and Jixun Zhan

BibTeX View Paper

@inproceedings{Cotner2020,
	author = {Cotner, Michael and Zhang, Zhen and Zhan, Jixun},
	booktitle = {International Workshop on Bio-Design Automation ({{IWBDA}})},
	pages = {82--83},
	title = {({{Abstract}}) {{Enhanced}} Microbial Production of Valuable Natural Products through Computational Metabolic Models},
	url = {https://www.iwbdaconf.org/2020/docs/IWBDA2020Proceedings.pdf},
	year = {2020}
}

2020 (Abstract) Genetic Circuit Hazard Analysis Using STAMINA International Workshop on Bio-Design Automation (IWBDA) Lukas Bücherl, Jeanet Mante, Pedro Fontanarrosa, Zhen Zhang, Brett Jepsen, Riley Roberts, and Chris J. Myers

BibTeX View Paper

@inproceedings{Bucherl2020,
	author = {B{\"u}cherl, Lukas and Mante, Jeanet and Fontanarrosa, Pedro and Zhang, Zhen and Jepsen, Brett and Roberts, Riley and Myers, Chris J.},
	booktitle = {International Workshop on Bio-Design Automation ({{IWBDA}})},
	month = {August},
	pages = {39--40},
	title = {({{Abstract}}) {{Genetic}} Circuit Hazard Analysis Using {{STAMINA}}},
	url = {https://www.iwbdaconf.org/2020/docs/IWBDA2020Proceedings.pdf},
	year = {2020}
}

2020 EFFORT: Enhancing Energy Efficiency and Error Resilience of a Near-Threshold Tensor Processing Unit 2020 25th Asia and South Pacific Design Automation Conference (ASP-DAC) Noel Daniel Gundi, Tahmoures Shabanian, Prabal Basu, Pramesh Pandey, Sanghamitra Roy, Koushik Chakraborty, and Zhen Zhang

BibTeX View Paper

@inproceedings{Gundi2020,
	author = {Gundi, Noel Daniel and Shabanian, Tahmoures and Basu, Prabal and Pandey, Pramesh and Roy, Sanghamitra and Chakraborty, Koushik and Zhang, Zhen},
	booktitle = {2020 25th {{Asia}} and {{South Pacific Design Automation Conference}} ({{ASP-DAC}})},
	doi = {10.1109/ASP-DAC47756.2020.9045479},
	issn = {2153-697X},
	month = {January},
	pages = {241--246},
	shorttitle = {{{EFFORT}}},
	title = {{{EFFORT}}: {{Enhancing Energy Efficiency}} and {{Error Resilience}} of a {{Near-Threshold Tensor Processing Unit}}},
	year = {2020}
}

2019

2019 Approximation Techniques for Stochastic Analysis of Biological Systems Automated Reasoning for Systems Biology and Medicine Thakur Neupane, Zhen Zhang, Curtis Madsen, Hao Zheng, and Chris J. Myers

BibTeX View Paper

@incollection{Neupane2019,
	address = {Cham},
	author = {Neupane, Thakur and Zhang, Zhen and Madsen, Curtis and Zheng, Hao and Myers, Chris J.},
	booktitle = {Automated {{Reasoning}} for {{Systems Biology}} and {{Medicine}}},
	doi = {10.1007/978-3-030-17297-8_12},
	editor = {Li{\`o}, Pietro and Zuliani, Paolo},
	isbn = {978-3-030-17296-1 978-3-030-17297-8},
	langid = {english},
	pages = {327--348},
	publisher = {Springer International Publishing},
	title = {Approximation {{Techniques}} for {{Stochastic Analysis}} of {{Biological Systems}}},
	urldate = {2022-04-05},
	volume = {30},
	year = {2019}
}

2019 iBioSim 3: A Tool for Model-Based Genetic Circuit Design ACS Synthetic Biology Leandro Watanabe, Tramy Nguyen, Michael Zhang, Zach Zundel, Zhen Zhang, Curtis Madsen, Nicholas Roehner, and Chris Myers

BibTeX View Paper

@article{Watanabe2019,
	author = {Watanabe, Leandro and Nguyen, Tramy and Zhang, Michael and Zundel, Zach and Zhang, Zhen and Madsen, Curtis and Roehner, Nicholas and Myers, Chris},
	doi = {10.1021/acssynbio.8b00078},
	journal = {ACS Synthetic Biology},
	month = {July},
	number = {7},
	pages = {1560--1563},
	publisher = {American Chemical Society},
	shorttitle = {{{iBioSim}} 3},
	title = {{{iBioSim}} 3: {{A Tool}} for {{Model-Based Genetic Circuit Design}}},
	urldate = {2023-02-22},
	volume = {8},
	year = {2019}
}

2019 Probabilistic Verification for Reliable Network-on-Chip System Design Formal Methods for Industrial Critical Systems Benjamin Lewis, Arnd Hartmanns, Prabal Basu, Rajesh Jayashankara Shridevi, Koushik Chakraborty, Sanghamitra Roy, and Zhen Zhang

BibTeX View Paper

@inproceedings{Lewis2019,
	address = {Cham},
	author = {Lewis, Benjamin and Hartmanns, Arnd and Basu, Prabal and Jayashankara Shridevi, Rajesh and Chakraborty, Koushik and Roy, Sanghamitra and Zhang, Zhen},
	booktitle = {Formal {{Methods}} for {{Industrial Critical Systems}}},
	doi = {10.1007/978-3-030-27008-7_7},
	editor = {Larsen, Kim Guldstrand and Willemse, Tim},
	isbn = {978-3-030-27007-0 978-3-030-27008-7},
	langid = {english},
	pages = {110--126},
	publisher = {Springer International Publishing},
	title = {Probabilistic {{Verification}} for {{Reliable Network-on-Chip System Design}}},
	urldate = {2022-04-05},
	volume = {11687},
	year = {2019}
}

2019 STAMINA: STochastic Approximate Model-Checker for INfinite-State Analysis Computer Aided Verification Thakur Neupane, Chris J. Myers, Curtis Madsen, Hao Zheng, and Zhen Zhang

BibTeX View Paper

@inproceedings{Neupane2019a,
	address = {Cham},
	author = {Neupane, Thakur and Myers, Chris J. and Madsen, Curtis and Zheng, Hao and Zhang, Zhen},
	booktitle = {Computer {{Aided Verification}}},
	doi = {10.1007/978-3-030-25540-4_31},
	editor = {Dillig, Isil and Tasiran, Serdar},
	isbn = {978-3-030-25539-8 978-3-030-25540-4},
	langid = {english},
	pages = {540--549},
	publisher = {Springer International Publishing},
	shorttitle = {{{STAMINA}}},
	title = {{{STAMINA}}: {{STochastic Approximate Model-Checker}} for {{INfinite-State Analysis}}},
	urldate = {2022-04-05},
	volume = {11561},
	year = {2019}
}

2019 Synthetic Biology Open Language (SBOL) Version 2.3 Journal of Integrative Bioinformatics Curtis Madsen, Angel Goñi Moreno, Umesh P, Zachary Palchick, Nicholas Roehner, Christian Atallah, Bryan Bartley, Kiri Choi, Robert Sidney Cox, Thomas Gorochowski, Raik Grünberg, Chris Macklin, James McLaughlin, Xianwei Meng, Tramy Nguyen, Matthew Pocock, Meher Samineni, James Scott-Brown, Ysis Tarter, Michael Zhang, Zhen Zhang, Zach Zundel, Jacob Beal, Michael Bissell, Kevin Clancy, John H. Gennari, Goksel Misirli, Chris Myers, Ernst Oberortner, Herbert Sauro, and Anil Wipat

BibTeX View Paper

@article{Madsen2019,
	author = {Madsen, Curtis and Moreno, Angel Go{\~n}i and P, Umesh and Palchick, Zachary and Roehner, Nicholas and Atallah, Christian and Bartley, Bryan and Choi, Kiri and Cox, Robert Sidney and Gorochowski, Thomas and Gr{\"u}nberg, Raik and Macklin, Chris and McLaughlin, James and Meng, Xianwei and Nguyen, Tramy and Pocock, Matthew and Samineni, Meher and {Scott-Brown}, James and Tarter, Ysis and Zhang, Michael and Zhang, Zhen and Zundel, Zach and Beal, Jacob and Bissell, Michael and Clancy, Kevin and Gennari, John H. and Misirli, Goksel and Myers, Chris and Oberortner, Ernst and Sauro, Herbert and Wipat, Anil},
	doi = {10.1515/jib-2019-0025},
	issn = {1613-4516},
	journal = {Journal of Integrative Bioinformatics},
	langid = {english},
	month = {June},
	number = {2},
	publisher = {De Gruyter},
	title = {Synthetic {{Biology Open Language}} ({{SBOL}}) {{Version}} 2.3},
	urldate = {2023-03-06},
	volume = {16},
	year = {2019}
}

2018

2018 Synthetic Biology Open Language (SBOL) Version 2.2.0 Journal of Integrative Bioinformatics Robert Sidney Cox, Curtis Madsen, James Alastair McLaughlin, Tramy Nguyen, Nicholas Roehner, Bryan Bartley, Jacob Beal, Michael Bissell, Kiri Choi, Kevin Clancy, Raik Grünberg, Chris Macklin, Goksel Misirli, Ernst Oberortner, Matthew Pocock, Meher Samineni, Michael Zhang, Zhen Zhang, Zach Zundel, John H. Gennari, Chris Myers, Herbert Sauro, and Anil Wipat

BibTeX View Paper

@article{Cox2018,
	author = {Cox, Robert Sidney and Madsen, Curtis and McLaughlin, James Alastair and Nguyen, Tramy and Roehner, Nicholas and Bartley, Bryan and Beal, Jacob and Bissell, Michael and Choi, Kiri and Clancy, Kevin and Gr{\"u}nberg, Raik and Macklin, Chris and Misirli, Goksel and Oberortner, Ernst and Pocock, Matthew and Samineni, Meher and Zhang, Michael and Zhang, Zhen and Zundel, Zach and Gennari, John H. and Myers, Chris and Sauro, Herbert and Wipat, Anil},
	doi = {10.1515/jib-2018-0001},
	issn = {1613-4516},
	journal = {Journal of Integrative Bioinformatics},
	langid = {english},
	month = {March},
	number = {1},
	publisher = {De Gruyter},
	title = {Synthetic {{Biology Open Language}} ({{SBOL}}) {{Version}} 2.2.0},
	urldate = {2023-03-06},
	volume = {15},
	year = {2018}
}

2017

2017 A Validator and Converter for the Synthetic Biology Open Language ACS Synthetic Biology Zach Zundel, Meher Samineni, Zhen Zhang, and Chris J. Myers

BibTeX View Paper

@article{Zundel2017,
	author = {Zundel, Zach and Samineni, Meher and Zhang, Zhen and Myers, Chris J.},
	doi = {10.1021/acssynbio.6b00277},
	journal = {ACS Synthetic Biology},
	month = {July},
	number = {7},
	pages = {1161--1168},
	publisher = {American Chemical Society},
	title = {A {{Validator}} and {{Converter}} for the {{Synthetic Biology Open Language}}},
	urldate = {2023-02-22},
	volume = {6},
	year = {2017}
}

2016

2016 An Improved Fault-Tolerant Routing Algorithm for a Network-on-Chip Derived with Formal Analysis Science of Computer Programming Zhen Zhang, Wendelin Serwe, Jian Wu, Tomohiro Yoneda, Hao Zheng, and Chris Myers

BibTeX View Paper

@article{Zhang2016,
	author = {Zhang, Zhen and Serwe, Wendelin and Wu, Jian and Yoneda, Tomohiro and Zheng, Hao and Myers, Chris},
	doi = {10.1016/j.scico.2016.01.002},
	issn = {0167-6423},
	journal = {Science of Computer Programming},
	langid = {english},
	month = {March},
	pages = {24--39},
	series = {Formal {{Methods}} for {{Industrial Critical Systems}} ({{FMICS}}'2014)},
	title = {An Improved Fault-Tolerant Routing Algorithm for a {{Network-on-Chip}} Derived with Formal Analysis},
	urldate = {2021-03-05},
	volume = {118},
	year = {2016}
}

2016 Sharing Structure and Function in Biological Design with SBOL 2.0 ACS Synthetic Biology Nicholas Roehner, Jacob Beal, Kevin Clancy, Bryan Bartley, Goksel Misirli, Raik Grünberg, Ernst Oberortner, Matthew Pocock, Michael Bissell, Curtis Madsen, Tramy Nguyen, Michael Zhang, Zhen Zhang, Zach Zundel, Douglas Densmore, John H. Gennari, Anil Wipat, Herbert M. Sauro, and Chris J. Myers

BibTeX View Paper

@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, Michael and Zhang, Zhen and Zundel, Zach and Densmore, Douglas and Gennari, John H. and Wipat, Anil and Sauro, Herbert M. and Myers, Chris J.},
	doi = {10.1021/acssynbio.5b00215},
	journal = {ACS Synthetic Biology},
	month = {June},
	number = {6},
	pages = {498--506},
	publisher = {American Chemical Society},
	title = {Sharing {{Structure}} and {{Function}} in {{Biological Design}} with {{SBOL}} 2.0},
	urldate = {2023-03-06},
	volume = {5},
	year = {2016}
}

2015

2015 Compositional Model Checking of Concurrent Systems IEEE Transactions on Computers Hao Zheng, Zhen Zhang, Chris J. Myers, Emmanuel Rodriguez, and Yingying Zhang

BibTeX View Paper

@article{Zheng2015,
	author = {Zheng, Hao and Zhang, Zhen and Myers, Chris J. and Rodriguez, Emmanuel and Zhang, Yingying},
	doi = {10.1109/TC.2014.2329701},
	issn = {1557-9956},
	journal = {IEEE Transactions on Computers},
	month = {June},
	number = {6},
	pages = {1607--1621},
	title = {Compositional {{Model Checking}} of {{Concurrent Systems}}},
	volume = {64},
	year = {2015}
}

2015 Efficient Analysis Methods in Synthetic Biology Computational Methods in Synthetic Biology Curtis Madsen, Chris Myers, Nicholas Roehner, Chris Winstead, and Zhen Zhang

BibTeX View Paper

@incollection{Madsen2015,
	address = {New York, NY},
	author = {Madsen, Curtis and Myers, Chris and Roehner, Nicholas and Winstead, Chris and Zhang, Zhen},
	booktitle = {Computational {{Methods}} in {{Synthetic Biology}}},
	doi = {10.1007/978-1-4939-1878-2_11},
	editor = {Marchisio, Mario Andrea},
	isbn = {978-1-4939-1878-2},
	langid = {english},
	pages = {217--257},
	publisher = {Springer},
	series = {Methods in {{Molecular Biology}}},
	title = {Efficient {{Analysis Methods}} in {{Synthetic Biology}}},
	urldate = {2023-02-22},
	year = {2015}
}

2015 Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language ACS Synthetic Biology Nicholas Roehner, Zhen Zhang, Tramy Nguyen, and Chris J. Myers

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@article{Roehner2015,
	author = {Roehner, Nicholas and Zhang, Zhen and Nguyen, Tramy and Myers, Chris J.},
	doi = {10.1021/sb5003289},
	journal = {ACS Synthetic Biology},
	month = {August},
	number = {8},
	pages = {873--879},
	publisher = {American Chemical Society},
	title = {Generating {{Systems Biology Markup Language Models}} from the {{Synthetic Biology Open Language}}},
	urldate = {2023-02-22},
	volume = {4},
	year = {2015}
}

2015 libSBOLj 2.0: A Java Library to Support SBOL 2.0 IEEE Life Sciences Letters Zhen Zhang, Tramy Nguyen, Nicholas Roehner, Göksel Misirli, Matthew Pocock, Ernst Oberortner, Meher Samineni, Zach Zundel, Jacob Beal, Kevin Clancy, Anil Wipat, and Chris J. Myers

BibTeX View Paper

@article{Zhang2015,
	author = {Zhang, Zhen and Nguyen, Tramy and Roehner, Nicholas and Misirli, G{\"o}ksel and Pocock, Matthew and Oberortner, Ernst and Samineni, Meher and Zundel, Zach and Beal, Jacob and Clancy, Kevin and Wipat, Anil and Myers, Chris J.},
	doi = {10.1109/LLS.2016.2546546},
	issn = {2332-7685},
	journal = {IEEE Life Sciences Letters},
	month = {December},
	number = {4},
	pages = {34--37},
	shorttitle = {{{libSBOLj}} 2.0},
	title = {{{libSBOLj}} 2.0: {{A Java Library}} to {{Support SBOL}} 2.0},
	volume = {1},
	year = {2015}
}

2015 Synthetic Biology Open Language (SBOL) Version 2.0.0 Journal of Integrative Bioinformatics Bryan Bartley, Jacob Beal, Kevin Clancy, Goksel Misirli, Nicholas Roehner, Ernst Oberortner, Matthew Pocock, Michael Bissell, Curtis Madsen, Tramy Nguyen, Zhen Zhang, John H. Gennari, Chris Myers, Anil Wipat, and Herbert Sauro

BibTeX View Paper

@article{Bartley2015,
	author = {Bartley, Bryan and Beal, Jacob and Clancy, Kevin and Misirli, Goksel and Roehner, Nicholas and Oberortner, Ernst and Pocock, Matthew and Bissell, Michael and Madsen, Curtis and Nguyen, Tramy and Zhang, Zhen and Gennari, John H. and Myers, Chris and Wipat, Anil and Sauro, Herbert},
	doi = {10.1515/jib-2015-272},
	issn = {1613-4516},
	journal = {Journal of Integrative Bioinformatics},
	langid = {english},
	month = {June},
	number = {2},
	pages = {902--991},
	publisher = {De Gruyter},
	title = {Synthetic {{Biology Open Language}} ({{SBOL}}) {{Version}} 2.0.0},
	urldate = {2023-03-06},
	volume = {12},
	year = {2015}
}

2014

2014 Formal Analysis of a Fault-Tolerant Routing Algorithm for a Network-on-Chip Formal Methods for Industrial Critical Systems Zhen Zhang, Wendelin Serwe, Jian Wu, Tomohiro Yoneda, Hao Zheng, and Chris Myers

BibTeX View Paper

@inproceedings{Zhang2014,
	address = {Cham},
	author = {Zhang, Zhen and Serwe, Wendelin and Wu, Jian and Yoneda, Tomohiro and Zheng, Hao and Myers, Chris},
	booktitle = {Formal {{Methods}} for {{Industrial Critical Systems}}},
	doi = {10.1007/978-3-319-10702-8_4},
	editor = {Lang, Fr{\'e}d{\'e}ric and Flammini, Francesco},
	isbn = {978-3-319-10702-8},
	langid = {english},
	pages = {48--62},
	publisher = {Springer International Publishing},
	title = {Formal {{Analysis}} of a {{Fault-Tolerant Routing Algorithm}} for a {{Network-on-Chip}}},
	year = {2014}
}

2014 Stochastic Model Checking of Genetic Circuits ACM Journal on Emerging Technologies in Computing Systems Curtis Madsen, Zhen Zhang, Nicholas Roehner, Chris Winstead, and Chris Myers

BibTeX View Paper

@article{Madsen2014,
	author = {Madsen, Curtis and Zhang, Zhen and Roehner, Nicholas and Winstead, Chris and Myers, Chris},
	doi = {10.1145/2644817},
	issn = {1550-4832, 1550-4840},
	journal = {ACM Journal on Emerging Technologies in Computing Systems},
	langid = {english},
	month = {December},
	number = {3},
	pages = {1--21},
	title = {Stochastic {{Model Checking}} of {{Genetic Circuits}}},
	urldate = {2022-04-05},
	volume = {11},
	year = {2014}
}

2012

2012 Utilizing Stochastic Model Checking to Analyze Genetic Circuits 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) Curtis Madsen, Chris J. Myers, Nicholas Roehner, Chris Winstead, and Zhen Zhang

BibTeX View Paper

@inproceedings{Madsen2012,
	author = {Madsen, Curtis and Myers, Chris J. and Roehner, Nicholas and Winstead, Chris and Zhang, Zhen},
	booktitle = {2012 {{IEEE Symposium}} on {{Computational Intelligence}} in {{Bioinformatics}} and {{Computational Biology}} ({{CIBCB}})},
	doi = {10.1109/CIBCB.2012.6217255},
	month = {May},
	pages = {379--386},
	title = {Utilizing Stochastic Model Checking to Analyze Genetic Circuits},
	year = {2012}
}

2011

2011 A Fault-Tolerant Routing Algorithm for a Network-on-Chip Using a Link Fault Model Virtual Worldwide Forum for PhD Researchers in Electronic Design Automation Jian Wu, Zhen Zhang, and Chris Myers

BibTeX View Paper

@inproceedings{Wu2011,
	author = {Wu, Jian and Zhang, Zhen and Myers, Chris},
	booktitle = {Virtual Worldwide Forum for {{PhD}} Researchers in Electronic Design Automation},
	title = {A {{Fault-Tolerant Routing Algorithm}} for a {{Network-on-Chip Using}} a {{Link Fault Model}}},
	url = {https://engineering.usu.edu/ece/faculty-sites/zhen-zhang/files/VW-FEDA2.pdf},
	year = {2011}
}

2008

2008 Performance Analysis of Two Synchronizers 20th UK Asynchronous Forum Z. Zhang and J. Garside

BibTeX View Paper

@inproceedings{Zhang2008,
	author = {Zhang, Z. and Garside, J.},
	booktitle = {20th {{UK}} Asynchronous Forum},
	title = {Performance Analysis of Two Synchronizers},
	url = {http://apt.cs.manchester.ac.uk/ftp/pub/apt/papers/AsyncForum08\_ZZhang.pdf},
	year = {2008}
}

Acknowledgements

This material is based upon work supported by the National Science Foundation under Grant No. 1856740. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

This research is generously supported by Adobe Research.