keywords
- Synthetic biology, genetic design automation, formal verification, stochastic model checking, data standards, asynchronous circuit design
- Contact Info
Myers, Christopher Professor and Palmer Leadership Chair
Positions
- Professor, Electrical, Computer and Energy Engineering (ECEE)
- Professor, Computer Science
- Chair, Electrical, Computer and Energy Engineering (ECEE)
- Endowed Chair, Electrical, Computer and Energy Engineering (ECEE)
Research Areas
Research
Publications
selected publications
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chapter
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Platforms for Genetic Design Automation.
Methods in Microbiology.
177-202.
2013
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Platforms for Genetic Design Automation.
Methods in Microbiology.
177-202.
2013
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conference proceeding
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STAMINA: STochastic Approximate Model-Checker for INfinite-State Analysis.
Lecture Notes in Artificial Intelligence.
540-549.
2019
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Approximation Techniques for Stochastic Analysis of Biological Systems.
Computational Biology.
327-348.
2016
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Efficient Analysis of Systems Biology Markup Language Models of Cellular Populations Using Arrays.
ACS Synthetic Biology.
835-841.
2015
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Reachability Analysis Using Extremal Rates.
Lecture Notes in Artificial Intelligence.
158-172.
2015
- LEMA: A Tool for the Formal Verification of Digitally-Intensive Analog/Mixed-Signal Circuits. The ... Midwest Symposium on Circuits and Systems conference proceedings : MWSCAS. Midwest Symposium on Circuits and Systems. 1017-1020. 2014
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Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language.
ACS Synthetic Biology.
873-879.
2014
- Using Decision Diagrams to Compactly Represent the State Space for Explicit Model Checking. Proceedings - IEEE International High-Level Design Validation and Test Workshop, HLDVT. 17-24. 2012
- Modeling and Design Automation of Biological Circuits and Systems. ICCAD / IEEE/ACM International Conference on Computer-Aided Design. IEEE/ACM International Conference on Computer-Aided Design. 291-293. 2012
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An Improvement in Partial Order Reduction Using Behavioral Analysis.
100-107.
2012
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Poster Abstract: Methods and Tools for Verification of Cyber-Physical Systems.
232-232.
2012
- State Space Reductions for Scalable Verification of Asynchronous Designs. Proceedings - IEEE International High-Level Design Validation and Test Workshop, HLDVT. 17-24. 2010
- iSSA: An Incremental Stochastic Simulation Algorithm for Genetic Circuits. IEEE International Symposium on Circuits and Systems proceedings. IEEE International Symposium on Circuits and Systems. 553-556. 2010
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A New Verification Method For Embedded Systems.
IEEE International Conference on Computer Design - VLSI in Computers and Processors.
193-+.
2009
- A Behavioral Synthesis Method for Asynchronous Circuits with Bundled-data Implementation. Proceedings - International Conference on Application of Concurrency to System Design, ACSD. 50-+. 2008
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Verification of Analog/Mixed-Signal Circuits Using Symbolic Methods.
IEEE Transactions on Computer - Aided Design of Integrated Circuits and Systems.
2223-2235.
2008
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Application of Automated Model Generation Techniques to Analog/Mixed-Signal Circuits.
Proceedings - International Workshop on Microprocessor Test and Verification.
109-+.
2007
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ANALOG/MIXED-SIGNAL CIRCUIT VERIFICATION USING MODELS GENERATED FROM SIMULATION TRACES.
International Journal of Foundations of Computer Science.
191-210.
2007
- Analog/mixed-signal circuit verification using models generated from simulation traces. Lecture Notes in Artificial Intelligence. 114-+. 2007
- Bounded model checking of analog and mixed-signal circuits using an SMT solver. Lecture Notes in Artificial Intelligence. 66-+. 2007
- Hazard Checking of Timed Asynchronous Circuits Revisited. Fundamenta Informaticae. 411-435. 2007
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Hazard checking of timed asynchronous circuits revisited.
Proceedings - International Conference on Application of Concurrency to System Design, ACSD.
51-+.
2007
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Production-passage-time approximation: A new approximation method to accelerate the simulation process of enzymatic reactions.
Journal of Computational Biology.
779-792.
2007
- Production-passage-time approximation: A new approximation method to accelerate the simulation process of enzymatic reactions. Lecture Notes in Artificial Intelligence. 166-+. 2007
- The design of a genetic muller C-element. Proceedings - International Symposium on Asynchronous Circuits and Systems. 95-+. 2007
- Symbolic model checking of Analog/Mixed-Signal circuits. 316-+. 2007
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A conservative framework for safety-failure checking.
IEICE Transactions on Information and Systems.
642-654.
2006
- Effective contraction of timed STGs for decomposition based timed circuit synthesis. Lecture Notes in Artificial Intelligence. 229-244. 2006
- Learning genetic regulatory network connectivity from time series data. Lecture Notes in Artificial Intelligence. 962-971. 2006
- Automated abstraction methodology for genetic regulatory networks. Lecture Notes in Artificial Intelligence. 150-+. 2005
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High level synthesis of timed asynchronous circuits.
Proceedings - International Symposium on Asynchronous Circuits and Systems.
178-189.
2005
- Partial order reduction for detecting safety and timing failures of timed circuits. Lecture Notes in Artificial Intelligence. 339-353. 2004
- Verification of analog and mixed-signal circuits using timed hybrid Petri nets. Lecture Notes in Artificial Intelligence. 426-440. 2004
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Synthesis of speed independent circuits based on decomposition.
Proceedings - International Symposium on Asynchronous Circuits and Systems.
135-145.
2004
- Efficient verification of hazard-freedom in gate-level timed asynchronous circuits. 424-431. 2003
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Verification of timed circuits with failure directed abstractions.
IEEE International Conference on Computer Design - VLSI in Computers and Processors.
28-35.
2003
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Level oriented formal model for asynchronous circuit verification and its efficient analysis method.
210-218.
2002
- Partial order reduction for timed circuit verification based on level oriented model. IEICE Transactions on Information and Systems. 2601-2611. 2002
- Synchronous interlocked pipelines. Proceedings - International Symposium on Asynchronous Circuits and Systems. 3-12. 2002
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Framework of timed trace theoretic verification revisited.
437-442.
2001
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Analog decoding of product codes.
131-133.
2001
- Automatic abstraction for verification of timed circuits and systems. Lecture Notes in Artificial Intelligence. 182-193. 2001
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A standard-cell self-timed multiplier for energy and area critical synchronous systems.
188-201.
2001
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Efficient exact two-level hazard-free logic minimization.
Proceedings - International Symposium on Asynchronous Circuits and Systems.
64-73.
2001
- Timed circuits: A new paradigm for high-speed design. 335-340. 2001
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Achieving fast and exact hazard-free logic minimization of extended burst-mode gC finite state machines.
303-310.
2000
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RAPPID: An asynchronous instruction length decoder.
Proceedings - International Symposium on Asynchronous Circuits and Systems.
60-70.
1999
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Verification of delayed-reset domino circuits using ATACS.
Proceedings - International Symposium on Asynchronous Circuits and Systems.
3-12.
1999
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Timed circuit synthesis using implicit methods.
181-188.
1999
- Verification of timed systems using POSETs. Lecture Notes in Artificial Intelligence. 403-415. 1998
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Interfacing synchronous and asynchronous modules within a high-speed pipeline.
47-61.
1997
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Efficient timing analysis algorithms for timed state space exploration.
88-100.
1997
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Technology mapping of timed circuits.
138-147.
1995
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STAMINA: STochastic Approximate Model-Checker for INfinite-State Analysis.
Lecture Notes in Artificial Intelligence.
540-549.
2019
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journal article
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Genetic Circuit Dynamics: Hazard and Glitch Analysis.
ACS Synthetic Biology.
2324-2338.
2020
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The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering.
Frontiers in Bioengineering and Biotechnology.
2020
- SBML Level 3: an extensible format for the exchange and reuse of biological models. Molecular Systems Biology. 2020
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The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE)..
Journal of Integrative Bioinformatics.
2020
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Specifications of standards in systems and synthetic biology: status and developments in 2020.
Journal of Integrative Bioinformatics.
2020
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Synthetic biology open language (SBOL) version 3.0.0.
Journal of Integrative Bioinformatics.
2020
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Synthetic biology open language visual (SBOL visual) version 2.2.
Journal of Integrative Bioinformatics.
2020
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Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1.
Journal of Integrative Bioinformatics.
2020
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Extending SynBioHub's Functionality with Plugins.
ACS Synthetic Biology.
1216-1220.
2020
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The long journey towards standards for engineering biosystems Are the Molecular Biology and the Biotech communities ready to standardise?.
EMBO Reports.
2020
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SBOL Visual 2 Ontology.
ACS Synthetic Biology.
972-977.
2020
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SBOLExplorer: Data Infrastructure and Data Mining for Genetic Design Repositories.
ACS Synthetic Biology.
2287-2294.
2019
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Toward reproducible disease models using the Systems Biology Markup Language.
Simulation: transactions of the Society for Modeling and Simulation International.
895-930.
2019
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Communicating Structure and Function in Synthetic Biology Diagrams.
ACS Synthetic Biology.
1818-1825.
2019
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A Computational Workflow for the Automated Generation of Models of Genetic Designs.
ACS Synthetic Biology.
1548-1559.
2019
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Design of Asynchronous Genetic Circuits.
Proceedings of the Institute of Electrical and Electronics Engineers (IEEE).
1356-1368.
2019
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SBOL-OWL: An Ontological Approach for Formal and Semantic Representation of Synthetic Biology Information.
ACS Synthetic Biology.
1498-1514.
2019
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Specifying Combinatorial Designs with the Synthetic Biology Open Language (SBOL).
ACS Synthetic Biology.
1519-1523.
2019
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iBioSim 3: A Tool for Model-Based Genetic Circuit Design.
ACS Synthetic Biology.
1560-1563.
2019
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pySBOL: A Python Package for Genetic Design Automation and Standardization.
ACS Synthetic Biology.
1515-1518.
2019
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Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019.
Journal of Integrative Bioinformatics.
2019
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Synthetic Biology Open Language (SBOL) Version 2.3.
Journal of Integrative Bioinformatics.
2019
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Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1.
Journal of Integrative Bioinformatics.
2019
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The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2.
Journal of Integrative Bioinformatics.
2019
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Harmonizing semantic annotations for computational models in biology..
Briefings in Bioinformatics.
540-550.
2019
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sboljs: Bringing the Synthetic Biology Open Language to the Web Browser.
ACS Synthetic Biology.
191-193.
2019
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Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE) (vol 9, 1285, 2014).
Standards in Genomic Sciences.
2018
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Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017.
Journal of Integrative Bioinformatics.
2018
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Synthetic Biology Open Language (SBOL) Version 2.2.0.
Journal of Integrative Bioinformatics.
2018
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Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0.
Journal of Integrative Bioinformatics.
2018
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The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core.
Journal of Integrative Bioinformatics.
2018
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The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core.
Journal of Integrative Bioinformatics.
2018
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SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology.
ACS Synthetic Biology.
682-688.
2018
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A Validator and Converter for the Synthetic Biology Open Language.
ACS Synthetic Biology.
1161-1168.
2017
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SBOLDesigner 2: An Intuitive Tool for Structural Genetic Design.
ACS Synthetic Biology.
1150-1160.
2017
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A standard-enabled workflow for synthetic biology.
Biochemical Society Transactions.
793-803.
2017
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SBOLme: a Repository of SBOL Parts for Metabolic Engineering.
ACS Synthetic Biology.
732-736.
2017
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Design of Mixed-Signal Systems With Asynchronous Control.
IEEE Design and Test.
44-55.
2016
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Guest Editors' Introduction: Challenges and Opportunities in Analog/Mixed-Signal CAD.
IEEE Design and Test.
5-6.
2016
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A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language.
ACS Synthetic Biology.
479-486.
2016
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Sharing Structure and Function in Biological Design with SBOL 2.0.
ACS Synthetic Biology.
498-506.
2016
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An improved fault-tolerant routing algorithm for a Network-on-Chip derived with formal analysis.
Science of Computer Programming.
24-39.
2016
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Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016.
Journal of Integrative Bioinformatics.
2016
-
Synthetic Biology Open Language (SBOL) Version 2.1.0.
Journal of Integrative Bioinformatics.
2016
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SBOL Visual: A Graphical Language for Genetic Designs.
PLoS Biology.
2015
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JSBML 1.0: providing a smorgasbord of options to encode systems biology models.
Bioinformatics.
3380-3383.
2015
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Compositional Model Checking of Concurrent Systems.
IEEE Transactions on Computers.
1607-1621.
2015
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Computational Synthetic Biology: Progress and the Road Ahead.
IEEE Transactions on Multi-Scale Computing Systems.
19-32.
2015
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Efficient analysis methods in synthetic biology..
Methods in Molecular Biology.
217-257.
2015
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Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative.
Frontiers in Bioengineering and Biotechnology.
2015
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Proposed Data Model for the Next Version of the Synthetic Biology Open Language.
ACS Synthetic Biology.
57-71.
2015
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SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3.
Journal of Integrative Bioinformatics.
2015
-
Specifications of Standards in Systems and Synthetic Biology.
Journal of Integrative Bioinformatics.
2015
-
Synthetic Biology Open Language (SBOL) Version 2.0.0.
Journal of Integrative Bioinformatics.
2015
-
Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions.
Journal of Integrative Bioinformatics.
2015
-
The synthetic biology open language..
Methods in Molecular Biology.
323-336.
2015
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Introduction to the Special Issue on Computational Synthetic Biology.
ACM Journal on Emerging Technologies in Computing Systems.
2014
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Stochastic Model Checking of Genetic Circuits.
ACM Journal on Emerging Technologies in Computing Systems.
2014
-
Directed Acyclic Graph-Based Technology Mapping of Genetic Circuit Models.
ACS Synthetic Biology.
543-555.
2014
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The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.
Nature Biotechnology.
545-550.
2014
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A Methodology to Annotate Systems Biology Markup Language Models with the Synthetic Biology Open Language.
ACS Synthetic Biology.
57-66.
2014
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Hierarchical Stochastic Simulation Algorithm for SBML Models of Genetic Circuits..
Frontiers in Bioengineering and Biotechnology.
55.
2014
-
Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE).
Standards in Genomic Sciences.
2014
-
Dynamic Modeling of Cellular Populations within iBioSim.
ACS Synthetic Biology.
223-229.
2013
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IWBDA 2012 Special Issue.
ACS Synthetic Biology.
203-203.
2013
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Design and Test of Genetic Circuits Using iBioSim.
IEEE Design and Test of Computers.
32-39.
2012
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Verification of Analog/Mixed-Signal Circuits Using Labeled Hybrid Petri Nets.
IEEE Transactions on Computer - Aided Design of Integrated Circuits and Systems.
617-630.
2011
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Learning Genetic Regulatory Network Connectivity from Time Series Data.
IEEE/ACM Transactions on Computational Biology and Bioinformatics.
152-165.
2011
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Design and analysis of a robust genetic Muller C-element.
Journal of Theoretical Biology.
174-187.
2010
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Temperature Control of Fimbriation Circuit Switch in Uropathogenic Escherichia coli: Quantitative Analysis via Automated Model Abstraction.
PLoS Computational Biology.
2010
-
iBioSim: a tool for the analysis and design of genetic circuits.
Bioinformatics.
2848-2849.
2009
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Scheduling methods for asynchronous circuits with bundled-data implementations based on the approximation of start times.
IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences.
2790-2799.
2007
-
Synthesis of timed circuits based on decomposition.
IEEE Transactions on Computer - Aided Design of Integrated Circuits and Systems.
1177-1195.
2007
-
Efficient verification of hazard-freedom in gate-level timed asynchronous circuits.
IEEE Transactions on Computer - Aided Design of Integrated Circuits and Systems.
592-605.
2007
-
Verification of timed circuits with failure-directed abstractions.
IEEE Transactions on Computer - Aided Design of Integrated Circuits and Systems.
403-412.
2006
-
Failure trace analysis of timed circuits for automatic timing constraints derivation.
IEICE Transactions on Information and Systems.
2555-2564.
2005
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Homeobox D10 induces phenotypic reversion of breast tumor cells in a three-dimensional culture model..
Cancer Research.
7177-7185.
2005
-
Partial order reduction for detecting safety and timing failures of timed circuits.
IEICE Transactions on Information and Systems.
1646-1661.
2005
-
HOXA3 induces cell migration in endothelial and epithelial cells promoting angiogenesis and wound repair..
Journal of Cell Science.
2567-2577.
2005
-
CMOS analog MAP decoder for (8,4) Hamming code.
IEEE Journal of Solid State Circuits.
122-131.
2004
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Relationship between Candida albicans virulence during experimental hematogenously disseminated infection and endothelial cell damage in vitro..
Infection and Immunity.
598-601.
2004
-
Modular verification of timed circuits using automatic abstraction.
IEEE Transactions on Computer - Aided Design of Integrated Circuits and Systems.
1138-1153.
2003
-
Breast cancer-induced angiogenesis: multiple mechanisms and the role of the microenvironment..
Breast Cancer Research.
140-146.
2003
- Modular synthesis of timed circuits using partial order reduction. IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences. 2684-2692. 2002
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Efficient algorithms for exact two-level hazard-free logic minimization.
IEEE Transactions on Computer - Aided Design of Integrated Circuits and Systems.
1269-1283.
2002
- Framework of timed trace theoretic verification revisited. IEICE Transactions on Information and Systems. 1595-1604. 2002
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Direct synthesis of timed circuits from free-choice STGs.
IEEE Transactions on Computer - Aided Design of Integrated Circuits and Systems.
275-290.
2002
-
An asynchronous instruction length decoder.
IEEE Journal of Solid State Circuits.
217-228.
2001
-
Timed circuit verification using TEL structures.
IEEE Transactions on Computer - Aided Design of Integrated Circuits and Systems.
129-146.
2001
-
Interfacing synchronous and asynchronous modules within a high-speed pipeline.
IEEE Transactions on Very Large Scale Integration Systems.
573-583.
2000
-
Timed state space exploration using POSET's.
IEEE Transactions on Computer - Aided Design of Integrated Circuits and Systems.
501-520.
2000
-
POSET timing and its application to the synthesis and verification of gate-level timed circuits.
IEEE Transactions on Computer - Aided Design of Integrated Circuits and Systems.
769-786.
1999
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Covering conditions and algorithms for the synthesis of speed-independent circuits.
IEEE Transactions on Computer - Aided Design of Integrated Circuits and Systems.
205-219.
1998
-
Genetic Circuit Dynamics: Hazard and Glitch Analysis.
ACS Synthetic Biology.
2324-2338.
2020
Background
education and training
- Ph.D., Stanford University 1995
- M.S., Stanford University 1993
- B.S., California Institute of Technology 1991
International Activities
global connections related to teaching and scholarly work (in recent years)
- United Kingdom Country