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List of results

• Engineering Logical Inflammation Sensing Circuit for Modulating Gut Conditions  + (2020i)
• Bistable State Switch Enables Ultrasensitive Feedback Control in Heterogeneous Microbial Populations  + (2020i)
• Systems Level Model of Dietary Effects on Cognition via the Microbiome-Gut-Brain Axis  + (2020i)
• Reactive motion planning with probabilistic safety guarantees  + (2020k)
• A MATLAB toolbox for modeling genetic circuits in cell-free systems  + (2021a)
• Rules of the Road: Safety and Liveness Guarantees for Autonomous Vehicles  + (2021c)
• Time-Optimal Navigation in Uncertain Environments with High-Level Specifications  + (2021c)
• Limits of probabilistic safety guarantees when considering human uncertainty  + (2021c)
• Failure-Tolerant Contract-Based Design of an Automated Valet Parking System using a Directive-Response Architecture  + (2021c)
• Robustness Guarantees for Structured Model Reduction of Dynamical Systems  + (2021c)
• The Python Control Systems Library (python-control)  + (2021c)
• Synthesis of Static Test Environments for Observing Sequence-like Behaviors in Autonomous Systems  + (2021e)
• A Method for Cost-Effective and Rapid Characterization of Genetic Parts  + (2021e)
• Constrained risk-averse Markov decision processes  + (2021e)
• Leveraging Classification Metrics for Quantitative System-Level Analysis with Temporal Logic Specifications  + (2021m)
• Data-driven network models for genetic circuits from time-series data with incomplete measurements  + (2021m)
• How to model DNA replication in stochastic models of synthetic genetic circuits (and why)  + (2021n)
• Risk-Averse Decision Making Under Uncertainty  + (2021n)
• Metabolic engineering of Pseudomonas putida for production of vanillylamine from lignin-derived substrates  + (2021x_)
• Robustness guarantees for structured model reduction of dynamical systems with applications to biomolecular models  + (2022a)
• Towards Better Test Coverage: Merging Unit Tests for Autonomous Systems  + (2022b)
• From Specification to Implementation: Assume-Guarantee Contracts for Synthetic Biology  + (2022b)
• Robust Safe Control Synthesis with Disturbance Observer-Based Control Barrier Functions  + (2022b)
• Evaluation Metrics for Object Detection for Autonomous Systems  + (2022c)
• Layered Feedback Control Overcomes Performance Trade-Off in Synthetic Biomolecular Networks  + (2022d)
• Synthesizing Reactive Test Environments for Autonomous Systems: Testing Reach-Avoid Specifications with Multi-Commodity Flows  + (2022d)

• Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape  + (2022k)
• Integrase-mediated differentiation circuits improve evolutionary stability of burdensome and toxic functions in E. coli  + (2022k)

• Minimally Constrained Testing for Autonomy with Temporal Logic Specifications  + (2022m)
• Characterization of Integrase and Excisionase Activity in Cell-free Protein Expression System Using a Modeling and Analysis Pipeline  + (2022n)
• BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts  + (2022o)
• Reasoning over Test Specifications using Assume-Guarantee Contracts  + (2023a)
• Barrier-Based Test Synthesis for Safety-Critical Systems Subject to Timed Reach-Avoid Specifications  + (2023a)
• Context-Aided Variable Elimination for Requirement Engineering  + (2023a)
• Evaluation Metrics of Object Detection for Quantitative System-Level Analysis of Autonomous Systems  + (2023b)
• A Model-Free Algorithm for Extremely Resilient Navigation  + (2023c)
• A 65nm CMOS Living-Cell Dynamic Fluorescence Sensor with 1.05fA Sensitivity at 600/700nm Wavelengths  + (2023c)
• Control education for societal-scale challenges: A community roadmap  + (2023c)
• Metabolic perturbations to an E. coli-based cell-free system reveal a trade-off between transcription and translation  + (2023c)
• Addressable and adaptable intercellular communication via DNA messaging  + (2023d)
• Development of cell-free transcription-translation systems in three soil Pseudomonads  + (2023f)
• Pacti: Scaling Assume-Guarantee Reasoning for System Analysis and Design  + (2023h)
• A chemical reaction network model of PURE  + (2023h)
• Efficient local validation of partially ordered models via Baysian directed sampling  + (2023i)
• Engineering the soil bacterium Pseudomonas synxantha 2-79 into a ratiometric bioreporter for phosphorus limitation  + (2023j)
• TRILL: Orchestrating Modular Deep-Learning Workflows for Democratized, Scalable Protein Analysis and Engineering  + (2023k)
• Optimizing protein expression in the One-Pot PURE system: Insights into reaction composition and translation efficiency  + (2024a)
• A Field-Deployable Arsenic Sensor Integrating Bacillus Megaterium with CMOS Technology  + (2024b)
• Specifying and Analyzing Networked and Layered Control Systems Operating on Multiple Clocks  + (2024c)
• Impact of Chemical Dynamics of Commercial PURE Systems on Malachite Green Aptamer Fluorescence  + (2024d)
• Flow-Based Synthesis of Reactive Tests for Discrete Decision-Making Systems with Temporal Logic Specifications  + (2024e)
• Theory-Based Engineering of Biomolecular Circuits in Living Cells  + (AFOSR BRI)