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List of results

• Enhancing tolerance to unexpected jumps in GR(1) games  + (2016g)
• Fast Automatic Verification of Large-Scale Systems with Lookup Tables  + (2016h)
• The Effect of Compositional Context on Synthetic Gene Networks  + (2016i)
• Quantifying Resource Competition and its Effects in the TX-TL System  + (2016k)
• A Bayesian approach to inferring chemical signal timing and amplitude in a temporal logic gate using the cell population distributional response  + (2016l)
• Engineering Transcriptional Regulator Effector Specificity Using Computational Design and In Vitro Rapid Prototyping: Developing a Vanillin Sensor  + (2016x)
• Quantitative Modeling of Integrase Dynamics Using a Novel Python Toolbox for Parameter Inference in Synthetic Biology  + (2017a)
• Repressing Integrase attachment site operation with CRISPR-Cas9 in E. coli  + (2017a)
• Engineering pulsatile communication in bacterial consortia  + (2017a)
• Decomposing GR(1) Games with Singleton Liveness Guarantees for Efficient Synthesis  + (2017b)
• Hiding variables when decomposing specifications into GR(1) contracts  + (2017b)
• Population regulation in microbial consortia using dual feedback control  + (2017b)
• Learning-Based Abstractions for Nonlinear Constraint Solving  + (2017c)
• Parallelizing Synthesis from Temporal Logic Specifications by Identifying Equicontrollable States  + (2017d)
• Biophysical Constraints Arising from Compositional Context in Synthetic Gene Networks  + (2017e)
• Synthesis of Correct-by-Construction Behavior Trees  + (2017e)
• Recursively constructing analytic expressions for equilibrium distributions of stochastic biochemical reaction networks  + (2017f)
• Cell-free and in vivo characterization of Lux, Las, and Rpa quorum activation systems in E. coli  + (2017g)
• Layering assume-guarantee contracts for hierarchical system design  + (2017h)
• System-level studies of a cell-free transcription-translation platform for metabolic engineering  + (2017i)
• Control Theory for Synthetic Biology: Recent Advances in System Characterization, Control Design, and Controller Implementation for Synthetic Biology  + (2017j)
• Control of bacterial population density with population feedback and molecular sequestration  + (2017k)
• Length and time scales of cell-cell signaling circuits in agar  + (2017k)
• Modeling Dynamic Transcriptional Circuits with CRISPRi  + (2017k)
• Toward Specification-Guided Active Mars Exploration for Cooperative Robot Teams  + (2017l)
• Temporal Logic Control of POMDPs via Label-based Stochastic Simulation Relations  + (2017m)
• Single day construction of multi-gene circuits with 3G assembly  + (2018a)
• Long-distance communication in synthetic bacterial consortia through active signal propagation  + (2018a)
• Voluntary lane-change policy synthesis with reactive control improvisation  + (2018b)
• Role of interaction network topology in controlling microbial population in consortia  + (2018b)
• Optimal Experiment Design and Leveraging Competition for Shared Resources in Cell-free Extracts  + (2018b)
• On-chip membrane protein cell-free expression enables development of a direct binding assay: A curious case of potassium channel KcsA-Kv1.3  + (2018c)
• Robust Estimation Framework with Semantic Measurements  + (2018d)
• Risk-aware motion planning for automated vehicle among human-driven cars  + (2018d)
• A modal interface contract theory for guarded input/output automata with an application in traffic system design  + (2018d)
• Cell-Free Extract Data Variability Reduction in the Presence of Structural Non-Identifiability  + (2018d)

• End-to-End Safe Reinforcement Learning through Barrier Functions for Safety-Critical Continuous Control Tasks  + (2018e)
• Inverse Abstraction of Neural Networks Using Symbolic Interpolation  + (2018e)

• Model of Paradoxical Signaling Regulated T-Cell Population Control for Design of Synthetic Circuits  + (2018f)
• Cooperation Enhances Robustness of Coexistence in Spatially Structured Consortia  + (2018f)
• Design Guidelines For Sequestration Feedback Networks  + (2018g)
• Hard Limits And Performance Tradeoffs In A Class Of Sequestration Feedback Systems  + (2018g)
• Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape  + (2019a)
• Design of a genetic layered feedback controller in synthetic biological circuitry  + (2019b)
• Proof of concept continuous event logging in living cells  + (2019b)
• Tunable integrase-mediated differentiation facilitates improved output of burdensome functions in E. coli  + (2019b)
• Control of density and composition in an engineered two-member bacterial community  + (2019b)
• Addressable, “Packet-Based” Intercellular Communication through Plasmid Conjugation  + (2019c)
• Quantitative characterization of random partitioning in the evolution of plasmid-encoded traits  + (2019c)
• Bacterial Controller Aided Wound Healing: A Case Study in Dynamical Population Controller Design  + (2019c)
• Towards Assume-Guarantee Profiles for Autonomous Vehicles  + (2019d)
• A Method for Cost-Effective and Rapid Characterization of Engineered T7-based Transcription Factors by Cell-Free Protein Synthesis Reveals Insights into the Regulation of T7 RNA Polymerase-Driven Expression  + (2019e)
• An automated model reduction tool to guide the design and analysis of synthetic biological circuits  + (2019f)
• Contracts of Reactivity  + (2019g)
• Analysis of primitive genetic interactions for the design of a genetic signal differentiator  + (2019g)
• Counter-example Guided Learning of Bounds on Environment Behavior  + (2019h)
• Theoretical Design of Paradoxical Signaling-Based Synthetic Population Control Circuit in E. coli  + (2019i)
• A geometric and structural approach to the analysis and design of biological circuit dynamics: a theory tailored for synthetic biology  + (2019i)
• Layered Feedback Control Improves Robust Functionality across Heterogeneous Cell Populations  + (2019i)
• Model Reduction Tools For Phenomenological Modeling of Input-Controlled Biological Circuits  + (2019i)
• Intermittent Connectivity for Exploration in Communication-Constrained Multi-Agent Systems  + (2019k)
• Risk-Averse Planning Under Uncertainty  + (2019l)
• Invariant Sets for Integrators and Quadrotor Obstacle Avoidance  + (2019l)
• Formal Test Synthesis for Safety-Critical Autonomous Systems based on Control Barrier Functions  + (2020a)
• Theory-Based Engineering of Biomolecular Circuits in Living Cells  + (AFOSR BRI)
• Formal Methods for V&V and T&E of Autonomous Systems  + (AFOSR T&E)
• Field-Programmable, Recombinase-Based Biomolecular Circuits  + (AICB MRSB)
• Engineering Durable Cell-Free Biological Capabilities for Advanced Sensing and Prototyping  + (ARL cellfree)
• Enabling Technologies for Cell-Silicon Interfacing  + (ARL19 hybrid)
• Fundamental Biological Factors Underlying Human Performance: From Molecular Diagnostics and Detection to Behavior and Systems Biology  + (ARL19 zebrafish)
• Dissecting microbiome-gut-brain circuits for microbial modulation of host cognition in response to diet and stress  + (ARO GMB)
• Biomolecular Circuits for Rapid Detection and Response to Environmental Events  + (ARO ICB)
• Cell-Free Expression of Membrane Proteins with Applications to Drug Discovery  + (Amgen TX-TL)
• Correct-by-Construction Synthesis of Control Protocols for Aerospace Systems  + (Boeing)
• Improvement of E. coli transcription-translation (TX-TL) system  + (Caltech Grubstake)
• Assurance for Learning Enabled Systems  + (DARPA ALES)
• Robust Multi-Layer Control Systems for Cooperative Cellular Behaviors  + (DARPA BioCon)
• Temporal Logic Specifications for Control System Design in Automotive Systems  + (DENSO CPM)
• Programmable Molecular Technology Initiative  + (GBMF PMTI)
• Establishing microfluidic cell-free systems for the rapid prototyping of synthetic genetic networks  + (HFSP TX-TL)
• Design of Digitally Controlled Bacterial Circuits for Bioenabled Materials  + (ICB Materials)
• Genetic Circuits for Multi-Cellular Machines  + (ICB Microbial)
• Synthesizing flight software (FSW) discrete controllers from formal specifications  + (JPL CIF17)
• Safety-Critical Autonomy and Verification for Space Missions  + (JPL PDF17)
• Resilient Risk-Aware Autonomy for the Exploration of Uncertain and Extreme Environments  + (KISS RSS)
• A Brain Circuit Program for Understanding the Sensorimotor Basis of Behavior  + (NIH U19)
• Developing Standardized Cell-Free Platforms for Rapid Prototyping of Synthetic Biology Circuits and Pathways  + (NSF Cell-Free)
• Actuation of Synthetic Cells Via Proto-Flagellar Motors  + (NSF EAGER)
• Molecular Programming Project  + (NSF MPP)
• Molecular Programming Architectures, Abstractions, Algorithms, and Applications  + (NSF MPP2)
• VeHICaL: Verified Human Interfaces, Control, and Learning for Semi-Autonomous Systems  + (NSF VehiCaL)
• Model-guided Discovery and Optimization of Cell-based Sensors  + (ONR MURI)
• An Open Synthetic Biology Toolkit for Engineering Reliable Genetic Circuits in Microbes in Soil  + (RSI Soil Syn Bio)
• Engineering Replication-, Growth-, and Division-Deficient E. coli for Safe, Stable and Efficient Function  + (Rosen Simple Cell)
• The TerraSwarm Research Center  + (SRC TerraSwarm)
• Rapid, Reliable and Repeatable Platforms for Cell-Free Prototyping  + (Synvitrobio SBIR)