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List of results

• Quantification and Minimization of Crosstalk Sensitivity in Networks  + (2010m)
• TuLiP: A Software Toolbox for Receding Horizon Temporal Logic Planning  + (2010n)
• Fault-Tolerant Controller Design with Applications in Power Systems and Synthetic Biology  + (2010p)
• A group-theoretic approach to formalizing bootstrapping problems  + (2011a)
• Geometric trajectory filtering via numerical conformal mapping  + (2011b)
• Distributed Power Allocation for Vehicle Management Systems  + (2011c)
• Uncertain semantics, representation nuisances, and necessary invariance properties of bootstrapping agents  + (2011d)
• Analysis and design of a synthetic transcriptional network for exact adaptation  + (2011e)
• A hovercraft robot that uses insect-inspired visual autocorrelation for motion control in a corridor  + (2011g)
• Backtracking temporal logic synthesis for uncertain environments  + (2011h)
• Learning diffeomorphism models of robotic sensorimotor cascades  + (2011i)
• Fault detection and isolation from uninterpreted data in robotic sensorimotor cascades  + (2011j)
• Decentralised minimal-time dynamic consensus  + (2011k)
• Delay-Based Approximations of Biological Systems for Analysis and Design  + (2011l)
• Robust Control of Uncertain Markov Decision Processes with Temporal Logic Specifications  + (2011m)
• Parametric Delay-margin Maximization of Consensus Network Using Local Control Scheme  + (2011n)
• Temporal Logic Control of Switched Affine Systems with an Application in Fuel Balancing  + (2011o)
• Synthesis of Switching Protocols from Temporal Logic Specifications  + (2011p)
• On Synthesizing Robust Discrete Controllers under Modeling Uncertainty  + (2011q)
• Timing molecular motion and production with a synthetic transcriptional clock  + (2011r)
• Extremal Properties of Complex Networks  + (2011s)
• Stabilization of Feedback Systems via Distribution of Delays  + (2012a)
• Towards Formal Synthesis of Reactive Controllers for Dexterous Robotic Manipulation  + (2012b)
• Synthesis of Reactive Control Protocols for Differentially Flat Systems  + (2012c)
• Bisimulations for Reasoning about Input-to-State Stability Properties of Hybrid Systems  + (2012d)
• Performance Metrics for a Biomolecular Step Response  + (2012e)
• Reactive Protocols for Aircraft Electric Power Distribution  + (2012g)
• Quantifying Crosstalk in Biochemical Systems  + (2012h)
• Optimal Control with Weighted Average Costs and Temporal Logic Specifications  + (2012i)
• Synthesis of Reactive Switching Protocols from Temporal Logic Specifications  + (2012j)
• Robot Navigation in Dense Human Crowds: the Case for Cooperation  + (2012k)
• Motion planning in observations space with learned diffeomorphism models  + (2012l)
• Patching task-level robot controllers based on a local μ-calculus formula  + (2012m)
• Efficient reactive controller synthesis for a fragment of linear temporal logic  + (2012n)
• Just-in-time synthesis for motion planning with temporal logic  + (2012o)
• Biomolecular resource utilization in elementary cell-free gene circuits  + (2012p)

• Design and Implementation of a Biomolecular Circuit for Tracking Protein Concentration  + (2012q)

• Convex optimal uncertainty quantification: Algorithms and a case study in energy storage placement for power grids  + (2012r)
• Computing Augmented Finite Transition Systems to Synthesize Switching Protocols for Polynomial Switched Systems  + (2012s)
• Feedback architectures to regulate flux of components in artificial gene networks  + (2012t)
• Pre-orders for Reasoning about Input-to-State Stability Properties of Hybrid Systems  + (2012u)
• An Aircraft Electric Power Testbed for Validating Automatically Synthesized Reactive Control Protocols  + (2012v)
• A Domain-Specific Language for Reactive Control Protocols for Aircraft Electric Power Systems  + (2012w)
• Stability of Discrete Time Systems with Stochastically Delayed Feedback  + (2012x)
• Synergistic dual positive feedback loops established by molecular sequestration generate robust bimodal response  + (2012y)
• Synthesis of Control Protocols for Autonomous Systems  + (2012z)
• Synthesis of Reactive Protocols for Vehicle-to-Vehicle Communication  + (2012z)
• Optimal Control of Non-deterministic Systems for a Computationally Efficient Fragment of Temporal Logic  + (2013b)
• Temperature Dependence of Biomolecular Circuit Designs  + (2013b)
• Dynamic State Estimation in Distributed Aircraft Electric Control Systems via Adaptive Submodularity  + (2013b)
• Reverse Engineering Combination Therapies for Evolutionary Dynamics of Disease: An Hinfty Approach  + (2013b)
• An In Silico Modeling Toolbox for Rapid Prototyping of Circuits in a Biomolecular “Breadboard” System  + (2013b)
• Resource Competition as a Source of Non-Minimum Phase Behavior in Transcription-Translation Systems  + (2013b)
• Modeling Environmental Disturbances with the Chemical Master Equation  + (2013b)
• Automaton-Guided Controller Synthesis for Nonlinear Systems with Temporal Logic  + (2013c)
• Optimal Control of Nonlinear Systems with Temporal Logic Specifications  + (2013d)
• A robust model predictive control algorithm augmented with a reactive safety mode  + (2013e)
• Synthesis and Validation of Control Software For A Vehicular Electric Power Distribution Testbed  + (2013f)
• Optimization-based Control of Nonlinear Systems with Linear Temporal Logic Specifications  + (2013g)
• Moving bounding boxes and incremental synthesis for dynamic obstacles  + (2013g)
• Linear DNA for rapid prototyping of synthetic biological circuits in an Escherichia coli based TX-TL cell-free system  + (2013h)
• Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology  + (2013i)
• Efficient control synthesis for augmented finite transition systems with an application to switching protocols  + (2013j)
• Collaborative System Identification via Parameter Consensus  + (2013j)
• Synthesis of Correct-by-construction Control Protocols for Hybrid Systems Using Partial State Information  + (2013j)
• A Scalable Formulation for Engineering Combination Therapies for Evolutionary Dynamics of Disease  + (2013j)
• A Compositional Approach to Stochastic Optimal Control with Temporal Logic Specifications  + (2013j)
• Time-Delayed Feedback Channel Design: Discrete Time H infty Approach  + (2013j)
• Exact Stability Analysis of Discrete-Time Linear Systems with Stochastic Delays  + (2013j)
• Negative autoregulation matches production and demand in synthetic transcriptional networks  + (2013k)
• System identification of phosophorylation based insulator in a cell-free in vitro transcription-translation system  + (2013l)
• Implementation And Simulation Of Phosphorylation-Based Insulator In Transcription-Translation Platform  + (2013l)
• Analysis of Delays in Transcriptional Signaling Networks with Time-Varying Temperature-Dependent Rate Coefficients  + (2013l)
• Specification and Synthesis of Reactive Protocols for Aircraft Electric Power Distribution  + (2013m)
• Design and implementation of a synthetic biomolecular concentration tracker  + (2013n)
• Resource usage and gene circuit performance characterization in a cell-free ‘breadboard’  + (2013o)
• Convex Optimal Uncertainty Quantification  + (2013p)
• Bootstrapping bilinear models of simple vehicles  + (2013q)
• Pre-orders for Reasoning about Stability Properties with respect to Input of Hybrid Systems  + (2013r)
• Population diversification in a yeast metabolic program promotes anticipation of environmental shifts  + (2014a)
• A Contract-Based Methodology for Aircraft Electric Power System Design  + (2014b)
• Negative Feedback Facilitates Temperature Robustness in Biomolecular Circuit Dynamics  + (2014c)
• Modeling the Effects of Compositional Context on Promoter Activity in an E. Coli Extract based Transcription-Translation System  + (2014d)
• Designing Robustness to Temperature in a Feedforward Loop Circuit  + (2014d)
• Model Predictive Control with Signal Temporal Logic Specifications  + (2014d)
• Privacy Preserving Average Consensus  + (2014d)
• Hot-swapping robot task goals in reactive formal synthesis  + (2014d)
• Synthesizing Combination Therapies for Evolutionary Dynamics of Disease for Nonlinear Pharmacodynamics  + (2014d)
• Strategy-Driven Partitioning into Switching Modes for Piecewise-Affine Systems with Continuous Environments  + (2014d)
• Synthetic circuit for exact adaptation and fold-change detection  + (2014e)
• A Compositional Approach to Stochastic Optimal Control with Co-safe Temporal Logic Specifications  + (2014f)
• Engineering Transcriptional Regulator Effector Specificity Through Rational Design and Rapid Prototyping  + (2014g)
• Protein degradation in a TX-TL cell-free expression system using ClpXP protease  + (2014g)
• Synthetic logic circuits using RNA aptamer against T7 RNA polymerase  + (2014h)
• Variable Elimination for Scalable Receding Horizon Temporal Logic Planning  + (2014i)
• An Iterative Abstraction Algorithm for Reactive Correct-by-Construction Controller Synthesis  + (2014j)
• Online Horizon Selection in Receding Horizon Temporal Logic Planning  + (2014j)
• Reactive Synthesis from Signal Temporal Logic Specifications  + (2014j)
• Cross-entropy Temporal Logic Motion Planning  + (2014j)
• A State-space Realization Approach to Set Identification of Biochemical Kinetic Parameters  + (2014k)
• A Risk-Aware Architecture for Resilient Spacecraft Operations  + (2014l)
• Characterization of minimum inducer separation time for a two-input integrase-based event detector  + (2014m)
• Systematic Design and Implementation of a Novel Synthetic Fold-Change Detector Biocircuit In Vivo  + (2014m)
• Robust Model Predictive Control for Signal Temporal Logic Synthesis  + (2014n)
• Multi-dimensional state estimation in adversarial environment  + (2015a)
• Rapid prototyping of biomolecular circuits through module characterization in cell-free expression systems  + (2015a)
• Prototyping 1,4-butanediol (BDO) biosynthesis pathway in a cell-free transcription-translation (TX-TL) system  + (2015b)
• Design of a Toolbox of RNA Thermometers  + (2015b)
• Engineering Transcriptional Regulator Effector Specificity using Computational Design and In Vitro Rapid Prototyping: Developing a Vanillin Sensor  + (2015b)
• Synthesis from multi-paradigm specifications  + (2015c)
• Global Dynamical Structure Reconstruction from Reconstructed Dynamical Structure Subnetworks: Applications to Biochemical Reaction Networks  + (2015d)
• Quantitative Performance Bounds in Biomolecular Circuits due to Temperature Uncertainty  + (2015d)
• Control System Analysis on Symmetric Cones  + (2015d)
• Synthesis of Distributed Longitudinal Control 1 Protocols for a Platoon of Autonomous Vehicles  + (2015d)
• Engineering Principles of Synthetic Biochemical Oscillators with Negative Cyclic Feedback  + (2015d)
• A stochastic framework for the design of transient and steady state behavior of biochemical reaction networks  + (2015d)
• Characterizing and Prototyping Genetic Networks with Cell-Free Transcription-Translation Reactions  + (2015e)
• Application of Correct-by-Construction Principles for a Resilient Risk-Aware Architecture  + (2015f)
• The effects of time-varying temperature on delays in genetic networks  + (2015g)
• Symbolic construction of GR(1) contracts for systems with full information  + (2015h)
• Linear System Identifiability from Distributional and Time Series Data  + (2015h)
• Rapid cell-free forward engineering of novel genetic ring oscillators  + (2015i)
• Finding stationary solutions to the chemical master equation by gluing state spaces at one or two states recursively  + (2015j)
• Rapid in vitro engineering of 16 two-input logic gates  + (2015j)
• Use of population-level cell-state switching for recording transient inducer pulses  + (2015j)
• Identifying and exploiting tolerance to unexpected jumps in synthesized strategies for GR(1) specifications  + (2015k)
• An analytical approach to bistable biological circuit discrimination using real algebraic geometry  + (2015l)
• Interfacing TuLiP with the JPL Statechart Autocoder: Initial progress toward synthesis of flight software from formal specifications  + (2015m)
• Model Predictive Control for an Uncertain Smart Thermal Grid  + (2015n)
• Model Predictive Control for Signal Temporal Logic Specifications  + (2016a)
• Design Space Exploration of the Violacein Pathway in Escherichia coli Based Cell-Free System  + (2016b)
• Design and application of stationary phase combinatorial promoters  + (2016b)
• The role of single occupancy effects on integrase dynamics in a cell-free system  + (2016b)
• Stochastic Gene Expression in Single Gene Oscillator Variants  + (2016b)
• Synthesis of Control Protocols for Switched Electrical Power Systems for Commercial Applications with Safety Specifications  + (2016c)
• A population-based temporal logic gate for timing and recording chemical events  + (2016d)
• Control design for hybrid systems with TuLiP: The temporal logic planning toolbox  + (2016e)
• Connected Cruise Control Design Using Probabilistic Model Checking  + (2016f)
• 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)
• Engineering pulsatile communication in bacterial consortia  + (2017a)
• Repressing Integrase attachment site operation with CRISPR-Cas9 in E. coli  + (2017a)
• Quantitative Modeling of Integrase Dynamics Using a Novel Python Toolbox for Parameter Inference in Synthetic Biology  + (2017a)
• Population regulation in microbial consortia using dual feedback control  + (2017b)
• Hiding variables when decomposing specifications into GR(1) contracts  + (2017b)
• Decomposing GR(1) Games with Singleton Liveness Guarantees for Efficient Synthesis  + (2017b)
• Learning-Based Abstractions for Nonlinear Constraint Solving  + (2017c)
• Parallelizing Synthesis from Temporal Logic Specifications by Identifying Equicontrollable States  + (2017d)
• Synthesis of Correct-by-Construction Behavior Trees  + (2017e)
• Biophysical Constraints Arising from Compositional Context in Synthetic Gene Networks  + (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)
• Modeling Dynamic Transcriptional Circuits with CRISPRi  + (2017k)
• Length and time scales of cell-cell signaling circuits in agar  + (2017k)
• Control of bacterial population density with population feedback and molecular sequestration  + (2017k)
• Toward Specification-Guided Active Mars Exploration for Cooperative Robot Teams  + (2017l)
• Temporal Logic Control of POMDPs via Label-based Stochastic Simulation Relations  + (2017m)
• Long-distance communication in synthetic bacterial consortia through active signal propagation  + (2018a)
• Single day construction of multi-gene circuits with 3G assembly  + (2018a)
• Role of interaction network topology in controlling microbial population in consortia  + (2018b)
• Voluntary lane-change policy synthesis with reactive control improvisation  + (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)
• Cell-Free Extract Data Variability Reduction in the Presence of Structural Non-Identifiability  + (2018d)
• A modal interface contract theory for guarded input/output automata with an application in traffic system design  + (2018d)
• Risk-aware motion planning for automated vehicle among human-driven cars  + (2018d)
• Robust Estimation Framework with Semantic Measurements  + (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)
• Hard Limits And Performance Tradeoffs In A Class Of Sequestration Feedback Systems  + (2018g)
• Design Guidelines For Sequestration Feedback Networks  + (2018g)
• Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape  + (2019a)
• 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)
• Design of a genetic layered feedback controller in synthetic biological circuitry  + (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)
• Model Reduction Tools For Phenomenological Modeling of Input-Controlled Biological Circuits  + (2019i)
• 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)
• Intermittent Connectivity for Exploration in Communication-Constrained Multi-Agent Systems  + (2019k)
• Invariant Sets for Integrators and Quadrotor Obstacle Avoidance  + (2019l)
• Risk-Averse Planning Under Uncertainty  + (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)