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List of results

• Metabolic perturbations to an E. coli-based cell-free system reveal a trade-off between transcription and translation  + (KM23-SEED)
• Construction of an inducible amyloid expression circuit in Bacillus megaterium: A case study with CsgA and TasA  + (LMM19-biorxiv)
• Engineering the soil bacterium Pseudomonas synxantha 2-79 into a ratiometric bioreporter for phosphorus limitation  + (LMN23-ACSSynBio)
• Engineering Logical Inflammation Sensing Circuit for Modulating Gut Conditions  + (LNM+20-ime)
• Constrained risk-averse Markov decision processes  + (MA+21-aaai)
• Control of bacterial population density with population feedback and molecular sequestration  + (MHGM18-wqbio)
• Development of cell-free transcription-translation systems in three soil Pseudomonads  + (MLM23-ACSSynBio)
• Addressable, “Packet-Based” Intercellular Communication through Plasmid Conjugation  + (MM19-qbio)
• Addressable and adaptable intercellular communication via DNA messaging  + (MM23-NatureComms)
• 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  + (MMEL19-abb)
• TRILL: Orchestrating Modular Deep-Learning Workflows for Democratized, Scalable Protein Analysis and Engineering  + (MMT23-SEED)
• Control of density and composition in an engineered two-member bacterial community  + (MPM19-seed)
• From Specification to Implementation: Assume-Guarantee Contracts for Synthetic Biology  + (PISM22-IWBDA)
• An automated model reduction tool to guide the design and analysis of synthetic biological circuits  + (PM19-iwbda)
• A two-state ribosome and protein model can robustly capture the chemical reaction dynamics of gene expression  + (PM21-wqbio)
• Robustness guarantees for structured model reduction of dynamical systems with applications to biomolecular models  + (PM22-IJRNC)
• Assessment of Robustness to Temperature in a Negative Feedback Loop and a Feedforward Loop  + (PMS20-ACSsynbio)
• Characterization of Integrase and Excisionase Activity in Cell-free Protein Expression System Using a Modeling and Analysis Pipeline  + (PRPM22-biorxiv)
• Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape  + (Pan+23-JOSS)
• Time-Optimal Navigation in Uncertain Environments with High-Level Specifications  + (RAMA21-cdc)
• Bistable State Switch Enables Ultrasensitive Feedback Control in Heterogeneous Microbial Populations  + (RCMF21-acc)
• Control education for societal-scale challenges: A community roadmap  + (Ros+23:ARC)
• A Model-Free Algorithm for Extremely Resilient Navigation  + (SGRM23-ICRA)
• Proof of concept continuous event logging in living cells  + (SM19-seed)
• A MATLAB toolbox for modeling genetic circuits in cell-free systems  + (STSM21-oupsynbio)

• Analysis of Circuits for Dosage Control in Microbial Populations  + (WCM20-biorxiv)
• Tunable integrase-mediated differentiation facilitates improved output of burdensome functions in E. coli  + (WM19-biorxiv)
• Integrase-mediated differentiation circuits improve evolutionary stability of burdensome and toxic functions in E. coli  + (WM22-NatureComms)
• Reactive motion planning with probabilistic safety guarantees  + (YC+20-corl)
• Synthetic mammalian signaling circuits for robust cell population control  + (YM+20-biorxiv)
• Data-driven network models for genetic circuits from time-series data with incomplete measurements  + (Yeu+21-JRSI)
• Optimizing protein expression in the One-Pot PURE system: Insights into reaction composition and translation efficiency  + (Zha+24-SEED)
• Aspects of Geometric Mechanics and Control of Mechanical Systems  + (adl95-phd)
• Rapid prototyping of biomolecular circuits through module characterization in cell-free expression systems  + (af15-ms)
• Feasible Trajectories of Linear Dynamic Systems with Inequality Constraints Using Higher-Order Representations  + (afm99-ifac)
• The role of single occupancy effects on integrase dynamics in a cell-free system  + (ahhm16-seed)
• Risk-Averse Planning Under Uncertainty  + (ahm+20-acc)
• Fast Automatic Verification of Large-Scale Systems with Lookup Tables  + (ari+17-hscc)
• A Bayesian approach to inferring chemical signal timing and amplitude in a temporal logic gate using the cell population distributional response  + (bae+17-qbio)
• Control of Rotating Stall in a Low-Speed Axial Flow Compressor Using Pulsed Air Injection: Modeling, Simulations, and Experimental Validation  + (bdm95-cdc)
• Ellipsoidal Cones and Rendezvous of Multiple Agents  + (bftm04-cdc)
• Cone invariance and rendezvous of multiple agents  + (bftm09-jae)
• Reasoning over Test Specifications using Assume-Guarantee Contracts  + (bgim23-nfm)
• On Measures of Non-Integrability of Pfaffian Systems  + (bhsm96-ifac)
• Nonholonomic Mechanical Systems and Symmetry  + (bkmm94-cds)
• Nonholonomic Mechanical Systems with Symmetry  + (bkmm96-arma)
• Characterizing the Effects of Air Injection on Compressor Performance for Use in Active Control of Rotating Stall  + (blm97-turbo)
• Guidelines for Designing the Antithetic Feedback Motif  + (blom18-cellsys)
• Conversion and Verification Procedure for Goal-Based Control Programs  + (bm07-cds)
• Safety Verification of Fault Tolerant Goal-based Control Programs with Estimation Uncertainty  + (bm08-acc)