Murray, Richard

Monograph from CaltechAUTHORS

• Marken, John P. and Maxon, Mary E., et el. (2024) Policy Recommendations for the Regulation of Engineered Microbes for Environmental Release; 10.57959/bgny-v542
• Martinez, Zachary A and Murray, Richard M., et el. (2023) TRILL: Orchestrating Modular Deep-Learning Workflows for Democratized, Scalable Protein Analysis and Engineering; bioRxiv; 2023.10.24.563881; PMCID PMC10659302; 10.1101/2023.10.24.563881
• Kapasiawala, Manisha and Murray, Richard M. (2023) Probing metabolism in an E. coli-based cell-free system reveals a trade-off between transcription and translation; 10.1101/2023.03.22.533877
• Pandey, Ayush and Rodriguez, Makena L., et el. (2023) Characterization of Integrase and Excisionase Activity in Cell-free Protein Expression System Using a Modeling and Analysis Pipeline; 10.1101/2022.10.05.511053
• Marken, John P. and Murray, Richard M. (2023) Addressable and adaptable intercellular communication via DNA messaging; 10.1101/2022.11.17.516988
• Akella, Prithvi and Ahmadi, Mohamadreza, et el. (2023) Barrier-Based Test Synthesis for Safety-Critical Systems Subject to Timed Reach-Avoid Specifications
• Badithela, Apurva and Graebener, Josefine B., et el. (2022) Synthesizing Reactive Test Environments for Autonomous Systems: Testing Reach-Avoid Specifications with Multi-Commodity Flows; 10.48550/arXiv.2210.10304
• Badithela, Apurva and Wongpiromsarn, Tichakorn, et el. (2022) Evaluation Metrics for Object Detection for Autonomous Systems; 10.48550/arXiv.2210.10298
• Han, SooJean and Effros, Michelle, et el. (2022) OUTformation: Distributed Data-Gathering with Feedback under Unknown Environment and Communication Delay Constraints; 10.48550/arXiv.2208.06395
• Pandey, Ayush and Incer, Inigo, et el. (2022) From Specification to Implementation: Assume-Guarantee Contracts for Synthetic Biology; 10.1101/2022.04.08.487709
• Badithela, Apurva and Murray, Richard M. (2022) Synthesis of Static Test Environments for Observing Sequence-like Behaviors in Autonomous Systems; 10.48550/arXiv.2108.05911
• Daş, Ersin and Murray, Richard M. (2022) Robust Safe Control Synthesis with Disturbance Observer-Based Control Barrier Functions; 10.48550/arXiv.2201.05758
• Ahmadi, Mohamadreza and Rosolia, Ugo, et el. (2022) Risk-Averse Decision Making Under Uncertainty; 10.48550/arXiv.2109.04082
• Clamons, Samuel E. and Murray, Richard M. (2021) How to model DNA replication in stochastic models of synthetic gene circuits (and why); 10.1101/2021.09.26.461880
• Hu, Chelsea Y. and Murray, Richard M. (2021) Layered Feedback Control Overcomes Performance Trade-off in Synthetic Biomolecular Networks; 10.1101/2021.09.12.459953
• Graebener, Josefine B. and Phan-Minh, Tung, et el. (2021) Failure-Tolerant Contract-Based Design of an Automated Valet Parking System using a Directive-Response Architecture; 10.48550/arXiv.2103.12919
• McManus, John B. and Bernhards, Casey B., et el. (2021) A Method for Cost-Effective and Rapid Characterization of Genetic Parts; 10.1101/2021.04.30.440836
• Cai, Karena X. and Phan-Minh, Tung, et el. (2021) Rules of the Road: Towards Safety and Liveness Guarantees for Autonomous Vehicles; 10.48550/arXiv.2011.14148
• Chen, Yuxiao and Rosolia, Ugo, et el. (2021) Reactive motion planning with probabilistic safety guarantees; 10.48550/arXiv.2011.03590
• Walton, Sophie J. and Clamons, Samuel E., et el. (2020) Analysis of Circuits for Dosage Control in Microbial Populations; 10.1101/2020.12.18.423556
• Pandey, Ayush and Murray, Richard M. (2020) A two-state ribosome and protein model can robustly capture the chemical reaction dynamics of gene expression; 10.1101/2020.11.25.399287
• Merk, Liana N. and Shur, Andrey S., et el. (2020) Engineering Logical Inflammation Sensing Circuit for Modulating Gut Conditions; 10.1101/2020.11.10.377085
• Chen, Yuxiao and Dathathri, Sumanth, et el. (2020) Counter-example Guided Learning of Bounds on Environment Behavior; 10.48550/arXiv.2001.07233
• Ren, Xinying and Murray, Richard M. (2020) Layered Feedback Control Improves Robust Functionality across Heterogeneous Cell Populations; 10.1101/2020.03.24.006528
• Marken, John P. and Xiao, Fangzhou, et el. (2020) A geometric and structural approach to the analysis and design of biological circuit dynamics: a theory tailored for synthetic biology; 10.1101/2020.02.18.953620
• Pandey, Ayush and Murray, Richard M. (2020) Model Reduction Tools For Phenomenological Modeling of Input-Controlled Biological Circuits; 10.1101/2020.02.15.950840
• Guo, Shaobin and Hori, Yutaka, et el. (2020) Systematic Design and Implementation of a Novel Synthetic Fold-Change Detector Biocircuit In Vivo
• Farahani, Samira S. and Raman, Vasumathi, et el. (2020) Robust Model Predictive Control for Signal Temporal Logic Synthesis
• Hsiao, Victoria and Cheng, Aileen, et el. (2020) Design and application of stationary phase combinatorial promoters
• Yeung, Enoch and Kim, Jongmin, et el. (2020) Global Dynamical Structure Reconstruction from Reconstructed Dynamical Structure Subnetworks: Applications to Biochemical Reaction Networks
• Han, Duo and Mo, Yilin, et el. (2020) Synthesis of Distributed Longitudinal Control Protocols for a Platoon of Autonomous Vehicles
• Meng, Xianglin and Baetica, Ania A., et el. (2020) Finding stationary solutions to the chemical master equation by gluing state spaces at one or two states recursively
• Swaminathan, Anandh and Gomez, Marcella M., et el. (2020) Stochastic Gene Expression in Single Gene Oscillator Variants
• Dathathri, Sumanth and Livingston, Scott C., et el. (2020) Identifying and exploiting tolerance to unexpected jumps in synthesized strategies for GR(1) specifications
• Sen, Shaunak and Murray, Richard M. (2020) Quantitative Performance Bounds in Biomolecular Circuits due to Temperature Uncertainty
• Arichega, Nikos and Dathathri, Sumanth, et el. (2020) Fast Automatic Verification of Large-Scale Systems with Lookup Tables
• McCardell, Reed D. and Pandey, Ayush, et el. (2020) Control of density and composition in an engineered two-member bacterial community; 10.1101/632174
• Singhal, Vipul and Murray, Richard M. (2020) Cell-Free Extract Data Variability Reduction in the Presence of Structural Non-Identifiability
• Filippidis, Ioannis and Murray, Richard M. (2020) Hiding variables when decomposing specifications into GR(1) contracts
• Mayalu, Michaëlle N. and Murray, Richard M. (2020) Theoretical Design of Paradoxical Signaling-Based Synthetic Population Control Circuit in E. coli; 10.1101/2020.01.27.921734
• Larsson, Elin M. and McManus, John B., et el. (2019) Construction of an inducible amyloid expression circuit in Bacillus megaterium: A case study with CsgA and TasA; 10.1101/858266
• Ge, Jin I. and Murray, Richard M. (2019) Voluntary lane-change policy synthesis with reactive control improvisation
• Clamons, Samuel and Murray, Richard (2019) Modeling predicts that CRISPR-based activators, unlike CRISPR-based repressors, scale well with increasing gRNA competition and dCas9 bottlenecking; 10.1101/719278
• Green, Leopold N. and Hu, Chelsea Y., et el. (2019) Bacterial Controller Aided Wound Healing: A Case Study in Dynamical Population Controller Design; 10.1101/659714
• Hu, Chelsea Y. and Murray, Richard M. (2019) Design of a genetic layered feedback controller in synthetic biological circuitry; 10.1101/647057
• Pandey, Ayush and Murray, Richard M. (2019) An automated model reduction tool to guide the design and analysis of synthetic biological circuits; 10.1101/640276
• Williams, Rory L. and Murray, Richard M. (2019) Integrase-mediated differentiation circuits improve evolutionary stability of burdensome and toxic functions in E. coli; 10.1101/614529
• Barmpoutis, Dionysios and Murray, Richard M. (2019) Extremal Properties of Complex Networks; 10.48550/arXiv.1104.5532
• Barmpoutis, Dionysios and Murray, Richard M. (2019) Quantification and Minimization of Crosstalk Sensitivity in Networks; 10.48550/arXiv.1012.0606
• Wiltsche, Clemens and Topcu, Ufuk, et el. (2019) Synthesis of Reactive Protocols for Vehicle-to-Vehicle Communication; 10.48550/arXiv.1210.2035
• Raman, Vasumathi and Donzé, Alexandre, et el. (2019) Model Predictive Control for Signal Temporal Logic Specification; 10.48550/arXiv.1703.09563
• Halleran, Andrew D. and Flores-Bautista, Emanuel, et el. (2019) Quantitative characterization of random partitioning in the evolution of plasmid-encoded traits; 10.1101/594879
• Marken, John P. and Murray, Richard M. (2019) Addressable, "Packet-Based" Intercellular Communication through Plasmid Conjugation; 10.1101/591552
• Swaminathan, Anandh and Poole, William, et el. (2019) Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape; 10.1101/121152
• Murray, Richard M. and Day, John C., et el. (2019) Engineering Resilient Space Systems; 10.26206/WDX7-K192
• Dathathri, Sumanth and Zheng, Stephan, et el. (2019) Detecting Adversarial Examples via Neural Fingerprinting; 10.48550/arXiv.1803.03870
• Baetica, Ania-Ariadna and Leong, Yoke Peng, et el. (2018) Design Guidelines For Sequestration Feedback Networks; 10.1101/455493
• Shur, Andrey and Murray, Richard M. (2018) Proof of concept continuous event logging in living cells; 10.1101/225151
• Doong, Joy and Parkin, James, et el. (2018) Length and time scales of cell-cell signaling circuits in agar; 10.1101/220244
• Clamons, Samuel and Murray, Richard M. (2018) Modeling Dynamic Transcriptional Circuits with CRISPRi; 10.1101/225318
• Nguyen, Phuc H. B. and Wu, Yong Y., et el. (2018) Design Space Exploration of the Violacein Pathway in Escherichia coli Based Transcription Translation Cell-Free System (TX-TL); 10.1101/027656
• McCardell, Reed D. and Huang, Shan, et el. (2018) Control of bacterial population density with population feedback and molecular sequestration; 10.1101/225045
• Parkin, James M. and Murray, Richard M. (2018) Long-distance communication in synthetic bacterial consortia through active signal propagation; 10.1101/321307
• Catanach, Thomas A. and McCardell, Reed, et el. (2018) Context Dependence of Biological Circuits; 10.1101/360040
• Olsman, Noah and Baetica, Ania-Ariadna, et el. (2018) Hard Limits And Performance Tradeoffs In A Class Of Sequestration Feedback Systems; 10.1101/222042
• Wu, Yong Y. and Sato, Hirokazu, et el. (2018) System-level studies of a cell-free transcription-translation platform for metabolic engineering; 10.1101/172007
• Swaminathan, Anandh and Hsiao, Victoria, et el. (2017) Quantitative Modeling of Integrase Dynamics Using a Novel Python Toolbox for Parameter Inference in Synthetic Biology; 10.1101/121152
• Guo, Shaobin and Murray, Richard M. (2017) Prototyping And Implementation Of A Novel Feedforward Loop In A Cell-Free Transcription-Translation System And Cells; 10.1101/123190
• Guo, Shaobin and Yeung, Enoch, et el. (2017) Implementation and System Identification of a Phosphorylation-Based Insulator in a Cell-Free Transcription-Translation System; 10.1101/122606
• Shur, Andrey and Murray, Richard M. (2017) Repressing Integrase attachment site operation with CRISPR-Cas9 in E. coli; 10.1101/110254
• Parkin, James M. and Hsiao, Victoria, et el. (2017) Engineering pulsatile communication in bacterial consortia; 10.1101/111906
• Guo, Shaobin and Vaish, Amit, et el. (2017) Expressing Biologically Active Membrane Proteins in a Cell-Free Transcription-Translation Platform; 10.1101/104455
• Yeung, Enoch and Dy, Aaron J., et el. (2017) The Effect of Compositional Context on Synthetic Gene Networks; 10.1101/083329
• Baetica, Ania A. and Catanach, Thomas A., et el. (2017) A Bayesian approach to inferring chemical signal timing and amplitude in a temporal logic gate using the cell population distributional response; 10.1101/087379
• Filippidis, Ioannis and Murray, Richard M. (2016) Formalizing synthesis in TLA+
• Artavanis, Georgios and Hsiao, Victoria, et el. (2016) The role of single occupancy effects on integrase dynamics in a cell-free system; 10.1101/059675
• Filippidis, Ioannis and Murray, Richard M. (2016) Symbolic construction of GR(1) contracts for systems with full information; 10.1109/ACC.2016.7525009
• Sen, Shaunak and Murray, Richard M. (2016) Negative Feedback Facilitates Temperature Robustness in Biomolecular Circuit Dynamics; 10.1101/007385
• Chiao, Abel C. and Murray, Richard M., et el. (2016) Development of prokaryotic cell-free systems for synthetic biology; 10.1101/048710
• Dathathri, Sumanth and Livingston, Scott C., et el. (2016) Interfacing TuLiP with the JPL Statechart Autocoder: Initial progress toward synthesis of flight software from formal specifications
• Sun, Zachary Z. and Kim, Jongmin, et el. (2015) Protein degradation in a TX-TL cell-free expression system using ClpXP protease; 10.1101/019695
• Filippidis, Ioannis and Murray, Richard M. (2015) Revisiting the AMBA AHB bus case study
• Wu, Yong Y. and Culler, Stephanie, et el. (2015) Prototyping 1,4-butanediol (BDO) biosynthesis pathway in a cell-free transcription-translation (TX-TL) system; 10.1101/017814
• Filippidis, Ioannis and Murray, Richard M., et el. (2015) Synthesis from multi-paradigm specifications
• Livingston, Scott C. and Wolff, Eric M., et el. (2015) Cross-entropy Temporal Logic Motion Planning; 10.1145/2728606.2728635
• Raman, Vasumathi and Fält, Mattias, et el. (2015) Online Horizon Selection in Receding Horizon Temporal Logic Planning
• Gupta, Vijay and Chung, Timothy H., et el. (2015) Scheduling for Distributed Sensor Networks
• Livingston, Scott C. and Murray, Richard M. (2014) Hot-swapping robot task goals in reactive formal synthesis
• Cohen, Judith G. and Dekany, Richard, et el. (2014) California Extremely Large Telescope: Conceptual Design for a Thirty-Meter Telescope
• Wolff, Eric M. and Murray, Richard M. (2013) Optimal Control of Mixed Logical Dynamical Systems with Long-Term Temporal Logic Specifications
• Rogersten, Robert and Xu, Huan, et el. (2013) An Aircraft Electric Power Testbed for Validating Automatically Synthesized Reactive Control Protocols
• Censi, Andrea and Nilsson, Adam, et el. (2012) Motion planning in observations space with learned diffeomorphism models
• Livingston, Scott C. and Prabhakar, Pavithra, et el. (2012) Patching task-level robot controllers based on a local µ-calculus formula
• Wolff, Eric M. and Topcu, Ufuk, et el. (2011) Robust Control of Uncertain Markov Decision Processes with Temporal Logic Specifications
• Liu, Jun and Ozay, Necmiye, et el. (2011) Synthesis of Switching Protocols from Temporal Logic Specifications
• Censi, Andrea and Murray, Richard M. (2011) Bootstrapping, uncertain semantics, and invariance
• Censi, Andrea and Murray, Richard M. (2011) A group-theoretic approach to formalizing bootstrapping problems
• Censi, Andrea and Murray, Richard M. (2010) Bootstrapping bilinear models of robotic sensorimotor cascades
• Lavaei, Javad and Sojoudi, Somayeh, et el. (2010) Delay-Based Controller Design for Continuous-Time and Hybrid Applications
• Han, Shuo and Censi, Andrea, et el. (2010) A bio-plausible design for visual pose stabilization
• Tonetti, Stefania and Murray, Richard M. (2009) Limits on the Network Sensitivity Function for Multi-Agent Systems on a Graph
• Wongpiromsarn, Tichakorn and Mitra, Sayan, et el. (2008) Periodically Controlled Hybrid Systems: Verifying A Controller for An Autonomous Vehicle
• Braman, J. M. B. and Murray, R. M. (2007) Conversion and verification procedure for goal-based control programs
• Gupta, Vijay and Chung, Timothy H., et el. (2004) On a stochastic sensor selection algorithm with applications in sensor scheduling and sensor coverage
• Gupta, Vijay and Spanos, Demetri, et el. (2004) Optimal LQG Control Across a Packet-Dropping Link
• Gupta, Vijay and Hassibi, Babak, et el. (2004) A Sub-optimal Algorithm to Synthesize Control Laws for a Network of Dynamic Agents
• Dunbar, William B. and Murray, Richard M. (2004) Distributed Receding Horizon Control with Application to Multi-Vehicle Formation Stabilization
• Fax, J. Alexander and Murray, Richard M. (2003) Information Flow and Cooperative Control of Vehicle Formations
• Olfati-Saber, Reza and Murray, Richard M. (2003) Agreement Problems in Networks with Directed Graphs and Switching Topology
• Martin, Phillipe and Murray, Richard M., et el. (2003) Flat systems, equivalence and trajectory generation
• van Nieuwstadt, Michiel and Rathinam, Muruhan, et el. (2002) Differential Flatness and Absolute Equivalence
• Fax, J. Alexander and Murray, Richard M. (2001) Graph Laplacians and Stabilization of Vehicle Formations
• Murray, Richard M. (1999) Geometric Approaches to Control in the Presence of Magnitude and Rate Saturations
• Yeung, S. and Wang, Y., et el. (1998) Evaluation of Bleed Valve Rate Requirements in Nonlinear Control of Rotating Stall on Axial Flow Compressors
• Muruhan, Rathinam and Murray, Richard M. (1998) Discrete Function Approximation: Numerical Tools for Nonlinear Control
• Morin, Pascal and Murray, Richard M., et el. (1997) Nonlinear Rescaling of Control Laws with Application to Stabilization in the Presence of Magnitude Saturation
• Murray, Richard M. and Jacobsen, C.A., et el. (1997) System Identification for Limit Cycling Systems: A Case Study for Combustion Instabilities
• van Nieuwstadt, Michiel J. and Murray, Richard M. (1997) Real Time Trajectory Generation for Differentially Flat Systems
• Bullo, Francesco and Murray, Richard M. (1997) Tracking for Fully Actuated Mechanical Systems: A Geometric Framework
• Rathinam, Muruhan and Murray, Richard M. (1996) Configuration Flatness of Lagrangian Systems Underactuated by One Control
• D'Andrea, Raffaello and Behnken, Robert L., et el. (1996) Active Control of an Axial Flow Compressor via Pulsed Air Injection
• Lewis, Andrew D. and Murray, Richard M. (1996) Decomposition for Control Systems on Manifolds with an Affine Connection
• Rathinam, Muruhan and Murray, Richard M. (1996) Configuration Flatness of Lagrangian Systems Underactuated by One Control
• Sur, Sudipto and Murray, Richard M. (1996) An Experimental Comparison of Tradeoffs in Using Compliant Manipulators for Robotic Grasping Tasks
• Bullo, Francesco and Murray, Richard M., et el. (1995) Control on the Sphere and Reduced Attitude Stabilization
• M'Closkey, Robert T. and Murray, Richard M. (1995) Exponential Stabilization of Driftless Nonlinear Control Systems using Homogeneous Feedback
• Bloch, A. M. and Krishnaprasad, P. S., et el. (1995) Nonholonomic Mechanical Systems with Symmetry
• Bullo, Francesco and Murray, Richard M. (1995) Proportional Derivative (PD) Control on the Euclidean Group
• Tierno, Jorge E. and Murray, Richard M., et el. (1995) Numerically Efficient Robustness Analysis of Trajectory Tracking for Nonlinear Systems
• Sluis, Willem M. and Banaszuk, Andrzej, et el. (1995) A Homotopy Algorithm for Approximating Geometric Distributions by Integrable Systems
• Lewis, Andrew D. and Murray, Richard M. (1995) Configuration Controllability of Simple Mechanical Control Systems
• Kelly, Scott D. and Murray, Richard M. (1994) Geometric Phases and Robotic Locomotion
• Lewis, Andrew D. and Murray, Richard M. (1994) Variational Principles for Constrained Systems: Theory and Experiment
• Murray, Richard M. (1992) Nilpotent Bases for a Class of Non-Integrable Distributions with Applications to Trajectory Generation for Nonholonomic Systems