Murray, Richard

Monograph from CaltechAUTHORS

Larsson, Elin M. and Wang, Olivia Y., el al. (2025) A DNA part library for reliable engineering of the emerging model nematode symbiotic bacterium Xenorhabdus griffiniae HGB2511; 10.1101/2025.06.09.658710
Marken, John P. and Maxon, Mary E., el al. (2024) Policy Recommendations for the Regulation of Engineered Microbes for Environmental Release; 10.57959/bgny-v542
Martinez, Zachary A and Murray, Richard M., el al. (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
Marken, John P. and Murray, Richard M. (2022) Addressable and adaptable intercellular communication via DNA messaging; 10.1101/2022.11.17.516988
Badithela, Apurva and Graebener, Josefine B., el al. (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, el al. (2022) Evaluation Metrics for Object Detection for Autonomous Systems; 10.48550/arXiv.2210.10298
Pandey, Ayush and Rodriguez, Makena L., el al. (2022) Characterization of Integrase and Excisionase Activity in Cell-free Protein Expression System Using a Modeling and Analysis Pipeline; 10.1101/2022.10.05.511053
Han, SooJean and Effros, Michelle, el al. (2022) OUTformation: Distributed Data-Gathering with Feedback under Unknown Environment and Communication Delay Constraints; 10.48550/arXiv.2208.06395
Pandey, Ayush and Incer, Inigo, el al. (2022) From Specification to Implementation: Assume-Guarantee Contracts for Synthetic Biology; 10.1101/2022.04.08.487709
Daş, Ersin and Murray, Richard M. (2022) Robust Safe Control Synthesis with Disturbance Observer-Based Control Barrier Functions; 10.48550/arXiv.2201.05758
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
Ahmadi, Mohamadreza and Rosolia, Ugo, el al. (2021) Risk-Averse Decision Making Under Uncertainty; 10.48550/arXiv.2109.04082
Badithela, Apurva and Murray, Richard M. (2021) Synthesis of Static Test Environments for Observing Sequence-like Behaviors in Autonomous Systems; 10.48550/arXiv.2108.05911
McManus, John B. and Bernhards, Casey B., el al. (2021) A Method for Cost-Effective and Rapid Characterization of Genetic Parts; 10.1101/2021.04.30.440836
Graebener, Josefine B. and Phan-Minh, Tung, el al. (2021) Failure-Tolerant Contract-Based Design of an Automated Valet Parking System using a Directive-Response Architecture; 10.48550/arXiv.2103.12919
Walton, Sophie J. and Clamons, Samuel E., el al. (2020) Analysis of Circuits for Dosage Control in Microbial Populations; 10.1101/2020.12.18.423556
Cai, Karena X. and Phan-Minh, Tung, el al. (2020) Rules of the Road: Towards Safety and Liveness Guarantees for Autonomous Vehicles; 10.48550/arXiv.2011.14148
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., el al. (2020) Engineering Logical Inflammation Sensing Circuit for Modulating Gut Conditions; 10.1101/2020.11.10.377085
Chen, Yuxiao and Rosolia, Ugo, el al. (2020) Reactive motion planning with probabilistic safety guarantees; 10.48550/arXiv.2011.03590
Ren, Xinying and Murray, Richard M. (2020) Layered Feedback Control Improves Robust Functionality across Heterogeneous Cell Populations; 10.1101/2020.03.24.006528
Pandey, Ayush and Murray, Richard M. (2020) Model Reduction Tools For Phenomenological Modeling of Input-Controlled Biological Circuits; 10.1101/2020.02.15.950840
Marken, John P. and Xiao, Fangzhou, el al. (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
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
Chen, Yuxiao and Dathathri, Sumanth, el al. (2020) Counter-example Guided Learning of Bounds on Environment Behavior; 10.48550/arXiv.2001.07233
Larsson, Elin M. and McManus, John B., el al. (2019) Construction of an inducible amyloid expression circuit in Bacillus megaterium: A case study with CsgA and TasA; 10.1101/858266
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
Singhal, Vipul and Murray, Richard M. (2019) Cell-Free Extract Data Variability Reduction in the Presence of Structural Non-Identifiability
Green, Leopold N. and Hu, Chelsea Y., el al. (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
McCardell, Reed D. and Pandey, Ayush, el al. (2019) Control of density and composition in an engineered two-member bacterial community; 10.1101/632174
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
Halleran, Andrew D. and Flores-Bautista, Emanuel, el al. (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
Ge, Jin I. and Murray, Richard M. (2018) Voluntary lane-change policy synthesis with reactive control improvisation
Baetica, Ania-Ariadna and Leong, Yoke Peng, el al. (2018) Design Guidelines For Sequestration Feedback Networks; 10.1101/455493
Catanach, Thomas A. and McCardell, Reed, el al. (2018) Context Dependence of Biological Circuits; 10.1101/360040
Parkin, James M. and Murray, Richard M. (2018) Long-distance communication in synthetic bacterial consortia through active signal propagation; 10.1101/321307
Dathathri, Sumanth and Zheng, Stephan, el al. (2018) Detecting Adversarial Examples via Neural Fingerprinting; 10.48550/arXiv.1803.03870
Filippidis, Ioannis and Murray, Richard M. (2017) Hiding variables when decomposing specifications into GR(1) contracts
Clamons, Samuel and Murray, Richard M. (2017) Modeling Dynamic Transcriptional Circuits with CRISPRi; 10.1101/225318
McCardell, Reed D. and Huang, Shan, el al. (2017) Control of bacterial population density with population feedback and molecular sequestration; 10.1101/225045
Shur, Andrey and Murray, Richard M. (2017) Proof of concept continuous event logging in living cells; 10.1101/225151
Olsman, Noah and Baetica, Ania-Ariadna, el al. (2017) Hard Limits And Performance Tradeoffs In A Class Of Sequestration Feedback Systems; 10.1101/222042
Doong, Joy and Parkin, James, el al. (2017) Length and time scales of cell-cell signaling circuits in agar; 10.1101/220244
Wu, Yong Y. and Sato, Hirokazu, el al. (2017) System-level studies of a cell-free transcription-translation platform for metabolic engineering; 10.1101/172007
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, el al. (2017) Implementation and System Identification of a Phosphorylation-Based Insulator in a Cell-Free Transcription-Translation System; 10.1101/122606
Arichega, Nikos and Dathathri, Sumanth, el al. (2017) Fast Automatic Verification of Large-Scale Systems with Lookup Tables
Raman, Vasumathi and Donzé, Alexandre, el al. (2017) Model Predictive Control for Signal Temporal Logic Specification; 10.48550/arXiv.1703.09563
Swaminathan, Anandh and Hsiao, Victoria, el al. (2017) Quantitative Modeling of Integrase Dynamics Using a Novel Python Toolbox for Parameter Inference in Synthetic Biology; 10.1101/121152
Swaminathan, Anandh and Poole, William, el al. (2017) Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape; 10.1101/121152
Parkin, James M. and Hsiao, Victoria, el al. (2017) Engineering pulsatile communication in bacterial consortia; 10.1101/111906
Shur, Andrey and Murray, Richard M. (2017) Repressing Integrase attachment site operation with CRISPR-Cas9 in E. coli; 10.1101/110254
Guo, Shaobin and Vaish, Amit, el al. (2017) Expressing Biologically Active Membrane Proteins in a Cell-Free Transcription-Translation Platform; 10.1101/104455
Filippidis, Ioannis and Murray, Richard M. (2016) Formalizing synthesis in TLA+
Dathathri, Sumanth and Livingston, Scott C., el al. (2016) Identifying and exploiting tolerance to unexpected jumps in synthesized strategies for GR(1) specifications
Yeung, Enoch and Dy, Aaron J., el al. (2016) The Effect of Compositional Context on Synthetic Gene Networks; 10.1101/083329
Baetica, Ania A. and Catanach, Thomas A., el al. (2016) 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) Symbolic construction of GR(1) contracts for systems with full information; 10.1109/ACC.2016.7525009
Swaminathan, Anandh and Gomez, Marcella M., el al. (2016) Stochastic Gene Expression in Single Gene Oscillator Variants
Artavanis, Georgios and Hsiao, Victoria, el al. (2016) The role of single occupancy effects on integrase dynamics in a cell-free system; 10.1101/059675
Chiao, Abel C. and Murray, Richard M., el al. (2016) Development of prokaryotic cell-free systems for synthetic biology; 10.1101/048710
Hsiao, Victoria and Cheng, Aileen, el al. (2016) Design and application of stationary phase combinatorial promoters
Dathathri, Sumanth and Livingston, Scott C., el al. (2016) Interfacing TuLiP with the JPL Statechart Autocoder: Initial progress toward synthesis of flight software from formal specifications
Yeung, Enoch and Kim, Jongmin, el al. (2015) Global Dynamical Structure Reconstruction from Reconstructed Dynamical Structure Subnetworks: Applications to Biochemical Reaction Networks
Sen, Shaunak and Murray, Richard M. (2015) Quantitative Performance Bounds in Biomolecular Circuits due to Temperature Uncertainty
Han, Duo and Mo, Yilin, el al. (2015) Synthesis of Distributed Longitudinal Control Protocols for a Platoon of Autonomous Vehicles
Meng, Xianglin and Baetica, Ania A., el al. (2015) Finding stationary solutions to the chemical master equation by gluing state spaces at one or two states recursively
Farahani, Samira S. and Raman, Vasumathi, el al. (2015) Robust Model Predictive Control for Signal Temporal Logic Synthesis
Nguyen, Phuc H. B. and Wu, Yong Y., el al. (2015) Design Space Exploration of the Violacein Pathway in Escherichia coli Based Transcription Translation Cell-Free System (TX-TL); 10.1101/027656
Sun, Zachary Z. and Kim, Jongmin, el al. (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, el al. (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., el al. (2015) Synthesis from multi-paradigm specifications
Livingston, Scott C. and Wolff, Eric M., el al. (2015) Cross-entropy Temporal Logic Motion Planning; 10.1145/2728606.2728635
Raman, Vasumathi and Fält, Mattias, el al. (2015) Online Horizon Selection in Receding Horizon Temporal Logic Planning
Guo, Shaobin and Hori, Yutaka, el al. (2015) Systematic Design and Implementation of a Novel Synthetic Fold-Change Detector Biocircuit In Vivo
Livingston, Scott C. and Murray, Richard M. (2014) Hot-swapping robot task goals in reactive formal synthesis
Sen, Shaunak and Murray, Richard M. (2014) Negative Feedback Facilitates Temperature Robustness in Biomolecular Circuit Dynamics; 10.1101/007385
Murray, Richard M. and Day, John C., el al. (2013) Engineering Resilient Space Systems; 10.26206/WDX7-K192
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, el al. (2013) An Aircraft Electric Power Testbed for Validating Automatically Synthesized Reactive Control Protocols
Wiltsche, Clemens and Topcu, Ufuk, el al. (2012) Synthesis of Reactive Protocols for Vehicle-to-Vehicle Communication; 10.48550/arXiv.1210.2035
Censi, Andrea and Nilsson, Adam, el al. (2012) Motion planning in observations space with learned diffeomorphism models
Livingston, Scott C. and Prabhakar, Pavithra, el al. (2012) Patching task-level robot controllers based on a local µ-calculus formula
Wolff, Eric M. and Topcu, Ufuk, el al. (2011) Robust Control of Uncertain Markov Decision Processes with Temporal Logic Specifications
Liu, Jun and Ozay, Necmiye, el al. (2011) Synthesis of Switching Protocols from Temporal Logic Specifications
Barmpoutis, Dionysios and Murray, Richard M. (2011) Extremal Properties of Complex Networks; 10.48550/arXiv.1104.5532
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
Barmpoutis, Dionysios and Murray, Richard M. (2010) Quantification and Minimization of Crosstalk Sensitivity in Networks; 10.48550/arXiv.1012.0606
Censi, Andrea and Murray, Richard M. (2010) Bootstrapping bilinear models of robotic sensorimotor cascades
Lavaei, Javad and Sojoudi, Somayeh, el al. (2010) Delay-Based Controller Design for Continuous-Time and Hybrid Applications
Han, Shuo and Censi, Andrea, el al. (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, el al. (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., el al. (2004) On a stochastic sensor selection algorithm with applications in sensor scheduling and sensor coverage
Gupta, Vijay and Spanos, Demetri, el al. (2004) Optimal LQG Control Across a Packet-Dropping Link
Gupta, Vijay and Hassibi, Babak, el al. (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
Gupta, Vijay and Chung, Timothy H., el al. (2004) Scheduling for Distributed Sensor Networks
Olfati-Saber, Reza and Murray, Richard M. (2003) Agreement Problems in Networks with Directed Graphs and Switching Topology
Fax, J. Alexander and Murray, Richard M. (2003) Information Flow and Cooperative Control of Vehicle Formations
Martin, Phillipe and Murray, Richard M., el al. (2003) Flat systems, equivalence and trajectory generation
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
Muruhan, Rathinam and Murray, Richard M. (1998) Discrete Function Approximation: Numerical Tools for Nonlinear Control
Yeung, S. and Wang, Y., el al. (1998) Evaluation of Bleed Valve Rate Requirements in Nonlinear Control of Rotating Stall on Axial Flow Compressors
Morin, Pascal and Murray, Richard M., el al. (1997) Nonlinear Rescaling of Control Laws with Application to Stabilization in the Presence of Magnitude Saturation
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
Murray, Richard M. and Jacobsen, C.A., el al. (1997) System Identification for Limit Cycling Systems: A Case Study for Combustion Instabilities
Rathinam, Muruhan and Murray, Richard M. (1996) Configuration Flatness of Lagrangian Systems Underactuated by One Control
D'Andrea, Raffaello and Behnken, Robert L., el al. (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
Sur, Sudipto and Murray, Richard M. (1996) An Experimental Comparison of Tradeoffs in Using Compliant Manipulators for Robotic Grasping Tasks
Rathinam, Muruhan and Murray, Richard M. (1996) Configuration Flatness of Lagrangian Systems Underactuated by One Control
van Nieuwstadt, Michiel and Rathinam, Muruhan, el al. (1995) Differential Flatness and Absolute Equivalence
Bloch, A. M. and Krishnaprasad, P. S., el al. (1995) Nonholonomic Mechanical Systems with Symmetry
Tierno, Jorge E. and Murray, Richard M., el al. (1995) Numerically Efficient Robustness Analysis of Trajectory Tracking for Nonlinear Systems
Bullo, Francesco and Murray, Richard M. (1995) Proportional Derivative (PD) Control on the Euclidean Group
Lewis, Andrew D. and Murray, Richard M. (1995) Configuration Controllability of Simple Mechanical Control Systems
Bullo, Francesco and Murray, Richard M., el al. (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
Sluis, Willem M. and Banaszuk, Andrzej, el al. (1995) A Homotopy Algorithm for Approximating Geometric Distributions by Integrable 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