- 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; 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; Ahmadi, Mohamadreza; et el. (2023) Barrier-Based
Test Synthesis for Safety-Critical Systems Subject to Timed Reach-Avoid
Specifications
- Badithela, Apurva; 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; Wongpiromsarn, Tichakorn; et el. (2022) Evaluation
Metrics for Object Detection for Autonomous Systems; 10.48550/arXiv.2210.10298
- Han, SooJean; 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; Incer, Inigo; et el. (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
- 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
- Ahmadi, Mohamadreza; 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.; 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.; Bernhards, Casey B.; et el. (2021) A
Method for Cost-Effective and Rapid Characterization of Genetic
Parts; 10.1101/2021.04.30.440836
- Chen, Yuxiao; Rosolia, Ugo; et el. (2021) Reactive
motion planning with probabilistic safety guarantees; 10.48550/arXiv.2011.03590
- Cai, Karena X.; Phan-Minh, Tung; et el. (2021) Rules
of the Road: Towards Safety and Liveness Guarantees for Autonomous
Vehicles; 10.48550/arXiv.2011.14148
- Walton, Sophie J.; 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.; Shur, Andrey S.; et el. (2020) Engineering
Logical Inflammation Sensing Circuit for Modulating Gut Conditions;
10.1101/2020.11.10.377085
- Chen, Yuxiao; 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.; 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
- Farahani, Samira S.; Raman, Vasumathi; et el. (2020) Robust
Model Predictive Control for Signal Temporal Logic Synthesis
- Guo, Shaobin; Hori, Yutaka; et el. (2020) Systematic
Design and Implementation of a Novel Synthetic Fold-Change Detector
Biocircuit In Vivo
- Hsiao, Victoria; Cheng, Aileen; et el. (2020) Design
and application of stationary phase combinatorial promoters
- Meng, Xianglin; Baetica, Ania A.; et el. (2020) Finding
stationary solutions to the chemical master equation by gluing state
spaces at one or two states recursively
- Yeung, Enoch; Kim, Jongmin; et el. (2020) Global
Dynamical Structure Reconstruction from Reconstructed Dynamical
Structure Subnetworks: Applications to Biochemical Reaction
Networks
- Han, Duo; Mo, Yilin; et el. (2020) Synthesis
of Distributed Longitudinal Control Protocols for a Platoon of
Autonomous Vehicles
- Dathathri, Sumanth; 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
- Swaminathan, Anandh; Gomez, Marcella M.; et el. (2020) Stochastic
Gene Expression in Single Gene Oscillator Variants
- Singhal, Vipul and Murray, Richard M. (2020) Cell-Free
Extract Data Variability Reduction in the Presence of Structural
Non-Identifiability
- McCardell, Reed D.; Pandey, Ayush; et el. (2020) Control
of density and composition in an engineered two-member bacterial
community; 10.1101/632174
- Arichega, Nikos; Dathathri, Sumanth; et el. (2020) Fast
Automatic Verification of Large-Scale Systems with Lookup
Tables
- 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.; 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.; 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
- Raman, Vasumathi; Donzé, Alexandre; et el. (2019) Model
Predictive Control for Signal Temporal Logic Specification; 10.48550/arXiv.1703.09563
- Barmpoutis, Dionysios and Murray, Richard M. (2019) Quantification
and Minimization of Crosstalk Sensitivity in Networks; 10.48550/arXiv.1012.0606
- Wiltsche, Clemens; Topcu, Ufuk; et el. (2019) Synthesis
of Reactive Protocols for Vehicle-to-Vehicle Communication; 10.48550/arXiv.1210.2035
- Halleran, Andrew D.; 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; Poole, William; et el. (2019) Fast
and flexible simulation and parameter estimation for synthetic biology
using bioscrape; 10.1101/121152
- Murray, Richard M.; Day, John C.; et el. (2019) Engineering
Resilient Space Systems; 10.26206/WDX7-K192
- Dathathri, Sumanth; Zheng, Stephan; et el. (2019) Detecting
Adversarial Examples via Neural Fingerprinting; 10.48550/arXiv.1803.03870
- Baetica, Ania-Ariadna; Leong, Yoke Peng; et el. (2018) Design
Guidelines For Sequestration Feedback Networks; 10.1101/455493
- Doong, Joy; 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
- Shur, Andrey and Murray, Richard M. (2018) Proof
of concept continuous event logging in living cells; 10.1101/225151
- McCardell, Reed D.; Huang, Shan; et el. (2018) Control
of bacterial population density with population feedback and molecular
sequestration; 10.1101/225045
- Nguyen, Phuc H. B.; 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
- 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.; McCardell, Reed; et el. (2018) Context
Dependence of Biological Circuits; 10.1101/360040
- Olsman, Noah; Baetica, Ania-Ariadna; et el. (2018) Hard
Limits And Performance Tradeoffs In A Class Of Sequestration Feedback
Systems; 10.1101/222042
- Wu, Yong Y.; Sato, Hirokazu; et el. (2018) System-level
studies of a cell-free transcription-translation platform for metabolic
engineering; 10.1101/172007
- Guo, Shaobin; Yeung, Enoch; et el. (2017) Implementation
and System Identification of a Phosphorylation-Based Insulator in a
Cell-Free Transcription-Translation System; 10.1101/122606
- 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
- Swaminathan, Anandh; Hsiao, Victoria; et el. (2017) Quantitative
Modeling of Integrase Dynamics Using a Novel Python Toolbox for
Parameter Inference in Synthetic Biology; 10.1101/121152
- Parkin, James M.; Hsiao, Victoria; et el. (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; Vaish, Amit; et el. (2017) Expressing
Biologically Active Membrane Proteins in a Cell-Free
Transcription-Translation Platform; 10.1101/104455
- Yeung, Enoch; Dy, Aaron J.; et el. (2017) The
Effect of Compositional Context on Synthetic Gene Networks; 10.1101/083329
- Baetica, Ania A.; 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+
- Filippidis, Ioannis and Murray, Richard M. (2016) Symbolic
construction of GR(1) contracts for systems with full information;
10.1109/ACC.2016.7525009
- Artavanis, Georgios; Hsiao, Victoria; et el. (2016) The
role of single occupancy effects on integrase dynamics in a cell-free
system; 10.1101/059675
- Sen, Shaunak and Murray, Richard M. (2016) Negative
Feedback Facilitates Temperature Robustness in Biomolecular Circuit
Dynamics; 10.1101/007385
- Chiao, Abel C.; Murray, Richard M.; et el. (2016) Development
of prokaryotic cell-free systems for synthetic biology; 10.1101/048710
- Dathathri, Sumanth; 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.; 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.; 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; Murray, Richard M.; et el. (2015) Synthesis from
multi-paradigm specifications
- Livingston, Scott C.; Wolff, Eric M.; et el. (2015) Cross-entropy
Temporal Logic Motion Planning; 10.1145/2728606.2728635
- Raman, Vasumathi; Fält, Mattias; et el. (2015) Online Horizon
Selection in Receding Horizon Temporal Logic Planning
- Gupta, Vijay; 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.; 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; Xu, Huan; et el. (2013) An
Aircraft Electric Power Testbed for Validating Automatically Synthesized
Reactive Control Protocols
- Censi, Andrea; Nilsson, Adam; et el. (2012) Motion
planning in observations space with learned diffeomorphism
models
- Livingston, Scott C.; Prabhakar, Pavithra; et el. (2012) Patching
task-level robot controllers based on a local µ-calculus
formula
- Wolff, Eric M.; Topcu, Ufuk; et el. (2011) Robust Control
of Uncertain Markov Decision Processes with Temporal Logic
Specifications
- Liu, Jun; 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; Sojoudi, Somayeh; et el. (2010) Delay-Based
Controller Design for Continuous-Time and Hybrid Applications
- Han, Shuo; 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; 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; Chung, Timothy H.; et el. (2004) On a
stochastic sensor selection algorithm with applications in sensor
scheduling and sensor coverage
- Gupta, Vijay; Hassibi, Babak; et el. (2004) A Sub-optimal
Algorithm to Synthesize Control Laws for a Network of Dynamic
Agents
- Gupta, Vijay; Spanos, Demetri; et el. (2004) Optimal LQG
Control Across a Packet-Dropping Link
- Dunbar, William B. and Murray, Richard M. (2004) Distributed
Receding Horizon Control with Application to Multi-Vehicle Formation
Stabilization
- Olfati-Saber, Reza and Murray, Richard M. (2003) Agreement
Problems in Networks with Directed Graphs and Switching
Topology
- Martin, Phillipe; Murray, Richard M.; et el. (2003) Flat systems,
equivalence and trajectory generation
- Fax, J. Alexander and Murray, Richard M. (2003) Information
Flow and Cooperative Control of Vehicle Formations
- van Nieuwstadt, Michiel; 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
- Muruhan, Rathinam and Murray, Richard M. (1998) Discrete
Function Approximation: Numerical Tools for Nonlinear Control
- Yeung, S.; Wang, Y.; et el. (1998) Evaluation
of Bleed Valve Rate Requirements in Nonlinear Control of Rotating Stall
on Axial Flow Compressors
- Morin, Pascal; Murray, Richard M.; et el. (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
- Murray, Richard M.; Jacobsen, C.A.; et el. (1997) System
Identification for Limit Cycling Systems: A Case Study for Combustion
Instabilities
- 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; Behnken, Robert L.; et el. (1996) Active
Control of an Axial Flow Compressor via Pulsed Air Injection
- 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
- Lewis, Andrew D. and Murray, Richard M. (1996) Decomposition
for Control Systems on Manifolds with an Affine Connection
- Sluis, Willem M.; 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
- Bullo, Francesco; 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.; Krishnaprasad, P. S.; et el. (1995) Nonholonomic
Mechanical Systems with Symmetry
- Tierno, Jorge E.; Murray, Richard M.; et el. (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
- 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