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2020b_PMS20-ACSsynbio

Assessment of Robustness to Temperature in a Negative Feedback Loop and a Feedforward Loop
Abhilash Patel, Richard M. Murray, Shaunak Sen
ACS Synthetic Biology, 9(7):1581-1590, 2020


2020a_AAMA20-cdc

Formal Test Synthesis for Safety-Critical Autonomous Systems based on Control Barrier Functions
Prithvi Akella, Mohamadreza Ahmadi, Richard M. Murray, Aaron D. Ames
To appear, 2020 Conference on Decision and Control (CDC)


2019x_WM19-biorxiv

Tunable integrase-mediated differentiation facilitates improved output of burdensome functions in E. coli
Rory L. Williams, Richard M. Murray
bioRxiv 614529, 2019 (revised 2020, 2022)


2019m_LMM19-biorxiv

Construction of an inducible amyloid expression circuit in Bacillus megaterium: A case study with CsgA and TasA
Elin M. Larsson, John B. McManus, Richard M. Murray
bioRxiv 858266


2019l_ahm+20-acc

Risk-Averse Planning Under Uncertainty
Mohamadreza Ahmadi, Masahiro Ono, Michel D. Ingham, Richard M. Murray, Aaron D. Ames
2020 American Control Conference (ACC)


2019l_dnam20-acc

Invariant Sets for Integrators and Quadrotor Obstacle Avoidance
Ludvig Doeser, Petter Nilsson, Aaron D. Ames, and Richard M. Murray
2020 American Control Conference (ACC)


2019k_knam20-iccps

Intermittent Connectivity for Exploration in Communication-Constrained Multi-Agent Systems
Filip Klaesson, Petter Nilsson, Aaron D. Ames, Richard M. Murray
2020 International Conference on Cyberphysical Systems (ICCPS)


2019i_BAM20-acc

Learning pose estimation for UAV autonomous navigation and landing using visual-inertial sensor data
Francesca Baldini, Animashree Anandkumar, Richard M. Murray
2020 American Control Conference (ACC)


2019i_rm20-wqbio

Layered Feedback Control Improves Robust Functionality across Heterogeneous Cell Populations
Xinying Ren, Richard M. Murray
2020 Winter q-bio


2019i_mxm20-wqbio

A geometric and structural approach to the analysis and design of biological circuit dynamics: a theory tailored for synthetic biology
John P. Marken, Fangzhou Xiao, Richard M. Murray
2020 Winter q-bio


2019i_mm20-wqbio

Theoretical Design of Paradoxical Signaling-Based Synthetic Population Control Circuit in E. coli
Michaëlle N. Mayalu, Richard M. Murray
2020 Winter q-bio


2019i_pm20-wqbio

Model Reduction Tools For Phenomenological Modeling of Input-Controlled Biological Circuits
Ayush Pandey, Richard M. Murray
2020 Winter q-bio


2019h_cdpm19-corl

Counter-example Guided Learning of Bounds on Environment Behavior
Yuxiao Chen, Sumanth Dathathri, Tung Phan-Minh, Richard M. Murray
2019 Conference on Robot Learning (CoRL)


2019g_CM19-biorxiv

Modeling predicts that CRISPR-based activators, unlike CRISPR-based repressors, scale well with increasing gRNA competition and dCas9 bottlenecking
Samuel Clamons, Richard M. Murray
bioRxiv preprint


2019g_ham19-oupsynbio

Analysis of primitive genetic interactions for the design of a genetic signal differentiator
Wolfgang Halter, Richard M. Murray, Frank Allgower
Submitted, OUP Synthetic Biology, May 2019


2019g_pm19-formats

Contracts of Reactivity
Tung Phan-Minh and Richard M. Murray
Submitted, Int'l Conf on Formal Modeling and Analysis of Timed Systems (FORMATS) 2019


2019f_PM19-iwbda

An automated model reduction tool to guide the design and analysis of synthetic biological circuits
Ayush Pandey, Richard M. Murray
2019 International Workshop on Biodesign Automation (IWBDA)


2019e_MMEL19-abb

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
John B. McManus, Richard M. Murray, Peter A. Emanuel, Matthew W. Lux
Archives of Biochemistry and Biophysics, Volume 674, 15 October 2019, 108045


2019d_pcm19-cdc

Towards Assume-Guarantee Profiles for Autonomous Vehicles
Tung Phan-Minh, Karena X. Cai, Richard M. Murray
Submitted, 2019 Conference on Decision and Control (CDC)


2019c_GHRM19-qbio

Bacterial Controller Aided Wound Healing: A Case Study in Dynamical Population Controller Design
Leopold N. Green, Chelsea Y. Hu, Xinying Y. Ren, Richard M. Murray
qBio Conference 2019


2019c_HFM19-qbio

Quantitative characterization of random partitioning in the evolution of plasmid-encoded traits
Andrew D. Halleran, Emanuel Flores-Bautista, Richard M. Murray
qBio 2019 Conference


2019c_MM19-qbio

Addressable, “Packet-Based” Intercellular Communication through Plasmid Conjugation
John P. Marken, Richard M. Murray
qBio 2019 Conference


2019b_HM19-seed

Design of a genetic layered feedback controller in synthetic biological circuitry
Chelsea Y. Hu, Richard M. Murray
2019 Synthetic Biology: Engineerinng, Evolution and Design (SEED) Conference


2019b_MPM19-seed

Control of density and composition in an engineered two-member bacterial community
Reed D. McCardell, Ayush Pandey, Richard M. Murray
Submitted, 2019 Synthetic Biology: Engineering, Evolution and Design (SEED) Conference


2019b_SM19-seed

Proof of concept continuous event logging in living cells
Andrey Shur, Richard M. Murray
2019 Synthetic Biology: Engineering, Evolution and Design (SEED) Conference


2018g_blom18-cellsys

Guidelines for Designing the Antithetic Feedback Motif
Ania-Ariadna Baetica, Yoke Peng Leong, Richard M. Murray
Physical Biology, 17(5):055002, 2020


2018g_ols+18-cellsys

Hard Limits And Performance Tradeoffs In A Class Of Sequestration Feedback Systems
Noah Olsman, Ania-Ariadna Baetica, Fangzhou Xiao, Yoke Peng Leong, John Doyle, Richard Murray
Submitted, Cell Systems (Nov 2018)


2018f_rm19-ecc

Cooperation Enhances Robustness of Coexistence in Spatially Structured Consortia
Xinying Ren, Richard M Murray
Submitted, 2019 European Control Conference


2018f_mhm19-ecc

Model of Paradoxical Signaling Regulated T-Cell Population Control for Design of Synthetic Circuits
Michaelle N. Mayalu, Harman Mehta and Richard M. Murray
Submitted, 2019 European Control Conference (ECC)


2018e_dgm19-aiaa

Inverse Abstraction of Neural Networks Using Symbolic Interpolation
Sumanth Dathathri, Sicun Gao, Richard M. Murray
To appear, 2019 AAAI Conference on Artificial Intelligence


2018e_comb19-aiaa

End-to-End Safe Reinforcement Learning through Barrier Functions for Safety-Critical Continuous Control Tasks
Richard Cheng, Gabor Orosz, Richard M. Murray, Joel W. Burdick
To appear, 2019 AAAI Conference on Artificial Intelligence


2018d_chmc19-acc

Robust Estimation Framework with Semantic Measurements
Karena X. Cai, Alexei Harvard, Richard M. Murray, Soon-Jo Chung
Submitted, 2019 American Control Conference (ACC)


2018d_gsma19-acc

Risk-aware motion planning for automated vehicle among human-driven cars
Jin I. Ge, Bastian Schurmann, Richard M. Murray, and Matthias Althoff
Submitted, 2019 American Control Conference (ACC)


2018d_pha+19-acc

A modal interface contract theory for guarded input/output automata with an application in traffic system design
Tung Phan-Minh, Steve Guo, Bastian Schürmann, Matthias Althoff, and Richard M. Murray
Submitted, 2019 American Control Conference (ACC)


2018d_sm19-acc

Cell-Free Extract Data Variability Reduction in the Presence of Structural Non-Identifiability
Vipul Singhal and Richard M. Murray
Submitted, 2019 American Control Conference (ACC)


2018c_vai+18-anbio

On-chip membrane protein cell-free expression enables development of a direct binding assay: A curious case of potassium channel KcsA-Kv1.3
A. Vaisha, S. Guo, R. M.Murray, P. J..Grandsard and Q. Chen
Analytical Biochemistry, 556:70-77, 2018


2018b_rm18-cdc

Role of interaction network topology in controlling microbial population in consortia
Xinying Ren, Richard M Murray
To appear, 2018 Conference on Decision and Control (CDC)


2018b_hamg18-cdc

Optimal Experiment Design and Leveraging Competition for Shared Resources in Cell-free Extracts
Wolfgang Halter, Frank Allgower, Richard M. Murray and Andras Gyorgy
To appear, 2018 Conference on Decision and Control (CDC)


2018b_gm18-cdc

Voluntary lane-change policy synthesis with reactive control improvisation
Jin I. Ge and Richard M. Murray
To appear, 2018 Conference on Decision and Control (CDC)


2018a_pm18-seed

Long-distance communication in synthetic bacterial consortia through active signal propagation
James M Parkin, Richard M Murray
2018 Synthetic Biology: Engineering, Evolution and Design (SEED) Conference


2018a_hsm18-seed

Single day construction of multi-gene circuits with 3G assembly
Andrew D Halleran, Anandh Swaminathan, Richard M Murray
2018 Synthetic Biology: Engineering, Evolution and Design (SEED) Conference


2017m_hae+18-adhs

Temporal Logic Control of POMDPs via Label-based Stochastic Simulation Relations
S. Haesaert, P. Nilsson, C. I. Vasile, R. Thakker, A. Agha-mohammadi, A. D. Ames and R. M. Murray
To appear in IFAC Conference on Analysis and Design of Hybrid Systems (ADHS), 2018


2017l_nil+18-rss

Toward Specification-Guided Active Mars Exploration for Cooperative Robot Teams
P. Nilsson, S. Haesaert, C. Vasile, R. Thakker, A. Agha-mohammadi. R. M. Murray and A. D. Ames
To appear in Robotics: Science and Systems (RSS), 2018.


2017k_cm18-wqbio

Modeling Dynamic Transcriptional Circuits with CRISPRi
Samuel E Clamons, Richard M Murray
2018 Winter q-bio


2017k_MHGM18-wqbio

Control of bacterial population density with population feedback and molecular sequestration
Reed D McCardell, Shan Huang, Leopold N Green, Richard M Murray
2018 Winter q-bio


2017k_dpm18-wqbio

Length and time scales of cell-cell signaling circuits in agar
Joy Doong, James Parkin, Richard M. Murray
2018 Winter q-bio


2017j_hsm17-ieeecsm

Control Theory for Synthetic Biology: Recent Advances in System Characterization, Control Design, and Controller Implementation for Synthetic Biology
Victoria Hsiao, Anandh Swaminathan, and Richard M. Murray
IEEE Control Systems Magazine, 38(3):32-62 , June 2018


2017i_wu+17-biorxiv

System-level studies of a cell-free transcription-translation platform for metabolic engineering
Yong Y. Wu, Hirokazu Sato, Hongjun Huang, Stephanie J. Culler, Julia Khandurina, Harish Nagarajan, Tae Hoon Yang, Stephen Van Dien, Richard M. Murray
bioRxiv Technical Report


2017h_fm18-pieee

Layering assume-guarantee contracts for hierarchical system design
Ioannis Filippidis and Richard M. Murray
Proceedings of the IEEE, 2018


2017g_HM17-biorxiv

Cell-free and in vivo characterization of Lux, Las, and Rpa quorum activation systems in E. coli
Andrew Halleran, Richard M. Murray
ACS Synthetic Biology, 7(2):752–755, 2017