User:Murray/Papers: Difference between revisions

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Revision as of 05:40, 15 May 2016

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  1. Flow-Based Synthesis of Reactive Tests for Discrete Decision-Making Systems with Temporal Logic Specifications (Josefine B. Graebener, Apurva S. Badithela, Denizalp Goktas, Wyatt Ubellacker, Eric V. Mazumdar, Aaron D. Ames, Richard M. Murray, Submitted, IEEE Transactions on Robotics, 2024)
  2. Impact of Chemical Dynamics of Commercial PURE Systems on Malachite Green Aptamer Fluorescence (Zoila Jurado, Richard M. Murray, Submitted, ACS Synthetic Biology, 2024)
  3. Specifying and Analyzing Networked and Layered Control Systems Operating on Multiple Clocks (Inigo Incer, Noel Csomay-Shanklin, Aaron Ames, Richard M. Murray, To appear, 2024 Conference on Decision and Control (CDC))
  4. A Field-Deployable Arsenic Sensor Integrating Bacillus Megaterium with CMOS Technology (Chelsea Y Hu, John B McManus, Fatemeh Aghlmand, Elin M Larsson, Azita Emami, Richard M Murray, Submitted, ACS Synthetic Biology, 2024)
  5. Optimizing protein expression in the One-Pot PURE system: Insights into reaction composition and translation efficiency (Y. Zhang, Y. Qiu, M. Deveikis, Z. A. Martinez, T.-F. Chou, P. Freemont, R. M. Murray, SEED, 2024)
  6. TRILL: Orchestrating Modular Deep-Learning Workflows for Democratized, Scalable Protein Analysis and Engineering (Zachary A Martinez, Richard M. Murray, Matt W. Thomson, Submitted, 2024 SEED)
  7. Engineering the soil bacterium Pseudomonas synxantha 2-79 into a ratiometric bioreporter for phosphorus limitation (Elin M. Larsson, Richard M. Murray, Dianne K. Newman, ACS Synthetic Biology, 2024)
  8. Efficient local validation of partially ordered models via Baysian directed sampling (Kellan Moorse and Richard Murray, Submitted, 2024 American Control Conference (ACC))
  9. A chemical reaction network model of PURE (Zoila Jurado, Ayush Pandey, Richard M. Murray, BioRxiv preprint, 2023)
  10. Pacti: Scaling Assume-Guarantee Reasoning for System Analysis and Design (Inigo Incer, Apurva Badithela, Josefine Graebener, Piergiuseppe Mallozzi, Ayush Pandey, Sheng-Jung Yu, Albert Benveniste, Benoit Caillaud, Richard M. Murray, Alberto Sangiovanni-Vincentelli, Sanjit A. Seshia, Submitted, ACM Transactions on Cyber-Physical Systems (TCPS), Aug 2023)
  11. Development of cell-free transcription-translation systems in three soil Pseudomonads (Joseph T. Meyerowitz, Elin M. Larsson, Richard M. Murray, To appear, ACS Synthetic Biology, 2024)
  12. Addressable and adaptable intercellular communication via DNA messaging (John P. Marken and Richard M. Murray, Nature Communications, 14:2358, 2023)
  13. A Model-Free Algorithm for Extremely Resilient Navigation (Christian J. Stromberger, Josefine B. Graebener, James F. Ragan, and Richard M. Murray, Submitted, 2024 International Conference on Robotics and Automation (ICRA))
  14. Metabolic perturbations to an E. coli-based cell-free system reveal a trade-off between transcription and translation (Manisha Kapasiawala and Richard M. Murray, SEED 2023)
  15. Control education for societal-scale challenges: A community roadmap (John Anthony Rossiter, Christos G. Cassandras, João Hespanha, Sebastian Dormido, Luis de la Torre, Gireeja Ranade, Antonio Visioli, John Hedengren, Richard M. Murray, Panos Antsaklis, Francoise Lamnabhi-Lagarrigue, Thomas Parisini, Annual Reviews in Control, 55:1-17, 2023)
  16. A 65nm CMOS Living-Cell Dynamic Fluorescence Sensor with 1.05fA Sensitivity at 600/700nm Wavelengths (Fatemeh Aghimand, Chelsea Hu, Saransh Sharma, Krishna K. Pochana, Richard M. Murray, Azita Emami, 2023 IEEE International Solid-State Circuits Conference (ISSCC))
  17. Evaluation Metrics of Object Detection for Quantitative System-Level Analysis of Autonomous Systems (Apurva Badithela, Tichakorn Wongpiromsarn, and Richard M. Murray, To appear, 2023 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS))
  18. Context-Aided Variable Elimination for Requirement Engineering (Inigo Incer, Albert Benveniste, Richard M. Murray, Alberto Sangiovanni-Vincentelli, Sanjit A. Seshia, Submitted, 2023 Formal Methods in Computer-Aided Design (FMCAD))
  19. Reasoning over Test Specifications using Assume-Guarantee Contracts (Apurva Badithela, Josefine B. Graebener, Inigo Incer, and Richard M. Murray, Submitted, NASA Formal Methods (NFM), 2023)
  20. Barrier-Based Test Synthesis for Safety-Critical Systems Subject to Timed Reach-Avoid Specifications (Prithvi Akella, Mohamadreza Ahmadi, Richard M. Murray, Aaron D. Ames, Submitted, IEEE Transactions on Automatic Control, 2023)
  21. BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts (William Poole, Ayush Pandey, Zoltan Tuza, Andrey Shur, Richard M. Murray, PLoS Computational Biology, 18(4), e1009987, 2022)
  22. Characterization of Integrase and Excisionase Activity in Cell-free Protein Expression System Using a Modeling and Analysis Pipeline (Ayush Pandey, Makena L. Rodriguez, William Poole, Richard M. Murray, ACS Synthetic Biology, 12(2):511–523, 2023)
  23. Minimally Constrained Testing for Autonomy with Temporal Logic Specifications (Apurva Badithela, Josefine Graebener, Richard M. Murray, RSS 2022 Workshop on Envisioning an Infrastructure for Multi-Robot and Collaborative Autonomy Testing and Evaluation)
  24. Integrase-mediated differentiation circuits improve evolutionary stability of burdensome and toxic functions in E. coli (Rory L. Williams and Richard M. Murray, Nature Communications, 13:6822, 2022)
  25. Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape (Anandh Swaminathan, William Poole, Victoria Hsiao, Ayush Pandey, and Richard M. Murray, Journal of Open Source Software (JOSS), 2023)
  26. Synthesizing Reactive Test Environments for Autonomous Systems: Testing Reach-Avoid Specifications with Multi-Commodity Flows (Apurva Badithela, Josefine B. Graebener, Wyatt Ubellacker, Eric V. Mazumdar, Aaron D. Ames, Richard M. Murray, Submitted, 2023 International Conference on Robotics and Automation (ICRA))
  27. Layered Feedback Control Overcomes Performance Trade-Off in Synthetic Biomolecular Networks (Chelsea Hu, Richard M. Murray, Nature Communications 13(1):1-13, 2022)
  28. Evaluation Metrics for Object Detection for Autonomous Systems (Apurva Badithela, Tichakorn Wongpiromsarn, Richard M. Murray, Submitted, 2023 International Conference on Robotics and Automation (ICRA))
  29. From Specification to Implementation: Assume-Guarantee Contracts for Synthetic Biology (Ayush Pandey, Inigo Incer, Alberto Sangiovanni-Vincentelli, Richard M. Murray, 2022 International Workshop on Biodesign Automation (IWBDA))
  30. Towards Better Test Coverage: Merging Unit Tests for Autonomous Systems (Josefine Graebener, Apurva Badithela, Richard M. Murray, 2022 NASA Formal Methods Symposium (NFM))
  31. Robust Safe Control Synthesis with Disturbance Observer-Based Control Barrier Functions (Ersin Das, Richard M. Murray, To appear, 2022 Conference on Decision and Control (CDC))
  32. Robustness guarantees for structured model reduction of dynamical systems with applications to biomolecular models (Ayush Pandey, Richard M. Murray, International Journal on Robust and Nonlinear Control (IJRNC), 1-29, 2022)
  33. How to model DNA replication in stochastic models of synthetic genetic circuits (and why) (Samuel E. Clamons, Richard M. Murray, bioRxiv 2021.09.26.461880)
  34. Risk-Averse Decision Making Under Uncertainty (Mohamadreza Ahmadi, Ugo Rosolia, Michel D. Ingham, Richard M. Murray, Aaron D. Ames, 2021 AAAI Conference on Artificial Intelligence (AAAI-21))
  35. Data-driven network models for genetic circuits from time-series data with incomplete measurements (Enoch Yeung, Jim Kim, Ye Yuan, Jorge Gonçalves, Richard M. Murray, Journal of the Royal Society Interface 18 (182), 20210413)
  36. Leveraging Classification Metrics for Quantitative System-Level Analysis with Temporal Logic Specifications (Apurva Badithela, Tichakorn Wongpiromsarn, Richard M Murray, To appear, 2021 Conference on Decision and Control)
  37. A Method for Cost-Effective and Rapid Characterization of Genetic Parts (John B. McManus, Casey B. Bernhards, Caitlin E. Sharpes, David C. Garcia, Stephanie D. Cole, Richard M. Murray, Peter A. Emanuel, Matthew W. Lux, To appear, Journal of Visualized Experiments (JoVE))
  38. Synthesis of Static Test Environments for Observing Sequence-like Behaviors in Autonomous Systems (Apurva Badithela, Richard M. Murray, Submitted, 2021 NASA Formal Methods (NFM))
  39. Constrained risk-averse Markov decision processes (Mohamadreza Ahmadi, Ugo Rosolia, Michel D Ingham, Richard M Murray, Aaron D Ames, 35th AAAI Conference on Artificial Intelligence (AAAI-21))
  40. Failure-Tolerant Contract-Based Design of an Automated Valet Parking System using a Directive-Response Architecture (Josefine Graebener, Tung Phan-Minh, Jiaqi Yan, Qiming Zhao, Richard M. Murray, Submitted, 2021 Conference on Decision and Control (CDC))
  41. Rules of the Road: Safety and Liveness Guarantees for Autonomous Vehicles (Karena X. Cai, Tung Phan-Minh, Soon-Jo Chung, Richard M. Murray, IEEE Transactions on Robotics, 39(3))
  42. The Python Control Systems Library (python-control) (Sawyer Fuller, Ben Greiner, Jason Moore, Richard M. Murray, Renee van Paassen, Rory Yorke, IEEE Conference on Decision and Control (CDC), 2021)
  43. Robustness Guarantees for Structured Model Reduction of Dynamical Systems (Ayush Pandey, Richard M. Murray, IEEE Conference on Decision and Control (CDC), 2021)
  44. Limits of probabilistic safety guarantees when considering human uncertainty (Richard Cheng, Richard M. Murray, Joel W. Burdick, Submitted, 2021 Conference on Decision and Control (CDC))
  45. Time-Optimal Navigation in Uncertain Environments with High-Level Specifications (Ugo Rosolia, Mohamadreza Ahmadi, Richard M. Murray, Aaron D. Ames, To appear, 2021 Conference on Decision and Control (CDC))
  46. A MATLAB toolbox for modeling genetic circuits in cell-free systems (Vipul Singhal, Zoltan A. Tuza, Zachary Z. Sun, Richard M. Murray, Synthetic Biology, 6(1):ysab007, 2021)
  47. Reactive motion planning with probabilistic safety guarantees (Yuxiao Chen, Ugo Rosolia, Chuchu Fan, Aaron D. Ames, Richard M. Murray, Submitted, Conference on Robotic Learning (CoRL))
  48. Synthetic mammalian signaling circuits for robust cell population control (Yitong Ma, Mark W. Budde, Michaëlle N. Mayalu, Junqin Zhu, Richard M. Murray, Michael B. Elowitz, Submitted, Cell Systems)
  49. Bistable State Switch Enables Ultrasensitive Feedback Control in Heterogeneous Microbial Populations (Xinying Ren, Christian Cuba Samaniego, Richard M. Murray, Elisa Franco, 2021 American Control Conference (ACC))
  50. Systems Level Model of Dietary Effects on Cognition via the Microbiome-Gut-Brain Axis (Michaëlle N. Mayalu, Anish Sarma, Fangzhou Xiao, John C. Doyle and Richard M. Murray, 2021 European Control Conference (ECC))

... further results

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