Papers

    2023

  • M. Scott, O. de Lange, X. Quaranto, R. Cardiff, and Eric Klavins, Open-source workflow design and management software to interrogate duckweed growth conditions and stress responses, Plant Methods. Vol. 19, No. 95. 2023.
  • O. Roth, S. Yechezkel, O. Serero, A. Eliyahu, I. Vints, P. Tzeela, A. Carignano, D.P. Janacek, V. Peters, A. Kessel, V. Dwivedi, M. Carmeli-Weissberg, F. Shaya, A. Faigenboim-Doron, J. Riov, E. Klavins, C. Dawid, U.Z. Hammes, N. Ben-Tal, R. Napier, E. Sadot and R. Weinstain, Alleviating the barrier of adventitious roots formation in recalcitrant mature tissue by slow release of a synthetic auxin, Biorxiv. 2023.

    • 2022

  • J.D. Vrana, N. Panpradist, N. Higa, D. Ko, P. Ruth, R. Kanthula, J.J. Lai, Y. Yang, S.R. Sakr, B. Chohan, M.H. Chung, L.M. Frenkel, B.R. Lutz, E. Klavins, I.A. Beck, Implementation of an interactive mobile application to pilot a rapid assay to detect HIV drug resistance mutations in Kenya, PLOS Global Public Health. 2022.

    • Alberto Carignano's bistable yeast consortium (ELife 2022)

  • A. Carignano, D.H. Chen, C. Mallory, C. Wright, G. Seelig, and E. Klavins, Modular, robust and extendible multicellular circuit design in yeast, ELife. 2022.
  • J.M Singer, S. Novotney, D. Strickland, H. K. Haddox, N. Leiby, G. J. Rocklin, C. M. Chow, A. Roy, A. K. Bera, F. C. Motta, L. Cao, E-M. Strauch, T. M. Chidyausiku, A. Ford, E. Ho, C. O. Mackenzie, H. Eramian, F. DiMaio, G. Grigoryan, M. Vaughn, L. J. Stewart, D. Baker and E. Klavins, Large-scale design and refinement of stable proteins using sequence-only models, PloS One. Vol. 17, No. 3. 2022.

    • 2021

  • J. Vrana, O. de Lange, Y. Yang, G. Newman, A. Saleem, Ayesha, A. Miller, C. Cordray, Cameron, S. Halabiya, M. Parks, E. Lopez, S. Goldberg, B. Keller, D. Strickland, Devin and E. Klavins, Aquarium: open-source laboratory software for design, execution and data management, Oxford Synthetic Biology. 2021.

    • 2020

  • A. Hossain, E. Lopez, S. M. Halper, D. P. Cetnar, A. C. Reis, D. Strickland, E. Klavins, and H. M. Salis, Automated design of thousands of nonrepetitive parts for engineering stable genetic systems, Nature Biotechnology. 2020.
  • J. Maguire, H. Haddox, D. Strickland, S. Halabiya, B. Coventry, M. Cummins, D. Thieker, E. Klavins, F. DiMaio, D. Baker, and B. Kuhlman, Perturbing the energy landscape for improved packing during computational protein design, Proteins. 2020.

    • 2019

    A snapshot of the Aquarium Software guiding clinicians through an HIV test

  • N. Panpradist, I. A. Beck,, J. Vrana, N. Higa, D. McIntyre, P. S. Ruth, I. So, E.C. Kline, R. Kanthula, Annie Wong-On-Wing, J. Lim, D. Ko, R. Milne, T. Rossou, U. D. Feuch, M. Chung, G. Jourdain, N. Ngo-Giang-Huong, L. Laomanit, J. Sori, J. Lai, E. Klavins, L. M. Frenkel and B. R. Lutz, OLA-Simple: A software-guided HIV-1 drug resistance test for low-resource laboratories, EBioMedicine. 2019.
  • Y. Yang, J. L. Nemhauser, and E. Klavins, Synthetic Bistability and Differentiation in Yeast, ACS Synthetic Biology. 2019.

    • 2018

  • A. Khakhar, A. R Leydon, A. C. Lemmex, E. Klavins, and J. L. Nemhauser, Synthetic hormone-responsive transcription factors can monitor and re-program plant development, eLIFE. 2018. Ian Haydon wrote a nice article about this paper for synbiobeta.

    • 2017

  • D. A. Younger, S. Berger, D. Baker and E. Klavins, High-Throughput Characterization of Protein-Protein Interactions by Reprogramming Yeast Mating, Proceedings of the National Academy of Science. 2017. Ian Haydon wrote a nice article about this paper for The Conversation.
  • C. Takahashi, L. Zaman, and E. Klavins, Accelerating Evolutionary Hill Climbs in Parallel Turbidostats, BioRxiv (preprint). 2017.
  • O. de Lange, E. Klavins, and J. Nemhauser, Synthetic genetic circuits in crop plants, Current Opinion in Biotechnology. Vol. 49. pp. 16-22. 2017.

    • Justin's impression of our dCas9 based NOR gate.

  • M. Gander, J. Vrana, W. Voje, J. Carothers, and E. Klavins, Digital logic circuits in yeast with CRISPR/dCas9 NOR gates, Nature Communications. 2017. The UW News wrote a nice article about this paper.

    • 2016

  • R. Egbert, L. Brettner, D. Zong, and E. Klavins, Self-destructive altruism in a synthetic developmental program enables complex feedstock utilization, BioRxiv (preprint). 2016.

    • 2015

  • A. Khakhar, N. Bolten, J. Nemhauser, and E. Klavins, Cell-cell communication in yeast using auxin biosynthesis and auxin responsive CRISPR transcription factors, ACS Synthetic Biology. pp. DOI: 10.1021/acssynbio.5b00064. 2015. The UW News wrote a nice article about this paper.
  • J.M. Guseman, A. Hellmuth, A. Lanctot, T.P. Feldman, B.L. Moss, E. Klavins, L.I.A. Calderón, Villalobos, J.L. Nemhauser, Auxin-induced degradation dynamics set the pace for lateral root development, Development. Vol. 152. pp. 1-5. 2015.

    • 2014

  • E. Klavins, Lightening the load in synthetic biology (News and Views), Nature Biotechnology. Vol. 32. pp. 1198–1200. 2014.
  • C. Takahashi, A. Miller, F. Ekness, M. Dunham and E. Klavins, A low cost, customizable turbidostat for use in synthetic circuit characterization, ACS Synthetic Biology. 2014. See the turbidostat wiki page for more information.
  • E. Pierre-Jerome* S. S. Jang*, K. A. Havens, J. L. Nemhauser and E. Klavins, Recapitulation of the forward nuclear auxin response pathway in yeast, Proceedings of the National Academy of Science. 2014. Click here for data and associated code.
  • K. Oishi and E. Klavins, A Framework for Implementing Finite State Machines in Gene Regulatory Networks, ACS Synthetic Biology. 2014.

    • 2013

  • H. Yu, B. Moss, S. Jang, M. Prigge, E. Klavins, J. Nemhauser, and M. Estelle, Mutations in the TIR1 auxin receptor that increase affinity for Aux/IAA proteins result in auxin hypersensitivity, Plant Physiology. pp. 113.215582. March 2013.

    • 2012

    In our 2012 PNAS paper, Rob Egbert introduced a genetic tuning method and precisely balanced the number of cells in each state of a synthetic genetic switch.

  • D. Thorsley and E. Klavins, Estimation and Discrimination of Stochastic Biochemical Circuits From Time-Lapse Microscopy Data, PLoS One. Nov 2012.
  • J. Bishop and E. Klavins, Characterization of a Biomolecular Fuel Delivery Device under Load, Proceedings of the 51st IEEE Conference on Decision and Control. Dec 2012.
  • R.G. Egbert and E. Klavins, Fine-tuning gene networks using simple sequence repeats, Proceedings of the National Academy of Science. Vol. 109, No. 42. pp. 16817-16822. Oct 2012. Featured on the cover. See also the commentary by Prindle and Hasty.
  • S.S. Jang, K.T. Oishi, R.G. Egbert, and E. Klavins, Specification and simulation of multicelled behaviors, ACS Synthetic Biology. Vol. 1, No. 8. pp. 365-374. 2012.
  • K. Havens*, E. Pierre-Jerome*, S. Jang*, J. Guseman*, N. Bolten, E. Klavins, and J. Nemhauser, A synthetic approach reveals extensive tunability of auxin perception, Plant Physiology. pp. 112.202184. July 2012.

    • 2011

  • K. Oishi and E. Klavins, A biomolecular implementation of linear I/O systems, IET Systems Biology. Vol. 5, No. 4. pp. 252–260. July 2011.

    • In our 2012 ACS synthetic biology paper, we designed cell programs that could someday control cells to undergo synthetic morphogenesis.

  • N. Napp and E. Klavins, Load balancing for multi-robot construction, 2011 IEEE Conf. on Robotics and Automation. pp. pages 254-260. 2011.
  • N. Napp and E. Klavins, A Compositional Framework for Programming Stochastically Interacting Robots, The International Journal of Robotics Research. Vol. 30, No. 6. pp. 713-729. May 2011.

    • 2010

  • E. Klavins, Proportional-Integral Control of Stochastic Gene Regulatory Networks, Conference on Decision and Control (CDC). pp. 2547-2553. Dec 2010.
  • N. Napp, S. Burden, and E. Klavins, Setpoint Regulation for Stochastically Interacting Robots, Autonomous Robotics. Vol. 30, No. 1. pp. 57-71. Sep 2010.
  • D. Thorsley and E. Klavins, Approximating Stochastic Biochemical Processes With Wasserstein Pseudometrics, IET Systems Biology. Vol. 4, No. 3. pp. 193-211. May 2010.
  • N. Napp and E. Klavins, Robust by Composition: Programs for Multi Robot Systems, IEEE Conf. on Robotics and Automation. pp. 2459-2466. 2010.
  • D. Georgiev, M. Fazel, and E. Klavins, Model Discrimination of Chemical Reaction Networks by Linearization, American Control Conference (ACC). pp. 5916 - 5922. 2010.

    • 2009

    In our 2010 AR paper, Nils Napp and Sam Burden build robots that react like molecules.

  • N. Napp, S. Burden and E. Klavins, Setpoint Regulation for Stochastically Interacting Robots, Robotics: Science and Systems V. 2009.
  • F. W. Shaw and E. Klavins., Distributed Estimation and State Assignment For Stochastically Interacting Robots, Workshop on Network Estimation and Control. 2009.
  • N. Napp, D. Thorsley and E. Klavins, Hidden Markov Models for Non-Well-Mixed Reaction Networks, Proceedings of the American Control Conference. 2009.
  • D. Thorsley and E. Klavins, A Theory of Approximation for Stochastic Biochemical Networks, Control Theory and Systems Biology, Eds. B. Ingalls and P. Iglesias. 2009.

    • 2008

  • D. Georgiev and E. Klavins, Model Discrimination of Polynomial Systems via Stochastic Inputs, Conference on Decision and Control. 2008.
  • F. Shaw and E. Klavins, Distributed Estimation and Control For Stochastically Interacting Robots, Conference on Decision and Control. 2008.
  • J. M. McNew and E. Klavins, Non-deterministic Reconfiguration of Tree Formations, American Control Conference. pp. 690-697. June 2008.
  • D. Thorsley and E. Klavins, Model Reduction of Stochastic Processes Using Wasserstein Pseudometrics, American Control Conference. pp. 1374-1381. June 2008.

    • 2007

  • J. Bishop and E. Klavins, An Improved Autonomous DNA Nanomotor, Nanoletters. Vol. 7, No. 9. pp. 2574-7. Sep 2007.
  • E. Klavins, Programmable Self-Assembly, Control Systems Magazine. Vol. 24, No. 4. pp. 43-56. Aug 2007.
  • W. B. Dunbar, N. A. Wilson, J. Schaeffer, E. Klavins, J. Bishop and B. Tanner, Dynamics and control of biomolecules: Research venues and opportunites, 46th Conference on Decision and Control. pp. 3297-3307. Dec 2007.

    • In our 2007 Nanoletters paper, Josh Bishop developed a new molecular nanomotor that is robust to its own waste products!

  • M. Yim, W.M. Shen, B. Salemi, D. Rus, M. Moll, H. Lipson, E. Klavins and G.S. Chirickjian, Modular Self-Reconfigurable Robot Systems, IEEE Robotics and Automation Magazine. Vol. 14, No. 1. pp. 43-42. Mar 2007.
  • C. Belta, A. Bicchi, M. Egerstedt, E. Frazzoli, E. Klavins and G.J. Pappas, Symbolic Planning and Control of Robot Motion, IEEE Robotics and Automation Magazine. Vol. 14, No. 1. pp. 61-70. Mar 2007.
  • J. M. McNew, E. Klavins and M. Egerstedt, Solving Coverage Problems with Embedded Graph Grammars, Hybrid Systems: Computation and Control. 2007.
  • S. Waydo, J. Hauser and R. Bailey, E. Klavins and R. Murray, UAV as a Reliable Wingman: A Flight Demonstration, IEEE Transactions on Control Systems Technology. Vol. 15, No. 4. pp. 680--688. Jul 2007.

    • 2006

  • E. Klavins, S. Burden and N. Napp, Optimal Rules for Programmed Stochastic Self-Assembly, Robotics: Science and Systems II. pp. 9-16. 2006.
  • J. Bishop and E. Klavins, Collective Sensing with Self-Organizing Robots, 45th IEEE Conference on Decision and Control, . pp. 4175-81. 2006.
  • J. M. McNew and E. Klavins, Locally Interacting Hybrid Systems with Embedded Graph Grammars, 45th IEEE Conference on Decision and Control. pp. 6080-87. 2006.
  • E. Klavins, Self-Assembly From the Point of View of Its Pieces, American Control Conference. Jun 2006.
  • J. M. McNew and E. Klavins, Model-Checking and Control of Self-Assembly, American Control Conference. Jun 2006.

    • In our 2006 RSS paper, we optimzed the rate of robotic self assembly with traingular robotic pieces.

  • S. Burden, N. Napp, E. Klavins, The Statistical Dynamics of Programmed Robotic Self-Assembly, International Conference on Robotics and Automation. pp. 1469--76. May 2006.
  • E. Klavins, R. Ghrist and D. Lipsky, A Grammatical Approach to Self-Organizing Robotic Systems, IEEE Transactions on Automatic Control. Vol. 51, No. 5. pp. 949-962. June 2006.
  • D. Del Vecchio, R. Murray and E. Klavins, Discrete State Estimators for Systems on a Lattice, Automatica. Vol. 42, No. 2. pp. 271-285. 2006.

    • 2005

  • J. M. McNew and E. Klavins, A Grammatical Approach to Cooperative Control: The wanderers and Scouts Example, Cooperative Control. 2005.
  • J. Bishop, S. Burden, E. Klavins, R. Kreisberg, W. Malone, N. Napp and T. Nguyen, Self-Organizing Programmable Parts, International Conference on Intelligent Robots and Systems. 2005.

    • 2004

  • E. Klavins, Universal Self-Replication Using Graph Grammars, International Conference on MEMs, NANO and Smart Systems. 2004.
  • E. Klavins, Directed Self-Assembly Using Graph Grammars, Foundations of Nanoscience: Self Assembled Architectures and Devices. 2004.

    • In my papers with Rob Ghrist (ICRA 2004, TAC 2006), we explored the power and limitations of graph grammers for self-assembly and robotic self-organization.

  • E. Klavins, R. Ghrist, and D. Lipsky, Graph Grammars for Self-Assembling Robotic Systems, Proceedings of the International Conference on Robotics and Automation. pp. 5293-5300. May 2004.
  • E. Klavins, A Language for Modeling and Programming Cooperative Control Systems, Proceedings of the International Conference on Robotics and Automation. pp. 3403-3410. May 2004.
  • E. Klavins and R. Murray, Distributed Algorithms for Cooperative Control, IEEE Pervasive Computing. Vol. 3, No. 1. pp. 56-65. 2004.

    • 2003

  • E. Klavins, A Formal Model of a Multi-Robot Control and Communication Task, 42nd IEEE Conference on Decision and Control. Dec 2003.
  • D. Del Vecchio and E. Klavins, Observation of Hybrid Guarded Command Programs, 42nd IEEE Conference on Decision and Control. Dec 2003.
  • S. Waydo. B. Dunbar and E. Klavins, Toward Feedback Stabilization of Faulty Software Systems: A Case Study, 42nd IEEE Conference on Decision and Control. Dec 2003.
  • E. Klavins, Communication Complexity of Multi-Robot Systems, Algorithmic Foundations of Robotics V. Eds. J.-D. Boissonnat, J. Burdick, K. Goldberg, S. Hutchinson. Vol. 7. pp. 275-292. 2003.
  • E. Klavins, Toward the Control of Self-Assembling Systems, Control Problems in Robotics. Eds. A. Bicchi, H. Christensen and D. Prattichizzo. Vol. 4. pp. 153-168. 2003.

    • 2002

  • E. Klavins, Automatically Synthesized Controllers for Distributed Assembly: Partial Correctness, Cooperative Control: Models, Applications and Algorithms. Eds. S. Butenko, R. Murphey and P. M. Pardalos. pp. 111-127. 2002.
  • E. Klavins and U. Saranli, Object Oriented State Machines, Embedded Systems Magazine. pp. 30-42.. May 2002.
  • E. Klavins, Automatic Synthesis of Controllers for Distributed Assembly and Formation Forming, Proceedings of the IEEE Conference on Robotics and Automation. May 2002.

    • In my 2002 IJRR paper, I showed that potential functions can be used to regulate phase for multi-legged robots.

  • E. Klavins and D. E. Koditschek, Phase Regulation of Decentralized Cyclic Robotic Systems, International Journal of Robotics Research. Vol. 21, No. 3. pp. 257-276. 2002.
  • T. Chung, L. Cremean, B. Dunbar, Z. Jin, E. Klavins, D. Moore, A. Tiwari, D. van Gogh and S. Waydo, A Platform for Cooperative and Coordinated Control of Multiple Vehicles: The Caltech Multi-Vehicle Wireless Testbed, Proceedings of the Conference on Cooperative Control and Optimization.. 2002.
  • L. Cremean, B. Dunbar, D. van Gogh, J. Hickey, E. Klavins, J. Meltzer and R. M. Murray, The Caltech Multi-Vehicle Wireless Testbed, 41st IEEE Conference on Decision and Control. Dec 2002.

    • 2001

  • E. Klavins, H. Komsuoglu, R. J. Full and D. E. Koditschek, The Role of Reflexes Versus Central Pattern Generators in Dynamical Legged Locomotion, Neurotechnology for Biomimetic Robots. Eds. J. Ayers, J. Davis and A. Rudolph. MIT Press. 2001.
  • E. Klavins and D. E. Koditschek, Stability of Hybrid Coupled Oscillators, International Conference on Robotics and Automation. 2001.
  • E. Klavins, Decentralized Phase Regulation of Cyclic Robotic Systems, Ph.D. Thesis, University of Michigan. June 2001.

    • 2000

  • E. Klavins, Automatic Compilation of Concurrent Hybrid Factories from Product Assembly Specifications, Hybrid Systems: Computation and Control. LNCS 1790. Springer-Verlag. pp. 174-187. 2000.
  • E. Klavins and D. E. Koditschek, A Formalism for the Composition of Concurrent Robot Behaviors, In Proceedings of the IEEE Conference on Robotics and Automation. 2000.

    • Eric's first paper: A phase transition between satisfiable and unsatisfiable 3-valued logic propositions. Exciting!

  • E. Klavins, D. E. Koditschek and R. Ghrist, Toward the Regulation and Composition of Cyclic Behaviors, Algorithmic and Computational Robotics: New Directions (2000 WAFR). Eds. B. R. Donald, K. M. Lynch and D. Rus. pp. 205-220.. 2000.

    • 1998

  • E. Klavins, W. C. Rounds, and Q.-Q. Zhang, Experimenting with Power Default Reasoning, Proceedings of AAAI-98. 1998.

2015

  • David Younger, Toward an S. cerevisiae mating assay as a tool for protein engineering, extracellular target detection, and synthetic ecology, DYF15. 2015.

    • 2014

  • Chris Takahashi, Evolutionary Dynamics in a Turbidostat, CTF14. 2014.
  • Stephen Rettie, Review of Fusion Assay Design: Strategies for the Construction of a Rapid Assay for the Detection of Cell Fusion, StRF14. 2014.
  • David Younger, Toward a Saccharomyces cerevisiae mating assay as a novel diagnostic platform, DYF14. 2014.
  • Miles Gander and William Voje, Design and Implementation of CRISPR/Cas9 Transcription Factor Wires Using RNA Polymerase II, MGF14. 2014.
  • Harrison Haghanegi, Current Klavins Lab Research in Comparison to Global Trends in Synthetic Biology, HHF14. 2014.
  • Luis Zaman, A Brief History and Prospectus of Applied Coevolution, LZF14. 2014.
  • Nick Bolten and Arjun Khakhar, Engineering orthogonal, auxin-based cell-to-cell communication into yeast, AK-NBF14. 2014.
  • Yaoyu Yang, Design and Construction of an Inducible Bistable Switch in Yeast, YYF14. 2014.
  • T. Amimeur, Review of Bayesian Approaches: for Potential Applications in Synthetic Biology Design-Space Mapping, TASU14. 2014.
  • N. Bolten, Yeast Intercellular Oscillator and Activator-Inhibitor Pattern Formation System, NBSU14. 2014.
  • L. Brettner, No Man (or Microbe) is an Island: The Potential Effects of Community Structure on the Performance of Synthetic Behaviors, LBSU14. 2014.
  • M. Gander, Toward Rational Design of Complex Transcriptionally Controlled Gene Circuits in Saccharomyces Cerevisiae, MGSU14. 2014.
  • H. Haghanegi, Quantification of RNA via Real-Time qPCR: Methods and Procedures, HHSU14. 2014.
  • A. Khakhar, Enhancing CRISPR Based Transcription Factors with Plant Like Tunability, AKSU14. 2014.
  • C. Takahashi, A Review of Recombineering in a Semiautomated Workflow, CTSU14. 2014.
  • Y. Yang, Design and Analysis of a Plant Hormone Induced Oscillator in Yeast, YYSU14. 2014.
  • D. Younger, The Role of Sexual Agglutinin Proteins in the Mating of S. cerevisiae, DYSU14. 2014.

    • 2000

  • E. Klavins, The Construction of Attention Functions for Phase Regulation, University of Michigan Technical Report. No. CSE-TR-422-00. 2000.

    • 1999

  • E. Klavins, A Formalism for the Composition of Loosely Coupled Robot Behaviors, University of Michigan Technical Report. No. CSE-TR-412-99. 1999.

    • 2017

  • D. Younger, High Throughput Characterization of Protein-Protein Interactions by Reprogramming Yeast Mating, Ph.D. Thesis, University of Washington. 2017.

    • 2016

  • Y. Yang, Design and Construction of a Genetic Bistable Switch in S. cerevisiae, Ph.D. Thesis, University of Washington. 2016.

    • 2015

  • C. N. Takahashi, Directed Evolution in a Turbidostat, Ph.D. Thesis, University of Washington. 2015.

    • 2014

  • S. S. Jang, Parameter-Component Dependency: Identifying the Biological Functions of Interchangeable Genetic Components, Ph.D. Thesis, University of Washington. 2014.
  • K. Oishi, Programming Molecules and Cells: Design Architectures for Chemical Reaction and Gene Regulatory Networks, Ph.D. Thesis, University of Washington. 2014.

    • 2012

  • R. Egbert, Fine-tuning Gene Networks Using Simple Sequence Repeats, Ph.D. Thesis, University of Washington. 2012.
  • F. Shaw, Decentralized Estimation for Stochastic Multi-Agent Systems, Ph.D. Thesis, University of Washington. 2012.
  • J. Bishop, Engineering the Feedback Dynamics of in vitro Synthetic Biological Systems, Ph.D. Thesis, University of Washington. 2012.

    • 2011

  • N. Napp, Control of Stochastically Interacting Particles with Applications to Robotics, Ph.D. Thesis, University of Washington. 2011.

    • 2008

  • J. M. McNew, Nondeterministic Modeling and Verification of Networked Robotic Systems, Ph.D. Thesis, University of Washington. 2008.

    • 2001

  • E. Klavins, Decentralized Phase Regulation of Cyclic Robotic Systems, Ph.D. Thesis, University of Michigan. 2001.