Erik Winfree

Summary

Affiliation: California Institute of Technology
Country: USA

Publications

  1. pmc Synthetic in vitro transcriptional oscillators
    JongMin Kim
    Department of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Mol Syst Biol 7:465. 2011
  2. pmc A simple DNA gate motif for synthesizing large-scale circuits
    Lulu Qian
    Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
    J R Soc Interface 8:1281-97. 2011
  3. pmc Construction of an in vitro bistable circuit from synthetic transcriptional switches
    JongMin Kim
    Biology, California Institute of Technology, Pasadena, CA, USA
    Mol Syst Biol 2:68. 2006
  4. pmc On the biophysics and kinetics of toehold-mediated DNA strand displacement
    Niranjan Srinivas
    Computation and Neural Systems, California Institute of Technology, Pasadena, CA 91125, USA, Rudolph Peierls Centre for Theoretical Physics, Department of Physics, University of Oxford, Oxford OX1 3NP, UK, Computer Science, California Institute of Technology, Pasadena, CA 91125, USA, Departments of Electrical and Computer Engineering, Materials Science and Engineering, Boise State University, ID83725, USA, Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK and Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
    Nucleic Acids Res 41:10641-58. 2013
  5. pmc Algorithmic self-assembly of DNA Sierpinski triangles
    Paul W K Rothemund
    Computation and Neural Systems, California Institute of Technology, Pasadena, USA
    PLoS Biol 2:e424. 2004
  6. pmc Paradigms for computational nucleic acid design
    Robert M Dirks
    Chemistry Department, California Institute of Technology, Pasadena, CA 91125, USA
    Nucleic Acids Res 32:1392-403. 2004
  7. ncbi request reprint Engineering entropy-driven reactions and networks catalyzed by DNA
    David Yu Zhang
    Computation and Neural Systems, California Institute of Technology, MC 136 93, 1200 East California Boulevard, Pasadena, CA91125, USA
    Science 318:1121-5. 2007
  8. pmc Integrating DNA strand-displacement circuitry with DNA tile self-assembly
    David Yu Zhang
    Department of Computation and Neural Systems, California Institute of Technology, Pasadena, California, USA
    Nat Commun 4:1965. 2013
  9. pmc An information-bearing seed for nucleating algorithmic self-assembly
    Robert D Barish
    California Institute of Technology, Pasadena, CA 91125, USA
    Proc Natl Acad Sci U S A 106:6054-9. 2009
  10. doi request reprint Scaling up digital circuit computation with DNA strand displacement cascades
    Lulu Qian
    Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
    Science 332:1196-201. 2011

Collaborators

Detail Information

Publications25

  1. pmc Synthetic in vitro transcriptional oscillators
    JongMin Kim
    Department of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Mol Syst Biol 7:465. 2011
    ..Synthetic transcriptional oscillators could prove valuable for systematic exploration of biochemical circuit design principles and for controlling nanoscale devices and orchestrating processes within artificial cells...
  2. pmc A simple DNA gate motif for synthesizing large-scale circuits
    Lulu Qian
    Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
    J R Soc Interface 8:1281-97. 2011
    ..Here, we propose a simple DNA gate architecture that appears suitable for practical synthesis of large-scale circuits involving possibly thousands of gates...
  3. pmc Construction of an in vitro bistable circuit from synthetic transcriptional switches
    JongMin Kim
    Biology, California Institute of Technology, Pasadena, CA, USA
    Mol Syst Biol 2:68. 2006
    ..Construction of larger synthetic circuits provides a unique opportunity for evaluating model inference, prediction, and design of complex biochemical systems and could be used to control nanoscale devices and artificial cells...
  4. pmc On the biophysics and kinetics of toehold-mediated DNA strand displacement
    Niranjan Srinivas
    Computation and Neural Systems, California Institute of Technology, Pasadena, CA 91125, USA, Rudolph Peierls Centre for Theoretical Physics, Department of Physics, University of Oxford, Oxford OX1 3NP, UK, Computer Science, California Institute of Technology, Pasadena, CA 91125, USA, Departments of Electrical and Computer Engineering, Materials Science and Engineering, Boise State University, ID83725, USA, Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK and Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
    Nucleic Acids Res 41:10641-58. 2013
    ..Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems. ..
  5. pmc Algorithmic self-assembly of DNA Sierpinski triangles
    Paul W K Rothemund
    Computation and Neural Systems, California Institute of Technology, Pasadena, USA
    PLoS Biol 2:e424. 2004
    ..This shows that engineered DNA self-assembly can be treated as a Turing-universal biomolecular system, capable of implementing any desired algorithm for computation or construction tasks...
  6. pmc Paradigms for computational nucleic acid design
    Robert M Dirks
    Chemistry Department, California Institute of Technology, Pasadena, CA 91125, USA
    Nucleic Acids Res 32:1392-403. 2004
    ..Finally, we observe that designing for thermodynamic stability does not determine folding kinetics, emphasizing the opportunity for extending design criteria to target kinetic features of the energy landscape...
  7. ncbi request reprint Engineering entropy-driven reactions and networks catalyzed by DNA
    David Yu Zhang
    Computation and Neural Systems, California Institute of Technology, MC 136 93, 1200 East California Boulevard, Pasadena, CA91125, USA
    Science 318:1121-5. 2007
    ..We have constructed and characterized several circuits that amplify nucleic acid signals, including a feedforward cascade with quadratic kinetics and a positive feedback circuit with exponential growth kinetics...
  8. pmc Integrating DNA strand-displacement circuitry with DNA tile self-assembly
    David Yu Zhang
    Department of Computation and Neural Systems, California Institute of Technology, Pasadena, California, USA
    Nat Commun 4:1965. 2013
    ..Integrating more sophisticated control circuits and tile systems could enable precise spatial and temporal organization of dynamic molecular structures...
  9. pmc An information-bearing seed for nucleating algorithmic self-assembly
    Robert D Barish
    California Institute of Technology, Pasadena, CA 91125, USA
    Proc Natl Acad Sci U S A 106:6054-9. 2009
    ..In sum, this work demonstrates how DNA origami seeds enable the easy, high-yield, low-error-rate growth of algorithmic crystals as a route toward programmable bottom-up fabrication...
  10. doi request reprint Scaling up digital circuit computation with DNA strand displacement cascades
    Lulu Qian
    Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
    Science 332:1196-201. 2011
    ..The design naturally incorporates other crucial elements for large-scale circuitry, such as general debugging tools, parallel circuit preparation, and an abstraction hierarchy supported by an automated circuit compiler...
  11. pmc Synthesis of crystals with a programmable kinetic barrier to nucleation
    Rebecca Schulman
    Department of Computation and Neural Systems, California Institute of Technology, Pasadena, CA 91125, USA
    Proc Natl Acad Sci U S A 104:15236-41. 2007
    ..More generally, this work shows how a self-assembly subroutine can be initiated...
  12. doi request reprint Ensemble Bayesian analysis of bistability in a synthetic transcriptional switch
    Pakpoom Subsoontorn
    Department of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    ACS Synth Biol 1:299-316. 2012
    ..Our work demonstrates that programmable in vitro biochemical circuits can serve as a testing ground for evaluating methods for the design and analysis of more complex biochemical systems such as living cells...
  13. ncbi request reprint Enzyme-free nucleic acid logic circuits
    Georg Seelig
    Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA
    Science 314:1585-8. 2006
    ..Biological nucleic acids such as microRNAs can serve as inputs, suggesting applications in biotechnology and bioengineering...
  14. pmc Robustness and modularity properties of a non-covalent DNA catalytic reaction
    David Yu Zhang
    California Institute of Technology, MC 136 93, 1200 E California Blvd, Pasadena, CA 91125, USA
    Nucleic Acids Res 38:4182-97. 2010
    ..These properties facilitate the incorporation of strand displacement-based DNA components in synthetic chemical and biological reaction networks...
  15. ncbi request reprint Two computational primitives for algorithmic self-assembly: copying and counting
    Robert D Barish
    Department of Computer Science, California Institute of Technology and Computation and Neural Systems, Pasadena, CA 91125, USA
    Nano Lett 5:2586-92. 2005
    ..A subset of the tiles for counting form information-bearing DNA tubes that copy bit strings from layer to layer along their length...
  16. ncbi request reprint Catalyzed relaxation of a metastable DNA fuel
    Georg Seelig
    Department of Applied Physics, California Institute of Technology, Pasadena, California 91125, USA
    J Am Chem Soc 128:12211-20. 2006
    ..The amplifier uses a single strand of DNA as input and releases a second strand with unrelated sequence as output. A single input strand can catalytically trigger the release of more than 10 output strands...
  17. pmc Robust self-replication of combinatorial information via crystal growth and scission
    Rebecca Schulman
    Computer Science, California Institute of Technology, Pasadena, CA 91125, USA
    Proc Natl Acad Sci U S A 109:6405-10. 2012
    ..The form of the replicated information is also compatible with the replication and evolution of a wide class of materials with precise nanoscale geometry such as plasmonic nanostructures or heterogeneous protein assemblies...
  18. doi request reprint Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates
    Hareem T Maune
    California Institute of Technology, Pasadena, California 91125, USA
    Nat Nanotechnol 5:61-6. 2010
    ..In such organizations of electronic components, DNA origami serves as a programmable nanobreadboard; thus, DNA origami may allow the rapid prototyping of complex nanotube-based structures...
  19. doi request reprint Neural network computation with DNA strand displacement cascades
    Lulu Qian
    Bioengineering, California Institute of Technology, Pasadena, California 91125, USA
    Nature 475:368-72. 2011
    ..Our results suggest that DNA strand displacement cascades could be used to endow autonomous chemical systems with the capability of recognizing patterns of molecular events, making decisions and responding to the environment...
  20. ncbi request reprint Design and characterization of programmable DNA nanotubes
    Paul W K Rothemund
    Department of Computer Science, California Institute of Technology, Pasadena, California 91125, USA
    J Am Chem Soc 126:16344-52. 2004
    ..Supported by these results, nanotube structure is explained by a simple model based on the geometry and energetics of B-form DNA...
  21. doi request reprint Dynamic allosteric control of noncovalent DNA catalysis reactions
    David Yu Zhang
    California Institute of Technology, MC 136 93, 1200 East California Boulevard, Pasadena, California 91125, USA
    J Am Chem Soc 130:13921-6. 2008
    ..Unlike previous works, both the allosteric receptor and catalytic core are designed, rather than evolved. This allows flexibility in the sequence design and modularity in synthetic network construction...
  22. doi request reprint Control of DNA strand displacement kinetics using toehold exchange
    David Yu Zhang
    California Institute of Technology, MC 136 93, 1200 E California Boulevard, Pasadena, California 91125, USA
    J Am Chem Soc 131:17303-14. 2009
    ..This work improves the understanding of the kinetics of nucleic acid reactions and will be useful in the rational design of dynamic DNA and RNA circuits and nanodevices...
  23. doi request reprint Direct atomic force microscopy observation of DNA tile crystal growth at the single-molecule level
    Constantine G Evans
    Physics, California Institute of Technology, Pasadena, California 91125, USA
    J Am Chem Soc 134:10485-92. 2012
    ..We show that these statistics fit the widely used kinetic Tile Assembly Model and demonstrate AFM movies as a viable technique for directly investigating DNA tile systems during growth rather than after assembly...
  24. pmc Timing molecular motion and production with a synthetic transcriptional clock
    Elisa Franco
    Control and Dynamical Systems, California Institute of Technology, Pasadena, CA 91125, USA
    Proc Natl Acad Sci U S A 108:E784-93. 2011
    ..Understanding how to design effective insulation between biochemical subsystems will be critical for the synthesis of larger and more complex systems...
  25. ncbi request reprint Protein design is NP-hard
    Niles A Pierce
    Applied and Computational Mathematics, California Institute of Technology, Pasadena, CA 91125, USA
    Protein Eng 15:779-82. 2002
    ..The purpose of this paper is to explain the context of this observation, to provide a simple illustrative proof and to discuss the implications for future progress on algorithms for computational protein design...