Winfree, Erik

Book Chapter from CaltechAUTHORS

• Zolaktaf, Sedigheh and Dannenberg, Frits, el al. (2019) Efficient Parameter Estimation for DNA Kinetics Modeled as Continuous-Time Markov Chains; ISBN 978-3-030-26806-0; DNA Computing and Molecular Programming; 80-99; 10.1007/978-3-030-26807-7_5
• Winfree, Erik (2019) Chemical Reaction Networks and Stochastic Local Search; ISBN 978-3-030-26806-0; DNA Computing and Molecular Programming; 1-20; 10.1007/978-3-030-26807-7_1
• Brailovskaya, Tatiana and Gowri, Gokul, el al. (2019) Reversible Computation Using Swap Reactions on a Surface; ISBN 978-3-030-26806-0; DNA Computing and Molecular Programming; 174-196; 10.1007/978-3-030-26807-7_10
• Evans, Constantine G. and Winfree, Erik (2018) Optimizing Tile Set Size While Preserving Proofreading with a DNA Self-assembly Compiler; ISBN 978-3-030-00029-5; DNA Computing and Molecular Programming; 37-54; 10.1007/978-3-030-00030-1_3
• Zolaktaf, Sedigheh and Dannenberg, Frits, el al. (2017) Inferring Parameters for an Elementary Step Model of DNA Structure Kinetics with Locally Context-Dependent Arrhenius Rates; ISBN 978-3-319-66798-0; DNA Computing and Molecular Programming; 172-187; 10.1007/978-3-319-66799-7_12
• Poole, William and Ortiz-Muñoz, Andrés, el al. (2017) Chemical Boltzmann Machines; ISBN 978-3-319-66798-0; DNA Computing and Molecular Programming; 210-231; 10.1007/978-3-319-66799-7_14
• Badelt, Stefan and Shin, Seung Woo, el al. (2017) A General-Purpose CRN-to-DSD Compiler with Formal Verification, Optimization, and Simulation Capabilities; ISBN 978-3-319-66798-0; DNA Computing and Molecular Programming; 232-248; 10.1007/978-3-319-66799-7_15
• Schiefer, Nicholas and Winfree, Erik (2016) Time Complexity of Computation and Construction in the Chemical Reaction Network-Controlled Tile Assembly Model; ISBN 978-3-319-43993-8; DNA Computing and Molecular Programming; 165-182; 10.1007/978-3-319-43994-5_11
• Johnson, Robert F. and Dong, Qing, el al. (2016) Verifying Chemical Reaction Network Implementations: A Bisimulation Approach; ISBN 9783319439938; DNA Computing and Molecular Programming; 114-134; 10.1007/978-3-319-43994-5_8
• Thachuk, Chris and Winfree, Erik, el al. (2015) Leakless DNA Strand Displacement Systems; ISBN 978-3-319-21998-1; DNA Computing and Molecular Programming; 133-153; 10.1007/978-3-319-21999-8_9
• Schaeffer, Joseph Malcolm and Thachuk, Chris, el al. (2015) Stochastic Simulation of the Kinetics of Multiple Interacting Nucleic Acid Strands; ISBN 978-3-319-21998-1; DNA Computing and Molecular Programming; 194-211; 10.1007/978-3-319-21999-8_13
• Schiefer, Nicholas and Winfree, Erik (2015) Universal Computation and Optimal Construction in the Chemical Reaction Network-Controlled Tile Assembly Model; ISBN 978-3-319-21998-1; DNA Computing and Molecular Programming: 21st International Conference, DNA 21, Boston and Cambridge, MA, USA, August 17-21, 2015. Proceedings; 34-54; 10.1007/978-3-319-21999-8_3
• Qian, Lulu and Winfree, Erik (2014) Parallel and Scalable Computation and Spatial Dynamics with DNA-Based Chemical Reaction Networks on a Surface; ISBN 978-3-319-11294-7; DNA Computing and Molecular Programming; 114-131; 10.1007/978-3-319-11295-4_8
• Woods, Damien and Chen, Ho-Lin, el al. (2013) Active Self-Assembly of Algorithmic Shapes and Patterns in Polylogarithmic Time; ISBN 978-1-4503-1859-4; Proceedings of the 4th conference on Innovations in Theoretical Computer Science; 353-354; 10.1145/2422436.2422476
• Evans, Constantine G. and Winfree, Erik (2013) DNA Sticky End Design and Assignment for Robust Algorithmic Self-assembly; ISBN 978-3-319-01927-7; DNA Computing and Molecular Programming; 61-75; 10.1007/978-3-319-01928-4_5
• Densmore, Douglas and Horowitz, Mark, el al. (2011) Joint DAC/IWBDA special session design and synthesis of biological circuits; ISBN 978-1-4503-0636-2; Proceedings of the 48th Design Automation Conference; 114-115; 10.1145/2024724.2024750
• Schulman, Rebecca and Winfree, Erik (2011) Simple Evolution of Complex Crystal Species; ISBN 978-3-642-18304-1; DNA Computing and Molecular Programming; 147-161; 10.1007/978-3-642-18305-8_14
• Qian, Lulu and Soloveichik, David, el al. (2011) Efficient Turing-Universal Computation with DNA Polymers; ISBN 978-3-642-18304-1; DNA computing and molecular programming; 123-140; 10.1007/978-3-642-18305-8_12
• Cook, Matthew and Soloveichik, David, el al. (2009) Programmability of Chemical Reaction Networks; ISBN 978-3-540-88868-0; Algorithmic Bioprocesses; 543-584; 10.1007/978-3-540-88869-7_27
• Soloveichik, David and Seelig, Georg, el al. (2009) DNA as a Universal Substrate for Chemical Kinetics; ISBN 978-3-642-03075-8; DNA Computing; 57-69; 10.1007/978-3-642-03076-5_6
• Qian, Lulu and Winfree, Erik (2009) A Simple DNA Gate Motif for Synthesizing Large-Scale Circuits; ISBN 978-3-642-03075-8; DNA computing : 14th International Meeting on DNA Computing, DNA 14, Prague, Czech Republic, June 2-9, 2008 : revised selected papers; 70-89; 10.1007/978-3-642-03076-5
• Winfree, Erik (2008) Toward molecular programming with DNA; ISBN 978-1-59593-958-6; ASPLOS XIII Proceedings of the 13th international conference on Architectural support for programming languages and operating systems; 10.1145/1346281.1346282
• Winfree, Erik (2006) Algorithmic Self-Assembly of DNA; ISBN 978-1-4244-0337-0; Proceedings of the 2006 International Conference on Microtechnologies in Medicine and Biology; 4-4
• Winfree, Erik (2006) Self-Healing Tile Sets; ISBN 9783540302964; Nanotechnology: Science and Computation; 55-78; 10.1007/3-540-30296-4_4
• Winfree, Erik (2006) Fault-Tolerance in Biochemical Systems; ISBN 978-3-540-38593-6; Unconventional Computation; 26; 10.1007/11839132_3
• Soloveichik, David and Winfree, Erik (2006) Complexity of compact proofreading for self-assembled patterns; ISBN 3-540-34161-7; DNA Computing; 305-324; 10.1007/11753681_24
• Seelig, Georg and Yurke, Bernard, el al. (2005) DNA hybridization catalysts and catalyst circuits; ISBN 3-540-26174-5; DNA Computing; 329-343; 10.1007/11493785_29
• Schulman, Rebecca and Winfree, Erik (2005) Programmable Control of Nucleation for Algorithmic Self-assembly; ISBN 978-3-540-26174-2; DNA Computing; 319-328; 10.1007/11493785_28
• Soloveichik, David and Winfree, Erik (2005) Complexity of Self-assembled Shapes (Extended Abstract); ISBN 978-3-540-26174-2; DNA Computing; 344-354; 10.1007/11493785_30
• Schulman, Rebecca and Winfree, Erik (2005) Self-replication and evolution of DNA crystals; ISBN 3-540-28848-1; Advances in Artificial Life; 734-743; 10.1007/11553090_74
• Winfree, Erik and Bekbolatov, Renat (2004) Proofreading tile sets: Error correction for algorithmic self-assembly; ISBN 3-540-20930-1; DNA Computing; 126-144; 10.1007/978-3-540-24628-2_13
• Schulman, Rebecca and Lee, Shaun, el al. (2004) One dimensional boundaries for DNA tile self-assembly; ISBN 3-540-20930-1; DNA Computing; 108-125; 10.1007/978-3-540-24628-2_12
• Cook, Matthew and Rothemund, Paul W. K., el al. (2004) Self-assembled circuit patterns; ISBN 3-540-20930-1; DNA Computing; 91-107; 10.1007/978-3-540-24628-2_11
• Winfree, Erik and Landweber, Laura F. (2002) Introduction: Evolution and Computation: Where Do They Meet?; ISBN 978-3-642-63081-1; Evolution as Computation: DIMACS Workshop, Princeton, January 1999; v-ix
• Winfree, Erik and Eng, Tony, el al. (2001) String tile models for DNA computing by self-assembly; ISBN 978-3-540-42076-7; DNA Computing; 63-88; 10.1007/3-540-44992-2_6
• Winfree, Erik (2001) In Vitro Transcriptional Circuits; ISBN 978-1-85233-415-4; Unconventional Models of Computation, UMC'2K; 121-122; 10.1007/978-1-4471-0313-4_10
• Rothemund, Paul W. K. and Winfree, Erik (2000) The program-size complexity of self-assembled squares; ISBN 1-58113-184-4; STOC '00 Proceedings of the thirty-second annual ACM symposium on Theory of computing; 459-468; 10.1145/335305.335358
• Chen, Kevin and Winfree, Erik (2000) Error Correction in DNA Computing: Misclassification and Strand Loss; ISBN 9780821820537; DNA Based Computers V; 49-63
• LaBean, Thomas H. and Winfree, Erik, el al. (2000) Experimental Progress in Computation by Self-Assembly of DNA Tilings; ISBN 9780821820537; DNA Based Computers V; 123-40
• Winfree, Erik and Yang, Xiaoping, el al. (1999) Universal Computation via Self-assembly of DNA: Some Theory and Experiments; ISBN 0821807560; DNA Based Computers II; 191-213
• Winfree, Erik (1996) On the Computational Power of DNA Annealing and Ligation; ISBN 0821805185; DNA Based Computers; 199-221
• Winfree, Erik (1996) Complexity of Restricted and Unrestricted Models of Molecular Computation; ISBN 0821805185; DNA based computers; 187-198