<h1>Winfree, Erik</h1>
<h2>Book Chapter from <a href="https://authors.library.caltech.edu">CaltechAUTHORS</a></h2>
<ul>
<li>Winfree, Erik (2019) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200810-152243847">Chemical Reaction Networks and Stochastic Local Search</a>; ISBN 978-3-030-26806-0; DNA Computing and Molecular Programming; 1-20; <a href="https://doi.org/10.1007/978-3-030-26807-7_1">10.1007/978-3-030-26807-7_1</a></li>
<li>Zolaktaf, Sedigheh and Dannenberg, Frits, el al. (2019) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200811-134907797">Efficient Parameter Estimation for DNA Kinetics Modeled as Continuous-Time Markov Chains</a>; ISBN 978-3-030-26806-0; DNA Computing and Molecular Programming; 80-99; <a href="https://doi.org/10.1007/978-3-030-26807-7_5">10.1007/978-3-030-26807-7_5</a></li>
<li>Brailovskaya, Tatiana and Gowri, Gokul, el al. (2019) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20190730-094203386">Reversible Computation Using Swap Reactions on a Surface</a>; ISBN 978-3-030-26806-0; DNA Computing and Molecular Programming; 174-196; <a href="https://doi.org/10.1007/978-3-030-26807-7_10">10.1007/978-3-030-26807-7_10</a></li>
<li>Evans, Constantine G. and Winfree, Erik (2018) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200811-140005797">Optimizing Tile Set Size While Preserving Proofreading with a DNA Self-assembly Compiler</a>; ISBN 978-3-030-00029-5; DNA Computing and Molecular Programming; 37-54; <a href="https://doi.org/10.1007/978-3-030-00030-1_3">10.1007/978-3-030-00030-1_3</a></li>
<li>Poole, William and Ortiz-Muñoz, Andrés, el al. (2017) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20181126-090207704">Chemical Boltzmann Machines</a>; ISBN 978-3-319-66798-0; DNA Computing and Molecular Programming; 210-231; <a href="https://doi.org/10.1007/978-3-319-66799-7_14">10.1007/978-3-319-66799-7_14</a></li>
<li>Badelt, Stefan and Shin, Seung Woo, el al. (2017) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20181126-085056720">A General-Purpose CRN-to-DSD Compiler with Formal Verification, Optimization, and Simulation Capabilities</a>; ISBN 978-3-319-66798-0; DNA Computing and Molecular Programming; 232-248; <a href="https://doi.org/10.1007/978-3-319-66799-7_15">10.1007/978-3-319-66799-7_15</a></li>
<li>Zolaktaf, Sedigheh and Dannenberg, Frits, el al. (2017) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20181126-091545698">Inferring Parameters for an Elementary Step Model of DNA Structure Kinetics with Locally Context-Dependent Arrhenius Rates</a>; ISBN 978-3-319-66798-0; DNA Computing and Molecular Programming; 172-187; <a href="https://doi.org/10.1007/978-3-319-66799-7_12">10.1007/978-3-319-66799-7_12</a></li>
<li>Johnson, Robert F. and Dong, Qing, el al. (2016) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20191007-155606936">Verifying Chemical Reaction Network Implementations: A Bisimulation Approach</a>; ISBN 9783319439938; DNA Computing and Molecular Programming; 114-134; <a href="https://doi.org/10.1007/978-3-319-43994-5_8">10.1007/978-3-319-43994-5_8</a></li>
<li>Schiefer, Nicholas and Winfree, Erik (2016) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170718-122926337">Time Complexity of Computation and Construction in the Chemical Reaction Network-Controlled Tile Assembly Model</a>; ISBN 978-3-319-43993-8; DNA Computing and Molecular Programming; 165-182; <a href="https://doi.org/10.1007/978-3-319-43994-5_11">10.1007/978-3-319-43994-5_11</a></li>
<li>Schaeffer, Joseph Malcolm and Thachuk, Chris, el al. (2015) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200811-152309514">Stochastic Simulation of the Kinetics of Multiple Interacting Nucleic Acid Strands</a>; ISBN 978-3-319-21998-1; DNA Computing and Molecular Programming; 194-211; <a href="https://doi.org/10.1007/978-3-319-21999-8_13">10.1007/978-3-319-21999-8_13</a></li>
<li>Thachuk, Chris and Winfree, Erik, el al. (2015) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200812-120743269">Leakless DNA Strand Displacement Systems</a>; ISBN 978-3-319-21998-1; DNA Computing and Molecular Programming; 133-153; <a href="https://doi.org/10.1007/978-3-319-21999-8_9">10.1007/978-3-319-21999-8_9</a></li>
<li>Schiefer, Nicholas and Winfree, Erik (2015) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20150904-111819530">Universal Computation and Optimal Construction in the Chemical Reaction Network-Controlled Tile Assembly Model</a>; 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; <a href="https://doi.org/10.1007/978-3-319-21999-8_3">10.1007/978-3-319-21999-8_3</a></li>
<li>Qian, Lulu and Winfree, Erik (2014) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170719-084200345">Parallel and Scalable Computation and Spatial Dynamics with DNA-Based Chemical Reaction Networks on a Surface</a>; ISBN 978-3-319-11294-7; DNA Computing and Molecular Programming; 114-131; <a href="https://doi.org/10.1007/978-3-319-11295-4_8">10.1007/978-3-319-11295-4_8</a></li>
<li>Woods, Damien and Chen, Ho-Lin, el al. (2013) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20130128-100842529">Active Self-Assembly of Algorithmic Shapes and Patterns  in Polylogarithmic Time</a>; ISBN 978-1-4503-1859-4; Proceedings of the 4th conference on Innovations in Theoretical Computer Science; 353-354; <a href="https://doi.org/10.1145/2422436.2422476">10.1145/2422436.2422476</a></li>
<li>Evans, Constantine G. and Winfree, Erik (2013) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20140530-150254025">DNA Sticky End Design and Assignment for Robust Algorithmic Self-assembly</a>; ISBN 978-3-319-01927-7; DNA Computing and Molecular Programming; 61-75; <a href="https://doi.org/10.1007/978-3-319-01928-4_5">10.1007/978-3-319-01928-4_5</a></li>
<li>Densmore, Douglas and Horowitz, Mark, el al. (2011) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20120521-113649301">Joint DAC/IWBDA special session design and synthesis of biological circuits</a>; ISBN 978-1-4503-0636-2; Proceedings of the 48th Design Automation Conference; 114-115; <a href="https://doi.org/10.1145/2024724.2024750">10.1145/2024724.2024750</a></li>
<li>Qian, Lulu and Soloveichik, David, el al. (2011) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20111006-081731222">Efficient Turing-Universal Computation with DNA Polymers</a>; ISBN 978-3-642-18304-1; DNA computing and molecular programming; 123-140; <a href="https://doi.org/10.1007/978-3-642-18305-8_12">10.1007/978-3-642-18305-8_12</a></li>
<li>Schulman, Rebecca and Winfree, Erik (2011) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20111025-131913963">Simple Evolution of Complex Crystal Species</a>; ISBN 978-3-642-18304-1; DNA Computing and Molecular Programming; 147-161; <a href="https://doi.org/10.1007/978-3-642-18305-8_14">10.1007/978-3-642-18305-8_14</a></li>
<li>Cook, Matthew and Soloveichik, David, el al. (2009) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20111020-103016495">Programmability of Chemical Reaction Networks</a>; ISBN 978-3-540-88868-0; Algorithmic Bioprocesses; 543-584; <a href="https://doi.org/10.1007/978-3-540-88869-7_27">10.1007/978-3-540-88869-7_27</a></li>
<li>Qian, Lulu and Winfree, Erik (2009) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20100707-102356969">A Simple DNA Gate Motif for Synthesizing Large-Scale Circuits</a>; 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; <a href="https://doi.org/10.1007/978-3-642-03076-5">10.1007/978-3-642-03076-5</a></li>
<li>Soloveichik, David and Seelig, Georg, el al. (2009) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200812-121640271">DNA as a Universal Substrate for Chemical Kinetics</a>; ISBN 978-3-642-03075-8; DNA Computing; 57-69; <a href="https://doi.org/10.1007/978-3-642-03076-5_6">10.1007/978-3-642-03076-5_6</a></li>
<li>Winfree, Erik (2008) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170105-124404623">Toward molecular programming with DNA</a>; ISBN 978-1-59593-958-6; ASPLOS XIII Proceedings of the 13th international conference on Architectural support for programming languages and operating systems; <a href="https://doi.org/10.1145/1346281.1346282">10.1145/1346281.1346282</a></li>
<li>Soloveichik, David and Winfree, Erik (2006) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20110309-104201054">Complexity of compact proofreading for self-assembled patterns</a>; ISBN 3-540-34161-7; DNA Computing; 305-324; <a href="https://doi.org/10.1007/11753681_24">10.1007/11753681_24</a></li>
<li>Winfree, Erik (2006) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20110810-095116353">Algorithmic Self-Assembly of DNA</a>; ISBN 978-1-4244-0337-0; Proceedings of the 2006 International Conference on Microtechnologies in Medicine and Biology; 4-4</li>
<li>Winfree, Erik (2006) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20190822-092012516">Fault-Tolerance in Biochemical Systems</a>; ISBN 978-3-540-38593-6; Unconventional Computation; 26; <a href="https://doi.org/10.1007/11839132_3">10.1007/11839132_3</a></li>
<li>Winfree, Erik (2006) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20111021-093324589">Self-Healing Tile Sets</a>; ISBN 9783540302964; Nanotechnology: Science and Computation; 55-78; <a href="https://doi.org/10.1007/3-540-30296-4_4">10.1007/3-540-30296-4_4</a></li>
<li>Soloveichik, David and Winfree, Erik (2005) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200221-095747956">Complexity of Self-assembled Shapes (Extended Abstract)</a>; ISBN 978-3-540-26174-2; DNA Computing; 344-354; <a href="https://doi.org/10.1007/11493785_30">10.1007/11493785_30</a></li>
<li>Schulman, Rebecca and Winfree, Erik (2005) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200221-152848969">Programmable Control of Nucleation for Algorithmic Self-assembly</a>; ISBN 978-3-540-26174-2; DNA Computing; 319-328; <a href="https://doi.org/10.1007/11493785_28">10.1007/11493785_28</a></li>
<li>Schulman, Rebecca and Winfree, Erik (2005) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20110309-104201367">Self-replication and evolution of DNA crystals</a>; ISBN 3-540-28848-1; Advances in Artificial Life; 734-743; <a href="https://doi.org/10.1007/11553090_74">10.1007/11553090_74</a></li>
<li>Seelig, Georg and Yurke, Bernard, el al. (2005) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20110309-104201845">DNA hybridization catalysts and catalyst circuits</a>; ISBN 3-540-26174-5; DNA Computing; 329-343; <a href="https://doi.org/10.1007/11493785_29">10.1007/11493785_29</a></li>
<li>Cook, Matthew and Rothemund, Paul W. K., el al. (2004) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20110309-104202667">Self-assembled circuit patterns</a>; ISBN 3-540-20930-1; DNA Computing; 91-107; <a href="https://doi.org/10.1007/978-3-540-24628-2_11">10.1007/978-3-540-24628-2_11</a></li>
<li>Schulman, Rebecca and Lee, Shaun, el al. (2004) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20110309-104202835">One dimensional boundaries for DNA tile self-assembly</a>; ISBN 3-540-20930-1; DNA Computing; 108-125; <a href="https://doi.org/10.1007/978-3-540-24628-2_12">10.1007/978-3-540-24628-2_12</a></li>
<li>Winfree, Erik and Bekbolatov, Renat (2004) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20110309-104203016">Proofreading tile sets: Error correction for algorithmic self-assembly</a>; ISBN 3-540-20930-1; DNA Computing; 126-144; <a href="https://doi.org/10.1007/978-3-540-24628-2_13">10.1007/978-3-540-24628-2_13</a></li>
<li>Winfree, Erik and Landweber, Laura F. (2002) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20110309-104203989">Introduction: Evolution and Computation: Where Do They Meet?</a>; ISBN 978-3-642-63081-1; Evolution as Computation: DIMACS Workshop, Princeton, January 1999; v-ix</li>
<li>Winfree, Erik and Eng, Tony, el al. (2001) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20111024-092612665">String tile models for DNA computing by self-assembly</a>; ISBN 978-3-540-42076-7; DNA Computing; 63-88; <a href="https://doi.org/10.1007/3-540-44992-2_6">10.1007/3-540-44992-2_6</a></li>
<li>Winfree, Erik (2001) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200812-123245128">In Vitro Transcriptional Circuits</a>; ISBN 978-1-85233-415-4; Unconventional Models of Computation, UMC'2K; 121-122; <a href="https://doi.org/10.1007/978-1-4471-0313-4_10">10.1007/978-1-4471-0313-4_10</a></li>
<li>Rothemund, Paul W. K. and Winfree, Erik (2000) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20161213-162052032">The program-size complexity of self-assembled squares</a>; ISBN 1-58113-184-4; STOC '00 Proceedings of the thirty-second annual ACM symposium on Theory of computing; 459-468; <a href="https://doi.org/10.1145/335305.335358">10.1145/335305.335358</a></li>
<li>LaBean, Thomas H. and Winfree, Erik, el al. (2000) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20111101-150157119">Experimental Progress in Computation by Self-Assembly of DNA Tilings</a>; ISBN 9780821820537; DNA Based Computers V; 123-40</li>
<li>Chen, Kevin and Winfree, Erik (2000) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20111102-073137217">Error Correction in DNA Computing: Misclassification and
Strand Loss</a>; ISBN 9780821820537; DNA Based Computers V; 49-63</li>
<li>Winfree, Erik and Yang, Xiaoping, el al. (1999) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20111024-101156919">Universal Computation via Self-assembly of DNA: Some Theory and Experiments</a>; ISBN 0821807560; DNA Based Computers II; 191-213</li>
<li>Winfree, Erik (1996) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20111024-134249923">Complexity of Restricted and Unrestricted Models of Molecular Computation</a>; ISBN 0821805185; DNA based computers; 187-198</li>
<li>Winfree, Erik (1996) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20111024-133436564">On the Computational Power of DNA Annealing and Ligation</a>; ISBN 0821805185; DNA Based Computers; 199-221</li>
</ul>