Winfree, Erik (2019) Chemical
Reaction Networks and Stochastic Local Search ; ISBN
978-3-030-26806-0; DNA Computing and Molecular Programming; Springer:
Cham; 1-20; 10.1007/978-3-030-26807-7_1
Zolaktaf, Sedigheh; Dannenberg, Frits; et el. (2019) Efficient
Parameter Estimation for DNA Kinetics Modeled as Continuous-Time Markov
Chains ; ISBN 978-3-030-26806-0; DNA Computing and Molecular
Programming; Springer: Cham; 80-99; 10.1007/978-3-030-26807-7_5
Brailovskaya, Tatiana; Gowri, Gokul; et el. (2019) Reversible
Computation Using Swap Reactions on a Surface ; ISBN
978-3-030-26806-0; DNA Computing and Molecular Programming; Springer:
Cham; 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; Springer: Cham; 37-54; 10.1007/978-3-030-00030-1_3
Badelt, Stefan; Shin, Seung Woo; et el. (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; Springer: Cham, Switzerland;
232-248; 10.1007/978-3-319-66799-7_15
Poole, William; Ortiz-Muñoz, Andrés; et el. (2017) Chemical
Boltzmann Machines ; ISBN 978-3-319-66798-0; DNA Computing and
Molecular Programming; Springer: Cham, Switzerland; 210-231; 10.1007/978-3-319-66799-7_14
Zolaktaf, Sedigheh; Dannenberg, Frits; et el. (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; Springer: Cham, Switzerland;
172-187; 10.1007/978-3-319-66799-7_12
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; Springer: Cham, Switzerland;
165-182; 10.1007/978-3-319-43994-5_11
Johnson, Robert F.; Dong, Qing; et el. (2016) Verifying
Chemical Reaction Network Implementations: A Bisimulation Approach ;
ISBN 9783319439938; DNA Computing and Molecular Programming; Springer:
Cham; 114-134; 10.1007/978-3-319-43994-5_8
Thachuk, Chris; Winfree, Erik; et el. (2015) Leakless
DNA Strand Displacement Systems ; ISBN 978-3-319-21998-1; DNA
Computing and Molecular Programming; Springer: Cham; 133-153; 10.1007/978-3-319-21999-8_9
Schaeffer, Joseph Malcolm; Thachuk, Chris; et el. (2015) Stochastic
Simulation of the Kinetics of Multiple Interacting Nucleic Acid
Strands ; ISBN 978-3-319-21998-1; DNA Computing and Molecular
Programming; Springer: Cham; 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;
Springer: Cham, Switzerland; 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; Springer: Cham, Switzerland;
114-131; 10.1007/978-3-319-11295-4_8
Woods, Damien; Chen, Ho-Lin; et el. (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; ACM: New York, NY; 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; Springer: Cham, Switzerland; 61-75; 10.1007/978-3-319-01928-4_5
Densmore, Douglas; Horowitz, Mark; et el. (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; Association for Computing Machinery (ACM): New
York; 114-115; 10.1145/2024724.2024750
Qian, Lulu; Soloveichik, David; et el. (2011) Efficient
Turing-Universal Computation with DNA Polymers ; ISBN
978-3-642-18304-1; DNA computing and molecular programming; Springer:
Berlin; 123-140; 10.1007/978-3-642-18305-8_12
Schulman, Rebecca and Winfree, Erik (2011) Simple
Evolution of Complex Crystal Species ; ISBN 978-3-642-18304-1; DNA
Computing and Molecular Programming; Springer: Berlin; 147-161; 10.1007/978-3-642-18305-8_14
Cook, Matthew; Soloveichik, David; et el. (2009) Programmability
of Chemical Reaction Networks ; ISBN 978-3-540-88868-0; Algorithmic
Bioprocesses; Springer-Verlag: Berlin; 543-584; 10.1007/978-3-540-88869-7_27
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; Springer: New York; 70-89; 10.1007/978-3-642-03076-5
Soloveichik, David; Seelig, Georg; et el. (2009) DNA
as a Universal Substrate for Chemical Kinetics ; ISBN
978-3-642-03075-8; DNA Computing; Springer: Berlin; 57-69; 10.1007/978-3-642-03076-5_6
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; ACM: New York,
NY; 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; IEEE: Piscataway, NJ; 4-4
Soloveichik, David and Winfree, Erik (2006) Complexity
of compact proofreading for self-assembled patterns ; ISBN
3-540-34161-7; DNA Computing; Springer: Berlin; 305-324; 10.1007/11753681_24
Winfree, Erik (2006) Fault-Tolerance
in Biochemical Systems ; ISBN 978-3-540-38593-6; Unconventional
Computation; Springer: Berlin; 26; 10.1007/11839132_3
Winfree, Erik (2006) Self-Healing
Tile Sets ; ISBN 9783540302964; Nanotechnology: Science and
Computation; Springer: Berlin; 55-78; 10.1007/3-540-30296-4_4
Soloveichik, David and Winfree, Erik (2005) Complexity
of Self-assembled Shapes (Extended Abstract) ; ISBN
978-3-540-26174-2; DNA Computing; Springer: Berlin; 344-354; 10.1007/11493785_30
Seelig, Georg; Yurke, Bernard; et el. (2005) DNA
hybridization catalysts and catalyst circuits ; ISBN 3-540-26174-5;
DNA Computing; Springer: Berlin; 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; Springer: Berlin; 319-328; 10.1007/11493785_28
Schulman, Rebecca and Winfree, Erik (2005) Self-replication
and evolution of DNA crystals ; ISBN 3-540-28848-1; Advances in
Artificial Life; Springer: Berlin; 734-743; 10.1007/11553090_74
Schulman, Rebecca; Lee, Shaun; et el. (2004) One
dimensional boundaries for DNA tile self-assembly ; ISBN
3-540-20930-1; DNA Computing; Springer: Berlin; 108-125; 10.1007/978-3-540-24628-2_12
Winfree, Erik and Bekbolatov, Renat (2004) Proofreading
tile sets: Error correction for algorithmic self-assembly ; ISBN
3-540-20930-1; DNA Computing; Springer: Berlin; 126-144; 10.1007/978-3-540-24628-2_13
Cook, Matthew; Rothemund, Paul W. K.; et el. (2004) Self-assembled
circuit patterns ; ISBN 3-540-20930-1; DNA Computing; Springer:
Berlin; 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; Springer: Berlin, Germany; v-ix
Winfree, Erik (2001) In
Vitro Transcriptional Circuits ; ISBN 978-1-85233-415-4;
Unconventional Models of Computation, UMC’2K; Springer: London; 121-122;
10.1007/978-1-4471-0313-4_10
Winfree, Erik; Eng, Tony; et el. (2001) String
tile models for DNA computing by self-assembly ; ISBN
978-3-540-42076-7; DNA Computing; Springer: Berlin; 63-88; 10.1007/3-540-44992-2_6
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; ACM: New York, NY; 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; American Mathematical Society:
Providence, RI; 49-63
LaBean, Thomas H.; Winfree, Erik; et el. (2000) Experimental
Progress in Computation by Self-Assembly of DNA Tilings ; ISBN
9780821820537; DNA Based Computers V; American Mathematical Society:
Providence, RI; 123-40
Winfree, Erik; Yang, Xiaoping; et el. (1999) Universal
Computation via Self-assembly of DNA: Some Theory and Experiments ;
ISBN 821807560; DNA Based Computers II; American Mathematical Society:
Providence, RI; 191-213
Winfree, Erik (1996) Complexity
of Restricted and Unrestricted Models of Molecular Computation ; ISBN
821805185; DNA based computers; American Mathematical Society:
Providence, RI; 187-198
Winfree, Erik (1996) On
the Computational Power of DNA Annealing and Ligation ; ISBN
821805185; DNA Based Computers; American Mathematical Society:
Providence, RI; 199-221