Erik Winfree - RankMe

78 papers A* 3A 1B 28C 1Journal 29Unranked 14

Year	Rank	Type	Title / Venue / Authors
2025	B	`conf`	Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems. DNA Inhoo Lee, Salvador Buse, Erik Winfree
2024	B	`conf`	Learning and Inference in a Lattice Model of Multicomponent Condensates. DNA Cameron T. Chalk, Salvador Buse, Krishna Shrinivas, Arvind Murugan, Erik Winfree
2023	J	`jnl`	Predicting DNA kinetics with a truncated continuous-time Markov chain method. Comput. Biol. Chem. Sedigheh Zolaktaf, Frits Dannenberg, Mark Schmidt, Anne Condon, Erik Winfree
2023	B	`conf`	Revisiting Hybridization Kinetics with Improved Elementary Step Simulation. DNA Jordan Lovrod, Boyan Beronov, Chenwei Zhang, Erik Winfree, Anne Condon
2023	—	`conf`	The Tall Thin Molecular Programmer. ISSCC Erik Winfree
2023	J	`jnl`	Two-dimensional tile displacement can simulate cellular automata. CoRR Erik Winfree, Lulu Qian
2022	J	`jnl`	Detailed Balanced Chemical Reaction Networks as Generalized Boltzmann Machines. CoRR William Poole, Thomas E. Ouldridge, Manoj Gopalkrishnan, Erik Winfree
2022	J	`jnl`	Pattern recognition in the nucleation kinetics of non-equilibrium self-assembly. CoRR Constantine Glen Evans, Jackson O'Brien, Erik Winfree, Arvind Murugan
2020	J	`jnl`	Stochastic chemical reaction networks for robustly approximating arbitrary probability distributions. Theor. Comput. Sci. Daniele Cappelletti, Andrés Ortiz-Muñoz, David F. Anderson, Erik Winfree
2020	J	`jnl`	Verifying polymer reaction networks using bisimulation. Theor. Comput. Sci. Robert F. Johnson, Erik Winfree
2019	B	`conf`	Chemical Reaction Networks and Stochastic Local Search. DNA Erik Winfree
2019	J	`jnl`	Diverse and robust molecular algorithms using reprogrammable DNA self-assembly. Nat. Damien Woods, David Doty, Cameron Myhrvold, Joy Hui, Felix Zhou, Peng Yin, Erik Winfree
2019	B	`conf`	Efficient Parameter Estimation for DNA Kinetics Modeled as Continuous-Time Markov Chains. DNA Sedigheh Zolaktaf, Frits Dannenberg, Erik Winfree, Alexandre Bouchard-Côté, Mark Schmidt, Anne Condon
2019	B	`conf`	Reversible Computation Using Swap Reactions on a Surface. DNA Tatiana Brailovskaya, Gokul Gowri, Sean Yu, Erik Winfree
2019	J	`jnl`	Verifying chemical reaction network implementations: A bisimulation approach. Theor. Comput. Sci. Robert F. Johnson, Qing Dong, Erik Winfree
2019	J	`jnl`	Verifying chemical reaction network implementations: A pathway decomposition approach. Theor. Comput. Sci. Seung Woo Shin, Chris Thachuk, Erik Winfree
2018	B	`conf`	Optimizing Tile Set Size While Preserving Proofreading with a DNA Self-assembly Compiler. DNA Constantine G. Evans, Erik Winfree
2018	J	`jnl`	Stochastic Chemical Reaction Networks for Robustly Approximating Arbitrary Probability Distributions. CoRR Daniele Cappelletti, Andrés Ortiz-Muñoz, David F. Anderson, Erik Winfree
2017	B	`conf`	A General-Purpose CRN-to-DSD Compiler with Formal Verification, Optimization, and Simulation Capabilities. DNA Stefan Badelt, Seung Woo Shin, Robert F. Johnson, Qing Dong, Chris Thachuk, Erik Winfree
2017	B	`conf`	Chemical Boltzmann Machines. DNA William Poole, Andrés Ortiz-Muñoz, Abhishek Behera, Nick S. Jones, Thomas E. Ouldridge, Erik Winfree, Manoj Gopalkrishnan
2017	B	`conf`	Inferring Parameters for an Elementary Step Model of DNA Structure Kinetics with Locally Context-Dependent Arrhenius Rates. DNA Sedigheh Zolaktaf, Frits Dannenberg, Xander Rudelis, Anne Condon, Joseph M. Schaeffer, Mark Schmidt, Chris Thachuk, Erik Winfree
2016	B	`conf`	Time Complexity of Computation and Construction in the Chemical Reaction Network-Controlled Tile Assembly Model. DNA Nicholas Schiefer, Erik Winfree
2016	B	`conf`	Verifying Chemical Reaction Network Implementations: A Bisimulation Approach. DNA Robert F. Johnson, Qing Dong, Erik Winfree
2015	J	`jnl`	A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures. CoRR Casey Grun, Karthik Sarma, Brian Wolfe, Seung Woo Shin, Erik Winfree
2015	B	`conf`	Leakless DNA Strand Displacement Systems. DNA Chris Thachuk, Erik Winfree, David Soloveichik
2015	B	`conf`	Stochastic Simulation of the Kinetics of Multiple Interacting Nucleic Acid Strands. DNA Joseph Malcolm Schaeffer, Chris Thachuk, Erik Winfree
2015	B	`conf`	Universal Computation and Optimal Construction in the Chemical Reaction Network-Controlled Tile Assembly Model. DNA Nicholas Schiefer, Erik Winfree
2014	B	`conf`	Parallel and Scalable Computation and Spatial Dynamics with DNA-Based Chemical Reaction Networks on a Surface. DNA Lulu Qian, Erik Winfree
2014	J	`jnl`	Verifying Chemical Reaction Network Implementations: A Pathway Decomposition Approach. CoRR Seung Woo Shin, Chris Thachuk, Erik Winfree
2013	J	`jnl`	Active Self-Assembly of Algorithmic Shapes and Patterns in Polylogarithmic Time CoRR Damien Woods, Ho-Lin Chen, Scott Goodfriend, Nadine Dabby, Erik Winfree, Peng Yin
2013	A	`conf`	Active self-assembly of algorithmic shapes and patterns in polylogarithmic time. ITCS Damien Woods, Ho-Lin Chen, Scott Goodfriend, Nadine Dabby, Erik Winfree, Peng Yin
2013	B	`conf`	DNA Sticky End Design and Assignment for Robust Algorithmic Self-assembly. DNA Constantine G. Evans, Erik Winfree
2012	J	`jnl`	Simple evolution of complex crystal species. Nat. Comput. Rebecca Schulman, Erik Winfree
2011	J	`jnl`	Erratum to "The computational power of Benenson automata" [Theoret. Comput. Sci. 344 (2005) 279-297] Theor. Comput. Sci. David Soloveichik, Erik Winfree
2011	A*	`conf`	Joint DAC/IWBDA special session design and synthesis of biological circuits. DAC Douglas Densmore, Mark Horowitz, Smita Krishnaswamy, Xiling Shen, Adam P. Arkin, Erik Winfree, Chris Voigt
2011	J	`jnl`	Neural network computation with DNA strand displacement cascades. Nat. Lulu Qian, Erik Winfree, Jehoshua Bruck
2010	B	`conf`	Efficient Turing-Universal Computation with DNA Polymers. DNA Lulu Qian, David Soloveichik, Erik Winfree
2010	B	`conf`	Simple Evolution of Complex Crystal Species. DNA Rebecca Schulman, Erik Winfree
2009	—	`ed.`	Algorithmic Bioprocesses Anne Condon, David Harel, Joost N. Kok, Arto Salomaa, Erik Winfree
2009	J	`jnl`	Error suppression mechanisms for DNA tile self-assembly and their simulation. Nat. Comput. Kenichi Fujibayashi, David Yu Zhang, Erik Winfree, Satoshi Murata
2009	—	`conf`	Programmability of Chemical Reaction Networks. Algorithmic Bioprocesses Matthew Cook, David Soloveichik, Erik Winfree, Jehoshua Bruck
2009	J	`jnl`	Programmable Control of Nucleation for Algorithmic Self-Assembly. SIAM J. Comput. Rebecca Schulman, Erik Winfree
2008	B	`conf`	A Simple DNA Gate Motif for Synthesizing Large-Scale Circuits. DNA Lulu Qian, Erik Winfree
2008	J	`jnl`	Combining self-healing and proofreading in self-assembly. Nat. Comput. David Soloveichik, Matthew Cook, Erik Winfree
2008	J	`jnl`	Computation with finite stochastic chemical reaction networks. Nat. Comput. David Soloveichik, Matthew Cook, Erik Winfree, Jehoshua Bruck
2008	B	`conf`	DNA as a Universal Substrate for Chemical Kinetics. DNA David Soloveichik, Georg Seelig, Erik Winfree
2008	J	`jnl`	How crystals that sense and respond to their environments could evolve. Nat. Comput. Rebecca Schulman, Erik Winfree
2008	A*	`conf`	Toward molecular programming with DNA. ASPLOS Erik Winfree
2007	J	`jnl`	Complexity of Self-Assembled Shapes. SIAM J. Comput. David Soloveichik, Erik Winfree
2007	J	`jnl`	Thermodynamic Analysis of Interacting Nucleic Acid Strands. SIAM Rev. Robert M. Dirks, Justin S. Bois, Joseph M. Schaeffer, Erik Winfree, Niles A. Pierce
2006	C	`conf`	Fault-Tolerance in Biochemical Systems. UC Erik Winfree
2006	—	`conf`	Self-healing Tile Sets. Nanotechnology: Science and Computation Erik Winfree
2005	B	`conf`	Complexity of Compact Proofreading for Self-assembled Patterns. DNA David Soloveichik, Erik Winfree
2005	—	`conf`	Self-replication and Evolution of DNA Crystals. ECAL Rebecca Schulman, Erik Winfree
2005	J	`jnl`	The computational power of Benenson automata. Theor. Comput. Sci. David Soloveichik, Erik Winfree
2004	J	`jnl`	Complexity of Self-Assembled Shapes CoRR David Soloveichik, Erik Winfree
2004	B	`conf`	Complexity of Self-assembled Shapes. DNA David Soloveichik, Erik Winfree
2004	B	`conf`	DNA Hybridization Catalysts and Catalyst Circuits. DNA Georg Seelig, Bernard Yurke, Erik Winfree
2004	—	`conf`	Neural Network Computation by In Vitro Transcriptional Circuits. NIPS Jongmin Kim, John J. Hopfield, Erik Winfree
2004	B	`conf`	Programmable Control of Nucleation for Algorithmic Self-assembly. DNA Rebecca Schulman, Erik Winfree
2004	J	`jnl`	The Computational Power of Benenson Automata CoRR David Soloveichik, Erik Winfree
2003	B	`conf`	One Dimensional Boundaries for DNA Tile Self-Assembly. DNA Rebecca Schulman, Shaun Lee, Nick Papadakis, Erik Winfree
2003	B	`conf`	Proofreading Tile Sets: Error Correction for Algorithmic Self-Assembly. DNA Erik Winfree, Renat Bekbolatov
2003	B	`conf`	Self-Assembled Circuit Patterns. DNA Matthew Cook, Paul W. K. Rothemund, Erik Winfree
2000	—	`ed.`	DNA Based Computers, Proceedings of a DIMACS Workshop, New Brunswick, New Jersey, USA, June 14-15, 1999 DNA Based Computers Erik Winfree, David K. Gifford
2000	—	`conf`	In-vitro Transcriptional Circuits. UMC Erik Winfree
2000	—	`conf`	String Tile Models for DNA Computing by Self-Assembly. DNA Computing Erik Winfree, Tony Eng, Grzegorz Rozenberg
2000	A*	`conf`	The program-size complexity of self-assembled squares (extended abstract). STOC Paul W. K. Rothemund, Erik Winfree
1999	—	`conf`	Error correction in DNA computing: Misclassification and strand loss. DNA Based Computers Kevin Chen, Erik Winfree
1999	—	`conf`	Experimental progress in computation by self-assembly of DNA tilings. DNA Based Computers Thomas H. LaBean, Erik Winfree, John H. Reif
1999	J	`jnl`	On Applying Molecular Computation to the Data Encryption Standard. J. Comput. Biol. Leonard M. Adleman, Paul W. K. Rothemund, Sam T. Roweis, Erik Winfree
1999	J	`jnl`	On the Reduction of Errors in DNA Computation. J. Comput. Biol. Sam T. Roweis, Erik Winfree
1998	J	`jnl`	A Sticker-Based Model for DNA Computation. J. Comput. Biol. Sam T. Roweis, Erik Winfree, Richard Burgoyne, Nickolas V. Chelyapov, Myron F. Goodman, Paul W. K. Rothemund, Leonard M. Adleman
1996	—	`conf`	A sticker based model for DNA computation. DNA Based Computers Sam T. Roweis, Erik Winfree, Richard Burgoyne, Nickolas V. Chelyapov, Myron F. Goodman, Paul W. K. Rothemund, Leonard M. Adleman
1996	—	`conf`	On applying molecular computation to the data encryption standard. DNA Based Computers Leonard M. Adleman, Paul W. K. Rothemund, Sam T. Roweis, Erik Winfree
1996	—	`conf`	Universal computation via self-assembly of DNA: Some theory and experiments. DNA Based Computers Erik Winfree, Xiaoping Yang, Nadrian C. Seeman
1995	—	`conf`	Complexity of restricted and unrestricted models of molecular computation. DNA Based Computers Erik Winfree
1995	—	`conf`	On the computational power of DNA annealing and ligation. DNA Based Computers Erik Winfree