Automated sequence-level analysis of kinetics and thermodynamics for domain-level DNA strand-displacement systems

Probabilistic switching circuits in DNA

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Verifying chemical reaction network implementations: A bisimulation approach

(2018) Robert Johnson et al.   THEORETICAL COMPUTER SCIENCE

Scaling up molecular pattern recognition with DNA-based winner-take-all neural networks

(2018) Kevin M. Cherry et al.   NATURE

Constrained Multistate Sequence Design for Nucleic Acid Reaction Pathway Engineering

(2017) Brian R. Wolfe et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Multi-Arm Junctions for Dynamic DNA Nanotechnology

(2017) Shohei Kotani et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Enzyme-free nucleic acid dynamical systems

(2017) Niranjan Srinivas et al.   SCIENCE

Verifying chemical reaction network implementations: A pathway decomposition approach

(2017) Seung Woo Shin et al.   THEORETICAL COMPUTER SCIENCE

Compiler-aided systematic construction of large-scale DNA strand displacement circuits using unpurified components

(2017) Anupama J. Thubagere et al.   Nature Communications

Modular verification of chemical reaction network encodings via serializability analysis

(2016) Matthew R. Lakin et al.   THEORETICAL COMPUTER SCIENCE

A strand graph semantics for DNA-based computation

(2016) Rasmus L. Petersen et al.   THEORETICAL COMPUTER SCIENCE

Analog Computation by DNA Strand Displacement Circuits

(2016) Tianqi Song et al.   ACS Synthetic Biology

Supervised Learning in Adaptive DNA Strand Displacement Networks

(2016) Matthew R. Lakin et al.   ACS Synthetic Biology

Simulation-guided DNA probe design for consistently ultraspecific hybridization

(2015) Juexiao Sherry Wang et al.   Nature Chemistry

Computing in mammalian cells with nucleic acid strand exchange

(2015) Benjamin Groves et al.   Nature Nanotechnology

Scaling down DNA circuits with competitive neural networks

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Two-domain DNA strand displacement

(2013) LUCA CARDELLI   MATHEMATICAL STRUCTURES IN COMPUTER SCIENCE

Three-Input Majority Logic Gate and Multiple Input Logic Circuit Based on DNA Strand Displacement

(2013) Wei Li et al.   NANO LETTERS

Programmable chemical controllers made from DNA

(2013) Yuan-Jyue Chen et al.   Nature Nanotechnology

On the biophysics and kinetics of toehold-mediated DNA strand displacement

(2013) Niranjan Srinivas et al.   NUCLEIC ACIDS RESEARCH

Stacking nonenzymatic circuits for high signal gain

(2013) X. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Combinatorial Displacement of DNA Strands: Application to Matrix Multiplication and Weighted Sums

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Visual DSD: a design and analysis tool for DNA strand displacement systems

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Biomolecular implementation of linear I/O systems

(2011) K. Oishi et al.   IET Systems Biology

Expanding the Rule Set of DNA Circuitry with Associative Toehold Activation

(2011) Xi Chen   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Reversible Logic Circuits Made of DNA

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A simple DNA gate motif for synthesizing large-scale circuits

(2011) L. Qian et al.   Journal of the Royal Society Interface

Neural network computation with DNA strand displacement cascades

(2011) Lulu Qian et al.   NATURE

Dynamic DNA nanotechnology using strand-displacement reactions

(2011) David Yu Zhang et al.   Nature Chemistry

Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades

(2011) L. Qian et al.   SCIENCE

NUPACK: Analysis and design of nucleic acid systems

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Cooperative Hybridization of Oligonucleotides

(2010) David Yu Zhang   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Strand algebras for DNA computing

(2010) Luca Cardelli   Natural Computing

DNA as a universal substrate for chemical kinetics

(2010) D. Soloveichik et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Forward flux sampling for rare event simulations

(2009) Rosalind J Allen et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Control of DNA Strand Displacement Kinetics Using Toehold Exchange

(2009) David Yu Zhang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A programming language for composable DNA circuits

(2009) A. Phillips et al.   Journal of the Royal Society Interface

Programming biomolecular self-assembly pathways

(2008) Peng Yin et al.   NATURE