Journal Publications:

PDF Zhang, David Y; Chen, Sherry X; Yin, Peng. "Optimizing the specificity of nucleic acid hybridization" Nature Chemistry 4: 208-214 (2012).

PDF Genot, Anthony J; Zhang, David Y; Bath, Jonathan; Turberfield, Andrew J. "Remote Toehold: A Mechanism for Flexible Control of DNA Hybridization Kinetics." J. Am. Chem. Soc. 133: 2177-2182 (2011).

PDF Zhang, David Y; Seelig, Georg. "Dynamic DNA Nanotechnology using Strand Displacement Reactions." Nature Chemistry. 3: 103-113 (2011).

PDF Zhang, David Y. "Cooperative Hybridization of Oligonucleotides" J. Am. Chem. Soc. 133: 1077-1086 (2011).

PDF Zhang, David Y; Seelig, Georg. "DNA-Based Fixed Gain Amplifiers and Linear Classifier Circuits." Lecture Notes in Computer Science 6518: 176-186 (2011).

PDF Zhang, David Y. "Towards Domain-Based Sequence Design for DNA Strand Displacement Reactions." Lecture Notes in Computer Science 6518: 162-175 (2011).

PDF Zhang, David Y; Winfree, Erik. "Robustness and Modularity Properties of a Non-covalent DNA Catalytic Reaction." Nuc. Acids Res. 38: 4182-4197 (2010).

PDF Zhang, David Y; Winfree, Erik. "Control of DNA Strand Displacement Kinetics Using Toehold Exchange." J. Am. Chem. Soc. 131: 17303-17314 (2009).
PDF Supporting Materials

PDF Fujibayashi, K; Zhang, David Y; Winfree E; Murata S. "Error suppression mechanisms for DNA tile self-assembly." Natural Computing 8: 589-612 (2009).

PDF Zhang, David Y; Winfree, Erik. "Dynamic Allosteric Control of Non-covalent DNA Catalysis Reactions." J. Am. Chem. Soc. 130: 13921-13926 (2008).

PDF Zhang, David Y; Turberfield, Andrew J; Yurke, Bernard; Winfree, Erik. "Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA." Science 318: 1121-1125 (2007).
PDF Supporting Materials

PDF Seelig, Georg; Soloveichik, David; Zhang, David Y; Winfree, Erik. "Enzyme-free nucleic acid-based logic circuits." Science 314: 1585-1588 (2006).
PDF Supporting Materials

PDF Zhang, David Yu and Yurke, Bernard. "A Superstructure-Based Self Replicator Without Product Inhibition." Natural Computing 5: 183-202 (2006).

PDF Schoenmyer, Tor and Zhang, David Yu. "FFT-based Algorithms for the String Matching with Mismatches Problem." J. Algorithms 57: 130-139 (2005).

PDF Yurke, Bernard and Zhang, David Yu. "A Clocked DNA-Based Replicator." Lecture Notes in Computer Science 3384: 445 (2005).


Patents:

PDF Schaus, Thomas E.; Zhang, David Yu; Sun, Wei; Yin, Peng. "Spatial Sequestration of Dynamic Nucleic Acid Circuits." US Provisional Patent filed May 2011.

PDF Zhang, David Yu; Yin, Peng. "Nucleic Acid Probe Systems." US Provisional Patent filed Oct 2010.

PDF Zhang, David Yu. "Cooperative DNA Strand Displacement and its Applications in Nucleic Acid Detection, Quantitation, and Logic." US Provisional Patent filed March 2010.

PDF Zhang, David Yu; Turberfield, Andrew J; Winfree, Erik. "Versatile Entropy-Driven DNA Catalyst and Applications." US Provisional Patent filed Jan 2007.

PDF Seelig, Georg; Solovechik, David; Zhang, David; Winfree, Erik. "Enzyme-Free DNA Logic Gates and Circuits." US Non-Provisional Patent number 7,745,594. Filed July 2005.

PDF Zhang, David Yu; Yurke, Bernard; Winfree, Erik. "Enzyme-Free DNA Amplifier." US Non-Provisional patent number 7,538,202. Filed 9 December 2004.