| 2009 | NP-Completeness of the Direct Energy Barrier Problem without Pseudoknots. | Jn Manuch, Chris Thachuk, Ladislav Stacho, Anne Condon |
| 2009 | Design of a Biomolecular Device That Executes Process Algebra. | Urmi Majumder, John H. Reif |
| 2009 | Automatic Design of DNA Logic Gates Based on Kinetic Simulation. | Ibuki Kawamata, Fumiaki Tanaka, Masami Hagiya |
| 2009 | Self-assembly of the Discrete Sierpinski Carpet and Related Fractals. | Steven M. Kautz, James I. Lathrop |
| 2009 | Renewable, Time-Responsive DNA Logic Gates for Scalable Digital Circuits. | Ashish Goel, Morteza Ibrahimi |
| 2009 | DNA Chips for Species Identification and Biological Phylogenies. | Max H. Garzon, Tit-Yee Wong, Vinhthuy T. Phan |
| 2009 | Advancing the Deoxyribozyme-Based Logic Gate Design Process. | M. Leigh Fanning, Joanne Macdonald, Darko Stefanovic |
| 2009 | Limitations of Self-assembly at Temperature One. | David Doty, Matthew J. Patitz, Scott M. Summers |
| 2009 | A Domain-Specific Language for Programming in the Tile Assembly Model. | David Doty, Matthew J. Patitz |
| 2009 | Strand Algebras for DNA Computing. | Luca Cardelli |
| 2009 | Filter Position in Networks of Evolutionary Processors Does Not Matter: A Direct Proof. | Paolo Bottoni, Anna Labella, Florin Manea, Victor Mitrana, Jos M. Sempere |
| 2008 | Tiamat: A Three-Dimensional Editing Tool for Complex DNA Structures. | Sean Williams, Kyle Lund, Chenxiang Lin, Peter Wonka, Stuart Lindsay, Hao Yan |
| 2008 | Towards DNA Comparator: The Machine That Compares DNA Concentrations. | Fumiaki Tanaka, Takashi Tsuda, Masami Hagiya |
| 2008 | DNA as a Universal Substrate for Chemical Kinetics. | David Soloveichik, Georg Seelig, Erik Winfree |
| 2008 | Isothermal Reactivating Whiplash PCR for Locally Programmable Molecular Computation. | John H. Reif, Urmi Majumder |
| 2008 | A Simple DNA Gate Motif for Synthesizing Large-Scale Circuits. | Lulu Qian, Erik Winfree |
| 2008 | Self-assembly of Discrete Self-similar Fractals. | Matthew J. Patitz, Scott M. Summers |
| 2008 | Operon Structure Optimization by Random Self-assembly. | Yusuke Nakagawa, Katsuyuki Yugi, Kenji Tsuge, Mitsuhiro Itaya, Hiroshi Yanagawa, Yasubumi Sakakibara |
| 2008 | Polyomino-Safe DNA Self-assembly via Block Replacement. | Chris Luhrs |
| 2008 | Construction of Photon-Fueled DNA Nanomachines by Tethering Azobenzenes as Engines. | Xingguo Liang, Hidenori Nishioka, Nobutaka Takenaka, Hiroyuki Asanuma |
| 2008 | Experimental Validation of Signal Dependent Operation in Whiplash PCR. | Ken Komiya, Masayuki Yamamura, John A. Rose |
| 2008 | Speeding Up Local-Search Type Algorithms for Designing DNA Sequences under Thermodynamical Constraints. | Suguru Kawashimo, Yen Kaow Ng, Hirotaka Ono, Kunihiko Sadakane, Masafumi Yamashita |
| 2008 | Sequentiality Induced by Spike Number in SNP Systems. | Oscar H. Ibarra, Andrei Paun, Alfonso Rodrguez-Patn |
| 2008 | Connecting the Dots: Molecular Machinery for Distributed Robotics. | Yuriy Brun, Dustin Reishus |
| 2008 | Time Optimal Self-assembly for 2D and 3D Shapes: The Case of Squares and Cubes. | Florent Becker, Eric Rmila, Nicolas Schabanel |