| 2000 | String Tile Models for DNA Computing by Self-Assembly. | Erik Winfree, Tony Eng, Grzegorz Rozenberg |
| 2000 | Engineered Communications for Microbial Robotics. | Ron Weiss, Thomas F. Knight Jr. |
| 2000 | Solving Computational Learning Problems of Boolean Formulae on DNA Computers. | Yasubumi Sakakibara |
| 2000 | The Fidelity of Annealing-Ligation: A Theoretical Analysis. | John A. Rose, Russell J. Deaton |
| 2000 | Challenges and Applications for Self-Assembled DNA Nanostructures. | John H. Reif, Thomas H. LaBean, Nadrian C. Seeman |
| 2000 | Computationally Inspired Biotechnologies: Improved DNA Synthesis and Associative Search Using Error-Correcting Codes and Vector-Quantization. | John H. Reif, Thomas H. LaBean |
| 2000 | Steady Flow Micro-Reactor Module for Pipelined DNA Computations. | John S. McCaskill, Robert Penchovsky, Marlies Gohlke, Jrg Ackermann, Thomas Rcker |
| 2000 | Graph Replacement Chemistry for DNA Processing. | John S. McCaskill, Ulrich Niemann |
| 2000 | About Time-Varying Distributed H Systems. | Maurice Margenstern, Yurii Rogozhin |
| 2000 | Successive State Transitions with I/O Interface by Molecules. | Ken Komiya, Kensaku Sakamoto, Hidetaka Gouzu, Shigeyuki Yokoyama, Masanori Arita, Akio Nishikawa, Masami Hagiya |
| 2000 | From Molecular Computing to Molecular Programming. | Masami Hagiya |
| 2000 | DNA Implementation of a Royal Road Fitness Evaluation. | Elizabeth Goode, David Harlan Wood, Junghuei Chen |
| 2000 | Diophantine Equations and Splicing: A New Demonstration of the Generative Capability of H Systems. | Pierluigi Frisco |
| 2000 | Molecular Computing with Generalized Homogeneous P-Systems. | Rudolf Freund, Franziska Freund |
| 2000 | A DNA-Based Random Walk Method for Solving k-SAT. | Sergio Daz, Juan Luis Esteban, Mitsunori Ogihara |
| 2000 | A Space-Efficient Randomized DNA Algorithm for k-SAT. | Kevin Chen, Vijay Ramachandran |
| 2000 | Solution of a Satisfiability Problem on a Gel-Based DNA Computer. | Ravinderjit S. Braich, Cliff Johnson, Paul W. K. Rothemund, Darryl Hwang, Nickolas V. Chelyapov, Leonard M. Adleman |
| 2000 | DNA and Circular Splicing. | Paola Bonizzoni, Clelia de Felice, Giancarlo Mauri, Rosalba Zizza |