| 141 | -- | 0 | Dan Gusfield, Ming-Yang Kao. Guest Editors Foreword |
| 142 | -- | 175 | John H. Reif. Parallel Biomolecular Computation: Models and Simulations |
| 176 | -- | 195 | Bhaskar DasGupta, Xin He, Tao Jiang, Ming Li, John Tromp. On the Linear-Cost Subtree-Transfer Distance between Phylogenetic Trees |
| 196 | -- | 221 | Paul E. Kearney, Ryan Hayward, Henk Meijer. Evolutionary Trees and Ordinal Assertions |
| 222 | -- | 238 | Richard Beigel, Bin Fu. Molecular Computing, Bounded Nondeterminism, and Efficient Recursion |
| 239 | -- | 250 | Mitsunori Ogihara, Animesh Ray. Simulating Boolean Circuits on a DNA Computer |
| 251 | -- | 278 | Kevin Atteson. The Performance of Neighbor-Joining Methods of Phylogenetic Reconstruction |
| 279 | -- | 294 | John Atkins, William E. Hart. On the Intractability of Protein Folding with a Finite Alphabet of Amino Acids |
| 295 | -- | 310 | Laxmi Parida, Dan Geiger. Mass Estimation of DNA Molecules and Extraction of Ordered Restriction Maps in Optical Mapping Imagery |
| 311 | -- | 329 | Mary Cryan, Leslie Ann Goldberg, Cynthia A. Phillips. Approximation Algorithms for the Fixed-Topology Phylogenetic Number Problem |
| 330 | -- | 346 | T. C. Ip, Vincent A. Fischetti, Jeanette P. Schmidt. An Algorithm for Identifying Similar Amino Acid Clusters among Different Alpha-Helical Coiled-Coil Proteins Using Their Secondary Structure |
| 347 | -- | 371 | Paul W. Finn, Lydia E. Kavraki. Computational Approaches to Drug Design |
| 372 | -- | 402 | Ioannis Z. Emiris, Bernard Mourrain. Computer Algebra Methods for Studying and Computing Molecular Conformations |