| 5 | -- | 22 | Nataraj Akkiraju, Herbert Edelsbrunner. Triangulating the Surface of a Molecule |
| 23 | -- | 40 | Jonathan E. Atkins, Martin Middendorf. On Physical Mapping and the Consecutive Ones Property for Sparse Matrices |
| 41 | -- | 53 | Vineet Bafna, Babu O. Narayanan, R. Ravi. Nonoverlapping Local Alignments (weighted Independent Sets of Axis-parallel Rectangles) |
| 55 | -- | 77 | Hans Leo Bodlaender, Babette van Antwerpen-de Fluiter. On Intervalizing K-colored Graphs for DNA Physical Mapping |
| 79 | -- | 94 | Dan Boneh, Christopher Dunworth, Richard J. Lipton, Jiri Sgall. On the Computational Power of DNA |
| 95 | -- | 109 | Andreas W. M. Dress, Daniel H. Huson, Vincent Moulton. Analyzing and Visualizing Sequence and Distance Data Using SplitsTree |
| 111 | -- | 136 | Leslie Ann Goldberg, Paul W. Goldberg, Cynthia A. Phillips, Elizabeth Sweedyk, Tandy Warnow. Minimizing Phylogenetic Number To Find Good Evolutionary Trees |
| 137 | -- | 151 | Sridhar Hannenhalli. Polynomial-time Algorithm for Computing Translocation Distance Between Genomes |
| 153 | -- | 169 | Jotun Hein, Tao Jiang, Lusheng Wang, Kaizhong Zhang. On the Complexity of Comparing Evolutionary Trees |
| 171 | -- | 185 | Denise B. Kandel, Yossi Matias, Ron Unger, Peter Winkler. Shuffling Biological Sequences |
| 187 | -- | 215 | J. MacGregor Smith, Badri Toppur. Euclidean Steiner Minimal Trees, Minimum Energy Configurations, and the Embedding Problem of Weighted Graphs in E:::3::: |
| 217 | -- | 230 | Mike Paterson, Teresa M. Przytycka. On the Complexity of String Folding |
| 231 | -- | 246 | William R. Pearson, Gabriel Robins, Dallas E. Wrege, Tongtong Zhang. On the Primer Selection Problem in Polymerase Chain Reaction Experiments |
| 247 | -- | 257 | David Sankoff, Joseph H. Nadeau. Conserved Synteny As a Measure of Genomic Distance |
| 259 | -- | 268 | Thomas D. Schneider, David N. Mastronarde. Fast Multiple Alignment of Ungapped DNA Sequences Using Information Theory and a Relaxation Method |
| 269 | -- | 295 | Ting Chen, Steven Skiena. Sorting with Fixed-length Reversals |
| 297 | -- | 309 | Martin Vingron, Michael S. Waterman. Alignment Networks and Electrical Networks |
| 311 | -- | 335 | Cynthia A. Phillips, Tandy Warnow. The Asymmetric Median Tree - A New Model for Building Consensus Trees |
| 337 | -- | 365 | Z. Zhang, B. He, Webb C. Miller. Local Multiple Alignment Via Subgraph Enumeration |