| 1 | -- | 2 | Sorin Istrail, Pavel A. Pevzner, Ron Shamir. Foreword |
| 3 | -- | 44 | Richa Agarwala, Leslie G. Biesecker, Alejandro A. Schäffer. Inverse inbreeding coefficient problems with an application to linkage analysis of recessive diseases in inbred populations |
| 45 | -- | 62 | Tatsuya Akutsu. Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots |
| 63 | -- | 96 | Richard Arratia, Béla Bollobás, Don Coppersmith, Gregory B. Sorkin. Euler circuits and DNA sequencing by hybridization |
| 97 | -- | 111 | Bonnie Berger, Jonathan A. King, Russell Schwartz, Peter W. Shor. Local rule mechanism for selecting icosahedral shell geometry |
| 113 | -- | 142 | Ralf Bundschuh, Terence Hwa. An analytic study of the phase transition line in local sequence alignment with gaps |
| 143 | -- | 186 | John D. Kececioglu, Hans-Peter Lenhof, Kurt Mehlhorn, Petra Mutzel, Knut Reinert, Martin Vingron. A polyhedral approach to sequence alignment problems |
| 187 | -- | 201 | Brendan Mumey. Probe location in the presence of errors: a problem from DNA mapping |
| 203 | -- | 227 | Laxmi Parida, Bud Mishra. Partitioning single-molecule maps into multiple populations: algorithms and probabilistic analysis |
| 229 | -- | 258 | Manuela S. Pereira, Lucio Andrade, Sameh El Difrawy, Barry L. Karger, Elias S. Manolakos. Statistical learning formulation of the DNA base-calling problem and its solution in a Bayesian EM framework |
| 259 | -- | 280 | Mireille Régnier. A unified approach to word occurrence probabilities |
| 281 | -- | 300 | Lusheng Wang, Bin Ma, Ming Li. Fixed topology alignment with recombination |