| 1 | -- | 2 | Junhyong Kim, Inge Jonassen. Guest Editorial: WABI Special Section Part II |
| 3 | -- | 14 | Julien Allali, Marie-France Sagot. A New Distance for High Level RNA Secondary Structure Comparison |
| 15 | -- | 28 | Denis Bertrand, Olivier Gascuel. Topological Rearrangements and Local Search Method for Tandem Duplication Trees |
| 29 | -- | 38 | Daniel G. Brown. Optimizing Multiple Seeds for Protein Homology Search |
| 39 | -- | 0 | Dan Gusfield. Editorial-State of the Transaction |
| 40 | -- | 50 | Nadia Pisanti, Maxime Crochemore, Roberto Grossi, Marie-France Sagot. Bases of Motifs for Generating Repeated Patterns with Wild Cards |
| 51 | -- | 61 | Gregory Kucherov, Laurent Noé, Mikhail A. Roytberg. Multiseed Lossless Filtration |
| 62 | -- | 76 | Ying Liu, Shamkant B. Navathe, Jorge Civera, Venu Dasigi, Ashwin Ram, Brian J. Ciliax, Ray Dingledine. Text Mining Biomedical Literature for Discovering Gene-to-Gene Relationships: A Comparative Study of Algorithms |