| 1998 | A Bit-Parallel Approach to Suffix Automata: Fast Extended String Matching. Gonzalo Navarro, Mathieu Raffinot |
| 1998 | A Dictionary Matching Algorithm Fast on the Average for Terms of Varying Length. Michal Ziv-Ukelson, Aaron Kershenbaum |
| 1998 | A Fast Bit-Vector Algorithm for Approximate String Matching Based on Dynamic Programming. Gene Myers |
| 1998 | A Rotation Invariant Filter for Two-Dimensional String Matching. Kimmo Fredriksson, Esko Ukkonen |
| 1998 | A Very Fast String Matching Algorithm for Small Alphabeths and Long Patterns (Extended Abstract). Christian Charras, Thierry Lecroq, Joseph Daniel Pehoushek |
| 1998 | Aligning Alignments. John D. Kececioglu, Weiqing Zhang |
| 1998 | Aligning DNA Sequences to Minimize the Change in Protein (Extended Abstract). Yufang Hua, Tao Jiang, Bin Wu |
| 1998 | An Approximate Oracle for Distance in Metric Spaces. Yanling Yang, Kaizhong Zhang, Xiong Wang, Jason Tsong-Li Wang, Dennis E. Shasha |
| 1998 | Approximate Word Sequence Matching over Sparse Suffix Trees. Knut Magne Risvik |
| 1998 | Combinatorial Pattern Matching, 9th Annual Symposium, CPM 98, Piscataway, New Jersey, USA, July 20-22, 1998, Proceedings Martin Farach-Colton |
| 1998 | Comparison of Coding DNA. Christian N. S. Pedersen, Rune B. Lyngsø, Jotun Hein |
| 1998 | Constructing Suffix Arrays for Multi-dimensional Matrices. Dong Kyue Kim, Yoo Ah Kim, Kunsoo Park |
| 1998 | Efficient Parallel Algorithm for the Editing Distance between Ordered Trees. Kaizhong Zhang |
| 1998 | Efficient Special Cases of Pattern Matching with Swaps. Amihood Amir, Gad M. Landau, Moshe Lewenstein, Noa Lewenstein |
| 1998 | Fixed Topology Alignment with Recombination. Bin Ma, Lusheng Wang, Ming Li |
| 1998 | Genome Halving. Nadia El-Mabrouk, Joseph H. Nadeau, David Sankoff |
| 1998 | Reporting Exact and Approximate Regular Expression Matches. Eugene W. Myers, Paulo Oliva, Katia S. Guimarães |
| 1998 | Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree (Preliminary Version). Jens Stoye, Dan Gusfield |