| 1999 | On the Complexity of Positional Sequencing by Hybridization. | Amir Ben-Dor, Itsik Pe'er, Ron Shamir, Roded Sharan |
| 1999 | Physical Mapping with Repeated Probes: The Hypergraph Superstring Problem. | Serafim Batzoglou, Sorin Istrail |
| 1999 | Matching of Spots in 2D Electrophoresis Images. Point Matching Under Non-uniform Distortions. | Tatsuya Akutsu, Kyotetsu Kanaya, Akira Ohyama, Asao Fujiyama |
| 1998 | A Dictionary Matching Algorithm Fast on the Average for Terms of Varying Length. | Michal Ziv-Ukelson, Aaron Kershenbaum |
| 1998 | Efficient Parallel Algorithm for the Editing Distance between Ordered Trees. | Kaizhong Zhang |
| 1998 | An Approximate Oracle for Distance in Metric Spaces. | Yanling Yang, Kaizhong Zhang, Xiong Wang, Jason Tsong-Li Wang, Dennis E. Shasha |
| 1998 | Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree (Preliminary Version). | Jens Stoye, Dan Gusfield |
| 1998 | Approximate Word Sequence Matching over Sparse Suffix Trees. | Knut Magne Risvik |
| 1998 | Comparison of Coding DNA. | Christian N. S. Pedersen, Rune B. Lyngs, Jotun Hein |
| 1998 | A Bit-Parallel Approach to Suffix Automata: Fast Extended String Matching. | Gonzalo Navarro, Mathieu Raffinot |
| 1998 | Reporting Exact and Approximate Regular Expression Matches. | Eugene W. Myers, Paulo Oliva, Katia S. Guimares |
| 1998 | A Fast Bit-Vector Algorithm for Approximate String Matching Based on Dynamic Programming. | Gene Myers |
| 1998 | Fixed Topology Alignment with Recombination. | Bin Ma, Lusheng Wang, Ming Li |
| 1998 | Constructing Suffix Arrays for Multi-dimensional Matrices. | Dong Kyue Kim, Yoo Ah Kim, Kunsoo Park |
| 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 | A Rotation Invariant Filter for Two-Dimensional String Matching. | Kimmo Fredriksson, Esko Ukkonen |
| 1998 | Genome Halving. | Nadia El-Mabrouk, Joseph H. Nadeau, David Sankoff |
| 1998 | A Very Fast String Matching Algorithm for Small Alphabeths and Long Patterns (Extended Abstract). | Christian Charras, Thierry Lecroq, Joseph Daniel Pehoushek |
| 1998 | Efficient Special Cases of Pattern Matching with Swaps. | Amihood Amir, Gad M. Landau, Moshe Lewenstein, Noa Lewenstein |
| 1997 | An Easy Case of Sorting by Reversals. | Nicholas Q. Trn |
| 1997 | On the Nadeau-Taylor Theory of Conserved Chromosome Segments. | David Sankoff, Marie-Noelle Parent, Isabelle Marchand, Vincent Ferretti |
| 1997 | Flexible Identification of Structural Objects in Nucleic Acid Sequences: Palindromes, Mirror Repeats, Pseudoknots and Triple Helices. | Marie-France Sagot, Alain Viari |
| 1997 | A New Algorithm for the Ordered Tree Inclusion Problem. | Thorsten Richter |
| 1997 | A Filter Method for the Weighted Local Similarity Search Problem. | Enno Ohlebusch |