| 1999 | A Dynamic Data Structure for Reverse Lexicographically Sorted Prefixes. Hidetoshi Yokoo |
| 1999 | A General Practical Approach to Pattern Matching over Ziv-Lempel Compressed Text. Gonzalo Navarro, Mathieu Raffinot |
| 1999 | A New Indexing Method for Approximate String Matching. Gonzalo Navarro, Ricardo A. Baeza-Yates |
| 1999 | Applying an Edit Distance to the Matching of Tree Ring Sequences in Dendrochronology. Carola Wenk |
| 1999 | Approximate Periods of Strings. Jeong Seop Sim, Costas S. Iliopoulos, Kunsoo Park, William F. Smyth |
| 1999 | Bounds on the Number of String Subsequences. Daniel S. Hirschberg |
| 1999 | Combinatorial Pattern Matching, 10th Annual Symposium, CPM 99, Warwick University, UK, July 22-24, 1999, Proceedings Maxime Crochemore, Mike Paterson |
| 1999 | Computing Similarity between RNA Structures. Kaizhong Zhang, Lusheng Wang, Bin Ma |
| 1999 | Fast Multi-dimensional Approximate Pattern Matching. Gonzalo Navarro, Ricardo A. Baeza-Yates |
| 1999 | Finding Common RNA Secondary Structures from RNA Sequences. Zhuozhi Wang, Kaizhong Zhang |
| 1999 | Finding Common Subsequences with Arcs and Pseudoknots. Patricia A. Evans |
| 1999 | Finding Maximal Pairs with Bounded Gap. Gerth Stølting Brodal, Rune B. Lyngsø, Christian N. S. Pedersen, Jens Stoye |
| 1999 | GESTALT: Genomic Steiner Alignments. Giuseppe Lancia, R. Ravi |
| 1999 | Hybridization and Genome Rearrangement. Nadia El-Mabrouk, David Sankoff |
| 1999 | Matching of Spots in 2D Electrophoresis Images. Point Matching Under Non-uniform Distortions. Tatsuya Akutsu, Kyotetsu Kanaya, Akira Ohyama, Asao Fujiyama |
| 1999 | On the Complexity of Positional Sequencing by Hybridization. Amir Ben-Dor, Itsik Pe'er, Ron Shamir, Roded Sharan |
| 1999 | On the Structure of Syntenic Distance. David Liben-Nowell |
| 1999 | Pattern Matching in Text Compressed by Using Antidictionaries. Yusuke Shibata, Masayuki Takeda, Ayumi Shinohara, Setsuo Arikawa |
| 1999 | Physical Mapping with Repeated Probes: The Hypergraph Superstring Problem. Serafim Batzoglou, Sorin Istrail |
| 1999 | Shift-And Approach to Pattern Matching in LZW Compressed Text. Takuya Kida, Masayuki Takeda, Ayumi Shinohara, Setsuo Arikawa |
| 1999 | The Compression of Subsegments of Images Described by Finite Automata. Juhani Karhumäki, Wojciech Plandowski, Wojciech Rytter |
| 1999 | Ziv Lempel Compression of Huge Natural Language Data Tries Using Suffix Arrays. Strahil Ristov, Eric Laporte |