| 2000 | Algorithmic Aspects of Speech Recognition: A Synopsis. | Adam L. Buchsbaum, Raffaele Giancarlo |
| 2000 | A Lower Bound for the Breakpoint Phylogeny Problem. | David Bryant |
| 2000 | Identifying and Filtering Near-Duplicate Documents. | Andrei Z. Broder |
| 2000 | Finding Maximal Quasiperiodicities in Strings. | Gerth Stlting Brodal, Christian N. S. Pedersen |
| 2000 | Approximating the Maximum Isomorphic Agreement Subtree Is Hard. | Paola Bonizzoni, Gianluca Della Vedova, Giancarlo Mauri |
| 2000 | An Upper Bound for Number of Contacts in the HP-Model on the Face-Centered-Cubic Lattice (FCC). | Rolf Backofen |
| 2000 | Simple Optimal String Matching Algorithm. | Cyril Allauzen, Mathieu Raffinot |
| 1999 | Computing Similarity between RNA Structures. | Kaizhong Zhang, Lusheng Wang, Bin Ma |
| 1999 | A Dynamic Data Structure for Reverse Lexicographically Sorted Prefixes. | Hidetoshi Yokoo |
| 1999 | Applying an Edit Distance to the Matching of Tree Ring Sequences in Dendrochronology. | Carola Wenk |
| 1999 | Finding Common RNA Secondary Structures from RNA Sequences. | Zhuozhi Wang, Kaizhong Zhang |
| 1999 | Approximate Periods of Strings. | Jeong Seop Sim, Costas S. Iliopoulos, Kunsoo Park, William F. Smyth |
| 1999 | Pattern Matching in Text Compressed by Using Antidictionaries. | Yusuke Shibata, Masayuki Takeda, Ayumi Shinohara, Setsuo Arikawa |
| 1999 | Ziv Lempel Compression of Huge Natural Language Data Tries Using Suffix Arrays. | Strahil Ristov, Eric Laporte |
| 1999 | A General Practical Approach to Pattern Matching over Ziv-Lempel Compressed Text. | Gonzalo Navarro, Mathieu Raffinot |
| 1999 | Fast Multi-dimensional Approximate Pattern Matching. | Gonzalo Navarro, Ricardo A. Baeza-Yates |
| 1999 | A New Indexing Method for Approximate String Matching. | Gonzalo Navarro, Ricardo A. Baeza-Yates |
| 1999 | On the Structure of Syntenic Distance. | David Liben-Nowell |
| 1999 | GESTALT: Genomic Steiner Alignments. | Giuseppe Lancia, R. Ravi |
| 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 Karhumki, Wojciech Plandowski, Wojciech Rytter |
| 1999 | Bounds on the Number of String Subsequences. | Daniel S. Hirschberg |
| 1999 | Finding Common Subsequences with Arcs and Pseudoknots. | Patricia A. Evans |
| 1999 | Hybridization and Genome Rearrangement. | Nadia El-Mabrouk, David Sankoff |
| 1999 | Finding Maximal Pairs with Bounded Gap. | Gerth Stlting Brodal, Rune B. Lyngs, Christian N. S. Pedersen, Jens Stoye |