| 2000 | A Boyer-Moore Type Algorithm for Compressed Pattern Matching. | Yusuke Shibata, Tetsuya Matsumoto, Masayuki Takeda, Ayumi Shinohara, Setsuo Arikawa |
| 2000 | Using Suffix Trees for Gapped Motif Discovery. | Emily Rocke |
| 2000 | Periods and Quasiperiods Characterization. | Mireille Rgnier, Laurent Mouchard |
| 2000 | Exact and Efficient Computation of the Expected Number of Missing and Common Words in Random Texts. | Sven Rahmann, Eric Rivals |
| 2000 | Machine Learning for Efficient Natural-Language Processing. | Fernando C. N. Pereira |
| 2000 | Incomplete Directed Perfect Phylogeny. | Itsik Pe'er, Ron Shamir, Roded Sharan |
| 2000 | Some Results on Flexible-Pattern Discovery. | Laxmi Parida |
| 2000 | The Combinatorial Partitioning Method. | Matthew R. Nelson, Sharon L. R. Kardia, Charles F. Sing |
| 2000 | Boyer-Moore String Matching over Ziv-Lempel Compressed Text. | Gonzalo Navarro, Jorma Tarhio |
| 2000 | Indexing Text with Approximate q-Grams. | Gonzalo Navarro, Erkki Sutinen, Jani Tanninen, Jorma Tarhio |
| 2000 | Compact Suffix Array. | Veli Mkinen |
| 2000 | Linear Bidirectional On-Line Construction of Affix Trees. | Moritz G. Maa |
| 2000 | A Polynominal Time Approximation Scheme for the Closest Substring Problem. | Bin Ma |
| 2000 | Structural Properties and Tractability Results for Linear Synteny. | David Liben-Nowell, Jon M. Kleinberg |
| 2000 | Improving Static Compression Schemes by Alphabet Extension. | Shmuel T. Klein |
| 2000 | A Dynamic Edit Distance Table. | Sung-Ryul Kim, Kunsoo Park |
| 2000 | Approximate String Matching over Ziv-Lempel Compressed Text. | Juha Krkkinen, Gonzalo Navarro, Esko Ukkonen |
| 2000 | A Faster and Unifying Algorithm for Comparing Trees. | Ming-Yang Kao, Tak Wah Lam, Wing-Kin Sung, Hing-Fung Ting |
| 2000 | The Longest Common Subsequence Problem for Arc-Annotated Sequences. | Tao Jiang, Guohui Lin, Bin Ma, Kaizhong Zhang |
| 2000 | Tsukuba BB: A Branch and Bound Algorithm for Local Multiple Sequence Alignment. | Paul Horton |
| 2000 | Explaining and Controlling Ambiguity in Dynamic Programming. | Robert Giegerich |
| 2000 | Approximation Algorithms for Hamming Clustering Problems. | Leszek Gasieniec, Jesper Jansson, Andrzej Lingas |
| 2000 | Parametric Multiple Sequence Alignment and Phylogeny Construction. | David Fernndez-Baca, Timo Sepplinen, Giora Slutzki |
| 2000 | Genome Rearrangement by Reversals and Insertions/Deletions of Contiguous Segments. | Nadia El-Mabrouk |
| 2000 | On the Complexity of Determining the Period of a String. | Artur Czumaj, Leszek Gasieniec |