| 2000 | A Boyer-Moore Type Algorithm for Compressed Pattern Matching. Yusuke Shibata, Tetsuya Matsumoto, Masayuki Takeda, Ayumi Shinohara, Setsuo Arikawa |
| 2000 | A Dynamic Edit Distance Table. Sung-Ryul Kim, Kunsoo Park |
| 2000 | A Faster and Unifying Algorithm for Comparing Trees. Ming-Yang Kao, Tak Wah Lam, Wing-Kin Sung, Hing-Fung Ting |
| 2000 | A Lower Bound for the Breakpoint Phylogeny Problem. David Bryant |
| 2000 | A Polynominal Time Approximation Scheme for the Closest Substring Problem. Bin Ma |
| 2000 | Algorithmic Aspects of Speech Recognition: A Synopsis. Adam L. Buchsbaum, Raffaele Giancarlo |
| 2000 | An Upper Bound for Number of Contacts in the HP-Model on the Face-Centered-Cubic Lattice (FCC). Rolf Backofen |
| 2000 | Approximate String Matching over Ziv-Lempel Compressed Text. Juha Kärkkäinen, Gonzalo Navarro, Esko Ukkonen |
| 2000 | Approximating the Maximum Isomorphic Agreement Subtree Is Hard. Paola Bonizzoni, Gianluca Della Vedova, Giancarlo Mauri |
| 2000 | Approximation Algorithms for Hamming Clustering Problems. Leszek Gasieniec, Jesper Jansson, Andrzej Lingas |
| 2000 | Boyer-Moore String Matching over Ziv-Lempel Compressed Text. Gonzalo Navarro, Jorma Tarhio |
| 2000 | Browsing around a Digital Library: Today and Tomorrow. Ian H. Witten |
| 2000 | Combinatorial Pattern Matching, 11th Annual Symposium, CPM 2000, Montreal, Canada, June 21-23, 2000, Proceedings Raffaele Giancarlo, David Sankoff |
| 2000 | Compact Suffix Array. Veli Mäkinen |
| 2000 | Exact and Efficient Computation of the Expected Number of Missing and Common Words in Random Texts. Sven Rahmann, Eric Rivals |
| 2000 | Explaining and Controlling Ambiguity in Dynamic Programming. Robert Giegerich |
| 2000 | Finding Maximal Quasiperiodicities in Strings. Gerth Stølting Brodal, Christian N. S. Pedersen |
| 2000 | Genome Rearrangement by Reversals and Insertions/Deletions of Contiguous Segments. Nadia El-Mabrouk |
| 2000 | Identifying and Filtering Near-Duplicate Documents. Andrei Z. Broder |
| 2000 | Improving Static Compression Schemes by Alphabet Extension. Shmuel T. Klein |
| 2000 | Incomplete Directed Perfect Phylogeny. Itsik Pe'er, Ron Shamir, Roded Sharan |
| 2000 | Indexing Text with Approximate q-Grams. Gonzalo Navarro, Erkki Sutinen, Jani Tanninen, Jorma Tarhio |
| 2000 | Linear Bidirectional On-Line Construction of Affix Trees. Moritz G. Maaß |
| 2000 | Machine Learning for Efficient Natural-Language Processing. Fernando C. N. Pereira |
| 2000 | On the Complexity of Determining the Period of a String. Artur Czumaj, Leszek Gasieniec |
| 2000 | Parametric Multiple Sequence Alignment and Phylogeny Construction. David Fernández-Baca, Timo Seppäläinen, Giora Slutzki |
| 2000 | Periods and Quasiperiods Characterization. Mireille Régnier, Laurent Mouchard |
| 2000 | Shift Error Detection in Standardized Exams. Steven Skiena, Pavel Sumazin |
| 2000 | Simple Optimal String Matching Algorithm. Cyril Allauzen, Mathieu Raffinot |
| 2000 | Some Results on Flexible-Pattern Discovery. Laxmi Parida |
| 2000 | Structural Properties and Tractability Results for Linear Synteny. David Liben-Nowell, Jon M. Kleinberg |
| 2000 | The Combinatorial Partitioning Method. Matthew R. Nelson, Sharon L. R. Kardia, Charles F. Sing |
| 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 | Using Suffix Trees for Gapped Motif Discovery. Emily Rocke |