| 2004 | On the Average Sequence Complexity. | Svante Janson, Stefano Lonardi, Wojciech Szpankowski |
| 2004 | Approximate String Matching Using Compressed Suffix Arrays. | Trinh N. D. Huynh, Wing-Kai Hon, Tak Wah Lam, Wing-Kin Sung |
| 2004 | Maximal Common Connected Sets of Interval Graphs. | Michel Habib, Christophe Paul, Mathieu Raffinot |
| 2004 | Small Phylogeny Problem: Character Evolution Trees. | Arvind Gupta, Jn Manuch, Ladislav Stacho, Chenchen Zhu |
| 2004 | A Simple Optimal Representation for Balanced Parentheses. | Richard F. Geary, Naila Rahman, Rajeev Raman, Venkatesh Raman |
| 2004 | Real-Time String Matching in Sublinear Space. | Leszek Gasieniec, Roman M. Kolpakov |
| 2004 | Improved Single and Multiple Approximate String Matching. | Kimmo Fredriksson, Gonzalo Navarro |
| 2004 | Sparse Normalized Local Alignment. | Nadav Efraty, Gad M. Landau |
| 2004 | Polynomial-Time Algorithms for the Ordered Maximum Agreement Subtree Problem. | Anders Dessmark, Jesper Jansson, Andrzej Lingas, Eva-Marta Lundell |
| 2004 | A Computational Model for RNA Multiple Structural Alignment.. | Eugene Davydov, Serafim Batzoglou |
| 2004 | Performing Local Similarity Searches with Variable Length Seeds. | Mikls Csrs |
| 2004 | A Trie-Based Approach for Compacting Automata. | Maxime Crochemore, Chiara Epifanio, Roberto Grossi, Filippo Mignosi |
| 2004 | A Combinatorial Shape Matching Algorithm for Rigid Protein Docking. | Vicky Choi, Navin Goyal |
| 2004 | Compressed Index for a Dynamic Collection of Texts. | Ho-Leung Chan, Wing-Kai Hon, Tak Wah Lam |
| 2004 | New Results for the 2-Interval Pattern Problem. | Guillaume Blin, Guillaume Fertin, Stphane Vialette |
| 2004 | Maximum Agreement and Compatible Supertrees (Extended Abstract). | Vincent Berry, Franois Nicolas |
| 2004 | The Protein Sequence Design Problem in Canonical Model on 2D and 3D Lattices. | Piotr Berman, Bhaskar DasGupta, Dhruv Mubayi, Robert H. Sloan, Gyrgy Turn, Yi Zhang |
| 2004 | Reversal Distance without Hurdles and Fortresses. | Anne Bergeron, Julia Mixtacki, Jens Stoye |
| 2004 | Computational Problems in Perfect Phylogeny Haplotyping: Xor-Genotypes and Tag SNPs. | Tamar Barzuza, Jacques S. Beckmann, Ron Shamir, Itsik Pe'er |
| 2004 | Efficient Algorithms for Finding Submasses in Weighted Strings. | Nikhil Bansal, Mark Cieliebak, Zsuzsanna Liptk |
| 2004 | A Fast Set Intersection Algorithm for Sorted Sequences. | Ricardo A. Baeza-Yates |
| 2004 | Computational Design of New and Recombinant Selenoproteins. | Rolf Backofen, Anke Busch |
| 2004 | Faster Two Dimensional Pattern Matching with Rotations. | Amihood Amir, Oren Kapah, Dekel Tsur |
| 2003 | Efficient Selection of Unique and Popular Oligos for Large EST Databases. | Jie Zheng, Timothy J. Close, Tao Jiang, Stefano Lonardi |
| 2003 | Working on the Problem of Sorting by Transpositions on Genome Rearrangements. | Maria Emlia Telles Walter, Luiz Reginaldo A. F. Curado, Adilton G. Oliveira |