| 2004 | A Combinatorial Shape Matching Algorithm for Rigid Protein Docking. Vicky Choi, Navin Goyal |
| 2004 | A Computational Model for RNA Multiple Structural Alignment.. Eugene Davydov, Serafim Batzoglou |
| 2004 | A Fast Set Intersection Algorithm for Sorted Sequences. Ricardo A. Baeza-Yates |
| 2004 | A Linear-Time Algorithm for Computing Translocation Distance between Signed Genomes. Guojun Li, Xingqin Qi, Xiaoli Wang, Binhai Zhu |
| 2004 | A Simple Optimal Representation for Balanced Parentheses. Richard F. Geary, Naila Rahman, Rajeev Raman, Venkatesh Raman |
| 2004 | A Trie-Based Approach for Compacting Automata. Maxime Crochemore, Chiara Epifanio, Roberto Grossi, Filippo Mignosi |
| 2004 | Approximate Labelled Subtree Homeomorphism. Ron Y. Pinter, Oleg Rokhlenko, Dekel Tsur, Michal Ziv-Ukelson |
| 2004 | Approximate Point Set Pattern Matching on Sequences and Planes. Tomoaki Suga, Shinichi Shimozono |
| 2004 | Approximate String Matching Using Compressed Suffix Arrays. Trinh N. D. Huynh, Wing-Kai Hon, Tak Wah Lam, Wing-Kin Sung |
| 2004 | Average-Case Analysis of Approximate Trie Search (Extended Abstract). Moritz G. Maaß |
| 2004 | Combinatorial Pattern Matching, 15th Annual Symposium, CPM 2004, Istanbul,Turkey, July 5-7, 2004, Proceedings Süleyman Cenk Sahinalp, S. Muthukrishnan, Ugur Dogrusöz |
| 2004 | Compressed Compact Suffix Arrays. Veli Mäkinen, Gonzalo Navarro |
| 2004 | Compressed Index for a Dynamic Collection of Texts. Ho-Leung Chan, Wing-Kai Hon, Tak Wah Lam |
| 2004 | Computational Design of New and Recombinant Selenoproteins. Rolf Backofen, Anke Busch |
| 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 Lipták |
| 2004 | Faster Two Dimensional Pattern Matching with Rotations. Amihood Amir, Oren Kapah, Dekel Tsur |
| 2004 | Finding Biclusters by Random Projections. Stefano Lonardi, Wojciech Szpankowski, Qiaofeng Yang |
| 2004 | Improved Single and Multiple Approximate String Matching. Kimmo Fredriksson, Gonzalo Navarro |
| 2004 | Maximal Common Connected Sets of Interval Graphs. Michel Habib, Christophe Paul, Mathieu Raffinot |
| 2004 | Maximum Agreement and Compatible Supertrees (Extended Abstract). Vincent Berry, François Nicolas |
| 2004 | Multi-seed Lossless Filtration (Extended Abstract). Gregory Kucherov, Laurent Noé, Mikhail A. Roytberg |
| 2004 | New Results for the 2-Interval Pattern Problem. Guillaume Blin, Guillaume Fertin, Stéphane Vialette |
| 2004 | On the Average Sequence Complexity. Svante Janson, Stefano Lonardi, Wojciech Szpankowski |
| 2004 | On the k-Closest Substring and k-Consensus Pattern Problems. Yishan Jiao, Jingyi Xu, Ming Li |
| 2004 | Optimizing Multiple Spaced Seeds for Homology Search. Jinbo Xu, Daniel G. Brown, Ming Li, Bin Ma |
| 2004 | Performing Local Similarity Searches with Variable Length Seeds. Miklós Csürös |
| 2004 | Polynomial-Time Algorithms for the Ordered Maximum Agreement Subtree Problem. Anders Dessmark, Jesper Jansson, Andrzej Lingas, Eva-Marta Lundell |
| 2004 | Quadratic Time Algorithms for Finding Common Intervals in Two and More Sequences. Thomas Schmidt, Jens Stoye |
| 2004 | Real-Time String Matching in Sublinear Space. Leszek Gasieniec, Roman M. Kolpakov |
| 2004 | Reversal Distance without Hurdles and Fortresses. Anne Bergeron, Julia Mixtacki, Jens Stoye |
| 2004 | Small Phylogeny Problem: Character Evolution Trees. Arvind Gupta, Ján Manuch, Ladislav Stacho, Chenchen Zhu |
| 2004 | Sorting by Length-Weighted Reversals: Dealing with Signs and Circularity. Firas Swidan, Michael A. Bender, Dongdong Ge, Simai He, Haodong Hu, Ron Y. Pinter |
| 2004 | Sorting by Reversals in Subquadratic Time. Eric Tannier, Marie-France Sagot |
| 2004 | Sparse Normalized Local Alignment. Nadav Efraty, Gad M. Landau |
| 2004 | The Protein Sequence Design Problem in Canonical Model on 2D and 3D Lattices. Piotr Berman, Bhaskar DasGupta, Dhruv Mubayi, Robert H. Sloan, György Turán, Yi Zhang |
| 2004 | Two Algorithms for LCS Consecutive Suffix Alignment. Gad M. Landau, Eugene W. Myers, Michal Ziv-Ukelson |