| 2003 | Constrained Tree Inclusion. | Gabriel Valiente |
| 2003 | A Fully Linear-Time Approximation Algorithm for Grammar-Based Compression. | Hiroshi Sakamoto |
| 2003 | Extracting Approximate Patterns. | Johann Pelfrne, Sad Abdeddam, Jol Alexandre |
| 2003 | Complexities of the Centre and Median String Problems. | Franois Nicolas, Eric Rivals |
| 2003 | More Efficient Left-to-Right Pattern Matching in Non-sequential Equational Programs. | Nadia Nedjah, Luiza de Macedo Mourelle |
| 2003 | An Effective Algorithm for the Peptide De Novo Sequencing from MS/MS Spectrum. | Bin Ma, Kaizhong Zhang, Chengzhi Liang |
| 2003 | Alignment between Two Multiple Alignments. | Bin Ma, Zhuozhi Wang, Kaizhong Zhang |
| 2003 | Pattern Discovery in RNA Secondary Structure Using Affix Trees. | Giancarlo Mauri, Giulio Pavesi |
| 2003 | On Minimizing Pattern Splitting in Multi-track String Matching. | Kjell Lemstrm, Veli Mkinen |
| 2003 | Sparse LCS Common Substring Alignment. | Gad M. Landau, Baruch Schieber, Michal Ziv-Ukelson |
| 2003 | Tuning String Matching for Huge Pattern Sets. | Jari Kytjoki, Leena Salmela, Jorma Tarhio |
| 2003 | Space Efficient Linear Time Construction of Suffix Arrays. | Pang Ko, Srinivas Aluru |
| 2003 | Linear-Time Construction of Suffix Arrays. | Dong Kyue Kim, Jeong Seop Sim, Heejin Park, Kunsoo Park |
| 2003 | Efficient Data Structures and a New Randomized Approach for Sorting Signed Permutations by Reversals. | Haim Kaplan, Elad Verbin |
| 2003 | A Simpler 1.5-Approximation Algorithm for Sorting by Transpositions. | Tzvika Hartman |
| 2003 | Haplotype Inference by Pure Parsimony. | Dan Gusfield |
| 2003 | Optimal Partitions of Strings: A New Class of Burrows-Wheeler Compression Algorithms. | Raffaele Giancarlo, Marinella Sciortino |
| 2003 | Average-Optimal Multiple Approximate String Matching. | Kimmo Fredriksson, Gonzalo Navarro |
| 2003 | An Exact and Polynomial Distance-Based Algorithm to Reconstruct Single Copy Tandem Duplication Trees. | Olivier Elemento, Olivier Gascuel |
| 2003 | Analysis of Tree Edit Distance Algorithms. | Serge Dulucq, Hlne Touzet |
| 2003 | Distributed and Paged Suffix Trees for Large Genetic Databases. | Raphal Clifford, Marek J. Sergot |
| 2003 | Fast Lightweight Suffix Array Construction and Checking. | Stefan Burkhardt, Juha Krkkinen |
| 2003 | Optimal Spaced Seeds for Hidden Markov Models, with Application to Homologous Coding Regions. | Brona Brejov, Daniel G. Brown, Toms Vinar |
| 2003 | An Improved Algorithm for Generalized Comparison of Minisatellites. | Behshad Behzadi, Jean-Marc Steyaert |
| 2003 | Two-Dimensional Pattern Matching with Rotations. | Amihood Amir, Ayelet Butman, Maxime Crochemore, Gad M. Landau, Malka Schaps |