| 2003 | A Fully Linear-Time Approximation Algorithm for Grammar-Based Compression. Hiroshi Sakamoto |
| 2003 | A Simpler 1.5-Approximation Algorithm for Sorting by Transpositions. Tzvika Hartman |
| 2003 | Alignment between Two Multiple Alignments. Bin Ma, Zhuozhi Wang, Kaizhong Zhang |
| 2003 | An Effective Algorithm for the Peptide De Novo Sequencing from MS/MS Spectrum. Bin Ma, Kaizhong Zhang, Chengzhi Liang |
| 2003 | An Exact and Polynomial Distance-Based Algorithm to Reconstruct Single Copy Tandem Duplication Trees. Olivier Elemento, Olivier Gascuel |
| 2003 | An Improved Algorithm for Generalized Comparison of Minisatellites. Behshad Behzadi, Jean-Marc Steyaert |
| 2003 | Analysis of Tree Edit Distance Algorithms. Serge Dulucq, Hélène Touzet |
| 2003 | Average-Optimal Multiple Approximate String Matching. Kimmo Fredriksson, Gonzalo Navarro |
| 2003 | Combinatorial Pattern Matching, 14th Annual Symposium, CPM 2003, Morelia, Michocán, Mexico, June 25-27, 2003, Proceedings Ricardo A. Baeza-Yates, Edgar Chávez, Maxime Crochemore |
| 2003 | Complexities of the Centre and Median String Problems. François Nicolas, Eric Rivals |
| 2003 | Constrained Tree Inclusion. Gabriel Valiente |
| 2003 | Distributed and Paged Suffix Trees for Large Genetic Databases. Raphaël Clifford, Marek J. Sergot |
| 2003 | Efficient Data Structures and a New Randomized Approach for Sorting Signed Permutations by Reversals. Haim Kaplan, Elad Verbin |
| 2003 | Efficient Selection of Unique and Popular Oligos for Large EST Databases. Jie Zheng, Timothy J. Close, Tao Jiang, Stefano Lonardi |
| 2003 | Extracting Approximate Patterns. Johann Pelfrêne, Saïd Abdeddaïm, Joël Alexandre |
| 2003 | Fast Lightweight Suffix Array Construction and Checking. Stefan Burkhardt, Juha Kärkkäinen |
| 2003 | Haplotype Inference by Pure Parsimony. Dan Gusfield |
| 2003 | Linear-Time Construction of Suffix Arrays. Dong Kyue Kim, Jeong Seop Sim, Heejin Park, Kunsoo Park |
| 2003 | More Efficient Left-to-Right Pattern Matching in Non-sequential Equational Programs. Nadia Nedjah, Luiza de Macedo Mourelle |
| 2003 | Multiple Genome Alignment: Chaining Algorithms Revisited. Mohamed Ibrahim Abouelhoda, Enno Ohlebusch |
| 2003 | On Minimizing Pattern Splitting in Multi-track String Matching. Kjell Lemström, Veli Mäkinen |
| 2003 | Optimal Partitions of Strings: A New Class of Burrows-Wheeler Compression Algorithms. Raffaele Giancarlo, Marinella Sciortino |
| 2003 | Optimal Spaced Seeds for Hidden Markov Models, with Application to Homologous Coding Regions. Brona Brejová, Daniel G. Brown, Tomás Vinar |
| 2003 | Pattern Discovery in RNA Secondary Structure Using Affix Trees. Giancarlo Mauri, Giulio Pavesi |
| 2003 | Space Efficient Linear Time Construction of Suffix Arrays. Pang Ko, Srinivas Aluru |
| 2003 | Sparse LCS Common Substring Alignment. Gad M. Landau, Baruch Schieber, Michal Ziv-Ukelson |
| 2003 | Tuning String Matching for Huge Pattern Sets. Jari Kytöjoki, Leena Salmela, Jorma Tarhio |
| 2003 | Two-Dimensional Pattern Matching with Rotations. Amihood Amir, Ayelet Butman, Maxime Crochemore, Gad M. Landau, Malka Schaps |
| 2003 | Working on the Problem of Sorting by Transpositions on Genome Rearrangements. Maria Emília Telles Walter, Luiz Reginaldo A. F. Curado, Adilton G. Oliveira |