| 2003 | A Combinatorial Approach to Automatic Discovery of Cluster-Patterns. Revital Eres, Gad M. Landau, Laxmi Parida |
| 2003 | A Large Version of the Small Parsimony Problem. Jakob Fredslund, Jotun Hein, Tejs Scharling |
| 2003 | A Linear-Time Majority Tree Algorithm. Nina Amenta, Frederick Clarke, Katherine St. John |
| 2003 | A Local Chaining Algorithm and Its Applications in Comparative Genomics. Mohamed Ibrahim Abouelhoda, Enno Ohlebusch |
| 2003 | A Method to Detect Gene Structure and Alternative Splice Sites by Agreeing ESTs to a Genomic Sequence. Paola Bonizzoni, Graziano Pesole, Raffaella Rizzi |
| 2003 | A Stochastic Approach to Count RNA Molecules Using DNA Sequencing Methods. Boris Hollas, Rainer Schuler |
| 2003 | A Systematic Statistical Analysis of Ion Trap Tandem Mass Spectra in View of Peptide Scoring. Jacques Colinge, Alexandre Masselot, Jérôme Magnin |
| 2003 | Algorithms in Bioinformatics, Third International Workshop, WABI 2003, Budapest, Hungary, September 15-20, 2003, Proceedings Gary Benson, Roderic D. M. Page |
| 2003 | Ancestral Maximum Likelihood of Evolutionary Trees Is Hard. Louigi Addario-Berry, Benny Chor, Michael T. Hallett, Jens Lagergren, Alessandro Panconesi, Todd Wareham |
| 2003 | Bayesian Phylogenetic Inference under a Statistical Insertion-Deletion Model. Gerton Lunter, István Miklós, Alexei J. Drummond, Jens Ledet Jensen, Jotun Hein |
| 2003 | Better Hill-Climbing Searches for Parsimony. Ganeshkumar Ganapathy, Vijaya Ramachandran, Tandy J. Warnow |
| 2003 | Bounds for Resquencing by Hybridization. Dekel Tsur |
| 2003 | Common Intervals of Two Sequences. Gilles Didier |
| 2003 | Composition Alignment. Gary Benson |
| 2003 | Computing Refined Buneman Trees in Cubic Time. Gerth Stølting Brodal, Rolf Fagerberg, Anna Östlin, Christian N. S. Pedersen, S. Srinivasa Rao |
| 2003 | Consensus Networks: A Method for Visualising Incompatibilities in Collections of Trees. Barbara R. Holland, Vincent Moulton |
| 2003 | Designing Optimally Multiplexed SNP Genotyping Assays. Yonatan Aumann, Efrat Manisterski, Zohar Yakhini |
| 2003 | Distance Corrections on Recombinant Sequences. David Bryant, Daniel H. Huson, Tobias H. Klöpper, Kay Nieselt-Struwe |
| 2003 | Dynamic Programming Algorithms for Two Statistical Problems in Computational Biology. Sven Rahmann |
| 2003 | Efficient Energy Computation for Monte Carlo Simulation of Proteins. Itay Lotan, Fabian Schwarzer, Jean-Claude Latombe |
| 2003 | Efficient Generation of Uniform Samples from Phylogenetic Trees. Paul E. Kearney, J. Ian Munro, Derek Phillips |
| 2003 | Homology Modeling of Proteins Using Multiple Models and Consensus Sequence Alignment. Jahnavi C. Prasad, Michael Silberstein, Carlos J. Camacho, Sandor Vajda |
| 2003 | Identifying Blocks and Sub-populations in Noisy SNP Data. Gad Kimmel, Roded Sharan, Ron Shamir |
| 2003 | Match Chaining Algorithms for cDNA Mapping. Tetsuo Shibuya, Igor Kurochkin |
| 2003 | Minimum Recombiant Haplotype Configuration on Tree Pedigrees. Koichiro Doi, Jing Li, Tao Jiang |
| 2003 | New Algorithm for the Simplified Partial Digest Problem. Jacek Blazewicz, Marcin Jaroszewski |
| 2003 | New Efficient Algorithm for Detection of Horizontal Gene Transfer Events. Alix Boc, Vladimir Makarenkov |
| 2003 | Noisy Data Make the Partial Digest Problem NP-hard. Mark Cieliebak, Stephan J. Eidenbenz, Paolo Penna |
| 2003 | Optimal DNA Signal Recognition Models with a Fixed Amount of Intrasignal Dependency. Brona Brejová, Daniel G. Brown, Tomás Vinar |
| 2003 | Optimal Multiple Parsimony Alignment with Affine Gap Cost Using a Phylogenetic Tree. Bjarne Knudsen |
| 2003 | Parsimonious Reconstruction of Sequence Evolution and Haplotype Blocks. Yun S. Song, Jotun Hein |
| 2003 | Pattern Discovery Allowing Wild-Cards, Substitution Matrices, and Multiple Score Functions. Alban Mancheron, Irena Rusu |
| 2003 | Selecting Degenerate Multiplex PCR Primers. Richard Souvenir, Jeremy Buhler, Gary D. Stormo, Weixiong Zhang |
| 2003 | Sequencing from Compomers: Using Mass Spectrometry for DNA De-Novo Sequencing of 200+ nt. Sebastian Böcker |
| 2003 | Side-Chain Structure Prediction Based on Dead-End Elimination: Single Split DEE-criterion Implementation and Elimination Power. Jan A. Spriet |
| 2003 | Speedup LP Approach to Protein Threading via Graph Reduction. Jinbo Xu |
| 2003 | Vector Seeds: An Extension to Spaced Seeds Allows Substantial Improvements in Sensitivity and Specifity. Brona Brejová, Daniel G. Brown, Tomás Vinar |