| 2004 | Multiple Vector Seeds for Protein Alignment. | Daniel G. Brown |
| 2004 | The Most Probable Labeling Problem in HMMs and Its Application to Bioinformatics. | Brona Brejov, Daniel G. Brown, Toms Vinar |
| 2004 | Topological Rearrangements and Local Search Method for Tandem Duplication Trees. | Denis Bertrand, Olivier Gascuel |
| 2004 | Reconstructing Ancestral Gene Orders Using Conserved Intervals. | Anne Bergeron, Mathieu Blanchette, Annie Chateau, Cdric Chauve |
| 2004 | Online Consensus and Agreement of Phylogenetic Trees. | Tanya Y. Berger-Wolf |
| 2004 | The Minisatellite Transformation Problem Revisited: A Run Length Encoded Approach. | Behshad Behzadi, Jean-Marc Steyaert |
| 2004 | Finding Optimal Pairs of Patterns. | Hideo Bannai, Heikki Hyyr, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano |
| 2004 | Solving the Protein Threading Problem by Lagrangian Relaxation. | Stefan Balev |
| 2004 | Monotone Scoring of Patterns with Mismatches: (Extended Abstract). | Alberto Apostolico, Cinzia Pizzi |
| 2004 | ATDD: An Algorithmic Tool for Domain Discovery in Protein Sequences. | Stanislav Angelov, Sanjeev Khanna, Li Li, Fernando Pereira |
| 2004 | Genome Identification and Classification by Short Oligo Arrays. | Stanislav Angelov, Boulos Harb, Sampath Kannan, Sanjeev Khanna, Junhyong Kim, Li-San Wang |
| 2004 | Novel Tree Edit Operations for RNA Secondary Structure Comparison. | Julien Allali, Marie-France Sagot |
| 2003 | Speedup LP Approach to Protein Threading via Graph Reduction. | Jinbo Xu |
| 2003 | Bounds for Resquencing by Hybridization. | Dekel Tsur |
| 2003 | Side-Chain Structure Prediction Based on Dead-End Elimination: Single Split DEE-criterion Implementation and Elimination Power. | Jan A. Spriet |
| 2003 | Selecting Degenerate Multiplex PCR Primers. | Richard Souvenir, Jeremy Buhler, Gary D. Stormo, Weixiong Zhang |
| 2003 | Parsimonious Reconstruction of Sequence Evolution and Haplotype Blocks. | Yun S. Song, Jotun Hein |
| 2003 | Match Chaining Algorithms for cDNA Mapping. | Tetsuo Shibuya, Igor Kurochkin |
| 2003 | Dynamic Programming Algorithms for Two Statistical Problems in Computational Biology. | Sven Rahmann |
| 2003 | Homology Modeling of Proteins Using Multiple Models and Consensus Sequence Alignment. | Jahnavi C. Prasad, Michael Silberstein, Carlos J. Camacho, Sandor Vajda |
| 2003 | Pattern Discovery Allowing Wild-Cards, Substitution Matrices, and Multiple Score Functions. | Alban Mancheron, Irena Rusu |
| 2003 | Bayesian Phylogenetic Inference under a Statistical Insertion-Deletion Model. | Gerton Lunter, Istvn Mikls, Alexei J. Drummond, Jens Ledet Jensen, Jotun Hein |
| 2003 | Efficient Energy Computation for Monte Carlo Simulation of Proteins. | Itay Lotan, Fabian Schwarzer, Jean-Claude Latombe |
| 2003 | Optimal Multiple Parsimony Alignment with Affine Gap Cost Using a Phylogenetic Tree. | Bjarne Knudsen |
| 2003 | Identifying Blocks and Sub-populations in Noisy SNP Data. | Gad Kimmel, Roded Sharan, Ron Shamir |