| 2004 | A Hypergraph Model for the Yeast Protein Complex Network. Emad Y. Ramadan, Arijit Tarafdar, Alex Pothen |
| 2004 | Constrained De Novo Peptide Identification via Multi-Objective Optimization. Joël M. Malard, Alejandro Heredia-Langner, Douglas J. Baxter, Kristin H. Jarman, William R. Cannon |
| 2004 | Dynamic Programming for LR-PCR Segmention of Bacterium Genomes. Rumen Andonov, Dominique Lavenier, Philippe Veber, Nicola Yanev |
| 2004 | High Performance Biosequence Database Scanning on Reconfigurable Platforms. Timothy F. Oliver, Bertil Schmidt |
| 2004 | High Performance Computational Tools for Motif Discovery. Nicole E. Baldwin, Rebecca L. Collins, Michael A. Langston, Christopher T. Symons, Michael R. Leuze, Brynn H. Voy |
| 2004 | Identification of Mycobacterium Species Using Curated Custom Databases. Dan Kuyper, Hesham H. Ali, Amr M. Mohamed, Steven H. Hinrichs |
| 2004 | Large-Scale Simulation of Eukaryotic Cell Signaling Processes. John H. Miller, Yan Fang Zheng |
| 2004 | New Fast and Accurate Heuristics for Inference of Large Phylogenetic Trees. Alexandros Stamatakis, Harald Meier, Thomas Ludwig |
| 2004 | Parallel Protein Folding with STAPL. Shawna L. Thomas, Nancy M. Amato |
| 2004 | Parallel RNA Sequence-Structure Alignment. Tong Liu, Bertil Schmidt |
| 2004 | Particle Swarm Optimization and Neural Network Application for QSAR. Zhiwei Wang, Gregory L. Durst, Russell C. Eberhart, Donald B. Boyd, Zina Ben-Miled |
| 2004 | Study of a Highly Accurate and Fast Protein-Ligand Docking Algorithm Based on Molecular Dynamics. Michela Taufer, Michael F. Crowley, Daniel J. Price, Andrew A. Chien, Charles L. Brooks III |