| 2004 | Symbolic Inference of Xenobiotic Metabolism. | Daniel C. McShan, M. Updadhayaya, Imran Shah |
| 2004 | Terminological Mapping for High Throughput Comparative Biology of Phenotypes. | Yves A. Lussier, Jianrong Li |
| 2004 | Modeling Cellular Processes with Variational Bayesian Cooperative Vector Quantizer. | Xinghua Lu, Milos Hauskrecht, Roger S. Day |
| 2004 | Discovery of Binding Motif Pairs from Protein Complex Structural Data and Protein Interaction Sequence Data. | Haiquan Li, Jinyan Li, Soon-Heng Tan, See-Kiong Ng |
| 2004 | A Biospi Model of Lymphocyte-Endothelial Interactions in Inflamed Brain Venules. | Paola Lecca, Corrado Priami, Carlo Laudanna, Gabriela Constantin |
| 2004 | Kernel-Based Data Fusion and Its Application to Protein Function Prediction in Yeast. | Gert R. G. Lanckriet, Minghua Deng, Nello Cristianini, Michael I. Jordan, William Stafford Noble |
| 2004 | A Comparison of Different Strategies for Computing Confidence Intervals of the Linkage Disequilibrium Measure. | Sung K. Kim, Kui Zhang, Fengzhu Sun |
| 2004 | Inferring Gene Regulatory Networks from Raw Data: A Molecular Epistemics Approach. | D. A. Kightley, Navin Chandra, Keith O. Elliston |
| 2004 | An Evidence Ontology for Use in Pathway/Genome Databases. | Peter D. Karp, Suzanne M. Paley, Cynthia J. Krieger, Peifen Zhang |
| 2004 | Tradeoff Between No-Call Reduction in Genotyping Error Rate and Loss of Sample Size for Genetic Case/Control Association Studies. | Sun Jun Kang, Derek Gordon, A. M. Brown, Jrg Ott, Stephen J. Finch |
| 2004 | Detection of Novel Splice Forms in Human and Mouse Using Cross-Species Approach. | Zhengyan Kan, John Castle, Jason M. Johnson, Nick Tsinoremas |
| 2004 | Session Introduction. | Trey Ideker, Erik K. Neumann, Vincent Schchter |
| 2004 | Accurate Classification of Protein Structural Families Using Coherent Subgraph Analysis. | Jun Huan, Wei Wang, Anglina Washington, Jan F. Prins, Ruchir Shah, Alexander Tropsha |
| 2004 | Predicting the Operon Structure of Bacillus subtilis Using Operon Length, Intergene Distance, and Gene Expression Information. | Michiel J. L. de Hoon, Seiya Imoto, Kazuo Kobayashi, Naotake Ogasawara, Satoru Miyano |
| 2004 | Session Introduction. | Alexander J. Hartemink, Eran Segal |
| 2004 | Genome-Wide Detection of Alternative Splicing in Expressed Sequences Using Partial Order Multiple Sequence Alignment Graphs. | Catherine S. Grasso, Barmak Modrek, Yi Xing, Christopher J. Lee |
| 2004 | Building Mouse Phenotype Ontologies. | Georgios V. Gkoutos, Eain C. J. Green, Ann-Marie Mallon, John M. Hancock, Duncan Davidson |
| 2004 | Reconstructing Chain Functions in Genetic Networks. | Irit Gat-Viks, Ron Shamir, Richard M. Karp, Roded Sharan |
| 2004 | Combining Text Mining and Sequence Analysis to Discover Protein Functional Regions. | Eleazar Eskin, Eugene Agichtein |
| 2004 | A Markov Chain Approach to Reconstruction of Long Haplotypes. | Lauri Eronen, Floris Geerts, Hannu Toivonen |
| 2004 | Clustering Protein Sequence and Structure Space with Infinite Gaussian Mixture Models. | Ananya Dubey, Seungwoo Hwang, Claudia Rangel, Carl Edward Rasmussen, Zoubin Ghahramani, David L. Wild |
| 2004 | A Mixed Integer Linear Programming (MILP) Framework for Inferring Time Delay in Gene Regulatory Networks. | Madhukar S. Dasika, Anshuman Gupta, Costas D. Maranas, Jeffrey D. Varner |
| 2004 | The Effects of Alternative Splicing on Transmembrane Proteins in the Mouse Genome. | Melissa S. Cline, Ron Shigeta, Raymond Wheeler, Michael A. Siani-Rose, David Kulp, Ann E. Loraine |
| 2004 | Protein Structure and Fold Prediction Using Tree-Augmented Bayesian Classifier. | Arunkumar Chinnasamy, Wing-Kin Sung, Ankush Mittal |
| 2004 | Design of a High-Throughput Assay for Alternative Splicing Using Polymerase Colonies. | Jeremy Buhler, Richard Souvenir, Weixiong Zhang, Rob Mitra |