Table of Contents

• PrefaceRuss B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein. [doi]
• Session IntroductionHui Wang, U. Yang, Christopher Lee, John Blume. 3-4 [doi]
• Design of a High-Throughput Assay for Alternative Splicing Using Polymerase ColoniesJeremy Buhler, Richard Souvenir, Weixiong Zhang, Rob Mitra. 5-16 [doi]
• The Effects of Alternative Splicing on Transmembrane Proteins in the Mouse GenomeMelissa S. Cline, Ron Shigeta, Raymond Wheeler, Michael A. Siani-Rose, David Kulp, Ann E. Loraine. 17-28 [doi]
• Genome-Wide Detection of Alternative Splicing in Expressed Sequences Using Partial Order Multiple Sequence Alignment GraphsCatherine Grasso, Barmak Modrek, Yi Xing, Christopher Lee. 29-41 [doi]
• Detection of Novel Splice Forms in Human and Mouse Using Cross-Species ApproachZhengyan Kan, John Castle, Jason M. Johnson, Nick Tsinoremas. 42-53 [doi]
• Extensive Search for Discriminative Features of Alternative SplicingHiroki Sakai, Osamu Maruyama. 54-65 [doi]
• Transcriptome and Genome Conservation of Alternative Splicing Events in Humans and MiceCharles W. Sugnet, W. James Kent, Manual Ares, David Haussler. 66-77 [doi]
• A Database Designed to Computationally Aid an Experimental Approach to Alternative SplicingChristina L. Zheng, T. Murlidharan Nair, Michael Gribskov, Y. S. Kwon, Hai-Ri Li, Xiang-Dong Fu. 78-88 [doi]
• Session IntroductionFrancisco M. de la Vega, Kenneth K. Kidd, Andrew Collins. 89-92
• Pedigree Generation for Analysis of Genetic Linkage and AssociationM. P. Bass, E. R. Martin, E. R. Hauser. 93-103 [doi]
• A Markov Chain Approach to Reconstruction of Long HaplotypesLauri Eronen, Floris Geerts, Hannu Toivonen. 104-115 [doi]
• Tradeoff Between No-Call Reduction in Genotyping Error Rate and Loss of Sample Size for Genetic Case/Control Association StudiesSun Jun Kang, Derek Gordon, A. M. Brown, Jürg Ott, Stephen J. Finch. 116-127 [doi]
• A Comparison of Different Strategies for Computing Confidence Intervals of the Linkage Disequilibrium MeasureSung K. Kim, Kui Zhang, Fengzhu Sun. 128-139 [doi]
• Multiplexing Schemes for Generic SNP Genotyping AssaysRoded Sharan, Amir Ben-Dor, Zohar Yakhini. 140-151 [doi]
• Haplotype Block Definition and Its ApplicationXiaofeng Zhu, Shuanglin Zhang, Donghai Kan, Richard S. Cooper. 152-163 [doi]
• Session IntroductionOlivier Bodenreider, Joyce A. Mitchell, Alexa T. McCray. 164-165 [doi]
• Part-of Relations in Anatomy Ontologies: A Proposal for RDFS and OWL FormalisationsJ. Stuart Aitken, Bonnie L. Webber, Jonathan Bard. 166-177 [doi]
• Building Mouse Phenotype OntologiesGeorgios V. Gkoutos, Eain C. J. Green, Ann-Marie Mallon, John M. Hancock, Duncan Davidson. 178-189 [doi]
• An Evidence Ontology for Use in Pathway/Genome DatabasesPeter D. Karp, Suzanne M. Paley, Cynthia J. Krieger, Peifen Zhang. 190-201 [doi]
• Terminological Mapping for High Throughput Comparative Biology of PhenotypesYves A. Lussier, Jianrong Li. 202-213 [doi]
• The Compositional Structure of Gene Ontology TermsPhilip V. Ogren, K. Bretonnel Cohen, George Acquaah-Mensah, Jens Eberlein, Lawrence Hunter. 214-225 [doi]
• Defaults, Context, and Knowledge: Alternatives for OWL-Indexed Knowledge BasesAlan L. Rector. 226-237 [doi]
• Biological Nomenclatures: A Source of Lexical Knowledge and AmbiguityOlivia Tuason, Lifeng Chen, Hongfang Liu, Judith A. Blake, Carol Friedman. 238-249 [doi]
• Investigating Implicit Knowledge in Ontologies with Application to the Anatomical DomainSongmao Zhang, Olivier Bodenreider. 250-261 [doi]
• Session IntroductionAlexander J. Hartemink, Eran Segal. 262-263 [doi]
• ProGreSS: Simultaneous Searching of Protein Databases by Sequence and StructureArnab Bhattacharya, Tolga Can, Tamer Kahveci, Ambuj K. Singh, Yuan-Fang Wang. 264-275 [doi]
• Predicting the Operon Structure of Bacillus subtilis Using Operon Length, Intergene Distance, and Gene Expression InformationMichiel J. L. de Hoon, Seiya Imoto, Kazuo Kobayashi, Naotake Ogasawara, Satoru Miyano. 276-287 [doi]
• Combining Text Mining and Sequence Analysis to Discover Protein Functional RegionsEleazar Eskin, Eugene Agichtein. 288-299 [doi]
• Kernel-Based Data Fusion and Its Application to Protein Function Prediction in YeastGert R. G. Lanckriet, Minghua Deng, Nello Cristianini, Michael I. Jordan, William Stafford Noble. 300-311 [doi]
• Discovery of Binding Motif Pairs from Protein Complex Structural Data and Protein Interaction Sequence DataHaiquan Li, Jinyan Li, Soon-Heng Tan, See-Kiong Ng. 312-32 [doi]
• Phylogenetic Motif Detection by Expectation-Maximization on Evolutionary MixturesAlan M. Moses, Derek Y. Chiang, Michael B. Eisen. 324-335 [doi]
• Using Protein-Protein Interactions for Refining Gene Networks Estimated from Microarray Data by Bayesian NetworksNaoki Nariai, SunYong Kim, Seiya Imoto, Satoru Miyano. 336-347 [doi]
• Motif Discovery in Heterogeneous Sequence DataAmol Prakash, Mathieu Blanchette, Saurabh Sinha, Martin Tompa. 348-359 [doi]
• Negative Information for Motif DiscoveryKen T. Takusagawa, David K. Gifford. 360-371 [doi]
• Session IntroductionSean D. Mooney, Philip E. Bourne, Patricia C. Babbitt. 372-374 [doi]
• The Status of Structural Genomics Defined Through the Analysis of Current Targets and StructuresPhilip E. Bourne, C. K. J. Allerston, Werner G. Krebs, Wilfred W. Li, Ilya N. Shindyalov, Adam Godzik, Iddo Friedberg, Tong Liu, David L. Wild, Seungwoo Hwang, Zoubin Ghahramani, Li Chen, John D. Westbrook. 375-386 [doi]
• Protein Structure and Fold Prediction Using Tree-Augmented Bayesian ClassifierArunkumar Chinnasamy, Wing-Kin Sung, Ankush Mittal. 387-398 [doi]
• Clustering Protein Sequence and Structure Space with Infinite Gaussian Mixture ModelsAnanya Dubey, Seungwoo Hwang, Claudia Rangel, Carl Edward Rasmussen, Zoubin Ghahramani, David L. Wild. 399-410 [doi]
• Accurate Classification of Protein Structural Families Using Coherent Subgraph AnalysisJun Huan, Wei Wang 0010, Anglina Washington, Jan Prins, Ruchir Shah, Alexander Tropsha. 411-422 [doi]
• Identifying Good Predictions of RNA Secondary StructureMarkus E. Nebel. 423-434 [doi]
• Exploring Bias in the Protein Data Bank Using Contrast ClassifiersKang Peng, Zoran Obradovic, Slobodan Vucetic. 435-446 [doi]
• Geometric Analysis of Cross-Linkability for Protein Fold DiscriminationShobha Potluri, Aly Azeem Khan, A. Kuzminykh, Janusz M. Bujnicki, Alan M. Friedman, Chris Bailey-Kellogg. 447-458 [doi]
• Protein Fold Recognition Through Application of Residual Dipolar Coupling DataYouxing Qu, Jun-tao Guo, Victor Olman, Ying Xu. 459-470 [doi]
• Session IntroductionTrey Ideker, Erik K. Neumann, Vincent Schächter. 471-473 [doi]
• A Mixed Integer Linear Programming (MILP) Framework for Inferring Time Delay in Gene Regulatory NetworksMadhukar S. Dasika, Anshuman Gupta, Costas D. Maranas, Jeffrey D. Varner. 474-485 [doi]
• Robust Identification of Large Genetic NetworksDiego di Bernardo, T. S. Gardner, James J. Collins. 486-497 [doi]
• Reconstructing Chain Functions in Genetic NetworksIrit Gat-Viks, Ron Shamir, Richard M. Karp, Roded Sharan. 498-509 [doi]
• Inferring Gene Regulatory Networks from Raw Data: A Molecular Epistemics ApproachD. A. Kightley, Navin Chandra, K. O. Elliston. 510-520 [doi]
• A Biospi Model of Lymphocyte-Endothelial Interactions in Inflamed Brain VenulesPaola Lecca, Corrado Priami, Carlo Laudanna, G. Constantin. 521-532 [doi]
• Modeling Cellular Processes with Variational Bayesian Cooperative Vector QuantizerXinghua Lu, Milos Hauskrecht, Roger S. Day. 533-544 [doi]
• Symbolic Inference of Xenobiotic MetabolismDaniel C. McShan, M. Updadhayaya, Imran Shah. 545-556 [doi]
• Finding Optimal Models for Small Gene NetworksSascha Ott, Seiya Imoto, Satoru Miyano. 557-567 [doi]
• Pathway Logic Modeling of Protein Functional Domains in Signal TransductionCarolyn L. Talcott, Steven Eker, Merrill Knapp, Patrick Lincoln, Keith Laderoute. 568-580 [doi]
• Modeling Gene Expression from Microarray Expression Data with State-Space EquationsFang-Xiang Wu, Wen-Jun Zhang, Anthony J. Kusalik. 581-592 [doi]