9. PSB 2004: Big Island of Hawaii, USA

• Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein:
  Preface.
  

Alternative Splicing

• Hui Wang, U. Yang, Christopher Lee, John Blume:
  Session Introduction. 3-4
  
• Jeremy Buhler, Richard Souvenir, Weixiong Zhang, Rob Mitra:
  Design of a High-Throughput Assay for Alternative Splicing Using Polymerase Colonies. 5-16
  
• Melissa S. Cline, Ron Shigeta, Raymond Wheeler, Michael A. Siani-Rose, David Kulp, Ann E. Loraine:
  The Effects of Alternative Splicing on Transmembrane Proteins in the Mouse Genome. 17-28
  
• Catherine Grasso, Barmak Modrek, Yi Xing, Christopher Lee:
  Genome-Wide Detection of Alternative Splicing in Expressed Sequences Using Partial Order Multiple Sequence Alignment Graphs. 29-41
  
• Zhengyan Kan, John Castle, Jason M. Johnson, Nick Tsinoremas:
  Detection of Novel Splice Forms in Human and Mouse Using Cross-Species Approach. 42-53
  
• Hiroki Sakai, Osamu Maruyama:
  Extensive Search for Discriminative Features of Alternative Splicing. 54-65
  
• Charles W. Sugnet, W. James Kent, Manuel Ares, David Haussler:
  Transcriptome and Genome Conservation of Alternative Splicing Events in Humans and Mice. 66-77
  
• Christina L. Zheng, T. Murlidharan Nair, Michael Gribskov, Y. S. Kwon, Hai-Ri Li, Xiang-Dong Fu:
  A Database Designed to Computationally Aid an Experimental Approach to Alternative Splicing. 78-88
  

Computational Tools for Complex Trait Gene Mapping

• Francisco M. de la Vega, Kenneth K. Kidd, Andrew Collins: Session Introduction. 89-92
• M. P. Bass, E. R. Martin, E. R. Hauser:
  Pedigree Generation for Analysis of Genetic Linkage and Association. 93-103
  
• Lauri Eronen, Floris Geerts, Hannu Toivonen:
  A Markov Chain Approach to Reconstruction of Long Haplotypes. 104-115
  
• Sun Jun Kang, Derek Gordon, A. M. Brown, Jürg Ott, Stephen J. Finch:
  Tradeoff Between No-Call Reduction in Genotyping Error Rate and Loss of Sample Size for Genetic Case/Control Association Studies. 116-127
  
• Sung K. Kim, Kui Zhang, Fengzhu Sun:
  A Comparison of Different Strategies for Computing Confidence Intervals of the Linkage Disequilibrium Measure. 128-139
  
• Roded Sharan, Amir Ben-Dor, Zohar Yakhini:
  Multiplexing Schemes for Generic SNP Genotyping Assays. 140-151
  
• Xiaofeng Zhu, Shuanglin Zhang, Donghai Kan, Richard S. Cooper:
  Haplotype Block Definition and Its Application. 152-163
  

Biomedical Ontologies

• Olivier Bodenreider, Joyce A. Mitchell, Alexa T. McCray:
  Session Introduction. 164-165
  
• J. Stuart Aitken, Bonnie L. Webber, Jonathan Bard:
  Part-of Relations in Anatomy Ontologies: A Proposal for RDFS and OWL Formalisations. 166-177
  
• Georgios V. Gkoutos, Eain C. J. Green, Ann-Marie Mallon, John M. Hancock, Duncan Davidson:
  Building Mouse Phenotype Ontologies. 178-189
  
• Peter D. Karp, Suzanne M. Paley, Cynthia J. Krieger, Peifen Zhang:
  An Evidence Ontology for Use in Pathway/Genome Databases. 190-201
  
• Yves A. Lussier, Jianrong Li:
  Terminological Mapping for High Throughput Comparative Biology of Phenotypes. 202-213
  
• Philip V. Ogren, K. Bretonnel Cohen, George K. Acquaah-Mensah, Jens Eberlein, Lawrence Hunter:
  The Compositional Structure of Gene Ontology Terms. 214-225
  
• Alan L. Rector:
  Defaults, Context, and Knowledge: Alternatives for OWL-Indexed Knowledge Bases. 226-237
  
• Olivia Tuason, Lifeng Chen, Hongfang Liu, Judith A. Blake, Carol Friedman:
  Biological Nomenclatures: A Source of Lexical Knowledge and Ambiguity. 238-249
  
• Songmao Zhang, Olivier Bodenreider:
  Investigating Implicit Knowledge in Ontologies with Application to the Anatomical Domain. 250-261
  

Joint Learning from Multiple Types of Genomic Data

• Alexander J. Hartemink, Eran Segal:
  Session Introduction. 262-263
  
• Arnab Bhattacharya, Tolga Can, Tamer Kahveci, Ambuj K. Singh, Yuan-Fang Wang:
  ProGreSS: Simultaneous Searching of Protein Databases by Sequence and Structure. 264-275
  
• Michiel J. L. de Hoon, Seiya Imoto, Kazuo Kobayashi, Naotake Ogasawara, Satoru Miyano:
  Predicting the Operon Structure of Bacillus subtilis Using Operon Length, Intergene Distance, and Gene Expression Information. 276-287
  
• Eleazar Eskin, Eugene Agichtein:
  Combining Text Mining and Sequence Analysis to Discover Protein Functional Regions. 288-299
  
• Gert R. G. Lanckriet, Minghua Deng, Nello Cristianini, Michael I. Jordan, William Stafford Noble:
  Kernel-Based Data Fusion and Its Application to Protein Function Prediction in Yeast. 300-311
  
• Haiquan Li, Jinyan Li, Soon-Heng Tan, See-Kiong Ng:
  Discovery of Binding Motif Pairs from Protein Complex Structural Data and Protein Interaction Sequence Data. 312-32
  
• Alan M. Moses, Derek Y. Chiang, Michael B. Eisen:
  Phylogenetic Motif Detection by Expectation-Maximization on Evolutionary Mixtures. 324-335
  
• Naoki Nariai, SunYong Kim, Seiya Imoto, Satoru Miyano:
  Using Protein-Protein Interactions for Refining Gene Networks Estimated from Microarray Data by Bayesian Networks. 336-347
  
• Amol Prakash, Mathieu Blanchette, Saurabh Sinha, Martin Tompa:
  Motif Discovery in Heterogeneous Sequence Data. 348-359
  
• Ken T. Takusagawa, David K. Gifford:
  Negative Information for Motif Discovery. 360-371
  

Informatics Approaches in Structural Genomics

• Sean D. Mooney, Philip E. Bourne, Patricia C. Babbitt:
  Session Introduction. 372-374
  
• Philip 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:
  The Status of Structural Genomics Defined Through the Analysis of Current Targets and Structures. 375-386
  
• Arunkumar Chinnasamy, Wing-Kin Sung, Ankush Mittal:
  Protein Structure and Fold Prediction Using Tree-Augmented Bayesian Classifier. 387-398
  
• Ananya Dubey, Seungwoo Hwang, Claudia Rangel, Carl Edward Rasmussen, Zoubin Ghahramani, David L. Wild:
  Clustering Protein Sequence and Structure Space with Infinite Gaussian Mixture Models. 399-410
  
• Jun Huan, Wei Wang, Anglina Washington, Jan Prins, Ruchir Shah, Alexander Tropsha:
  Accurate Classification of Protein Structural Families Using Coherent Subgraph Analysis. 411-422
  
• Markus E. Nebel:
  Identifying Good Predictions of RNA Secondary Structure. 423-434
  
• Kang Peng, Zoran Obradovic, Slobodan Vucetic:
  Exploring Bias in the Protein Data Bank Using Contrast Classifiers. 435-446
  
• Shobha Potluri, Aly Azeem Khan, A. Kuzminykh, Janusz M. Bujnicki, Alan M. Friedman, Chris Bailey-Kellogg:
  Geometric Analysis of Cross-Linkability for Protein Fold Discrimination. 447-458
  
• Youxing Qu, Jun-tao Guo, Victor Olman, Ying Xu:
  Protein Fold Recognition Through Application of Residual Dipolar Coupling Data. 459-470
  

Computational and Symbolic Systems Biology

• Trey Ideker, Erik K. Neumann, Vincent Schächter:
  Session Introduction. 471-473
  
• Madhukar S. Dasika, Anshuman Gupta, Costas D. Maranas, Jeffrey D. Varner:
  A Mixed Integer Linear Programming (MILP) Framework for Inferring Time Delay in Gene Regulatory Networks. 474-485
  
• Diego di Bernardo, T. S. Gardner, James J. Collins:
  Robust Identification of Large Genetic Networks. 486-497
  
• Irit Gat-Viks, Ron Shamir, Richard M. Karp, Roded Sharan:
  Reconstructing Chain Functions in Genetic Networks. 498-509
  
• D. A. Kightley, Navin Chandra, K. O. Elliston:
  Inferring Gene Regulatory Networks from Raw Data: A Molecular Epistemics Approach. 510-520
  
• Paola Lecca, Corrado Priami, Carlo Laudanna, G. Constantin:
  A Biospi Model of Lymphocyte-Endothelial Interactions in Inflamed Brain Venules. 521-532
  
• Xinghua Lu, Milos Hauskrecht, Roger S. Day:
  Modeling Cellular Processes with Variational Bayesian Cooperative Vector Quantizer. 533-544
  
• Daniel C. McShan, M. Updadhayaya, Imran Shah:
  Symbolic Inference of Xenobiotic Metabolism. 545-556
  
• Sascha Ott, Seiya Imoto, Satoru Miyano:
  Finding Optimal Models for Small Gene Networks. 557-567
  
• Carolyn L. Talcott, Steven Eker, Merrill Knapp, Patrick Lincoln, Keith Laderoute:
  Pathway Logic Modeling of Protein Functional Domains in Signal Transduction. 568-580
  
• Fang-Xiang Wu, Wen-Jun Zhang, Anthony J. Kusalik:
  Modeling Gene Expression from Microarray Expression Data with State-Space Equations. 581-592
  

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