9. PSB 2004: Big Island of Hawaii, USA

Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Tiffany A. Jung, Teri E. Klein (Eds.): Biocomputing 2004, Proceedings of the Pacific Symposium, Hawaii, USA, 6-10 January 2004. World Scientific 2004, ISBN 981-238-598-3 BibTeX

@proceedings{DBLP:conf/psb/2004,
  editor    = {Russ B. Altman and
               A. Keith Dunker and
               Lawrence Hunter and
               Tiffany A. Jung and
               Teri E. Klein},
  title     = {Biocomputing 2004, Proceedings of the Pacific Symposium, Hawaii,
               USA, 6-10 January 2004},
  booktitle = {Pacific Symposium on Biocomputing},
  publisher = {World Scientific},
  year      = {2004},
  isbn      = {981-238-598-3},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein:
Preface.
Electronic Edition (link) BibTeX

Alternative Splicing

Hui Wang, U. Yang, Christopher Lee, John Blume:
Session Introduction. 3-4
Electronic Edition (link) BibTeX
Jeremy Buhler, Richard Souvenir, Weixiong Zhang, Rob Mitra:
Design of a High-Throughput Assay for Alternative Splicing Using Polymerase Colonies. 5-16
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX
Zhengyan Kan, John Castle, Jason M. Johnson, Nick Tsinoremas:
Detection of Novel Splice Forms in Human and Mouse Using Cross-Species Approach. 42-53
Electronic Edition (link) BibTeX
Hiroki Sakai, Osamu Maruyama:
Extensive Search for Discriminative Features of Alternative Splicing. 54-65
Electronic Edition (link) BibTeX
Charles W. Sugnet, W. James Kent, Manual Ares, David Haussler:
Transcriptome and Genome Conservation of Alternative Splicing Events in Humans and Mice. 66-77
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX

Computational Tools for Complex Trait Gene Mapping

Francisco M. de la Vega, Kenneth K. Kidd, Andrew Collins: Session Introduction. 89-92 BibTeX
M. P. Bass, E. R. Martin, E. R. Hauser:
Pedigree Generation for Analysis of Genetic Linkage and Association. 93-103
Electronic Edition (link) BibTeX
Lauri Eronen, Floris Geerts, Hannu Toivonen:
A Markov Chain Approach to Reconstruction of Long Haplotypes. 104-115
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX
Sung K. Kim, Kui Zhang, Fengzhu Sun:
A Comparison of Different Strategies for Computing Confidence Intervals of the Linkage Disequilibrium Measure. 128-139
Electronic Edition (link) BibTeX
Roded Sharan, Amir Ben-Dor, Zohar Yakhini:
Multiplexing Schemes for Generic SNP Genotyping Assays. 140-151
Electronic Edition (link) BibTeX
Xiaofeng Zhu, Shuanglin Zhang, Donghai Kan, Richard S. Cooper:
Haplotype Block Definition and Its Application. 152-163
Electronic Edition (link) BibTeX

Biomedical Ontologies

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

Joint Learning from Multiple Types of Genomic Data

Alexander J. Hartemink, Eran Segal:
Session Introduction. 262-263
Electronic Edition (link) BibTeX
Arnab Bhattacharya, Tolga Can, Tamer Kahveci, Ambuj K. Singh, Yuan-Fang Wang:
ProGreSS: Simultaneous Searching of Protein Databases by Sequence and Structure. 264-275
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX
Eleazar Eskin, Eugene Agichtein:
Combining Text Mining and Sequence Analysis to Discover Protein Functional Regions. 288-299
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX
Alan M. Moses, Derek Y. Chiang, Michael B. Eisen:
Phylogenetic Motif Detection by Expectation-Maximization on Evolutionary Mixtures. 324-335
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX
Amol Prakash, Mathieu Blanchette, Saurabh Sinha, Martin Tompa:
Motif Discovery in Heterogeneous Sequence Data. 348-359
Electronic Edition (link) BibTeX
Ken T. Takusagawa, David K. Gifford:
Negative Information for Motif Discovery. 360-371
Electronic Edition (link) BibTeX

Informatics Approaches in Structural Genomics

Sean D. Mooney, Philip E. Bourne, Patricia C. Babbitt:
Session Introduction. 372-374
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX
Arunkumar Chinnasamy, Wing-Kin Sung, Ankush Mittal:
Protein Structure and Fold Prediction Using Tree-Augmented Bayesian Classifier. 387-398
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX
Jun Huan, Wei Wang, Anglina Washington, Jan Prins, Ruchir Shah, Alexander Tropsha:
Accurate Classification of Protein Structural Families Using Coherent Subgraph Analysis. 411-422
Electronic Edition (link) BibTeX
Markus E. Nebel:
Identifying Good Predictions of RNA Secondary Structure. 423-434
Electronic Edition (link) BibTeX
Kang Peng, Zoran Obradovic, Slobodan Vucetic:
Exploring Bias in the Protein Data Bank Using Contrast Classifiers. 435-446
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX
Youxing Qu, Jun-tao Guo, Victor Olman, Ying Xu:
Protein Fold Recognition Through Application of Residual Dipolar Coupling Data. 459-470
Electronic Edition (link) BibTeX

Computational and Symbolic Systems Biology

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