12. PSB 2007: Wailea, Maui, Hawaii, USA

Protein Interactions and Disease

• Maricel G. Kann, Yanay Ofran, Marco Punta, Predrag Radivojac:
  Session Introduction. 1-3
  
• Karsten M. Borgwardt, Hans-Peter Kriegel:
  Graph Kernels For Disease Outcome Prediction From Protein-Protein Interaction Networks. 4-15
  
• Daniel L. Cook, Jesse C. Wiley, John H. Gennari:
  Chalkboard: Ontology-Based Pathway Modeling And Qualitative Inference Of Disease Mechanisms. 16-27
  
• Graciela Gonzalez, Juan C. Uribe, Luis Tari, Colleen Brophy, Chitta Baral:
  Mining Gene-Disease Relationships from Biomedical Literature: Weighting Proteinprotein Interactions and Connectivity. 28-39
  
• Peter M. Kasson, Vijay S. Pande:
  Predicting Structure and Dynamics of Loosely-Ordered Protein Complexes: Influenza Hemagglutinin Fusion Peptide. 40-50
  
• Libusha Kelly, Rachel Karchin, Andrej Sali:
  Protein Interactions and Disease Phenotypes in the ABC Transporter Superfamily. 51-63
  
• Vinay Pulim, Jadwiga R. Bienkowska, Bonnie Berger:
  Lthreader: Prediction of Ligand-Receptor Interactions Using Localized Threading. 64-75
  
• Lee T. Sam, Yang Liu, Jianrong Li, Carol Friedman, Yves A. Lussier:
  Discovery of Protein Interaction Networks Shared by Diseases. 76-87
  
• Padmavati Sridhar, Tamer Kahveci, Sanjay Ranka:
  An Iterative Algorithm for Metabolic Network-Based Drug Target Identification. 88-99
  
• Willy Valdivia Granda, Maricel G. Kann, Jose Malaga:
  Transcriptional Interactions During Smallpox Infection and Identification of Early Infection Biomarkers. 100-111
  

Computational Approaches To Metabolomics

• David S. Wishart, Russell Greiner:
  Session Introduction. 112-114
  
• David Chang, Aalim Weljie, Jack Newton:
  Leveraging Latent Information In NMR For Robust Predictive Models. 115-126
  
• Natarajan Ganesan, Bala Kalyanasundaram, Mahe Velauthapillai:
  Bioinformatics Data Profiling Tools: A Prelude to Metabolic Profiling. 127-132
  
• Emre Karakoç, Süleyman Cenk Sahinalp, Artem Cherkasov:
  Comparative QSAR Analysis of Bacterial-, Fungalplant- and Human Metabolites. 133-144
  
• Craig Knox, Savita Shrivastava, Paul Stothard, Roman Eisner, David S. Wishart:
  Biospider: A Web Server for Automating Metabolome Annotations. 145-156
  
• John L. Markley, Mark E. Anderson, Qiu Cui, Hamid Eghbalnia, Ian A. Lewis, Adrian D. Hegeman, Jing Li, Christopher F. Schulte, Michael R. Sussman, William M. Westler, Eldon L. Ulrich, Zsolt Zolnai:
  New Bioinformatics Resources For Metabolomics. 157-168
  
• Martin Scholz, Oliver Fiehn:
  Setup X - A Public Study Design Database for Metabolomic Projects. 169-180
  
• Chen Yang, Adam D. Richardson, Jeffrey W. Smith, Andrei Osterman:
  Comparative Metabolomics of Breast Cancer. 181-192
  
• Jeongah Yoon, Kyongbum Lee:
  Metabolic Flux Profiling of Reaction Modules in Liver Drug Transformation. 193-204
  

New Frontiers In Biomedical Text Mining

• Pierre Zweigenbaum, Dina Demner-Fushman, Hong Yu, K. Bretonnel Cohen:
  Session Introduction. 205-208
  
• Caroline B. Ahlers, Marcelo Fiszman, Dina Demner-Fushman, François-Michel Lang, Thomas C. Rindflesch:
  Extracting Semantic Predications from Medline Citations for Pharmacogenomics. 209-220
  
• Ali Cakmak, Gultekin Özsoyoglu:
  Annotating Genes Using Textual Patterns. 221-232
  
• Helen L. Johnson, K. Bretonnel Cohen, Lawrence Hunter:
  A Fault Model for Ontology Mapping, Alignment, and Linking Systems. 233-268
  
• Nikiforos Karamanis, Ian Lewin, Ruth L. Seal, Rachel A. Drysdale, Edward John Briscoe:
  Integrating Natural Language Processing with Flybase Curation. 245-256
  
• Zhenzhen Kou, William W. Cohen, Robert F. Murphy:
  A Stacked Graphical Model for Associating Sub-Images with Sub-Captions. 257-268
  
• Zhiyong Lu, K. Bretonnel Cohen, Lawrence Hunter:
  Generif Quality Assurance as Summary Revision. 269-280
  
• Alexander A. Morgan, Benjamin Wellner, Jeffrey B. Colombe, Robert Arens, Marc E. Colosimo, Lynette Hirschman:
  Evaluating the Automatic Mapping of Human Gene and Protein Mentions to Unique Identifiers. 281-291
  
• Aurélie Névéol, Sonya E. Shooshan, Susanne M. Humphrey, Thomas C. Rindflesch, Alan R. Aronson:
  Multiple Approaches to Fine-Grained Indexing of the Biomedical Literature. 292-303
  
• James Rhodes, Stephen Boyer, Jeffrey T. Kreulen, Ying Chen, Patricia Ordonez:
  Mining Patents Using Molecular Similarity Search. 304-315
  
• Kazuhiro Seki, Javed Mostafa:
  Discovering Implicit Associations Between Genes and Hereditary Diseases. 316-327
  
• Hong Yu, David Kaufman:
  A Cognitive Evaluation of Four Online Search Engines for Answering Definitional Questions Posed by Physicians. 328-339
  

Biodiversity Informatics: Managing Knowledge Beyond Humans And Model Organisms

• Indra Neil Sarkar:
  Session Introduction. 340-342
  
• Eithon Cadag, Brenton Louie, Peter J. Myler, Peter Tarczy-Hornoch:
  Biomediator Data Integration and Inference for Functional Annotation of Anonymous Sequences. 343-354
  
• Gregory Hampikian, Tim Andersen:
  Absent Sequences: Nullomers and Primes. 355-366
  
• Anne M. Maglia, Jennifer L. Leopold, L. Anal'a Pugener, Susan Gauch:
  An Anatomical Ontology for Amphibians. 367-378
  
• David M. Ng, Marcos H. Woehrmann, Joshua M. Stuart:
  Recommending Pathway Genes Using a Compendium of Clustering Solutions. 379-390
  
• Guido Sautter, Klemens Böhm, Donat Agosti:
  Semi-Automated XML Markup of Biosystematic Legacy Literature with the Goldengate Editor. 391-402
  

Computational Proteomics: High-Throughput Analysis For Systems Biology

• William R. Cannon, Bobbie-Jo M. Webb-Robertson:
  Session Introduction. 403-408
  
• Pedro Alves, Randy J. Arnold, Milos V. Novotny, Predrag Radivojac, James P. Reilly, Haixu Tang:
  Advancement in Protein Inference from Shotgun Proteomics Using Peptide Detectability. 409-420
  
• Yan Fu, Wen Gao, Simin He, Ruixiang Sun, Hu Zhou, Rong Zeng:
  Mining Tandem Mass Spectral Data to Develop a More Accurate Mass Error Model for Peptide Identification. 421-432
  
• Sonia M. Leach, Aaron Gabow, Lawrence Hunter, Debra Goldberg:
  Assessing and Combining Reliability of Protein Interaction Sources. 433-444
  
• David Sontag, Rohit Singh, Bonnie Berger:
  Probabilistic Modeling of Systematic Errors in Two-Hybrid Experiments. 445-457
  
• Raf Van de Plas, Fabian Ojeda, Maarten Dewil, Ludo Van Den Bosch, Bart De Moor, Etienne Waelkens:
  Prospective Exploration of Biochemical Tissue Composition via Imaging Mass Spectrometry Guided by Principal Component Analysis. 458-469
  

DNA-Protein Interactions: Integrating Structure, Sequence, and Function

• Martha L. Bulyk, Alexander J. Hartemink, Ernest Fraenkel, Gary D. Stormo:
  Session Introduction. 470-471
  
• Henry C. M. Leung, Francis Y. L. Chin, Bethany Man-Yee Chan:
  Discovering Motifs With Transcription Factor Domain Knowledge. 472-483
  
• L. Angela Liu, Joel S. Bader:
  Ab initio Prediction of Transcription Factor Binding Sites. 484-495
  
• Jizhen Zhao, Dongsheng Che, Liming Cai:
  Comparative Pathway Annotation with Protein-DNA Interaction and Operon Information via Graph Tree Decomposition. 496-507
  

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