PSB 2007 Online Proceedings

PSB 2007

PSB Proceedings for All Years


Contents


Preface

Protein Interactions and Disease

Session Introduction
Maricel Kann, Yanay Ofran, Marco Punta, Predrag Radivojac; Pacific Symposium on Biocomputing 12:1-3(2007)
Graph Kernels For Disease Outcome Prediction From Protein-Protein Interaction Networks
Karsten M. Borgwardt, Hans-Peter Kriegel; Pacific Symposium on Biocomputing 12:4-15(2007)
Chalkboard: Ontology-Based Pathway Modeling And Qualitative Inference Of Disease Mechanisms
Daniel L. Cook, Jesse C. Wiley, John H. Gennari; Pacific Symposium on Biocomputing 12:16-27(2007)
Mining Gene-Disease Relationships from Biomedical Literature: Weighting Proteinprotein Interactions and Connectivity
Graciela Gonzalez, Juan C. Uribe, Luis Tari, Colleen Brophy, Chitta Baral; Pacific Symposium on Biocomputing 12:28-39(2007)
Predicting Structure and Dynamics of Loosely-Ordered Protein Complexes: Influenza Hemagglutinin Fusion Peptide
Peter M. Kasson, Vijay S. Pande; Pacific Symposium on Biocomputing 12:40-50(2007)
Protein Interactions and Disease Phenotypes in the ABC Transporter Superfamily
Libusha Kelly, Rachel Karchin, Andrej Sali; Pacific Symposium on Biocomputing 12:51-63(2007)
Lthreader: Prediction of Ligand-Receptor Interactions Using Localized Threading
Vinay Pulim, Jadwiga Bienkowska, Bonnie Berger; Pacific Symposium on Biocomputing 12:64-75(2007)
Discovery of Protein Interaction Networks Shared by Diseases
Lee Sam, Yang Liu, Jianrong Li, Carol Friedman, Yves A. Lussier; Pacific Symposium on Biocomputing 12:76-87(2007)
An Iterative Algorithm for Metabolic Network-Based Drug Target Identification
Padmavati Sridhar, Tamer Kahveci, Sanjay Ranka; Pacific Symposium on Biocomputing 12:88-99(2007)
Transcriptional Interactions During Smallpox Infection and Identification of Early Infection Biomarkers
Willy A. Valdivia-Granda, Maricel G. Kann, Jose Malaga; Pacific Symposium on Biocomputing 12:100-111(2007)

Computational Approaches To Metabolomics

Session Introduction
David S. Wishart, Russell Greiner; Pacific Symposium on Biocomputing 12:112-114(2007)
Leveraging Latent Information In NMR For Robust Predictive Models
David Chang, Aalim Weljie, Jack Newton; Pacific Symposium on Biocomputing 12:115-126(2007)
Bioinformatics Data Profiling Tools: A Prelude to Metabolic Profiling
Natarajan Ganesan, Bala Kalyanasundaram, Mahe Velauthapllai; Pacific Symposium on Biocomputing 12:127-132(2007)
Comparative QSAR Analysis of Bacterial-, Fungalplant- and Human Metabolites
Emre Karakoc, S. Cenk Sahinalp, Artem Cherkasov; Pacific Symposium on Biocomputing 12:133-144(2007)
Biospider: A Web Server for Automating Metabolome Annotations
Craig Knox, Savita Shrivastava, Paul Stothard, Roman Eisner, David S. Wishart; Pacific Symposium on Biocomputing 12:145-156(2007)
New Bioinformatics Resources For Metabolomics
John L. Markley, Mark E. Anderson, Qiu Cui, Hamid R. Eghbalnia, Ian A. Lewis, Adrian D. Hegeman, Jing Li, Christopher F. Schulte, Michael R. Sussman, William M. Westler, Eldon L. Ulrich, Zsolt Zolnai; Pacific Symposium on Biocomputing 12:157-168(2007)
Setup X – A Public Study Design Database for Metabolomic Projects
Martin Scholz, Oliver Fiehn; Pacific Symposium on Biocomputing 12:169-180(2007)
Comparative Metabolomics of Breast Cancer
Chen Yang, Adam D. Richardson, Jeffrey W. Smith, Andrei Osterman ; Pacific Symposium on Biocomputing 12:181-192(2007)
Metabolic Flux Profiling of Reaction Modules in Liver Drug Transformation
Jeongah Yoon, Kyongbum Lee ; Pacific Symposium on Biocomputing 12:193-204(2007)

New Frontiers In Biomedical Text Mining

Session Introduction
Pierre Zweigenbaum, Dina Demner-Fushman, Hong Yu, K. Bretonnel Cohen; Pacific Symposium on Biocomputing 12:205-208(2007)
Extracting Semantic Predications from Medline Citations for Pharmacogenomics
Caroline B. Ahlers, Marcelo Fiszman, Dina Demner-Fushman, Francois-Michel Lang, Thomas C. Rindflesch; Pacific Symposium on Biocomputing 12:209-220(2007)
Annotating Genes Using Textual Patterns
Ali Cakmak, Gultekin Ozsoyoglu; Pacific Symposium on Biocomputing 12:221-232(2007)
A Fault Model for Ontology Mapping, Alignment, and Linking Systems
Helen L. Johnson, K. Bretonnel Cohen, Lawrence Hunter; Pacific Symposium on Biocomputing 12:233-268(2007)
Integrating Natural Language Processing with Flybase Curation
Nikiforos Karamanis, Ian Lewin, Ruth Sealy, Rachel Drysdaley, Edward Briscoe ; Pacific Symposium on Biocomputing 12:245-256(2007)
A Stacked Graphical Model for Associating Sub-Images with Sub-Captions
Zhenzhen Kou, William W. Cohen, Robert F. Murphy; Pacific Symposium on Biocomputing 12:257-268(2007)
Generif Quality Assurance as Summary Revision
Zhiyong Lu, K. Bretonnel Cohen, and Lawrence Hunter; Pacific Symposium on Biocomputing 12:269-280(2007)
Evaluating the Automatic Mapping of Human Gene and Protein Mentions to Unique Identifiers
Alexander A. Morgan, Benjamin Wellner, Jeffrey B. Colombe, Robert Arens, Marc E. Colosimo, Lynette Hirschman; Pacific Symposium on Biocomputing 12:281-291(2007)
Multiple Approaches to Fine-Grained Indexing of the Biomedical Literature
Aurelie Neveol, Sonya E. Shooshan, Susanne M. Humphrey, Thomas C. Rindflesh, Alan R. Aronson; Pacific Symposium on Biocomputing 12:292-303(2007)
Mining Patents Using Molecular Similarity Search
James Rhodes, Stephen Boyer, Jeffrey Kreulen, Ying Chen, Patricia Ordonez; Pacific Symposium on Biocomputing 12:304-315(2007)
Discovering Implicit Associations Between Genes and Hereditary Diseases
Kazuhiro Seki, Javed Mostafa; Pacific Symposium on Biocomputing 12:316-327(2007)
A Cognitive Evaluation of Four Online Search Engines for Answering Definitional Questions Posed by Physicians
Hong Yu, David Kaufman; Pacific Symposium on Biocomputing 12:328-339(2007)

Biodiversity Informatics: Managing Knowledge Beyond Humans And Model Organisms

Session Introduction
Indra Neil Sarkar; Pacific Symposium on Biocomputing 12:340-342(2007)
Biomediator Data Integration and Inference for Functional Annotation of Anonymous Sequences
Eithon Cadag, Brent Louie, Peter J. Myler, Peter Tarczy-Hornoch; Pacific Symposium on Biocomputing 12:343-354(2007)
Absent Sequences: Nullomers and Primes
Greg Hampikian, Tim Andersen; Pacific Symposium on Biocomputing 12:355-366(2007)
An Anatomical Ontology for Amphibians
Anne M. Maglia, Jennifer L. Leopold, L. Analía Pugener, Susan Gauch; Pacific Symposium on Biocomputing 12:367-378(2007)
Recommending Pathway Genes Using a Compendium of Clustering Solutions
David M. Ng, Marcos H. Woehrmann, Joshua M. Stuart; Pacific Symposium on Biocomputing 12:379-390(2007)
Semi-Automated XML Markup of Biosystematic Legacy Literature with the Goldengate Editor
Guido Sautter, Klemens Bohm, Donat Agosti; Pacific Symposium on Biocomputing 12:391-402(2007)

Computational Proteomics: High-Throughput Analysis For Systems Biology

Session Introduction
William Cannon, Bobbie-Jo Webb-Robertson; Pacific Symposium on Biocomputing 12:403-408(2007)
Advancement in Protein Inference from Shotgun Proteomics Using Peptide Detectability
Pedro Alves, Randy J. Arnold, Milos V. Novotny, Predrag Radivojac, James P. Reilly, Haixu Tang; Pacific Symposium on Biocomputing 12:409-420(2007)
Mining Tandem Mass Spectral Data to Develop a More Accurate Mass Error Model for Peptide Identification
Yan Fu, Wen Gao, Simin He, Ruixiang Sun, Hu Zhou, Rong Zeng; Pacific Symposium on Biocomputing 12:421-432(2007)
Assessing and Combining Reliability of Protein Interaction Sources
Sonia Leach, Aaron Gabow, Lawrence Hunter, Debra S. Goldberg; Pacific Symposium on Biocomputing 12:433-444(2007)
Probabilistic Modeling of Systematic Errors in Two-Hybrid Experiments
David Sontag, Rohit Singh, Bonnie Berger; Pacific Symposium on Biocomputing 12:445-457(2007)
Prospective Exploration of Biochemical Tissue Composition via Imaging Mass Spectrometry Guided by Principal Component Analysis
Raf Van de Plas, Fabian Ojeda, Maarten Dewil, Ludo Van Den Bosch, Bart De Moor, Etienne Waelkens; Pacific Symposium on Biocomputing 12:458-469(2007)

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

Session Introduction
Martha L. Bulyk, Alexander J. Hartemink, Ernest Fraenkel, Gary Stormo ; Pacific Symposium on Biocomputing 12:470-471(2007)
Discovering Motifs With Transcription Factor Domain Knowledge
Henry C.M. Leung, Francis Y.L. Chin, Bethany M.Y. Chan; Pacific Symposium on Biocomputing 12:472-483(2007)
Ab initio Prediction of Transcription Factor Binding Sites
L. Angela Liu, Joel S. Bader ; Pacific Symposium on Biocomputing 12:484-495(2007)
Comparative Pathway Annotation with Protein-DNA Interaction and Operon Information via Graph Tree Decomposition
Jizhen Zhao, Dongsheng Che, Liming Cai; Pacific Symposium on Biocomputing 12:496-507(2007)

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