Pacific Symposium on Biocomputing 2008: Kohala Coast, Hawaii, USA 4-8 January 2008

by Altman, Russ B.

• ISBN13: 9789812776082
• ISBN10: 9812776087
• Edition: 1st
• Format: Hardcover
• Copyright: 2008-04-01
• Publisher: World Scientific Pub Co Inc

Summary

The Pacific Symposium on Biocomputing (PSB) 2008 is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. Presentations are rigorously peer reviewed and are published in an archival proceedings volume. PSB 2008 will be held on January 4-8, 2008 at the Fairmont Orchid, Big Island of Hawaii. Tutorials will be offered prior to the start of the conference.

Table of Contents

Preface	p. v
Beyond Gap Models: Reconstructing Alignments and Phylogenies Under Genomic-Scale Events
Session Introduction	p. 1
Fresco: Flexible Alignment with Rectangle Scoring Schemes	p. 3
Local Reliability Measures from Sets of Co-Optimal Multiple Sequence Alignments	p. 15
The Effect of the Guide Tree on Multiple Sequence Alignments and Subsequent Phylogenetic Analysis	p. 25
Sensitivity Analysis for Reversal Distance and Breakpoint Reuse in Genome Rearrangements	p. 37
Computational Challenges in the Study of Small Regulatory RNAs
Session Introduction	p. 49
Comparing Sequence and Expression for Predicting microRNA Targets Using GenMiR3	p. 52
Analysis of MicroRNA-Target Interactions by a Target Structure Based Hybridization Model	p. 64
A Probabilistic Model for Small RNA Flowgram Matching	p. 75
Computational Tools for Next-Generation Sequencing Applications
Session Introduction	p. 87
TRELLIS+: An Effective Approach for Indexing Genome-Scale Sequences Using Suffix Trees	p. 90
Pash 2.0: Scaleable Sequence Anchoring for Next-Generation Sequencing Technologies	p. 102
Population Sequencing Using Short Reads: HIV as a Case Study	p. 114
Analysis of Large-Scale Sequencing of Small RNAs	p. 126
Knowledge-Driven Analysis and Data Integration for High-Throughput Biological Data
Session Introduction	p. 137
SGDI: System for Genomic Data Integration	p. 141
Annotating Pathways of Interaction Networks	p. 153
Integrating Microarray and Proteomics Data to Predict the Response of Cetuximab in Patients with Rectal Cancer	p. 166
A Bayesian Framework for Data and Hypotheses Driven Fusion of High Throughput Data: Application to Mouse Organogenesis	p. 178
Gathering the Gold Dust: Methods for Assessing the Aggregate Impact of Small Effect Genes in Genomic Scans	p. 190
Multi-Scale Correlations in Continuous Genomic Data	p. 201
Analysis of MALDI-TOF Spectrometry Data for Detection of Glycan Biomarkers	p. 216
Molecular Bioinformatics for Disease: Protein Interactions and Phenomics
Session Introduction	p. 228
System-Wide Peripheral Biomarker Discovery Using Information Theory	p. 231
Novel Integration of Hospital Electronic Medical Records and Gene Expression Measurements to Identify Genetic Markers of Maturation	p. 243
Networking Pathways Unveils Association Between Obesity and Non-Insulin Dependent Diabetes Mellitus	p. 255
Extracting Gene Expression Profiles Common to Colon and Pancreatic Adenocarcinoma Using Simultaneous Nonnegative Matrix Factorization	p. 267
Integration of Microarray and Textual Data Improves the Prognosis Prediction of Breast, Lung and Ovarian Cancer Patients	p. 279
Mining Metabolic Networks for Optimal Drug Targets	p. 291
Global Alignment of Multiple Protein Interaction Networks	p. 303
Predicting DNA Methylation Susceptibility Using CpG Flanking Sequences	p. 315
Multiscale Modeling and Simulation Session: From Molecules to Cells to Organisms?
Session Introduction	p. 327
Combining Molecular Dynamics and Machine Learning to Improve Protein Function Recognition	p. 332
Prediction of Structure of G-Protein Coupled Receptors and of Bound Ligands with Applications for Drug Design	p. 344
Markov Chain Models of Coupled Intracellular Calcium Channels: Kronecker Structured Representations and Benchmark Stationary Distribution Calculations	p. 354
Spatially-Compressed Cardiac Myofilament Models Generate Hysteresis that Is Not Found in Real Muscle	p. 366
Modeling Ventricular Interaction: A Multiscale Approach from Sarcomere Mechanics to Cardiovascular System Hemodynamics	p. 378
Sub-Micrometer Anatomical Models of the Sarcolemma of Cardiac Myocytes Based on Confocal Imaging	p. 390
Efficient Multiscale Simulation of Circadian Rhythms Using Automated Phase Macromodelling Techniques	p. 402
Integration of Multi-Scale Biosimulation Models via Light-Weight Semantics	p. 414
Comparisons of Protein Family Dynamics	p. 426
Protein-Nucleic Acid Interactions: Integrating Structure, Sequence, and Function
Session Introduction	p. 438
Functional Trends in Structural Classes of the DNA Binding Domains of Regulatory Transcription Factors	p. 441
Using DNA Duplex Stability Information for Transcription Factor Binding Site Discovery	p. 453
A Parametric Joint Model of DNA-Protein Binding, Gene Expression and DNA Sequence Data to Detect Target Genes of a Transcription Factor	p. 465
An Analysis of Information Content Present in Protein-DNA Interactions	p. 477
Use of an Evolutionary Model to Provide Evidence for a Wide Heterogeneity of Required Affinities Between Transcription Factors and Their Binding Sites in Yeast	p. 489
Striking Similarities in Diverse Telomerase Proteins Revealed by Combining Structure Prediction and Machine Learning Approaches	p. 501
Tiling Microarray Data Analysis Methods and Algorithms
Session Introduction	p. 513
CMARRT: A Tool for the Analysis of ChIP-chip Data from Tiling Arrays by Incorporating the Correlation Structure	p. 515
Transcript Normalization and Segmentation of Tiling Array Dat	p. 527
GSE: A Comprehensive Database System for the Representation, Retrieval, and Analysis of Microarray Data	p. 539
Translating Biology: Text Mining Tools That Work
Session Introduction	p. 551
Assisted Curation: Does Text Mining Really Help?	p. 556
Evidence for Showing Gene/Protein Name Suggestions in Bioscience Literature Search Interfaces	p. 568
Enabling Integrative Genomic Analysis of High-Impact Human Diseases Through Text Mining	p. 580
Information Needs and the Role of Text Mining in Drug Development	p. 592
EpiLoc: A (Working) Text-Based System for Predicting Protein Subcellular Location	p. 604
Filling the Gaps Between Tools and Users: A Tool Comparator, Using Protein-Protein Interactions as an Example	p. 616
Comparing Usability of Matching Techniques for Normalising Biomedical Named Entities	p. 628
Intrinsic Evaluation of Text Mining Tools May Not Predict Performance on Realistic Tasks	p. 640
BANNER: An Executable Survey of Advances in Biomedical Named Entity Recognition	p. 652
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