Biocomputing 2011 - Proceedings Of The Pacific Symposium.

Biocomputing 2011 - Proceedings Of The Pacific Symposium.

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Bibliographic Details
:
Altman, Russ B.
TeilnehmendeR:
Dunker, A Keith.
Hunter, Lawrence.
Jung, Tiffany A.
Klein, Teri E.
Place / Publishing House:Singapore : : World Scientific Publishing Company,, 2010.
©2011.
Year of Publication:2010
Edition:1st ed.
Language:English
Online Access:
Physical Description:1 online resource (386 pages)
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Table of Contents:
  • Intro
  • CONTENTS
  • PREFACE
  • INTEGRATIVE -OMICS FOR TRANSLATIONAL SCIENCE
  • 1. Introduction
  • 2. Session Summary
  • 3. Acknowledgments
  • TOWARDS INTEGRATIVE GENE PRIORITIZATION IN ALZHEIMER'S DISEASE
  • 1. Introduction
  • 2. Material and methods
  • 3. Results
  • 4. Discussion and conclusion
  • 5. Acknowledgement
  • References
  • SYSTEMS BIOLOGY ANALYSES OF GENE EXPRESSION AND GENOME WIDEASSOCIATION STUDY DATA IN OBSTRUCTIVE SLEEP APNEA
  • 1. Introduction
  • 2. Material and Methods
  • 3. Results and Discussion
  • 4. Conclusion
  • 5. Acknowledgments
  • References
  • FINDING MOST LIKELY HAPLOTYPES IN GENERAL PEDIGREESTHROUGH PARALLEL SEARCH WITH DYNAMIC LOAD BALANCING
  • 1. Introduction
  • 2. Background
  • 3. Setup and Parallel Scheme
  • 4. Predicting Subproblem Size Using the Cost Function
  • 5. Experiments
  • 6. Conclusion &amp
  • FutureWork
  • Acknowledgements
  • References
  • DYNAMIC, MULTI-LEVEL NETWORK MODELS OF CLINICAL TRIALS
  • 1. Background
  • 2. The scope and construction of a clinical trials network
  • 3. Annotation of multiple network levels
  • 4. Assessment of network dynamics
  • 5. Network characteristics of "influential" trials
  • 6. Discussion
  • Acknowledgments
  • References
  • MINING FUNCTIONALLY RELEVANT GENE SETS FOR ANALYZINGPHYSIOLOGICALLY NOVEL CLINICAL EXPRESSION DATA
  • 1. Introduction
  • 2. Methods
  • 3. Results
  • 4. Discussion
  • References
  • GENOTYPE PHENOTYPE MAPPING IN RNA VIRUSES - DISJUNCTIVENORMAL FORM LEARNING
  • 1. INTRODUCTION
  • 2. Related computational work
  • 3. Disjunctive Normal Form (DNF) learning algorithms
  • 4. RESULTS
  • 5. CONCLUSIONS
  • 6. ACKNOWLEDGEMENTS
  • References
  • GENOME-WIDE ASSOCIATION MAPPING AND RARE ALLELES: FROMPOPULATION GENOMICS TO PERSONALIZED MEDICINE
  • References.
  • AN APPLICATION AND EMPIRICAL COMPARISON OF STATISTICAL ANALYSISMETHODS FOR ASSOCIATING RARE VARIANTS TO A COMPLEX PHENOTYPE
  • 1. Introduction
  • 2. Sequencing the MGLL and FAAH genes in obese and control individuals
  • 3. Statistical methods for rare variant associations
  • 4. Results
  • 5. Conclusions and Future Directions
  • Acknowledgments
  • References
  • 2. Sequencing the MGLL and FAAH genes in obese and control individuals
  • 3. Statistical methods for rare variant associations
  • 4. Results
  • 5. Conclusions and Future Directions
  • Acknowledgments
  • References
  • HAPLOTYPE PHASING BY MULTI-ASSEMBLY OF SHAREDHAPLOTYPES: PHASE-DEPENDENT INTERACTIONS BETWEEN RARE VARIANTS
  • 1. Introduction
  • 2. Multi-Assembly of Shared Haplotypes
  • 3. Algorithmic Strategies
  • 4. Results on Simulated Data
  • 5. Acknowledgments
  • References
  • AN EVALUATION OF POWER TO DETECT LOW-FREQUENCY VARIANTASSOCIATIONS USING ALLELE-MATCHING TESTS THAT ACCOUNTFOR UNCERTAINTY
  • 1. Introduction
  • 2. Allele-Matching Tests
  • 3. Simulation Study
  • 4. Discussion
  • References
  • PENALIZED REGRESSION FOR GENOME-WIDE ASSOCIATIONSCREENING OF SEQUENCE DATA
  • 1. Introduction
  • 2. Methods
  • 3. Analysis of Simulated Data
  • 4. Software Implementation and Illustration of Real Data
  • 5. Discussion
  • Acknowledgments
  • References
  • MICROBIOME STUDIES: PSB 2011 SPECIAL SESSION INTRODUCTION
  • 1. Introduction to Microbiome Studies
  • 2. Papers in this session
  • ESTIMATING THE NUMBER OF SPECIES WITH CATCHALL
  • 1. Introduction
  • 2. Analysis of a microbial diversity dataset
  • 3. Conclusions and future directions
  • Acknowledgments
  • References
  • A FRAMEWORK FOR ANALYSIS OF METAGENOMIC SEQUENCING DATA
  • 1. Background
  • 2. Framework
  • 3. Workflow
  • 4. Discussion and Future Work
  • 5. Conclusion
  • Acknowledgements
  • References.
  • VISUALIZATION AND STATISTICAL COMPARISONS OF MICROBIALCOMMUNITIES USING R PACKAGES ON PHYLOCHIP DATA
  • 1. Introduction
  • 2. Details of the Data Analysis Procedures
  • 3. Batch E ect Detection using projections on Principal Planes
  • 4. Incorporating and adjusting the phylogenetic information
  • 5. Summary
  • Acknowledgments
  • References
  • HUMAN MICROBIOME VISUALIZATION USING 3D TECHNOLOGY
  • 1. Introduction
  • 2. Methods
  • 3. Results
  • 4. Discussion
  • 5. Acknowledgments
  • References
  • COMPARING BACTERIAL COMMUNITIES INFERRED FROM 16S rRNA GENE SEQUENCING AND SHOTGUN METAGENOMICS
  • 1. Introduction
  • 2. Methods
  • 3. Results
  • 4. Discussion
  • 5. Availability
  • 6. Acknowledgments
  • References
  • MULTI-SCALE MODELLING OF BIOSYSTEMS: FROM MOLECULAR TOMESOCALE
  • 1. Background
  • 2. Session Summary
  • 3. Acknowledgements
  • COMPUTATIONAL GENERATION INHIBITOR-BOUND CONFORMERS OF P38 MAPKINASE AND COMPARISON WITH EXPERIMENTS
  • 1. Introduction
  • 2. Materials and Methods
  • 3. Results and Discussion
  • 4. Conclusion
  • Acknowledgements
  • References
  • MOLECULAR DYNAMICS SIMULATIONS OF THE FULL TRIPLE HELICALREGION OF COLLAGEN TYPE I PROVIDE AN ATOMIC SCALE VIEW OF THEPROTEIN'S REGIONAL HETEROGENEITY
  • 1. Introduction
  • 2. Materials and Methods
  • 3. Results
  • 4. Discussion
  • 5. Acknowledgments
  • References
  • STRUCTURAL INSIGHTS INTO PRE-TRANSLOCATION RIBOSOME MOTIONS
  • 1. Introduction
  • 2. Background
  • 3. Method
  • 4. Results
  • 5. Discussion
  • Acknowledgements and availability
  • References
  • NEW CONFORMATIONAL SEARCH METHOD USING GENETICALGORITHM AND KNOT THEORY FOR PROTEINS
  • 1. Introduction
  • 2. Method
  • 3. Results and Discussion
  • 4. Conclusions
  • Acknowledgments
  • References
  • PERSONAL GENOMICS
  • 1. Introduction
  • 2. Session Summary
  • 3. Acknowledgments.
  • THE REFERENCE HUMAN GENOME DEMONSTRATES HIGH RISK OF TYPE 1DIABETES AND OTHER DISORDERS
  • 1. Introduction
  • 2. Methods
  • 3. Results:
  • 4. Discussion
  • 5. Acknowledgements
  • References
  • MATCHING CANCER GENOMES TO ESTABLISHED CELL LINESFOR PERSONALIZED ONCOLOGY
  • 1. Introduction
  • 2. Methods
  • 3. Results
  • 4. Discussion
  • Acknowledgements
  • References
  • USE OF BIOLOGICAL KNOWLEDGE TO INFORM THE ANALYSIS OF GENE-GENEINTERACTIONS INVOLVED IN MODULATING VIROLOGIC FAILURE WITHEFAVIRENZ-CONTAINING TREATMENT REGIMENS IN ART-NAÏVE ACTG CLINICALTRIALS PARTICIPANTS
  • 1. Introduction
  • 2. Methods
  • 3. Results
  • 4. Discussion
  • 5. Acknowledgements
  • References
  • VISUAL INTEGRATION OF RESULTS FROM A LARGE DNA BIOBANK (BIOVU)USING SYNTHESIS-VIEW
  • 1. Introduction
  • 2. Methods
  • 3. Visualization of Results
  • 4. Conclusions
  • 5. Acknowledgments
  • 6. References
  • MULTIVARIATE ANALYSIS OF REGULATORY SNPS: EMPOWERING PERSONALGENOMICS BY CONSIDERING CIS-EPISTASIS AND HETEROGENEITY
  • 1. Introduction
  • 2. Methods
  • 3. Results
  • 4. Discussion
  • References
  • HAPLOTYPE INFERENCE FROM SHORT SEQUENCE READS USING APOPULATION GENEALOGICAL HISTORY MODEL
  • 1. Introduction
  • 2. Background
  • 3. Haplotyping with Short Reads
  • 4. Results
  • Funding and Acknowledgment
  • References
  • REVERSE ENGINEERING AND SYNTHESIS OF BIOMOLECULAR SYSTEMS
  • 1. Introduction
  • 2. Session Papers
  • Acknowledgments
  • References
  • BINARY COUNTING WITH CHEMICAL REACTIONS
  • 1. Introduction
  • 2. Counting in Binary
  • 3. Synchronization
  • 4. Simulation results
  • 5. Discussion
  • References
  • DEFINING THE PLAYERS IN HIGHER-ORDER NETWORKS: PREDICTIVE MODELINGFOR REVERSE ENGINEERING FUNCTIONAL INFLUENCE NETWORKS
  • 1. Introduction
  • 2. Methods
  • 3. Results and Discussion
  • 4. Conclusions
  • 5. Acknowledgements
  • 6. References.
  • RATE-INDEPENDENT CONSTRUCTS FOR CHEMICAL COMPUTATION
  • 1. Introduction
  • 2. Chemical Model
  • 3. Computational Constructs
  • 4. A Multiplier
  • 5. Simulation Results
  • 6. Discussion
  • References
  • TOWARDS REAL-TIME CONTROL OF GENE EXPRESSION:CONTROLLING THE HOG SIGNALING CASCADE
  • 1. Introduction
  • 2. A platform for real-time control of gene expression
  • 3. Controlling transcription factor nuclear localization using a simplecontrol approach
  • 4. Design of an improved control approach
  • 5. Discussion
  • References
  • IDENTIFYING TARGETS FOR INTERVENTION BY ANALYZING BASINSOF ATTRACTION
  • 1. Introduction
  • 2. Background
  • 3. Methods
  • 4. Results
  • 5. Conclusion and Future Work
  • Supplementary Material
  • Acknowledgement
  • References
  • MINING THE PHARMACOGENOMICS LITERATURE
  • Abstract:
  • Goals of the workshop:
  • IDENTIFICATION OF ABERRANT PATHWAY AND NETWORKACTIVITY FROM HIGH-THROUGHPUT DATA
  • 1. Introduction
  • 2. Pathways in Human Disease
  • 3. High-Throughput Data
  • 4. Analysis Approaches and Tools
  • 5. Conclusion
  • References
  • WORKSHOP ON THE VALIDATION AND MODELING OF ELECTRON CRYOMICROSCOPYSTRUCTURES OF BIOLOGICAL NANOMACHINES
  • 1. Electron Cryo-microscopy
  • 2. Challenges of CryoEM Map Interpretation
  • 3. The CryoEM Modeling Challenge 2010
  • 4. Available Modeling Techniques
  • 5. Conclusions
  • 6. Acknowledgements
  • References.

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