Biocomputing 2011 - Proceedings Of The Pacific Symposium.

• Author: 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
• Physical Description: 1 online resource (386 pages)

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.