Biocomputing 2010 - 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,, 2009.; ©2010.
• Year of Publication: 2009
• Edition: 1st ed.
• Language: English
• Physical Description: 1 online resource (502 pages)

Table of Contents

• Intro
• CONTENTS
• PREFACE
• COMPUTATIONAL CHALLENGES IN COMPARATIVE GENOMICS
• SESSION INTRODUCTION
• ACCURATE TAXONOMIC ASSIGNMENT OF SHORT PYROSEQUENCING READS
• BENCHMARKING BLAST ACCURACY OF GENUS/PHYLA CLASSIFICATION OF METAGENOMIC READS
• GUIDED GENOME HALVING: PROVABLY OPTIMAL SOLUTIONS PROVIDE GOOD INSIGHTS INTO THE PREDUPLICATION ANCESTRAL GENOME OF SACCHAROMYCES CEREVISIAE
• A PRACTICAL ALGORITHM FOR ESTIMATION OF THE MAXIMUM LIKELIHOOD ANCESTRAL RECONSTRUCTION ERROR
• OPTIMIZATION METHODS FOR SELECTING FOUNDER INDIVIDUALS FOR CAPTIVE BREEDING OR REINTRODUCTION OF ENDANGERED SPECIES
• COMPUTATIONAL STUDIES OF NON-CODING RNAS
• SESSION INTRODUCTION
• RNA STRUCTURAL SEGMENTATION
• RNAZ 2.0: IMPROVED NONCODING RNA DETECTION
• IDENTIFICATION AND CLASSIFICATION OF SMALL RNAS IN TRANSCRIPTOME SEQUENCE DATA
• IMPROVEMENT OF STRUCTURE CONSERVATION INDEX WITH CENTROID ESTIMATORS
• DYNAMIC PROGRAMMING ALGORITHMS FOR RNA STRUCTURE PREDICTION WITH BINDING SITES
• AN ALGORITHM FOR THE ENERGY BARRIER PROBLEM WITHOUT PSEUDOKNOTS AND TEMPORARY ARCS
• DYNAMICS OF BIOLOGICAL NETWORKS
• SESSION INTRODUCTION
• LOCAL OPTIMIZATION FOR GLOBAL ALIGNMENT OF PROTEIN INTERACTION NETWORKS
• IDENTIFICATION OF COORDINATELY DYSREGULATED SUBNETWORKS IN COMPLEX PHENOTYPES
• SUBSPACE DIFFERENTIAL COEXPRESSION ANALYSIS: PROBLEM DEFINITION AND A GENERAL APPROACH
• ESTIMATION OF PROTEIN AND DOMAIN INTERACTIONS IN THE SWITCHING MOTILITY SYSTEM OF MYXOCOCCUS XANTHUS
• EXPLORING BIOLOGICAL NETWORK DYNAMICS WITH ENSEMBLES OF GRAPH PARTITIONS
• GEOMETRIC EVOLUTIONARY DYNAMICS OF PROTEIN INTERACTION NETWORKS
• THE STEADY STATES AND DYNAMICS OF UROKINASE-MEDIATED PLASMIN ACTIVATION
• MULTI-RESOLUTION MODELING OF BIOLOGICAL MACROMOLECULES
• SESSION INTRODUCTION.
• MULTI-RESOLUTION APPROACH FOR INTERACTIVELY LOCATING FUNCTIONALLY LINKED ION BINDING SITES BY STEERING SMALL MOLECULES INTO ELECTROSTATIC POTENTIAL MAPS USING A HAPTIC DEVICE
• PREDICTING RNA STRUCTURE BY MULTIPLE TEMPLATE HOMOLOGY MODELING
• CONSTRUCTING MULTI-RESOLUTION MARKOV STATE MODELS (MSMS) TO ELUCIDATE RNA HAIRPIN FOLDING MECHANISMS
• MULTISCALE DYNAMICS OF MACROMOLECULES USING NORMAL MODE LANGEVIN
• INSIGHTS INTO THE INTRA-RING SUBUNIT ORDER OF TRIC/CCT: A STRUCTURAL AND EVOLUTIONARY ANALYSIS
• "CROSS-GRAINING:" EFFICIENT MULTI-SCALE SIMULATION VIA MARKOV STATE MODELS
• TOWARD UNDERSTANDING ALLOSTERIC SIGNALING MECHANISMS IN THE ATPASE DOMAIN OF MOLECULAR CHAPERONES
• 3D-BLAST: 3D PROTEIN STRUCTURE ALIGNMENT, COMPARISON, AND CLASSIFICATION USING SPHERICAL POLAR FOURIER CORRELATIONS
• STRUCTURAL PREDICTION OF PROTEIN-RNA INTERACTION BY COMPUTATIONAL DOCKING WITH PROPENSITY-BASED STATISTICAL POTENTIALS
• PERSONAL GENOMICS
• SESSION INTRODUCTION
• IMPROVING THE PREDICTION OF PHARMACOGENES USING TEXT-DERIVED DRUG-GENE RELATIONSHIPS
• FINDING UNIQUE FILTER SETS IN PLATO: A PRECURSOR TO EFFICIENT INTERACTION ANALYSIS IN GWAS DATA
• ENABLING PERSONAL GENOMICS WITH AN EXPLICIT TEST OF EPISTASIS
• LOSS OF POST-TRANSLATIONAL MODIFICATION SITES IN DISEASE
• DETECTING GENOME-WIDE HAPLOTYPE POLYMORPHISM BY COMBINED USE OF MENDELIAN CONSTRAINTS AND LOCAL POPULATION STRUCTURE
• SEQUENCE FEATURE VARIANT TYPE (SFVT) ANALYSIS OF THE HLA GENETIC ASSOCIATION IN JUVENILE IDIOPATHIC ARTHRITIS
• ÇOKGEN: A SOFTWARE FOR THE IDENTIFICATION OF RARE COPY NUMBER VARIATION FROM SNP MICROARRAYS
• REVERSE ENGINEERING AND SYNTHESIS OF BIOMOLECULAR SYSTEMS
• SESSION INTRODUCTION
• CO-DESIGN IN SYNTHETIC BIOLOGY: A SYSTEM-LEVEL ANALYSIS OF THE DEVELOPMENT OF AN ENVIRONMENTAL SENSING DEVICE.
• CRITICAL ANALYSIS OF TRANSCRIPTIONAL AND POST-TRANSCRIPTIONAL REGULATORY NETWORKS IN MULTIPLE MYELOMA
• A COMPUTATIONAL MODEL OF GENE EXPRESSION IN AN INDUCIBLE SYNTHETIC CIRCUIT
• RETROVIRUS HTLV-1 GENE CIRCUIT: A POTENTIAL OSCILLATOR FOR EUKARYOTES
• EMULSION BASED SELECTION OF T7 PROMOTERS OF VARYING ACTIVITY
• CLUSTERING CONTEXT-SPECIFIC GENE REGULATORY NETWORKS
• WRITING AND COMPILING CODE INTO BIOCHEMISTRY
• SYNTHESIS OF PHARMACOKINETIC PATHWAYS THROUGH KNOWLEDGE ACQUISITION AND AUTOMATED REASONING
• WORKSHOPS
• INSILICO BIOLOGY
• GENOMIC STANDARDS CONSORTIUM WORKSHOP: METAGENOMICS, METADATA AND METAANALYSIS (M3)
• EXTRACTION OF GENOTYPE-PHENOTYPE-DRUG RELATIONSHIPS FROM TEXT: FROM ENTITY RECOGNITION TO BIOINFORMATICS APPLICATION.