Biocomputing 2010 - Proceedings Of The Pacific Symposium.
- 1 online resource (502 pages)
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 -- �COKGEN: 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.