Biocomputing 2000 - Proceedings Of The Pacific Symposium

Russ B Altman, Kevin Lauderdale, A Keith Dunker

• Publisher: World Scientific
• Year: 1999
• Print ISBN: 9789810241889, 9789810241889
• eBook ISBN: 9789814447331
• Topic: Biowissenschaften
• Subtopic: Wissenschaft Allgemein

The Pacific Symposium on Biocomputing brings together key researchers from the international biocomputing community. It is designed to be maximally responsive to the need for critical mass in subdisciplines within biocomputing. This book contains peer-reviewed articles in computational biology.

Table of contents

• CONTENTS
• PACIFIC SYMPOSIUM ON BIOCOMPUTING 2000
• Thanks to reviewers . . .
• SessionIntroductions and Peer Reviewed Papers
• Protein Evolution and Structural Genomics
• Enzyme Evolution Explained
• MODELING EVOLUTION AT THE PROTEIN LEVEL USING AN ADJUSTABLE AMINO ACID FITNESS MODEL
• PROTEIN FOLDS IN THE WORM GENOME
• SENSITIVE SEQUENCE COMPARISON AS PROTEIN FUNCTION PREDICTOR
• HIGH-THROUGHPUT FUNCTIONAL ANNOTATION OF NOVEL GENE PRODUCTS USING DOCUMENT CLUSTERING
• THE EVOLUTION OF DUPLICATED GENES CONSIDERING PROTEIN STABILITY CONSTRAINTS
• RELATING PHYSICOCHEMMICAL PROPERTIES OF AMINO ACIDS TO VARIABLE NUCLEOTIDE SUBSTITUTION PATTERNS AMONG SITES
• PROTEIN STRUCTURE PREDICTION IN BIOLOGY AND MEDICINE
• ALGORITHMIC APPROACH TO QUANTIFYING THE HYDROPHOBIC FORCE CONTRIBUTION IN PROTEIN FOLDING
• ELIMINATING SUPERFLUOUS NEIGHBOR PAIRS WHILE THREADING FOLD MODELS
• Hybrid Fold Recognition: Combining Sequence Derived Propertie s with Evolutionary Information.
• FOLDING NUCLEI IN 3D PROTEIN STRUCTURES
• HOW UNIVERSAL ARE FOLD RECOGNITION PARAMETERS. A COMPREHENSIVE STUDY OF ALIGNMENT AND SCORING FUNCTION PARAMETERS INFLUENCE ON RECOGNITION OF DISTANT FOLDS.
• Pinpointing the putative heparin/sialic acid-binding residues in the 'sushi' domain 7 of factor H: a molecular modeling study.
• RECOGNITION OF PROTEIN STRUCTURE: DETERMINING THE RELATIVE ENERGETIC CONTRIBUTIONS OF β-STRANDS, α-HELICES AND LOOPS
• Probing structure-function relationships of the DNA polymerase alpha-associated zinc-finger protein using computational approaches
• FLEXIBILITY AND CRITICAL HYDROGEN BONDS IN CYTOCHROME C
• MOLECULES TO MAPS: TOOLS FOR VISUALIZATION AND INTERACTION IN COMPUTATIONAL BIOLOGY
• MAPPETSHOW: NON-LINEAR VISUALIZATION FOR GENOME DATA
• PROFEEL: LOW COST VISUAL-HAPTIC PERCEPTUALIZATION OF PROTEIN STRUCTURE-STRUCTURE ALIGNMENTS
• Integrated Tools for Structural and Sequence Alignment and Analysis
• In VEST: Interactive and Visual Edge Selection Tool for Constructing Evolutionary Trees
• THE ENSEMBLE/LEGACY CHIMERA EXTENSION: STANDARDIZED USER AND PROGRAMMER INTERFACE TO MOLECULAR ENSEMBLE DATA AND LEGACY MODELING PROGRAMS
• GENERATING INTERACTIVE MOLECULAR DOCUMENTARIES USING A LIBRARY OF GRAPHICAL ACTIONS
• Visual management of large scale data mining projects
• MOLECULAR NETWORK MODELING AND DATA ANALYSIS
• ALGORITHMS FOR INFERRING QUALITATIVE MODELS OF BIOLOGICAL NETWORKS
• DISCOVERY OF REGULATORY INTERACTIONS THROUGH PERTURBATION: INFERENCE AND EXPERIMENTAL DESIGN
• CONSTRUCTION OF A GENERALIZED SIMULATOR FOR MULTI-CELLULAR ORGANISMS AND ITS APPLICATION TO SMAD SIGNAL TRANSDUCTION
• DELTA-NOTCH LATERAL INHIBITORY PATTERNING IN THE EMERGENCE OF CILIATED CELLS IN XENOPUS: EXPERIMENTAL OBSERVATIONS AND A GENE NETWORK MODEL
• HYBRID PETRI NET REPRESENTATION OF GENE REGULATORY NETWORK
• THE EFFECT OF DYNAMIC RECEPTOR CLUSTERING ON THE SENSITIVITY OF BIOCHEMICAL SIGNALING
• References
• Data Mining and Knowledge Discovery in Molecular Databases
• MINING THE QUANTITATIVE TRAIT LOCI ASSOCIATED WITH ORAL GLUCOSE TOLERANCE IN THE OLETF RAT
• STOCHASTIC SEGMENT MODELS OF EUKARYOTIC PROMOTER REGIONS
• STOCHASTIC HEURISTIC ALGORITHMS FOR TARGET MOTIF IDENTIFICATION (EXTENDED ABSTRACT)
• IDENTIFYING AMINO ACID RESIDUES IN MEDIUM RESOLUTION CRITICAL POINT GRAPHS USING INSTANCE BASED QUERY GENERATION
• Identification of Coordinated Gene Expression and Regulatory Sequences
• MUTUAL INFORMATION RELEVANCE NETWORKS: FUNCTIONAL GENOMIC CLUSTERING USING PAIRWISE ENTROPY MEASUREMENTS
• EST databases as multi-conditional gene expression datasets
• IN SILICO ANALYSIS OF GENE EXPRESSION PATTERNS DURING EARLY DEVELOPMENT OF XENOPUS LAEVIS
• PRINCIPAL COMPONENTS ANALYSIS TO SUMMARIZE MICROARRAY EXPERIMENTS: APPLICATION TO SPORULATION TIME SERIES
• ANN-SPEC: A METHOD FOR DISCOVERING TRANSCRIPTION FACTOR BINDING SITES WITH IMPROVED SPECIFICITY
• CLUSTER, FUNCTION AND PROMOTER: ANALYSIS OF YEAST EXPRESSION ARRAY
• Natural Language Processing for Biology
• KNOWLEDGE REPRESENTATION AND INDEXING USING THE UNIFIED MEDICAL LANGUAGE SYSTEM
• Two Applications of Information Extraction to Biological Science Journal Articles: Enzyme Interactions and Protein Structures
• EDGAR: Extraction of Drugs, Genes And Relations from the Biomedical Literature
• BIOBIBLIOMETRICS: INFORMATION RETRIEVAL AND VISUALIZATION FROM CO-OCCURRENCES OF GENE NAMES IN MEDLINE ABSTRACTS.
• Automatic Extraction of Protein Interactions from Scientific Abstracts
• COMPUTER-AIDED COMBINATORIAL CHEMISTRY AND CHEMINFORMATICS
• Compound Acquisition Strategies
• SEARCHING FOR MOLECULES WITH SIMILAR BIOLOGICAL ACTIVITY: ANALYSIS BY FINGERPRINT PROFILING
• LIBRARY DESIGN AND VIRTUAL SCREENING USING MULTIPLE 4-POINT PHARMACOPHORE FINGERPRINTS
• PICCOLO: A TOOL FOR COMBINATORIAL LIBRARY DESIGN VIA MULTICRITERION OPTIMIZATION
• Applications of Information Theory to Biology
• INFORMATION DYNAMICS OF IN VITRO SELECTION-AMPLIFICATION SYSTEMS
• AVERAGE MUTUAL INFORMATION OF CODING AND NONCODING DNA
• Finite-temperature Sequence Alignment
• HUMAN GENOME VARIATION: ANALYSIS, MANAGEMENT AND APPLICATION OF SNP DATA
• ALFRED: A WEB-ACCESSIBLE ALLELE FREQUENCY DATABASE
• LINKAGE DISEQUILIBRIUM MAPPING USING SINGLE NUCLEOTTDE POLYMORPHISMS -WHICH POPULATION?
• AN ANALYTIC SOLUTION TO SINGLE NUCLEOTIDE POLYMORPHISM ERROR-DETECTION RATES IN NUCLEAR FAMILIES: IMPLICATIONS FOR STUDY DESIGN
• THE HAPLOTYPE LINKAGE DISEQUILIBRIUM TEST FOR GENOME-WIDE SCREENS: ITS POWER AND STUDY DESIGN