EVOLUTIONARY BIOINFORMATICS

By H. LIVIR

CONTENTS INTRODUCTION WHAT IS BIOINFORMATICS? WHAT CAN BIOINFORMATICS DO? REFERENCES PART I INFORMATION THE NATURE OF INFORMATION STRUCTURE AND QUANTITY THE GENERATION OF INFORMATION CONDITIONAL AND UNCONDITIONAL INFORMATION EXPERIMENTS AND OBSERVATIONS CONSTRAINT THE VALUE OF INFORMATION THE QUALITY OF INFORMATION ACCURACY, MEANING, AND EFFECT ACCURACY MEANING EFFECT SIGNIFICS FURTHER REMARKS ON INFORMATION GENERATION SUMMARY THE TRANSMISSION OF INFORMATION THE CAPACITY OF A CHANNEL CODING DECODING COMPRESSION USE OF COMPRESSION TO MEASURE DISTANCE ERGODICITY NOISE ERROR CORRECTION SETS AND COMBINATORICS THE NOTION OF SET COMBINATORICS ORDERED SAMPLING WITH REPLACEMENT ORDERED SAMPLING WITHOUT REPLACEMENT UNORDERED SAMPLING WITHOUT REPLACEMENT UNORDERED SAMPLING WITH REPLACEMENT THE BINOMIAL THEOREM PROBABILITY AND LIKELIHOOD THE NOTION OF PROBABILITY FUNDAMENTALS GENERALIZED UNION CONDITIONAL PROBABILITY BERNOULLI TRIALS MOMENTS OF DISTRIBUTIONS RUNS THE HYPERGEOMETRIC DISTRIBUTION MULTIPLICATIVE PROCESSES LIKELIHOOD THE MAXIMUM ENTROPY METHOD RANDOMNESS AND COMPLEXITY RANDOM PROCESSES MARKOV CHAINS RANDOM WALKS COMPLEXITY SYSTEMS, NETWORKS, AND CIRCUITS GENERAL SYSTEMS THEORY AUTOMATA CELLULAR AUTOMATA PERCOLATION NETWORKS (GRAPHS) TREES COMPLEXITY PARAMETERS DYNAMICAL PROPERTIES SYNERGETICS SOME EXAMPLES RECEPTION AND GENERATION OF INFORMATION HABITUATION EVOLUTIONARY SYSTEMS ALGORITHMS EVOLUTIONARY COMPUTING PATTERN RECOGNITION BOTRYOLOGY CLUSTERING PRINCIPAL COMPONENT AND LINEAR DISCRIMINANT ANALYSES WAVELETS MULTIDIMENSIONAL SCALING AND SERIATION VISUALIZATION PART II BIOLOGY INTRODUCTION TO PART II GENOTYPE, PHENOTYPE, AND SPECIES ADAPTATION TIMESCALES OF ADAPTATION THE RÔLE OF MEMORY THE INTEGRATING RÔLE OF DIRECTIVE CORRELATION REGULATION THE CONCEPT OF MACHINE THE ARCHITECTURE OF FUNCTIONAL SYSTEMS BIOLOGICAL COMPLEXITY SELF-ORGANIZATION CYBERNETICS THE NATURE OF LIVING THINGS THE CELL THE STRUCTURE OF A CELL MITOCHONDRIA OBSERVATIONAL OVERVIEW METABOLISM THE CELL CYCLE THE CHROMOSOME THE STRUCTURES OF GENOME AND GENES THE C-VALUE PARADOX THE STRUCTURE OF THE CHROMOSOME THE IMMUNE SYSTEM MOLECULAR MECHANISMS REPLICATION PROOFREADING AND REPAIR RECOMBINATION SUMMARY OF SOURCES OF GENOME VARIATION GENE EXPRESSION TRANSCRIPTION REGULATION OF TRANSCRIPTION PROKARYOTIC TRANSCRIPTIONAL REGULATION EUKARYOTIC TRANSCRIPTIONAL REGULATION MRNA PROCESSING TRANSLATION ONTOGENY (DEVELOPMENT) STEM CELLS EPIGENESIS THE EPIGENETIC LANDSCAPE R AND K SELECTION HOMEOTIC GENES PHYLOGENY AND EVOLUTION GROUP AND KIN SELECTION MODELS OF EVOLUTION FURTHER REMARKS ON SOURCES OF GENOME VARIATION THE ORIGIN OF PROTEINS TAXONOMY AND GEOLOGICAL ERAS THE MOLECULES OF LIFE MOLECULES AND SUPRAMOLECULAR STRUCTURE WATER DNA RNA PROTEINS AMINO ACIDS PROTEIN FOLDING AND INTERACTION EXPERIMENTAL TECHNIQUES FOR PROTEIN STRUCTURE DETERMINATION PROTEIN STRUCTURE OVERVIEW POLYSACCHARIDES LIPIDS PART III APPLICATIONS INTRODUCTION TO PART III GENOMICS DNA SEQUENCING EXTRACTION OF NUCLEIC ACIDS THE POLYMERASE CHAIN REACTION SEQUENCING EXPRESSED SEQUENCE TAGS DNA METHYLATION PROFILING GENE IDENTIFICATION EXTRINSIC METHODS DATABASE RELIABILITY SEQUENCE COMPARISON AND ALIGNMENT TRACE, ALIGNMENT AND LISTING DYNAMIC PROGRAMMING ALGORITHMS INTRINSIC METHODS SIGNALS HIDDEN MARKOV MODELS BEYOND SEQUENCE MINIMALIST APPROACHES PHYLOGENIES METAGENOMICS PROTEOMICS TRANSCRIPTOMICS TWO-DIMENSIONAL GEL ELECTROPHORESIS COLUMN CHROMATOGRAPHY OTHER KINDS OF ELECTROPHORESIS PROTEIN IDENTIFICATION ISOTOPE-CODED AFFINITY TAGS PROTEIN MICROARRAYS PROTEIN EXPRESSION PATTERNS—TEMPORAL AND SPATIAL THE KINOME BIOCHEMICAL SIGNALLING THE GLYCOME, LIPIDOME AND MICROBIOME GLYCOMICS LIPIDOMICS MICROBIOMICS INTERACTOMICS: INTERACTIONS AND REGULATORY NETWORKS INFERENCE OF REGULATORY NETWORKS THE PHYSICAL CHEMISTRY OF INTERACTIONS INTERMOLECULAR INTERACTIONS IN VIVO EXPERIMENTAL METHODS THE YEAST TWO-HYBRID ASSAY CROSSLINKING CORRELATED EXPRESSION OTHER METHODS IN VITRO EXPERIMENTAL METHODS CHROMATOGRAPHY DIRECT AFFINITY MEASUREMENT PROTEIN CHIPS INTERACTIONS FROM SEQUENCE GLOBAL STATISTICS OF INTERACTIONS THE NERVOUS SYSTEM THE NEURON AND NEURAL NETWORKS OUTSTANDING PROBLEMS ARTIFICIAL NEURAL NETWORKS METABOLOMICS AND METABONOMICS DATA COLLECTION DATA ANALYSIS METABOLIC REGULATION METABOLIC CONTROL ANALYSIS THE METABOLIC CODE METABOLIC NETWORKS PHENOMICS POLYGENIC DISEASE ACTIVITY-BASED PROTEIN PROFILING PHENOTYPE MICROARRAYS ETHOMICS MODELLING LIFE MEDICAL APPLICATIONS THE GENETIC BASIS OF DISEASE CANCER TOWARD AUTOMATED DIAGNOSIS DRUG DISCOVERY AND TESTING NANODRUGS PERSONALIZED MEDICINE BACTERIAL MULTIRESISTANCE TOXICOGENOMICS REPROGRAMMING STEM CELLS TRACING GENETICALLY MODIFIED INGREDIENTS IN FOOD ECOSYSTEMS MANAGEMENT THE ORGANIZATION OF KNOWLEDGE ONTOLOGY KNOWLEDGE REPRESENTATION THE PROBLEM OF BACTERIAL IDENTIFICATION TEXT MINING THE AUTOMATION OF RESEARCH BIBLIOGRAPHY