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Bibliografická citace

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BK
4th ed.
Oxford : Oxford University Press, c2014
xvi, 371 s., [8] s. obr. příl. : il. (některé barev.) ; 27 cm

ISBN 978-0-19-965156-6 (brož.)
Obsahuje bibliografie a rejstřík
000248897
CONTENTS // Preface to the first edition xiv // Preface to the second edition xvii // Preface to the third edition xvili // Preface to the fourth edition xix // Plan of the book xx // Introduction to bioinformatics on the web xxi // Acknowledgements xxii // 1 Introduction 1 // Life in space and time 3 // Phenotype = genotype - environment + life history + epigenetics 4 // Evolution is the change over time in the world of living things 4 // Dogmas: central and peripheral 6 // Statics and dynamics 9 // Networks 10 // Observables and data archives 10 // A database without effective modes of access is merely a data graveyard 12 // Information flow in bioinformatics 12 // Curation, annotation, and quality control 14 // The world-wide web 15 // Electronic publication 16 // Computers and computer science 16 // Programming 17 // Biological classification and nomenclature 21 // Use of sequences to determine phylogenetic relationships 23 // Use of SINES and LINES to derive phylogenetic relationships 29 // Searching for similar sequences in databases: PSI-BLAST 30 // Introduction to protein structure 38 // The hierarchical nature of protein architecture 40 // Classification of protein structures 41 // Protein structure prediction and engineering 46 // Critical Assessment of Structure Prediction 47 // Protein engineering 48 // Proteomics and transcriptomics 48 // DNA microarrays 49 // Transcriptomics and RNA sequencing 50 // Mass spectrometry 50 // Contents // Systems biology 50 // Clinical
implications 50 // The future 53 // Recommended reading 53 // Exercises and problems 55 // 2 Genome organization and evolution 59 // Genomes, transcriptomes, and proteomes 59 // Genes 60 // Proteomics and transcriptomics 62 // Eavesdropping on the transmission of genetic information 64 // Identification of genes associated with inherited diseases 64 // Mappings between the maps 66 // High-resolution maps 68 // Genome-wide association studies 69 // Picking out genes in genomes 70 // Genome-sequencing projects 71 // Genomes of prokaryotes 72 // The genome of the bacterium Escherichia coli 73 // The genome of the archaeon Methanococcus lannaschii 75 // The genome of one of the simplest organisms: Mycoplasma genitalium 76 // Metagenomics: the collection of genomes in a coherent environmental sample 76 The human microbiome 79 // Genomes of eukarya 79 // Gene families 82 // The genome of Saccharomyces cerevisiae (baker’s yeast) 82 // The genome of Caenorhabditis eiegans 84 // The genome of Drosophila melanogaster 85 // The genome of Arabidopsis thaliana 86 // The genome of Homo sapiens (the human genome) 88 // Protein-coding genes 88 // Repeat sequences 89 // RNA 90 // Single-nucleotide polymorphisms and haplotypes 90 // Systematic measurements and collections of single-nucleotide polymorphisms 92 // Ethical, legal, and social issues 94 // Genetic diversity in anthropology 95 // DNA sequences and languages 96 // Genetic diversity and personal identification 97 // Evolution of genomes
98 // Please pass the genes: horizontal gene transfer 100 // Comparative genomics of eukarya 101 // Recommended Reading 102 // Contents // Exercises and problems 103 // 3 Scientific publications and archives: media, content, and access 107 // The scientific literature 107 // Economic factors governing access to scholarly publications 109 // Open access 110 // The Public Library of Science 111 // Traditional and digital libraries 111 // How to populate a digital library 112 // The information explosion 113 // The web: higher dimensions 113 // New media: video, sound 113 // Searching the literature 114 // Bibliography management 114 // Databases 115 // Database contents 116 // The literature as a database 116 // Database organization 116 // Annotation 119 // Database quality control 120 // Database access 122 // Links 123 // Database interoperability 125 // Data mining 127 // Programming languages and tools 128 // Traditional programming languages 130 // Scripting languages 130 // Program libraries specialized for molecular biology 130 // Java: computing over the web 131 // Markup languages 131 // Natural language processing 133 // Natural language processing and mining the biomedical literature 134 // Applications of text mining 136 // Recommended reading 141 // Exercises and problems 142 // 4 Archives and information retrieval 144 // Database indexing and specification of search terms 144 // Follow-up questions 145 // Analysis and processing of retrieved data 146 // The archives
146 // Nucleic acid sequence databases 147 // Genome databases and genome browsers 148 // Protein sequence databases 149 // Databases of protein families 152 // Contents // Databases of structures 153 // Classifications of protein structures 157 // Accuracy and precision of protein structure determinations 157 // Specialized, or ’boutique’, databases 158 // Expression and proteomics databases 159 // Bibliographic databases 160 // Surveys of molecular biology databases and servers 161 // Gateways to archives 161 // Access to databases in molecular biology 162 // ENTREZ 162 // The Protein Identification Resource 171 // ExPASy: Expert Protein Analysis System 172 // Where do we go from here? 173 // Recommended reading 173 // Exercises and problems 174 // 5 Alignments and phylogenetic trees 175 // Introduction to sequence alignment 175 // Thedotplot 176 // Dotplols and sequence alignments 181 // Measures of sequence similarity 182 // Scoring schemes 184 // Derivation of substitution matrices: PAM and BLOSUM matrices 184 // Computing the alignment of two sequences 187 // Variations and generalizations 187 // Approximate methods for quick screening of databases 188 // The dynamic-programming algorithm for optimal pairwise // sequence alignment 188 // Significance of alignments 194 // Multiple sequence alignment 196 // Applications of multiple sequence alignments and database searching 198 // Profiles 198 // PSI-BLAST 200 // Hidden Markov models 201 // Phylogeny 203 // Determination of
taxonomic relationships from molecular properties 205 // Phylogenetic trees 207 // Clustering methods 209 // Cladistic methods 210 // Reconstruction of ancestral sequences 211 // The problem of varying rates of evolution 213 // Are trees the correct way to present phylogenetic relationships? 213 // Computational considerations 214 // Putting It all together 215 // Contents // Recommended reading 215 // Exercises and problems 216 // 6 Structural bioinformatics and drug discovery 222 // Introduction 222 // Protein stability and folding 224 // The Sasisekharan-Ramakrishnan-Ramachandran plot describes // allowed mainchain conformations 225 // The sidechains 226 // Protein stability and denaturation 227 // Protein folding 229 // Applications of hydrophobicity 230 // Coiled-coiled proteins 230 // Superposition of structures, and structural alignments 235 // DALI and MUSTANG 237 // Evolution of protein structures 238 // Classifications of protein structures 240 // Protein structure prediction and modelling 241 // A priori and empirical methods 241 // Critical Assessment of Structure Prediction 243 // Secondary structure prediction 246 // Homology modelling 249 // Fold recognition 250 // Conformational energy calculations and molecular dynamics 255 // Assignment of protein structures to genomes 260 // Prediction of protein function 261 // Divergence of function: orthologues and paralogues 261 // Drug discovery and development 264 // The lead compound 265 // Improving on the lead compound:
quantitative structure-activity relationships 266 // Bioinformatics in drug discovery and development 267 // Molecular modelling in drug discovery 268 // Recommended reading 274 // Exercises and problems 276 // 7 Introduction to systems biology 282 // Introduction 282 // Networks and graphs 284 // Connectivity in networks 285 // Dynamics, stability, and robustness 286 // Some sources of ideas for systems biology 288 // Complexity of sequences 288 // Computational complexity 291 // Contents // Static and dynamic complexity 291 // Chaos and predictability 293 // Recommended reading 294 // Exercises and problems 294 // 8 Metabolic pathways 297 // Classification and assignment of protein function 298 // The Enzyme Commission 298 // The Gene Ontology Consortium protein function classification 299 // Catalysis by enzymes 301 // Active sites 303 // Cofactors 303 // Protein-ligand binding equilibria 304 // Enzyme kinetics 305 // Measures of effectiveness of enzymes 306 // How do proteins evolve new functions? 307 // Control over enzyme activity 308 // Structural mechanisms of evolution of altered or novel protein functions 308 // Protein evolution at the level of domain assembly 311 // Databases of metabolic pathways 312 // EcoCyc 313 // The Kyoto Encyclopedia of Genes and Genomes 313 // Evolution and phylogeny of metabolic pathways 316 // Pathway comparison 316 // Alignment of metabolic pathways 320 // Comparing linear metabolic pathways 320 // Comparing nonlinear metabolic pathways:
the pentose phosphate // pathway and the Calvin-Benson cycle 321 // Dynamics of metabolic networks 322 // Robustness of metabolic networks 323 // Dynamic modelling of metabolism 324 // Recommended reading 326 // Exercises and problems 326 // 9 Gene expression and regulation 328 // DNA microarrays 329 // Microarray data are quantitative but imprecise 330 // Analysis of microarray data 330 // Mass spectrometry 335 // Identification of components of a complex mixture 335 // Protein sequencing by mass spectrometry 337 // Measuring deuterium exchange in proteins 338 // Genome sequence analysis by mass spectrometry 339 // Contents // Protein complexes and aggregates 342 // Properties of protein-protein complexes 343 // Protein interaction networks 345 // Regulatory networks 348 // Signal transduction and transcriptional control 349 // Structures of regulatory networks 350 // Structural biology of regulatory networks 350 // The genetic switch of bacteriophage X 352 // What are the characteristics of the switch that must be implemented // by DNA-protein interactions? 353 // The materials 354 // How to ’throw’ the switch 355 // The genetic regulatory network of Saccharomyces cerevisiae 356 // Adaptability of the yeast regulatory network 358 // Recommended reading 360 // Exercises and problems 360 // Conclusion 363 // Index 365

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