Introduction to bioinformatics:
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Oxford, United Kingdom
Oxford University Press
[2019]
|
| Ausgabe: | Fifth edition |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | xx, 408 Seiten Illustrationen, Diagramme |
| ISBN: | 9780198794141 |
Internformat
MARC
| LEADER | 00000nam a2200000 c 4500 | ||
|---|---|---|---|
| 001 | BV045462537 | ||
| 003 | DE-604 | ||
| 005 | 20230224 | ||
| 007 | t | ||
| 008 | 190214s2019 a||| |||| 00||| eng d | ||
| 020 | |a 9780198794141 |c Paperback |9 978-0-19-879414-1 | ||
| 035 | |a (OCoLC)1102422183 | ||
| 035 | |a (DE-599)BVBBV045462537 | ||
| 040 | |a DE-604 |b ger |e rda | ||
| 041 | 0 | |a eng | |
| 049 | |a DE-20 |a DE-29T |a DE-703 |a DE-11 |a DE-355 |a DE-M49 |a DE-91G |a DE-634 |a DE-19 |a DE-1050 | ||
| 050 | 0 | |a QH507 | |
| 082 | 0 | |a 572.80285 |2 22 | |
| 084 | |a ST 640 |0 (DE-625)143686: |2 rvk | ||
| 084 | |a ST 690 |0 (DE-625)143691: |2 rvk | ||
| 084 | |a WC 3420 |0 (DE-625)148084: |2 rvk | ||
| 084 | |a WC 7700 |0 (DE-625)148144: |2 rvk | ||
| 084 | |a WD 2100 |0 (DE-625)148162: |2 rvk | ||
| 084 | |a BIO 180f |2 stub | ||
| 084 | |a BIO 110f |2 stub | ||
| 084 | |a CHE 820f |2 stub | ||
| 084 | |a DAT 600f |2 stub | ||
| 100 | 1 | |a Lesk, Arthur M. |e Verfasser |0 (DE-588)1047454270 |4 aut | |
| 245 | 1 | 0 | |a Introduction to bioinformatics |c Arthur M. Lesk, the Pennsylvania State University |
| 246 | 1 | 3 | |a Bioinformatics |
| 250 | |a Fifth edition | ||
| 264 | 1 | |a Oxford, United Kingdom |b Oxford University Press |c [2019] | |
| 300 | |a xx, 408 Seiten |b Illustrationen, Diagramme | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 650 | 0 | 7 | |a Bioinformatik |0 (DE-588)4611085-9 |2 gnd |9 rswk-swf |
| 655 | 7 | |0 (DE-588)4123623-3 |a Lehrbuch |2 gnd-content | |
| 689 | 0 | 0 | |a Bioinformatik |0 (DE-588)4611085-9 |D s |
| 689 | 0 | |5 DE-604 | |
| 856 | 4 | 2 | |m Digitalisierung UB Regensburg - ADAM Catalogue Enrichment |q application/pdf |u http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=030847767&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |3 Inhaltsverzeichnis |
| 999 | |a oai:aleph.bib-bvb.de:BVB01-030847767 | ||
Datensatz im Suchindex
| _version_ | 1804179366275448832 |
|---|---|
| adam_text | CONTENTS Preface to the fifth edition Plan of the book Introduction to bioinformatics on the web Acknowledgements 1 xv xxi xxii xxiii Introduction 1 Life in space and time 4 Phenotype = genotype + environment + life history + epigenetics 4 Evolution is the change over time in the world of living things 5 Biological classification and nomenclature 6 Dogmas: central and peripheral 9 The structure of DNA 9 Transcription and translation 12 The structures of proteins 12 Statics and dynamics 17 Systems biology 17 The human genome 19 Variation in human genome sequences 20 The human genome and medicine 21 Databases in molecular biology 28 Observables and data archives 29 A database without effective modes of access is merely a data graveyard 29 Information flow in bioinformatics 31 Curation, annotation, and quality control 32 The World Wide Web 33 Electronic publication 34 Computers and computer science Programming Après moi, le déluge? Sorry—too late! How much sequencing power is there in the world? 34 35 38 41 How does the amount of data in bioinformatics compare with other large scientific information archives? 2 41 Recommended reading 42 Exercises and Problems 43 From genetics to genomes 48 The classical genetics background 49 DNA embodies genes 50
Contents Maps and tour guides M Linkage maps 51 Linkage 51 Chromosome banding 53 High-resolution maps, based directly on DNA sequences 55 Restriction maps 56 DNA sequencing 57 Frederick Sanger and the development of DNA sequencing 57 DNA sequencing by termination of chain replication 58 Automation of DNA sequencing 60 Next-generation sequencing :1 Paired-end reads 66 Life in the fast lane 67 Assembly—computational aspects Pattern matching 68 Suffix trees 68 Fragment assembly Genomics in personal identification DNA fingerprinting Г ’ 74 Personal identification by amplification of specific regions has superseded the RFLP approach Mitochondrial DNA 75 ~?,c Analysis of non-human DNA sequences 77 Parentage testing 78 Ethical, legal, and social issues Databases containing human DNA sequence information 80 Use of DNA sequencing in research on human subjects 82 Recommended reading Exercises and Problems 3 The panorama of life Genomes, transcriptomes, and proteomes 89 Genes 89 Proteomics and transcriptomics 91 Eavesdropping on the transmission of genetic information 93 Genome-sequencing projects 93 Genomes of prokaryotes 94 The genome of the bacterium Escherichia coli The genome of the archaeon Methanocaldococcus jannaschii 95 97 The genome of one of the simplest organisms: Mycoplasma genitalium Metagenomics: the collection of genomes in a coherent environmental sample The human microbiome 99 101
Genomes of eukarya 102 Gene families 103 The genome of Saccharomyces cerevisiae (Baker s yeast) 103 The genome of Caenorhabdltis elegans 105 The genome of Drosophila melanogaster 105 The genome of Arabldopsis thaliana 107 The genome of Homo sapiens (the human genome) 108 Protein-coding genes 109 Repeat sequences 109 RNA 110 Single-nucleotide polymorphisms and haplotypes 110 Systematic measurements and collections of single-nucleotide polymorphisms Genetic diversity in anthropology 114 DNA sequences and languages 116 Evolution of genomes Please pass the genes: horizontal gene transfer 4 113 116 118 Comparative genomics of eukarya 119 Recommended reading 120 Exercises and Problems 121 Alignments and phylogenetic trees 123 Introduction to sequence alignment 124 Dotplots and sequence alignments 130 Measures of sequence similarity 132 Scoring schemes 132 Derivation of substitution matrices: РАДА matrices 133 Computing the alignment of two sequences 135 Variations and generalizations 135 Approximate methods for quick screening of databases 135 The dynamic programming algorithm for optimal pairwise sequence alignment 137 Significance of alignments 141 Multiple sequence alignment 143 Applications of multiple sequence alignments to database searching 143 Profiles 146 PSI-BLAST 147 Complete pairwise sequence alignment of human PAX-6 protein and Drosophila melanogaster eyeless 151 Hidden Markov Models 152 Phylogeny Determination of taxonomic relationships from molecular properties 154 155 Use of sequences to determine phylogenetic relationships 159 Use of SINES and LINES to derive
phylogenetic relationships 161
Contents Phylogenetic trees 5 162 Clustering methods 164 The maximum-likelihood method 165 Reconstruction of ancestral sequences 165 Pyruvate decarboxylase: synthesis, activity, and crystal structure of predicted ancestor 167 The problem of varying rates of evolution 16Ξ Bayesian methods 169 Are trees the correct way to present phylogenetic relationships? 169 Computational considerations 170 Putting it all together 171 Recommended reading 77 Exercises and Problems 17, Structural bioinformatics and drug discovery Introduction Protein stability and folding The Sasisekharan-Ramakrishnan-Ramachandran plot describes allowed mainchain conformations The sidechains Protein stability and dénaturation 180 131 183 Protein folding as a process Applications of hydrophobicity Coiled-coiled proteins 187 Description of the variety of protein structures Superposition of structures, and structural alignments IK Evolution of protein structures 1SC Classifications of protein structures 1 SCOP Protein structure prediction and modelling 199 201 A priori and empirical methods 202 Critical Assessment of Structure Prediction 203 Secondary structure prediction 204 Homology modelling 205 Fold recognition 205 Conformational energy calculations and molecular dynamics 207 ROSETTA 209 Protein structure prediction from contact maps derived from correlated mutations in multiple sequence alignments Design of novel proteins Drug discovery and development 210 213 215 The lead compound 216 Improving on the lead compound: quantitative structure-activity relationships 217 Bioinformatics in drug discovery and
development 218 Molecular modelling in drug discovery 219
Contents 6 Recommended reading 225 Exercises and Problems 228 Scientific publications and archives:media, content, access, and presentation The scientific literature 234 Access to scholarly publications 235 Open access 236 The Public Library of Science 237 Traditional and digital libraries 237 How to populate a digital library 238 The information explosion 239 The web: higher dimensions 239 New media: video, sound 240 Searching the scientific literature 240 Bibliography management 241 Databases 242 Database contents 242 Database quality control 243 The literature as a database 244 Database organization 244 Annotation 246 Markup languages 248 Database access 250 Links 250 Database interoperability 251 Data mining 251 Programming languages and tools fordatabase construction and access 255 Traditional programming languages 255 Scripting languages 256 Program libraries specialized for molecularbiology 256 Java—computing over the web 256 Natural language processing Natural language processing in mining thebiomedical literature 7 233 257 258 Biomedical applications of text mining 260 Hypothesis generation 264 A glaucoma-related network derived bytextmining 265 Recommended reading 268 Exercises and Problems 269 Artificial intelligence and machinelearning 271 What are artificial Intelligence and machinelearning? 272 Classification and clustering 273 Binary classifier 276 Receiver Operating Characteristic (ROC)curves 277
Contents Artificial neural networks Self-organizing maps 281 Support vector machines (SVMs) 286 Clustering Clustering by graphspectral theory 286 287 291 Recommended reading 233 Exercises and Problems 232 Introduction to systemsbiology 2 2 Introduction 22 Networks and graphs ~9 Connectivity in networks 293* Dynamics, stability, and robustness 2 9 Some sources of ideas for systems biology 2 2 Complexity of sequences 302 Shannon s definition of entropy 303 Complexity of sequences 304 The relationship between complexity, randomness, and compressibility 305 The Burrows-Wheeler Transform 2з Inverting the Burrows-Wheeler Transform 306 The Burrows-Wheeler Transform brings repeats together, facilitating compression 306 Use of the Burrows-Wheeler transform for searching for patterns in strings 306 Complexity of other types of biological data Static and dynamic complexity Predictability and chaos Analysis and comparison of networks 9 281 Decision trees Kernei methods 8 273 32 308 30У 310 Analysis of graphs by matrix algebra 311 Graph isomorphism 332 Recommended reading 314 Exercises and Problems 314 Metabolic pathways 317 Introduction 318 Classification of protein function 320 The Enzyme Commission 320 The Gene Ontology™ Consortium protein function classification 320 Prediction of protein function 321 Catalysis by enzymes 324 Active sites 325 Cofactors 325
Protein-ligand binding equilibria 326 Enzyme kinetics 327 Measures of effectiveness of enzymes How do enzymes evolve new functions? 328 329 Control over enzyme activity 329 Structural mechanisms of evolution of altered or novel protein functions 329 Pathways and limits in the divergence of sequence, structure, and function Evolution by gene duplication 334 335 Databases of metabolic pathways 337 The Kyoto Encyclopedia of Genes and Genomes (KEGG) 339 Evolution and phylogeny of metabolic pathways Pathway comparison Alignment of metabolic pathways Comparing linear metabolic pathways 341 341 343 343 Comparing non-linear metabolic pathways: The pentose phosphate pathway and the Calvin-Benson cycle 346 Dynamics of metabolic networks 347 Robustness of metabolic networks 347 Dynamic modelling of metabolism 347 Simulation of metabolic pathways in Plasmodium falciparum 351 The Human Metabolome Database supports clinical applications to the study of inborn errors of metabolism, and to cancer 10 352 Recommended reading 353 Exercises and Problems 353 Control of organization and organization of control Transcriptomics The ENCODE Project Determination of RNA sequences 355 356 357 358 RNAseq v. microarrays 358 DNA microarrays 359 RNAseq 363 The Genotype-Tissue Expression (GTEx) project 366 Expression patterns in different physiological states 367 Variation of expression patterns during the life cycle of Drosophila melanogaster 368 Different life stages make different demands on different genes Protein complexes and aggregates Properties of protein-protein complexes Protein interaction
networks Components of the primosome assembly in Bacillus subtilis 370 373 373 375 378
Contents Regulatory networks 380 Signal transduction and transcriptional control 380 Structural biology of regulatory networks 382 Examples of relatively simple regulatory control networks 3S3 Regulation of the lactose operon in E. coli 383 The genetic switch of bacteriophage λ 385 The diauxic shift in Saccharomyces cerevisiae 389 Logical structure of regulatory networks ES ։ The transcriptional regulatory network of E. coli 391 The transcriptional regulatory network of Saccharomyces cerevisiae 392 Adaptability of the yeast regulatory network 393 Recommended reading B E Exercises and Problems BBS Conclusions Index
|
| any_adam_object | 1 |
| author | Lesk, Arthur M. |
| author_GND | (DE-588)1047454270 |
| author_facet | Lesk, Arthur M. |
| author_role | aut |
| author_sort | Lesk, Arthur M. |
| author_variant | a m l am aml |
| building | Verbundindex |
| bvnumber | BV045462537 |
| callnumber-first | Q - Science |
| callnumber-label | QH507 |
| callnumber-raw | QH507 |
| callnumber-search | QH507 |
| callnumber-sort | QH 3507 |
| callnumber-subject | QH - Natural History and Biology |
| classification_rvk | ST 640 ST 690 WC 3420 WC 7700 WD 2100 |
| classification_tum | BIO 180f BIO 110f CHE 820f DAT 600f |
| ctrlnum | (OCoLC)1102422183 (DE-599)BVBBV045462537 |
| dewey-full | 572.80285 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 572 - Biochemistry |
| dewey-raw | 572.80285 |
| dewey-search | 572.80285 |
| dewey-sort | 3572.80285 |
| dewey-tens | 570 - Biology |
| discipline | Biologie Informatik Chemie |
| edition | Fifth edition |
| format | Book |
| fullrecord | <?xml version="1.0" encoding="UTF-8"?><collection xmlns="http://www.loc.gov/MARC21/slim"><record><leader>01829nam a2200469 c 4500</leader><controlfield tag="001">BV045462537</controlfield><controlfield tag="003">DE-604</controlfield><controlfield tag="005">20230224 </controlfield><controlfield tag="007">t</controlfield><controlfield tag="008">190214s2019 a||| |||| 00||| eng d</controlfield><datafield tag="020" ind1=" " ind2=" "><subfield code="a">9780198794141</subfield><subfield code="c">Paperback</subfield><subfield code="9">978-0-19-879414-1</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(OCoLC)1102422183</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(DE-599)BVBBV045462537</subfield></datafield><datafield tag="040" ind1=" " ind2=" "><subfield code="a">DE-604</subfield><subfield code="b">ger</subfield><subfield code="e">rda</subfield></datafield><datafield tag="041" ind1="0" ind2=" "><subfield code="a">eng</subfield></datafield><datafield tag="049" ind1=" " ind2=" "><subfield code="a">DE-20</subfield><subfield code="a">DE-29T</subfield><subfield code="a">DE-703</subfield><subfield code="a">DE-11</subfield><subfield code="a">DE-355</subfield><subfield code="a">DE-M49</subfield><subfield code="a">DE-91G</subfield><subfield code="a">DE-634</subfield><subfield code="a">DE-19</subfield><subfield code="a">DE-1050</subfield></datafield><datafield tag="050" ind1=" " ind2="0"><subfield code="a">QH507</subfield></datafield><datafield tag="082" ind1="0" ind2=" "><subfield code="a">572.80285</subfield><subfield code="2">22</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">ST 640</subfield><subfield code="0">(DE-625)143686:</subfield><subfield code="2">rvk</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">ST 690</subfield><subfield code="0">(DE-625)143691:</subfield><subfield code="2">rvk</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">WC 3420</subfield><subfield code="0">(DE-625)148084:</subfield><subfield code="2">rvk</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">WC 7700</subfield><subfield code="0">(DE-625)148144:</subfield><subfield code="2">rvk</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">WD 2100</subfield><subfield code="0">(DE-625)148162:</subfield><subfield code="2">rvk</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">BIO 180f</subfield><subfield code="2">stub</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">BIO 110f</subfield><subfield code="2">stub</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">CHE 820f</subfield><subfield code="2">stub</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">DAT 600f</subfield><subfield code="2">stub</subfield></datafield><datafield tag="100" ind1="1" ind2=" "><subfield code="a">Lesk, Arthur M.</subfield><subfield code="e">Verfasser</subfield><subfield code="0">(DE-588)1047454270</subfield><subfield code="4">aut</subfield></datafield><datafield tag="245" ind1="1" ind2="0"><subfield code="a">Introduction to bioinformatics</subfield><subfield code="c">Arthur M. Lesk, the Pennsylvania State University</subfield></datafield><datafield tag="246" ind1="1" ind2="3"><subfield code="a">Bioinformatics</subfield></datafield><datafield tag="250" ind1=" " ind2=" "><subfield code="a">Fifth edition</subfield></datafield><datafield tag="264" ind1=" " ind2="1"><subfield code="a">Oxford, United Kingdom</subfield><subfield code="b">Oxford University Press</subfield><subfield code="c">[2019]</subfield></datafield><datafield tag="300" ind1=" " ind2=" "><subfield code="a">xx, 408 Seiten</subfield><subfield code="b">Illustrationen, Diagramme</subfield></datafield><datafield tag="336" ind1=" " ind2=" "><subfield code="b">txt</subfield><subfield code="2">rdacontent</subfield></datafield><datafield tag="337" ind1=" " ind2=" "><subfield code="b">n</subfield><subfield code="2">rdamedia</subfield></datafield><datafield tag="338" ind1=" " ind2=" "><subfield code="b">nc</subfield><subfield code="2">rdacarrier</subfield></datafield><datafield tag="650" ind1="0" ind2="7"><subfield code="a">Bioinformatik</subfield><subfield code="0">(DE-588)4611085-9</subfield><subfield code="2">gnd</subfield><subfield code="9">rswk-swf</subfield></datafield><datafield tag="655" ind1=" " ind2="7"><subfield code="0">(DE-588)4123623-3</subfield><subfield code="a">Lehrbuch</subfield><subfield code="2">gnd-content</subfield></datafield><datafield tag="689" ind1="0" ind2="0"><subfield code="a">Bioinformatik</subfield><subfield code="0">(DE-588)4611085-9</subfield><subfield code="D">s</subfield></datafield><datafield tag="689" ind1="0" ind2=" "><subfield code="5">DE-604</subfield></datafield><datafield tag="856" ind1="4" ind2="2"><subfield code="m">Digitalisierung UB Regensburg - ADAM Catalogue Enrichment</subfield><subfield code="q">application/pdf</subfield><subfield code="u">http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=030847767&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA</subfield><subfield code="3">Inhaltsverzeichnis</subfield></datafield><datafield tag="999" ind1=" " ind2=" "><subfield code="a">oai:aleph.bib-bvb.de:BVB01-030847767</subfield></datafield></record></collection> |
| genre | (DE-588)4123623-3 Lehrbuch gnd-content |
| genre_facet | Lehrbuch |
| id | DE-604.BV045462537 |
| illustrated | Illustrated |
| indexdate | 2024-07-10T08:18:43Z |
| institution | BVB |
| isbn | 9780198794141 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-030847767 |
| oclc_num | 1102422183 |
| open_access_boolean | |
| owner | DE-20 DE-29T DE-703 DE-11 DE-355 DE-BY-UBR DE-M49 DE-BY-TUM DE-91G DE-BY-TUM DE-634 DE-19 DE-BY-UBM DE-1050 |
| owner_facet | DE-20 DE-29T DE-703 DE-11 DE-355 DE-BY-UBR DE-M49 DE-BY-TUM DE-91G DE-BY-TUM DE-634 DE-19 DE-BY-UBM DE-1050 |
| physical | xx, 408 Seiten Illustrationen, Diagramme |
| publishDate | 2019 |
| publishDateSearch | 2019 |
| publishDateSort | 2019 |
| publisher | Oxford University Press |
| record_format | marc |
| spelling | Lesk, Arthur M. Verfasser (DE-588)1047454270 aut Introduction to bioinformatics Arthur M. Lesk, the Pennsylvania State University Bioinformatics Fifth edition Oxford, United Kingdom Oxford University Press [2019] xx, 408 Seiten Illustrationen, Diagramme txt rdacontent n rdamedia nc rdacarrier Bioinformatik (DE-588)4611085-9 gnd rswk-swf (DE-588)4123623-3 Lehrbuch gnd-content Bioinformatik (DE-588)4611085-9 s DE-604 Digitalisierung UB Regensburg - ADAM Catalogue Enrichment application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=030847767&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Lesk, Arthur M. Introduction to bioinformatics Bioinformatik (DE-588)4611085-9 gnd |
| subject_GND | (DE-588)4611085-9 (DE-588)4123623-3 |
| title | Introduction to bioinformatics |
| title_alt | Bioinformatics |
| title_auth | Introduction to bioinformatics |
| title_exact_search | Introduction to bioinformatics |
| title_full | Introduction to bioinformatics Arthur M. Lesk, the Pennsylvania State University |
| title_fullStr | Introduction to bioinformatics Arthur M. Lesk, the Pennsylvania State University |
| title_full_unstemmed | Introduction to bioinformatics Arthur M. Lesk, the Pennsylvania State University |
| title_short | Introduction to bioinformatics |
| title_sort | introduction to bioinformatics |
| topic | Bioinformatik (DE-588)4611085-9 gnd |
| topic_facet | Bioinformatik Lehrbuch |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=030847767&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT leskarthurm introductiontobioinformatics AT leskarthurm bioinformatics |