Bioinformatics : an introduction / / Jeremy Ramsden

• Autore: Ramsden Jeremy
• Pubblicazione: Cham, Switzerland : , : Springer, , [2023]; ©2023
• Edizione: Fourth edition.
• Descrizione fisica: 1 online resource (401 pages)
• Disciplina: 570.285
• Soggetto topico: Bioinformatics
• Nota di bibliografia: Includes bibliographical references and index.
• Nota di contenuto: Intro -- Preface to the Fourth Edition -- Preface to the Third Edition -- Preface to the Second Edition -- Preface to the First Edition -- Contents -- 1 Introduction -- 1.1 What is Bioinformatics? -- 1.2 What Can Bioinformatics Do? -- 1.3 An Ontology of Bioinformatics -- 1.4 The Organization of This Book -- References -- Part I Overview -- 2 Genotype, Phenotype, and Environment -- References -- 3 Regulation and Control -- 3.1 The Concept of Machine -- 3.2 Regulation -- 3.3 Cybernetics -- 3.4 Adaptation -- 3.5 The Integrating Rôle of Directive Correlation -- 3.6 Timescales of Adaptation -- 3.7 The Architecture of Functional Systems -- 3.8 Autonomy and Heterarchical Architecture -- 3.9 Biological Information Processing -- References -- 4 Evolution -- 4.1 Phylogeny and Evolution -- 4.1.1 Group and Kin Selection -- 4.1.2 Models of Evolution -- 4.2 Evolutionary Systems -- 4.3 Evolutionary Computing -- 4.4 Concluding Remarks on Evolution -- References -- 5 Origins of Life and Earth Prehistory -- References -- Part II Information -- 6 The Nature of Information -- 6.1 Structure and Quantity -- 6.1.1 The Generation of Information -- 6.1.2 Conditional and Unconditional Information -- 6.1.3 Experiments and Observations -- 6.2 Constraint -- 6.2.1 The Value of Information -- 6.2.2 The Quality of Information -- 6.3 Accuracy, Meaning, and Effect -- 6.3.1 Accuracy -- 6.3.2 Meaning -- 6.3.3 Effect -- 6.3.4 Significs -- 6.4 Further Remarks on Information Generation and Reception -- 6.5 Summary -- References -- 7 The Transmission of Information -- 7.1 The Capacity of a Channel -- 7.2 Coding -- 7.3 Decoding -- 7.4 Compression -- 7.4.1 Use of Compression to Measure Distance -- 7.4.2 Ergodicity -- 7.5 Noise -- 7.6 Error Correction -- 7.7 Summary -- References -- 8 Sets and Combinatorics -- 8.1 The Notion of Set -- 8.2 Combinatorics. ; 8.2.1 Ordered Sampling with Replacement -- 8.2.2 Ordered Sampling Without Replacement -- 8.2.3 Unordered Sampling Without Replacement -- 8.2.4 Unordered Sampling With Replacement -- 8.3 The Binomial Theorem -- 9 Probability and Likelihood -- 9.1 The Notion of Probability -- 9.2 Fundamentals -- 9.2.1 Generalized Union -- 9.2.2 Conditional Probability -- 9.2.3 Bernoulli Trials -- 9.3 Moments of Distributions -- 9.3.1 Runs -- 9.3.2 The Hypergeometric Distribution -- 9.3.3 The Law of Large Numbers -- 9.3.4 Additive and Multiplicative Processes -- 9.4 Likelihood -- References -- 10 Statistics and Causation -- 10.1 A Brief Outline of Statistics -- 10.2 The Calculus of Causation -- References -- 11 Randomness and Complexity -- 11.1 Random Processes -- 11.2 Markov Chains -- 11.3 Random Walks -- 11.4 The Generation of Noise -- 11.5 Complexity -- 11.6 Biological Complexity -- References -- 12 Systems and Networks -- 12.1 General Systems Theory -- 12.1.1 Automata -- 12.1.2 Cellular Automata -- 12.1.3 Percolation -- 12.1.4 Systems Biology -- 12.2 Networks (Graphs) -- 12.2.1 Trees -- 12.2.2 Complexity Parameters of Networks -- 12.2.3 Dynamical Properties -- 12.3 Synergetics -- 12.4 Self-organization -- References -- 13 Useful Algorithms -- 13.1 Pattern Recognition -- 13.2 Botryology -- 13.2.1 Clustering -- 13.2.2 Principal Component and Linear Discriminant Analyses -- 13.2.3 Wavelets -- 13.3 Multidimensional Scaling and Seriation -- 13.4 Visualization -- 13.5 The Maximum Entropy Method -- References -- Part III Biology -- 14 The Nature of Living Things -- 14.1 The Cell -- 14.2 Mitochondria -- 14.3 Metabolism -- 14.4 The Cell Cycle -- 14.4.1 The Chromosome -- 14.4.2 The Structures of Genome and Genes -- 14.4.3 The C-Value Paradox -- 14.4.4 The Structure of the Chromosome -- 14.5 Cancer -- 14.6 The Immune System -- 14.7 Molecular Mechanisms -- 14.7.1 Replication. ; 14.7.2 Proofreading and Repair -- 14.7.3 Recombination -- 14.7.4 Summary of Sources of Genome Variation -- 14.8 Gene Expression -- 14.8.1 Transcription -- 14.8.2 Regulation of Transcription -- 14.8.3 Prokaryotic Transcriptional Regulation -- 14.8.4 Eukaryotic Transcriptional Regulation -- 14.8.5 mRNA Processing -- 14.8.6 Translation -- 14.9 Ontogeny (Development) -- 14.9.1 Stem cells -- 14.9.2 Epigenesis -- 14.9.3 The Epigenetic Landscape -- 14.9.4 ps: [/EMC pdfmark [/objdef Equ /Subtype /Span /ActualText (r) /StPNE pdfmark [/StBMC pdfmarkto.ps: [/EMC pdfmark [/Artifact < -- < -- /Type /Pagination> -- > -- /BDC pdfmark rps: [/EMC pdfmark [/StBMC pdfmark ps: [/EMC pdfmark [/StPop pdfmark [/StBMC pdfmark and ps: [/EMC pdfmark [/objdef Equ /Subtype /Span /ActualText (upper K) /StPNE pdfmark [/StBMC pdfmarkto.ps: [/EMC pdfmark [/Artifact < -- < -- /Type /Pagination> -- > -- /BDC pdfmark Kps: [/EMC pdfmark [/StBMC pdfmark ps: [/EMC pdfmark [/StPop pdfmark [/StBMC pdf -- 14.9.5 Homeotic Genes -- References -- Chapter15TheMoleculesofLife -- 15.1MoleculesandSupramolecularStructure -- 15.1MoleculesandSupramolecularStructure -- thletterofthealphabet.Thenextstageofcomplexityistoconsidermolecules(Table15.2)andmacromolecules(Table15.3).Thisisstillhighlyreductionist,however,itcorrespondstocalculatingShannonentropyfromthevocabularyofMacbeth.Wordsare,however,groupedintosentences,which,inturn,arearrangedintoparagraphs.Thecellisanalogouslyhighlystructured-moleculesaregroupedintosupramolecularcomplexes,which,inturn,areassembledintoorganelles.Thisstructure,someofwhichisvisibleintheopticalmicroscope,butwhichmostlyneedsthehigherre -- . -- 15.1MoleculesandSupramolecularStructure -- Element -- 500 -- Notypes -- Element -- 1600 -- H -- Element -- . -- 15.2Water -- 10nm -- . -- Density -- . -- . -- 15.3DNA -- . -- TheO-Hinfraredspectrum(ofHODinliquidD. ; Bondedandnonbondedionsareinequilibrium: -- atroomtemperatureorabout2.4kJ/mol) -- . -- Fig.15.2PolymerizedDNA.Theso-called -- Fig.15.2PolymerizedDNA.Theso-called -- endisatthelowerright(afterAgeno,1967 -- reproducedwithpermissionoftheAccademiadeiLincei) -- to -- Fig.15.2PolymerizedDNA.Theso-called -- Fig.15.3Thehydrogen-bondingpatternsofcomplementarybases(thymine[T],adenine[A],gua-nine[G],cytosine[C],movingroundclockwisefromtheupperleft)(afterAgeno,1967 -- reproducedwithpermissionoftheAccademiadeiLincei).InRNA,uracil(U)replacesthymine(i.e.,themethylgrouponthebaseisreplacedbyhydrogen)andtheribosehasahydroxylgroup.ThelowerpairisdenotedbyCpG(Sect.14.8.4) -- Fig.15.3Thehydrogen-bondingpatternsofcomplementarybases(thymine[T],adenine[A],gua-nine[G],cytosine[C],movingroundclockwisefromtheupperleft)(afterAgeno,1967 -- reproducedwithpermissionoftheAccademiadeiLincei).InRNA,uracil(U)replacesthymine(i.e.,themethylgrouponthebaseisreplacedbyhydrogen)andtheribosehasahydroxylgroup.ThelowerpairisdenotedbyCpG(Sect.14.8.4) -- . -- Asexpectedfromtheiraromaticstructure,thebasesareplanar.Figure15.4showstheformationofthedoublehelix.Thegenesofmostorganismsareformedbysuchadoublehelix.ThemeltingoftheH-bondsasthetemperatureisraisedishighly coöperative(duetotherepulsiveelectrostaticforcebetweenthechargedphosphategroups).Onaverage,theseparationintosinglestrandedDNAoccursatabout80 -- Fig.15.3Thehydrogen-bondingpatternsofcomplementarybases(thymine[T],adenine[A],gua-nine[G],cytosine[C],movingroundclockwisefromtheupperleft)(afterAgeno,1967 -- reproducedwithpermissionoftheAccademiadeiLincei).InRNA,uracil(U)replacesthymine(i.e.,themethylgrouponthebaseisreplacedbyhydrogen)andtheribosehasahydroxylgroup.ThelowerpairisdenotedbyCpG(Sect.14.8.4) -- Table15.5summarizessomesigni cantdiscoveriesrelatingtoDNA. -- Discoveryorevent -- Example:UCSCGenomeBrowser -- Crick -- Discoveryorevent. ; Atetranucleotidestructureelucidated -- 1944 -- Principalworker(s) -- Discoveryorevent -- where -- (15.4) -- isBoltz-mann'sconstant,and -- . -- 15.4RNA -- . -- 15.4RNA -- .Theconceptcanbeillustratedbyfocusingonloopclo-sure,consideredtobethemostimportantfoldingevent.Thepotentialenergyistheenthalpy(i.e.,thenumber -- RNAhas vemainfunctions:asamessenger(mRNA),actingasanintermediaryinproteinsynthesis -- asanenzyme(ribozymes) -- aspart(about60%byweight,therestbeingprotein)oftheribosome(rRNA) -- asthecarrierfortransferringaminoacidstothegrowingpolypeptidechainsynthesizedattheribosome(tRNA) -- andasamodulatorofDNA4andmRNAinteractions-smallinterferingRNA(siRNA -- seeSect.14.8.4). -- 15.4RNA -- Fig.15.5ApieceofRNA(fromtheQ -- Fig.15.5ApieceofRNA(fromtheQ -- 15.5Proteins -- Globularproteins -- Fig.15.5ApieceofRNA(fromtheQ -- whichmaybeverylarge,suchthattheyformgelsbyentanglement.Thepolypeptidebackboneisextensivelydecoratedwithrelativelyshortpolysac-charides.Typicallytheyactaslubricantsandengulfers(example:mucin) -- -- . -- . -- whichmaybeverylarge,suchthattheyformgelsbyentanglement.Thepolypeptidebackboneisextensivelydecoratedwithrelativelyshortpolysac-charides.Typicallytheyactaslubricantsandengulfers(example:mucin) -- -- . -- whicharealsoglobular,butpermanentlyembedded(transversally)inalipidbilayermembrane.Theymainlyfunctionaschannels,energyandsignaltransducers,andmotors(examples:ATPase,bacteriorhodopsin,andporin). -- whichmaybeverylarge,suchthattheyformgelsbyentanglement.Thepolypeptidebackboneisextensivelydecoratedwithrelativelyshortpolysac-charides.Typicallytheyactaslubricantsandengulfers(example:mucin) -- -- . -- 4.4 -- . -- . -- denotesabenzenering.Squarebracketsdenotearingstructure -- . -- Fig.15.6Hydrogen-bondingcapabilitiesofthepeptidebackboneandthepolarresidues(afterBakerandHubbard).Residuesnotshownareincapableofhydrogenbondformation. ; Fig.15.6Hydrogen-bondingcapabilitiesofthepeptidebackboneandthepolarresidues(afterBakerandHubbard).Residuesnotshownareincapableofhydrogenbondformation.
• Titolo autorizzato: Bioinformatics
• ISBN: 3-030-45607-2
• Formato: Materiale a stampa
• Livello bibliografico: Monografia
• Lingua di pubblicazione: Inglese
• Record Nr.: 9910746070703321
• Lo trovi qui: Univ. Federico II
• Serie: Computational biology.