Bioinformatics for Systems Biology
Seiten
2009
|
2nd ed. 2009
Humana Press Inc. (Verlag)
978-1-934115-02-2 (ISBN)
Humana Press Inc. (Verlag)
978-1-934115-02-2 (ISBN)
Bioinformatics for Systems Biology bridges and unifies many disciplines. It presents the life scientist, computational biologist, and mathematician with a common framework. Only by linking the groups together may the true life sciences revolution move forward.
With the completion of the human genome project, followed by the rise in high-throughput technologies like the various microarray and now high throughput genomic sequencing platforms,weexperiencedthebirthofSystemsBiologyafteritslonggestation. Thisrevolutionis markedbyachangeintheresearchparadigmfromthesinglesmall-scaleexperiment,i. e. ,following thechangeofacomponentinamulticomponentsystem,toonethatattemptstosimultaneously monitorthechangeoftensofthousandsofmoleculeswithinthisbody. Thisclearlynecessitatesthe unparalleleduseofproject-specificinformatictools,which,todate,requiresanunprecedentedlevel ofdevelopmenttocollect,manageandminethedataforinterestingassociations. Tobegintounderstandthisinformationwenowrelyonstatisticalanalysistoaidinourselection ofthefruitfromthetree. However,thisoftentakesusonajourneyintoanewfieldforwhichweare notyetprepared. SamuelJohnson(1709-1784)foreshadowedthedilemmawewouldfaceand characterizeditasfollows:"Knowledgeisoftwokinds. Weknowasubjectourselves,orweknow wherewecanfindinformationonit. "Itisforthelatterthatweroutinelyturntotheliterature.
The rateofgrowthoftheliteratureparallelsthatofsequencingdataandthearraydataplacingan almostimpossibletaskbeforeeachinvestigator. Topartiallyeasethisburdenweareagainturning towardsdevelopinginformaticaidsthatminetheliteratureanddatatodevelopsummariesand associationstodirectlyaddressthequestionsposedandthenewhypothesesthataretobetested. Althoughmoreclearlyarticulated,weagainfacesimilarchallengesasthosetackledduringthe courseofthehumangenomeproject. Itisessentialthatthetrainingofthebiologistandcomput- scientistoccurinaninterdisciplinaryenvironmentofcross-fertilization. Withthisgoalinmindthe textbook"BioinformaticsforSystemsBiology"wasundertaken. WebeginthisexplorationwithPartI,toprovidethecomputerscientistwithanintroductiontothe underlyingprinciplesofcellbiology. ThisisfollowedbyabriefintroductioninPartIIasameansfor thebiologisttobecomefamiliarwithconceptsandthestatisticalanalysisoflargedatasets. PartIII thendescribes,todate,thebestcharacterizeduseofthemicroarrayplatformthatisnowmoving towardswholegenomeanalysis. Withallofthisdata,howdowebeginanalysisforcommonelements guidingtheunderlyingprinciples?ThisisdiscussedinPartIVwhichleadstoPartVandPartVIto test,insilico,therelationshipsonawidescaleinordertoassesstheirapplicability.
Upondeveloping theassociations,PartVIIaskshowdoesthisinformationrelatetowhatwasmeasured?Asthesebasic principlesaredevelopedfroman"omics"drivenbiologicalsystemsapproach,theyareappliedin PartVIIItotranslationalmedicine. Anexcellentexampleisthenewterm"personalizedmedicine" thatisbeginningtoreverberateinclinicalcare. ItistheculminationoftheSystemsBiologyrevolution wheretechnologicaladvancesandcross-fertilizationhavedriventhefieldtomaturetothepoint whereitisbeingincorporatedinatruebench-to-bedsidemanner. Asyoureadthechapters,youwillfindthattheycanstandalone,yetcanbecombinedto emphasizetheintegralroleofinformaticsinSystemsBiology. Mostofthefiguresandtablesarein greyscale. IwouldencourageyoutoviewthosethatbenefitfromcolorontheaccompanyingCD. ThematerialcontainedontheCDprovidesanexcellentsourceofslidesforyourlecturesand presentations. v vi Preface Thechapter-relatedGlossaryandAbbreviationssectionwillassistinfamiliarizingyouwiththe terms. Youwillalsofindtheliteratureandsuggestedreadingsections,includingkeyreferences, veryusefulasyoudelveintothesubjectmatter. Technology,byitsverymeaningimpliesrefinement and change.
The informatics approaches used in systems biology are continually subject to refinement. Withthisreality,youareencouragedtoutilizethewebsiteinformationprovidedin variouschapterstohelpaccessthemostcurrentinformationandresourcesavailable. AsSystems Biologydevelopsweareabletowitnessgrowingpainsandmilestones. Withcontinuedinformatic andbiologicalcross-fertilization,advancementsinSystemsBiologywillrevolutionizepersonalized medicineansweringquestionsbyintegratinginformationinunexpectedways. Contents PartI LifeofaCellandItsAnalysis...1 1 StructureandFunctionoftheNucleusandCellOrganelles...3 JonHolyandEdPerkins 2 TranscriptionandtheControlofGeneExpression...33 NadineWiper-BergeronandIlonaS. Skerjanc 3 RNAProcessingandTranslation...51 ChristinaKaramboulas,NadineWiper-Bergeron,andIlonaS. Skerjanc 4 DNAReplication,Recombination,andRepair...67 LindaB. Bloom 5 CellSignaling...89 DanielA. RappoleeandD. RandallArmant 6 EpigeneticsofSpermiogenesis-drivenbiologicalsystemsapproach,theyareappliedin PartVIIItotranslationalmedicine. Anexcellentexampleisthenewterm"personalizedmedicine" thatisbeginningtoreverberateinclinicalcare.
ItistheculminationoftheSystemsBiologyrevolution wheretechnologicaladvancesandcross-fertilizationhavedriventhefieldtomaturetothepoint whereitisbeingincorporatedinatruebench-to-bedsidemanner. Asyoureadthechapters,youwillfindthattheycanstandalone,yetcanbecombinedto emphasizetheintegralroleofinformaticsinSystemsBiology. Mostofthefiguresandtablesarein greyscale. IwouldencourageyoutoviewthosethatbenefitfromcolorontheaccompanyingCD. ThematerialcontainedontheCDprovidesanexcellentsourceofslidesforyourlecturesand presentations. v vi Preface Thechapter-relatedGlossaryandAbbreviationssectionwillassistinfamiliarizingyouwiththe terms. Youwillalsofindtheliteratureandsuggestedreadingsections,includingkeyreferences, veryusefulasyoudelveintothesubjectmatter. Technology,byitsverymeaningimpliesrefinement and change. The informatics approaches used in systems biology are continually subject to refinement. Withthisreality,youareencouragedtoutilizethewebsiteinformationprovidedin variouschapterstohelpaccessthemostcurrentinformationandresourcesavailable. AsSystems Biologydevelopsweareabletowitnessgrowingpainsandmilestones.
Withcontinuedinformatic andbiologicalcross-fertilization,advancementsinSystemsBiologywillrevolutionizepersonalized medicineansweringquestionsbyintegratinginformationinunexpectedways. Contents PartI LifeofaCellandItsAnalysis...1 1 StructureandFunctionoftheNucleusandCellOrganelles...3 JonHolyandEdPerkins 2 TranscriptionandtheControlofGeneExpression...33 NadineWiper-BergeronandIlonaS. Skerjanc 3 RNAProcessingandTranslation...51 ChristinaKaramboulas,NadineWiper-Bergeron,andIlonaS. Skerjanc 4 DNAReplication,Recombination,andRepair...67 LindaB. Bloom 5 CellSignaling...89 DanielA. RappoleeandD. RandallArmant 6 EpigeneticsofSpermiogenesis-CombiningInSilicoandProteomicApproaches intheMouseModel...105 SophieRousseauxandMyriamFerro 7 GenomicToolsforAnalyzingTranscriptionalRegulatoryNetworks...119 JohnJ. Wyrick PartII StatisticalToolsandTheirApplication...137 8 ProbabilityandHypothesisTesting...139 MichaelL. Kruger 9 StochasticModelsforBiologicalPatterns...151 GautamB. Singh 10 PopulationGenetics...163 JillS. Barnholtz-SloanandHemantK. Tiwari 11 StatisticalToolsforGeneExpressionAnalysisandSystemsBiology andRelatedWebResources...1
81 ChiaraRomualdiandGerolamoLanfranchi vii viii Contents PartIII TranscriptomeAnalysis...207 12 WhatGoesinisWhatComesOut:HowtoDesignandImplementaSuccessful MicroarrayExperiment...209 JeffreyA. LoebandThomasL. Beaumont 13 ToolsandApproachesforanEnd-to-EndExpressionArrayAnalysis...227 AdrianE. PlattsandStephenA. Krawetz 14 AnalysisofAlternativeSplicingwithMicroarrays...267 JingyiHui,ShivendraKishore,AmitKhanna,andStefanStamm PartIV StructuralandFunctionalSequenceAnalysis...281 15 AnIntroductiontoMultipleSequenceAlignment-andtheT-CoffeeShop. BeyondJust AligningSequences:HowGoodcanyouMakeyourAlignment,andsoWhat?...283 StevenM. Thompson 16 ASpectrumofPhylogenetic-BasedApproachesforPredictingProtein FunctionalSites...315 DukkaBahadurK. C. andDennisR. Livesay 17 TheRoleofTranscriptionFactorBindingSitesinPromotersandTheir InSilicoDetection...339 ThomasWerner 18 InSilicoDiscoveryofDNARegulatorySitesandModules...353 PanayiotisV. Benos PartV LiteratureMiningforAssociationandMeaning...367 19 MiningtheResearchLiteratureinSystemsBiology...369 KeirT. Reavie 20 GoPubMed:ExploringPubMedwithOntologicalBackgroundKnowledge...385 HeikoDietze,DimitraAlexopoulou,MichaelR.
With the completion of the human genome project, followed by the rise in high-throughput technologies like the various microarray and now high throughput genomic sequencing platforms,weexperiencedthebirthofSystemsBiologyafteritslonggestation. Thisrevolutionis markedbyachangeintheresearchparadigmfromthesinglesmall-scaleexperiment,i. e. ,following thechangeofacomponentinamulticomponentsystem,toonethatattemptstosimultaneously monitorthechangeoftensofthousandsofmoleculeswithinthisbody. Thisclearlynecessitatesthe unparalleleduseofproject-specificinformatictools,which,todate,requiresanunprecedentedlevel ofdevelopmenttocollect,manageandminethedataforinterestingassociations. Tobegintounderstandthisinformationwenowrelyonstatisticalanalysistoaidinourselection ofthefruitfromthetree. However,thisoftentakesusonajourneyintoanewfieldforwhichweare notyetprepared. SamuelJohnson(1709-1784)foreshadowedthedilemmawewouldfaceand characterizeditasfollows:"Knowledgeisoftwokinds. Weknowasubjectourselves,orweknow wherewecanfindinformationonit. "Itisforthelatterthatweroutinelyturntotheliterature.
The rateofgrowthoftheliteratureparallelsthatofsequencingdataandthearraydataplacingan almostimpossibletaskbeforeeachinvestigator. Topartiallyeasethisburdenweareagainturning towardsdevelopinginformaticaidsthatminetheliteratureanddatatodevelopsummariesand associationstodirectlyaddressthequestionsposedandthenewhypothesesthataretobetested. Althoughmoreclearlyarticulated,weagainfacesimilarchallengesasthosetackledduringthe courseofthehumangenomeproject. Itisessentialthatthetrainingofthebiologistandcomput- scientistoccurinaninterdisciplinaryenvironmentofcross-fertilization. Withthisgoalinmindthe textbook"BioinformaticsforSystemsBiology"wasundertaken. WebeginthisexplorationwithPartI,toprovidethecomputerscientistwithanintroductiontothe underlyingprinciplesofcellbiology. ThisisfollowedbyabriefintroductioninPartIIasameansfor thebiologisttobecomefamiliarwithconceptsandthestatisticalanalysisoflargedatasets. PartIII thendescribes,todate,thebestcharacterizeduseofthemicroarrayplatformthatisnowmoving towardswholegenomeanalysis. Withallofthisdata,howdowebeginanalysisforcommonelements guidingtheunderlyingprinciples?ThisisdiscussedinPartIVwhichleadstoPartVandPartVIto test,insilico,therelationshipsonawidescaleinordertoassesstheirapplicability.
Upondeveloping theassociations,PartVIIaskshowdoesthisinformationrelatetowhatwasmeasured?Asthesebasic principlesaredevelopedfroman"omics"drivenbiologicalsystemsapproach,theyareappliedin PartVIIItotranslationalmedicine. Anexcellentexampleisthenewterm"personalizedmedicine" thatisbeginningtoreverberateinclinicalcare. ItistheculminationoftheSystemsBiologyrevolution wheretechnologicaladvancesandcross-fertilizationhavedriventhefieldtomaturetothepoint whereitisbeingincorporatedinatruebench-to-bedsidemanner. Asyoureadthechapters,youwillfindthattheycanstandalone,yetcanbecombinedto emphasizetheintegralroleofinformaticsinSystemsBiology. Mostofthefiguresandtablesarein greyscale. IwouldencourageyoutoviewthosethatbenefitfromcolorontheaccompanyingCD. ThematerialcontainedontheCDprovidesanexcellentsourceofslidesforyourlecturesand presentations. v vi Preface Thechapter-relatedGlossaryandAbbreviationssectionwillassistinfamiliarizingyouwiththe terms. Youwillalsofindtheliteratureandsuggestedreadingsections,includingkeyreferences, veryusefulasyoudelveintothesubjectmatter. Technology,byitsverymeaningimpliesrefinement and change.
The informatics approaches used in systems biology are continually subject to refinement. Withthisreality,youareencouragedtoutilizethewebsiteinformationprovidedin variouschapterstohelpaccessthemostcurrentinformationandresourcesavailable. AsSystems Biologydevelopsweareabletowitnessgrowingpainsandmilestones. Withcontinuedinformatic andbiologicalcross-fertilization,advancementsinSystemsBiologywillrevolutionizepersonalized medicineansweringquestionsbyintegratinginformationinunexpectedways. Contents PartI LifeofaCellandItsAnalysis...1 1 StructureandFunctionoftheNucleusandCellOrganelles...3 JonHolyandEdPerkins 2 TranscriptionandtheControlofGeneExpression...33 NadineWiper-BergeronandIlonaS. Skerjanc 3 RNAProcessingandTranslation...51 ChristinaKaramboulas,NadineWiper-Bergeron,andIlonaS. Skerjanc 4 DNAReplication,Recombination,andRepair...67 LindaB. Bloom 5 CellSignaling...89 DanielA. RappoleeandD. RandallArmant 6 EpigeneticsofSpermiogenesis-drivenbiologicalsystemsapproach,theyareappliedin PartVIIItotranslationalmedicine. Anexcellentexampleisthenewterm"personalizedmedicine" thatisbeginningtoreverberateinclinicalcare.
ItistheculminationoftheSystemsBiologyrevolution wheretechnologicaladvancesandcross-fertilizationhavedriventhefieldtomaturetothepoint whereitisbeingincorporatedinatruebench-to-bedsidemanner. Asyoureadthechapters,youwillfindthattheycanstandalone,yetcanbecombinedto emphasizetheintegralroleofinformaticsinSystemsBiology. Mostofthefiguresandtablesarein greyscale. IwouldencourageyoutoviewthosethatbenefitfromcolorontheaccompanyingCD. ThematerialcontainedontheCDprovidesanexcellentsourceofslidesforyourlecturesand presentations. v vi Preface Thechapter-relatedGlossaryandAbbreviationssectionwillassistinfamiliarizingyouwiththe terms. Youwillalsofindtheliteratureandsuggestedreadingsections,includingkeyreferences, veryusefulasyoudelveintothesubjectmatter. Technology,byitsverymeaningimpliesrefinement and change. The informatics approaches used in systems biology are continually subject to refinement. Withthisreality,youareencouragedtoutilizethewebsiteinformationprovidedin variouschapterstohelpaccessthemostcurrentinformationandresourcesavailable. AsSystems Biologydevelopsweareabletowitnessgrowingpainsandmilestones.
Withcontinuedinformatic andbiologicalcross-fertilization,advancementsinSystemsBiologywillrevolutionizepersonalized medicineansweringquestionsbyintegratinginformationinunexpectedways. Contents PartI LifeofaCellandItsAnalysis...1 1 StructureandFunctionoftheNucleusandCellOrganelles...3 JonHolyandEdPerkins 2 TranscriptionandtheControlofGeneExpression...33 NadineWiper-BergeronandIlonaS. Skerjanc 3 RNAProcessingandTranslation...51 ChristinaKaramboulas,NadineWiper-Bergeron,andIlonaS. Skerjanc 4 DNAReplication,Recombination,andRepair...67 LindaB. Bloom 5 CellSignaling...89 DanielA. RappoleeandD. RandallArmant 6 EpigeneticsofSpermiogenesis-CombiningInSilicoandProteomicApproaches intheMouseModel...105 SophieRousseauxandMyriamFerro 7 GenomicToolsforAnalyzingTranscriptionalRegulatoryNetworks...119 JohnJ. Wyrick PartII StatisticalToolsandTheirApplication...137 8 ProbabilityandHypothesisTesting...139 MichaelL. Kruger 9 StochasticModelsforBiologicalPatterns...151 GautamB. Singh 10 PopulationGenetics...163 JillS. Barnholtz-SloanandHemantK. Tiwari 11 StatisticalToolsforGeneExpressionAnalysisandSystemsBiology andRelatedWebResources...1
81 ChiaraRomualdiandGerolamoLanfranchi vii viii Contents PartIII TranscriptomeAnalysis...207 12 WhatGoesinisWhatComesOut:HowtoDesignandImplementaSuccessful MicroarrayExperiment...209 JeffreyA. LoebandThomasL. Beaumont 13 ToolsandApproachesforanEnd-to-EndExpressionArrayAnalysis...227 AdrianE. PlattsandStephenA. Krawetz 14 AnalysisofAlternativeSplicingwithMicroarrays...267 JingyiHui,ShivendraKishore,AmitKhanna,andStefanStamm PartIV StructuralandFunctionalSequenceAnalysis...281 15 AnIntroductiontoMultipleSequenceAlignment-andtheT-CoffeeShop. BeyondJust AligningSequences:HowGoodcanyouMakeyourAlignment,andsoWhat?...283 StevenM. Thompson 16 ASpectrumofPhylogenetic-BasedApproachesforPredictingProtein FunctionalSites...315 DukkaBahadurK. C. andDennisR. Livesay 17 TheRoleofTranscriptionFactorBindingSitesinPromotersandTheir InSilicoDetection...339 ThomasWerner 18 InSilicoDiscoveryofDNARegulatorySitesandModules...353 PanayiotisV. Benos PartV LiteratureMiningforAssociationandMeaning...367 19 MiningtheResearchLiteratureinSystemsBiology...369 KeirT. Reavie 20 GoPubMed:ExploringPubMedwithOntologicalBackgroundKnowledge...385 HeikoDietze,DimitraAlexopoulou,MichaelR.
Life of a Cell and Its Analysis.- Structure and Function of the Nucleus and Cell Organelles.- Transcription and the Control of Gene Expression.- RNA Processing and Translation.- DNA Replication, Recombination, and Repair.- Cell Signaling.- Epigenetics of Spermiogenesis.- Genomic Tools for Analyzing Transcriptional Regulatory Networks.- Statistical Tools and Their Application.- Probability and Hypothesis Testing.- Stochastic Models for Biological Patterns.- Population Genetics.- Statistical Tools for Gene Expression Analysis and Systems Biology and Related Web Resources.- Transcriptome Analysis.- What Goes in is What Comes Out: How to Design and Implement a Successful Microarray Experiment.- Tools and Approaches for an End-to-End Expression Array Analysis.- Analysis of Alternative Splicing with Microarrays.- Structural and Functional Sequence Analysis.- An Introduction to Multiple Sequence Alignment — and the T-Coffee Shop. Beyond Just Aligning Sequences: How Good can you Make your Alignment, and so What?.- A Spectrum of Phylogenetic-Based Approaches for Predicting Protein Functional Sites.- The Role of Transcription Factor Binding Sites in Promoters and Their In Silico Detection.- In Silico Discovery of DNA Regulatory Sites and Modules.- Literature Mining for Association and Meaning.- Mining the Research Literature in Systems Biology.- GoPubMed: Exploring PubMed with Ontological Background Knowledge.- BiblioSphere — Hypothesis Generation in Regulatory Network Analysis.- Biological Knowledge Extraction.- Genomic Databases.- Using KEGG in the Transition from Genomics to Chemical Genomics.- Ensembl.- Management of Spatially Organized Biological Data using EMAGE.- Equality of the Sexes? Parent-of-Origin Effects on Transcription and de novo Mutations.- BiologicalNetworks.- Methods for Structural Inference and Functional Module Identification in Intracellular Networks.- Methods for Dynamical Inference in Intracellular Networks.- ASIAN: Network Inference Web Server.- Bridging the Gap.- Bioinformatics for Metabolomics.- Virtual Reality Meets Functional Genomics.- Systems Biology of Personalized Medicine.
| Zusatzinfo | X, 740 p. 196 illus., 6 illus. in color. |
|---|---|
| Verlagsort | Totowa, NJ |
| Sprache | englisch |
| Maße | 193 x 260 mm |
| Themenwelt | Informatik ► Weitere Themen ► Bioinformatik |
| Naturwissenschaften ► Biologie ► Genetik / Molekularbiologie | |
| ISBN-10 | 1-934115-02-9 / 1934115029 |
| ISBN-13 | 978-1-934115-02-2 / 9781934115022 |
| Zustand | Neuware |
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