Bioinformatics for Systems Biology (eBook, PDF)

Redaktion: Krawetz, Stephen

• Format: PDF

Produktbeschreibung

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-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. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181 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.

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Produktdetails

• Verlag: Humana Press
• Seitenzahl: 639
• Erscheinungstermin: 11. Dezember 2008
• Englisch
• ISBN-13: 9781597454407
• Artikelnr.: 37363791

Inhaltsangabe

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.