Bioinformatics for Systems Biology by Stephen Krawetz (English) Hardcover Book

Description: Bioinformatics for Systems Biology by Stephen Krawetz Estimated delivery 3-12 business days Format Hardcover Condition Brand New Description 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. Publisher Description 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...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. Details ISBN 1934115029 ISBN-13 9781934115022 Title Bioinformatics for Systems Biology Author Stephen Krawetz Format Hardcover Year 2009 Pages 639 Edition 2nd Publisher Humana Press Inc. GE_Item_ID:143832246; About Us Grand Eagle Retail is the ideal place for all your shopping needs! With fast shipping, low prices, friendly service and over 1,000,000 in stock items - you're bound to find what you want, at a price you'll love! Shipping & Delivery Times Shipping is FREE to any address in USA. Please view eBay estimated delivery times at the top of the listing. 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