Thisbookisrecommendedforuseassupplementarymaterialbothinsideandoutside classroomsorasaself-learningguideforstudents, scientists, andresearcherswhodealwith numericdatainmolecularbiologyandrelated?elds. Thosewhostartasbeginners, but desiretobeatanintermediatelevel, will?ndthisbookespeciallyusefulintheirlearning pathway. WewanttothankJohnWalker(serieseditor),PatrickMarton, DavidCasey, andAnne Meagher,(editorsatSpringerandHumana)andShanthyJaganathan(Integra-India). The followingpersonsprovidedusefuladviceandcommentsonselectionoftopics, referralto expertsineachtopic, and/orchapterreviewsthatwetrulyappreciate:StephenLooney(a former editor of this book), Stan Young, Dmitri Zaykin, Douglas Hawkins, Wei Pan, Alexandre Almeida, John Ho, Rebecca Doerge, Paula Trushin, Kevin Morgan, Jason Osborne, PeterWestfall, JennyXiang, Ya-linChiu, YolandaBarron, HuiboShao, Alvin Mushlin, andRonaldFanta. Drs. Bang, Zhou, andMazumdarwerepartiallysupported byClinicalTranslationalScienceCenter(CTSC)grant(UL1-RR024996). HeejungBang vii Contents Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi PARTIBASICSTATISTICS. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1. ExperimentalStatisticsforBiologicalSciences. . . . . . . . . . . . . . . . . . . 3 HeejungBangandMarieDavidian 2. NonparametricMethodsforMolecularBiology. . . . . . . . . . . . . . . . . . 105 KnutM. WittkowskiandTingtingSong 3. BasicsofBayesianMethods. . . . . . . . . . . . . . . . . . . . . . . . . . . . 155 SujitK. Ghosh 4. TheBayesiant-TestandBeyond . . . . . . . . . . . . . . . . . . . . . . . . . 179 MithatGönen PARTII DESIGNSANDMETHODSFORMOLECULARBIOLOGY. . . . . . . . . . 201 5. SampleSizeandPowerCalculationforMolecularBiologyStudies. . . . . . . . 203 Sin-HoJung 6. DesignsforLinkageAnalysisandAssociationStudiesofComplexDiseases. . . . 219 YuehuaCui, GengxinLi, ShaoyuLi, andRonglingWu 7. IntroductiontoEpigenomicsandEpigenome-WideAnalysis. . . . . . . . . . . 243 MelissaJ. FazzariandJohnM. Greally 8. Exploration, Visualization, andPreprocessingofHigh-DimensionalData. . . . 267 ZhijinWuandZhiqiangWu PARTIII STATISTICALMETHODSFORMICROARRAYDATA . . . . . . . . . . . . 285 9. IntroductiontotheStatisticalAnalysisofTwo-ColorMicroarrayData. . . . . . 287 MartinaBremer, EdwardHimelblau, andAndreasMadlung 10. BuildingNetworkswithMicroarrayData. . . . . . . . . . . . . . . . . . . . . 315 BradleyM. Broom, WareeRinsurongkawong, LajosPusztai, andKim-AnhDo PARTIV ADVANCEDORSPECIALIZEDMETHODSFORMOLECULARBIOLOGY. . 345 11. SupportVectorMachinesforClassi?cation:AStatisticalPortrait. . . . . . . . . 347 YoonkyungLee 12. AnOverviewofClusteringAppliedtoMolecularBiology . . . . . . . . . . . . 369 RebeccaNugentandMarinaMeila ix xContents 13. HiddenMarkovModelandItsApplicationsinMotifFindings. . . . . . . . . . 405 JingWuandJunXie 14. DimensionReductionforHigh-DimensionalData. . . . . . . . . . . . . . . . 417 LexinLi 15. IntroductiontotheDevelopmentandValidationofPredictiveBiomarker ModelsfromHigh-ThroughputDataSets . . . . . . . . . . . . . . . . . . . . 435 XutaoDengandFabienCampagne 16. Multi-geneExpression-basedStatisticalApproachestoPredicting Patients'ClinicalOutcomesandResponses. . . . . . . . . . . . . . . . . . . . 471 FengCheng, Sang-HoonCho, andJaeK. Lee 17. Two-StageTestingStrategiesforGenome-WideAssociationStudies inFamily-BasedDesigns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 485 AmyMurphy, ScottT. Weiss, andChristophLange 18. StatisticalMethodsforProteomics . . . . . . . . . . . . . . . . . . . . . . . . 497 KlausJung PARTVMETA-ANALYSISFORHIGH-DIMENSIONALDATA . . . . . . . . . . . . 509 19. StatisticalMethodsforIntegratingMultipleTypesofHigh-ThroughputData. . 511 YangXieandChulAhn 20. ABayesianHierarchicalModelforHigh-DimensionalMeta-analysis. . . . . . . 531 FeiLiu 21. MethodsforCombiningMultipleGenome-WideLinkageStudies. . . . . . . . 541 TreciaA. KippolaandStephanieA. Santorico PARTVI OTHERPRACTICALINFORMATION . . . . . . . . . . . . . . . . . . . . 561 22. ImprovedReportingofStatisticalDesignandAnalysis:Guidelines, Education, andEditorialPolicies. . . . . . . . . . . . . . . . . . . . . . . . . 563 MadhuMazumdar, SampritBanerjee, andHeatherL. VanEpps 23. StataCompanion. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 599 JenniferSousaBrennan SubjectIndex. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 627 Contributors CHULAHN• Division of Biostatistics, Department of Clinical Sciences, The Harold C. | Statistical Methods in Molecular Biology by Heejung Bang, Hardcover | Indigo Chapters