Bioinformatics algorithms : techniques and applications PDF
Preview Bioinformatics algorithms : techniques and applications
BIOINFORMATICS ALGORITHMS Techniques and Applications Editedby IonI.Ma˘ndoiuandAlexanderZelikovsky AJOHNWILEY&SONS,INC.,PUBLICATION BIOINFORMATICS ALGORITHMS BIOINFORMATICS ALGORITHMS Techniques and Applications Editedby IonI.Ma˘ndoiuandAlexanderZelikovsky AJOHNWILEY&SONS,INC.,PUBLICATION Copyright©2008byJohnWiley&Sons,Inc.Allrightsreserved. PublishedbyJohnWiley&Sons,Inc.,Hoboken,NewJersey PublishedsimultaneouslyinCanada Nopartofthispublicationmaybereproduced,storedinaretrievalsystemortransmittedinanyformor byanymeans,electronic,mechanical,photocopying,recording,scanningorotherwise,exceptas permittedunderSections107or108ofthe1976UnitedStatesCopyrightAct,withouteithertheprior writtenpermissionofthePublisher,orauthorizationthroughpaymentoftheappropriateper-copyfeeto theCopyrightClearanceCenter,Inc.,222RosewoodDrive,Danvers,MA01923,978-750-8400,fax 978-646-8600,oronthewebatwww.copyright.com.RequeststothePublisherforpermissionshouldbe addressedtothePermissionsDepartment,JohnWiley&Sons,Inc.,111RiverStreet,Hoboken,NJ 07030,(201)-748-6011,fax(201)-748-6008. LimitofLiability/DisclaimerofWarranty:Whilethepublisherandauthorhaveusedtheirbesteffortsin preparingthisbook,theymakenorepresentationsorwarrantieswithrespecttotheaccuracyor completenessofthecontentsofthisbookandspecificallydisclaimanyimpliedwarrantiesof merchantabilityorfitnessforaparticularpurpose.Nowarrantymaybecreatedorextendedbysales representativesorwrittensalesmaterials.Theadviceandstrategiescontainedhereinmaynotbesuitable foryoursituation.Youshouldconsultwithaprofessionalwhereappropriate.Neitherthepublishernor authorshallbeliableforanylossofprofitoranyothercommericaldamages,includingbutnotlimitedto special,incidental,consequential,orotherdamages. ForgeneralinformationonourotherproductsandservicespleasecontactourCustomerCareDepartment withintheU.S.at877-762-2974,outsidetheU.S.at317-572-3993orfax317-572-4002. Wileyalsopublishesitsbooksinavarietyofelectronicformats.Somecontentthatappearsinprint, however,maynotavailableinelectronicformat. LibraryofCongressCataloging-in-PublicationData: Bioinformaticsalgorithms:techniquesandapplications/editedbyIonI. MandoiuandAlexanderZelikovsky. p.cm. ISBN978-0-470-09773-1(cloth) 1. Bioinformatics.2. Algorithms. I.Mandoiu,Ion.II.Zelikovsky, Alexander. QH324.2B5472 2008 572.80285–dc22 2007034307 PrintedintheUnitedStatesofAmerica 10 9 8 7 6 5 4 3 2 1 CONTENTS Preface ix Contributors xi 1 EducatingBiologistsinthe21stCentury:BioinformaticsScientists versusBioinformaticsTechnicians 1 PavelPevzner PARTI TECHNIQUES 7 2 DynamicProgrammingAlgorithmsforBiologicalSequence andStructureComparison 9 YuzhenYeandHaixuTang 3 GraphTheoreticalApproachestoDelineateDynamics ofBiologicalProcesses 29 TeresaM.PrzytyckaandElenaZotenko 4 AdvancesinHiddenMarkovModelsforSequenceAnnotation 55 BronˇaBrejova´,DanielG.Brown,andToma´sˇVinarˇ 5 Sorting-andFFT-BasedTechniquesintheDiscoveryofBiopatterns 93 SudhaBalla,SanguthevarRajasekaran,andJaimeDavila v vi CONTENTS 6 ASurveyofSeedingforSequenceAlignment 117 DanielG.Brown 7 TheComparisonofPhylogeneticNetworks:Algorithms andComplexity 143 PaolaBonizzoni,GianlucaDellaVedova,RiccardoDondi,and GiancarloMauri PARTII GENOMEANDSEQUENCEANALYSIS 175 8 FormalModelsofGeneClusters 177 AnneBergeron,CedricChauve,andYannickGingras 9 IntegerLinearProgrammingTechniquesforDiscovering ApproximateGeneClusters 203 SvenRahmannandGunnarW.Klau 10 EfficientCombinatorialAlgorithmsforDNA SequenceProcessing 223 BhaskarDasGuptaandMing-YangKao 11 AlgorithmsforMultiplexPCRPrimerSetSelectionwith AmplificationLengthConstraints 241 K.M.Konwar,I.I.Ma˘ndoiu,A.C.Russell,andA.A.Shvartsman 12 RecentDevelopmentsinAlignmentandMotifFinding forSequencesandNetworks 259 Sing-HoiSze PARTIII MICROARRAYDESIGNANDDATAANALYSIS 277 13 AlgorithmsforOligonucleotideMicroarrayLayout 279 Se´rgioA.DeCarvalhoJr.andSvenRahmann 14 ClassificationAccuracyBasedMicroarrayMissingValue Imputation 303 YiShi,ZhipengCai,andGuohuiLin 15 Meta-AnalysisofMicroarrayData 329 SaumyadiptaPyne,SteveSkiena,andBruceFutcher CONTENTS vii PARTIV GENETICVARIATIONANALYSIS 353 16 PhasingGenotypesUsingaHiddenMarkovModel 355 P.Rastas,M.Koivisto,H.Mannila,andE.Ukkonen 17 AnalyticalandAlgorithmicMethodsforHaplotype FrequencyInference:WhatDoTheyTellUs? 373 StevenHechtOrzack,DanielGusfield,LakshmanSubrahmanyan, LaurentEssioux,andSebastienLissarrague 18 OptimizationMethodsforGenotypeDataAnalysis inEpidemiologicalStudies 395 DumitruBrinza,JingwuHe,andAlexanderZelikovsky PARTV STRUCTURALANDSYSTEMSBIOLOGY 417 19 TopologicalIndicesinCombinatorialChemistry 419 SergeyBereg 20 EfficientAlgorithmsforStructuralRecallinDatabases 439 HaoWang,PatraVolarath,andRobertW.Harrison 21 ComputationalApproachestoPredictProtein–Protein andDomain–DomainInteractions 465 RajaJothiandTeresaM.Przytycka Index 493
The list of books you might like
