Advances in Computational Biology PDF
Preview Advances in Computational Biology
Advances in Experimental Medicine and Biology Forfurthervolumes: http://www.springer.com/series/5584 Advances in Experimental Medicine and Biology Editorial Board: IrunR.Cohen,TheWeizmannInstituteofScience AbelLajtha,N.S.KlineInstituteforPsychiatricResearch JohnD.Lambris,UniversityofPennsylvania RodolfoPaoletti,UniversityofMilan Volumes published in the series Volume672 BIOSURFACTANTS EditedbyRamkrishnaSen Volume673 MODELLINGPARASITETRANSMISSIONANDCONTROL EditedbyEdwinMichaelandRobertC.Spear Volume674 INTEGRINSANDIONCHANNELS:MOLECULARCOMPLEXESANDSIGNALING EditedbyAndreaBecchettiandAnnarosaArcangeli Volume675 RECENTADVANCESINPHOTOTROPHICPROKARYOTES EditedbyPatrickC.Hallenbeck Volume676 POLYPLOIDIZATIONANDCANCER EditedbyRandyY.C.Poon Volume677 PROTEINS:MEMBRANEBINDINGANDPOREFORMATION EditedbyGregorAnderluhandJeremyLakey Volume678 CHEMOFOG:CANCERCHEMOTHERAPY-RELATEDCOGNITIVEIMPAIRMENT EditedbyRobertB.RaffaandRonaldJ.Tallarida Volume679 MIPSANDTHEIRROLEINTHEEXCHANGEOFMETALLOIDS EditedbyThomasP.JahnandGerdP.Bienert Volume680 ADVANCESINCOMPUTATIONALBIOLOGY EditedbyHamidR.Arabnia Hamid R. Arabnia Editor Advances in Computational Biology Editor HamidR.Arabnia UniversityofGeorgia Dept.ComputerScience 30602-7404AthensGeorgia 415BoydGraduateStudies ResearchCtr. USA ISSN0065-2598 ISBN978-1-4419-5912-6 e-ISBN978-1-4419-5913-3 DOI10.1007/978-1-4419-5913-3 SpringerNewYorkHeidelbergDordrechtLondon LibraryofCongressControlNumber:2010934907 #SpringerScienceþBusinessMedia,LLC2010 Allrightsreserved.Thisworkmaynotbetranslatedorcopiedinwholeorinpartwithoutthewritten permissionof the publisher (SpringerScience+Business Media, LLC, 233 SpringStreet, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. Theuseinthispublicationoftradenames,trademarks,servicemarks,andsimilarterms,evenifthey arenotidentifiedassuch,isnottobetakenasanexpressionofopinionastowhetherornottheyare subjecttoproprietaryrights. While the advice and information in this book are believed to be true and accurate at the date of goingtopress,neithertheauthorsnortheeditorsnorthepublishercanacceptanylegalresponsibility foranyerrorsoromissionsthatmaybemade.Thepublishermakesnowarranty,expressorimplied,with respecttothematerialcontainedherein. Printedonacid-freepaper SpringerispartofSpringerScience+BusinessMedia(www.springer.com) Preface Itgivesusgreatpleasuretointroducethebookentitled“AdvancesinComputational Biology."Thebook is composed ofa collection ofpapersreceivedin response to anannouncementthatwaswidelydistributedtoacademiciansandpractitionersin thebroadareaofcomputationalbiology.Also,selectedauthorsofacceptedpapers of BIOCOMP’09 proceedings (International Conference on Bioinformatics and Computational Biology:July 13–16, 2009; Las Vegas, NV, USA) were invited to submittheextendedversionsoftheirpapersforevaluation. ThecollectionofpapersinPartI,presentadvancesinBioinformaticsDatabases, Data Mining, and Pattern Discovery. Microarray, Gene Expression Analysis, and Gene Regulatory Networks are presented in Part II. Followed by Part III that is composed of a collection of papers in the areas of Protein Classification and Structure Prediction, and Computational Structural Biology. Part IV is composed ofanumberofarticlesthatdiscussessignificantissuesintheareasofComparative Sequence,GenomeAnalysis,GenomeAssembly,andGenomeScaleComputational Methods.DrugDesign,DrugScreening,andrelatedtopicsarediscussedinPartV. PartVIpresentsvariousComputationalMethodsandDiagnosticToolsinBiomed- icalapplications.Lastly,generaltopicsintheareaofBioinformaticsarepresented inPartVII. Weareverygratefultothemanycolleagueswhohelpedinmakingthisproject possible. In particular, we would like to thank the members of the BIOCOMP’09 (http://www.world-academy-of-science.org/) Program Committee who provided theireditorialservicesforthisbookproject.TheBIOCOMP’09ProgramCommittee memberswere: l Dr.NiloofarArshadi,UniversityofToronto,ON,Canada l Prof.RuzenaBajcsy,Member,NationalAcademyofEngineering;IEEEFellow; ACMFellow;UniversityofCalifornia,Berkeley,USA l Prof.AlessandroBrawerman,CEO,Globaltalk,BrazilandPositivoUniversity, Brazil v vi Preface l Dr.DongshengChe,EastStroudsburgUniversity,PA,USA l Dr.ChumingChen,DelawareBiotechnologyInstitute,UniversityofDelaware, Delaware,USA l Prof.VictorA.Clincy,MSACSDirector,KennesawStateUniversity,Kennesaw, Georgia,USA l Prof. Kevin Daimi, Director CS Programs, University of Detroit Mercy, Michigan,USA l Dr.YoupingDeng(ViceChair),UniversityofSouthernMississippi,USA l Prof. Madjid Fathi, Institute and Center Director, University of Siegen, Germany l Dr.GeorgeA.Gravvanis,DemocritusUniversityofThrace,Greece l Dr. Debraj GuhaThakurta, Merck & Co. (Rosetta Inpharmatics), Seattle, Washington,USA l Prof. Ray Hashemi, Yamacraw Professor of CS & Coordinator of Graduate Program,ArmstrongAtlanticStateUniversity,Georgia,USA l Dr. Haibo He, Graduate Program Director, Stevens Institute of Technology, NewJersey,USA l Dr.SeddikKhemaissia,RiyadhCollegeofTechnology,Riyadh,SaudiArabia l Dr.WheDarLin,TheOverseasChineseInstituteofTechnology,Taiwan,R.O.C. l Prof.Chien-TsaiLiu,TaipeiMedicalUniversity,Taipei,Taiwan l Dr.WeidongMao,VirginiaStateUniversity,Virginia,USA l SaraMoein,MultimediaUniversity,Cyberjaya,Malaysia l Prof. Frederick I. Moxley, Director of Research for Network Science, United StatesMilitaryAcademy,WestPoint,NewYork,USA l Prof. Juan J. Nieto, Director of the Institute of Mathematics, University of SantiagodeCompostela,Spain l Dr. Mehdi Pirooznia, The Johns Hopkins University, School of Medicine, Maryland,USA l Dr.JianhuaRuan,UniversityofTexasatSanAntonio,Texas,USA l Prof. Abdel-Badeeh M. Salem, Head of Medical Informatics & Knowledge EngineeringResearchUnit,AinShamsUniversity,Cairo,Egypt l Avinash Shankaranarayanan, Ritsumeikan Asia Pacific University (APU), Japan and Institutefor Applied MaterialsFlow Management (Ifas), TrierUni- versity,Birkenfeld,Germany Preface vii l AshuM.G.Solo(PublicityChair),Principal/R&DEng.,MaverickTechnologies AmericaInc. l Dr.Quoc-NamTran,LamarUniversity,Texas,USA l Prof.AliciaTroncoso,HeadofCSDept.,PablodeOlavideUniversity,Seville, Spain l Dr.MaryQuYang(ViceChair),NationalInstitutesofHealth,USA l Prof.LotfiA.Zadeh,Member,NationalAcademyofEngineering;IEEEFellow, ACM Fellow, AAAS Fellow, AAAI Fellow, IFSA Fellow; Director, BISC; Uni- versityofCalifornia,Berkeley,California,USA l Prof.YanqingZhang,GeorgiaStateUniversity,Atlanta,Georgia,USA l Dr.LemingZhou,UniversityofPittsburgh,Pittsburgh,PA,USA l MembersofWORLDCOMPTaskForceforArtificialIntelligence l MembersofWORLDCOMPTaskForceforComputationalBiology l MembersofWORLDCOMPTaskForceforHigh-PerformanceComputing l MembersofWORLDCOMPTaskForceforPatternRecognition Last but not least, we would like to thank the editorial staff at Springer; in particular,weareindebtedtoMs.MelanieWilichinsky(theeditorialmanager)and herassistant,Ms.MeredithClinton,whoprovidedexcellentprofessionalserviceto ustomakethisprojectfeasible. HamidR.Arabnia,PhD Professor, Computer Science; Fellow, Int’l Society of Intelligent Biological Medicine (ISIBM); Editor-in-Chief, The Journal of Supercomputing (Springer); Co-Editor/Board,JournalofComputationalScience(Elsevier);Member,Advisory Board,IEEETechnicalCommitteeonScalableComputing(TCSC);Departmentof ComputerScience,TheUniversityofGeorgia,Athens,GA30602-7404,USA . Contents PartI BioinformaticsDatabases,DataMining,andPatternDiscovery 1 AClassificationMethodBasedonSimilarityMeasures ofGeneralizedFuzzyNumbersinBuildingExpertSystem forPostoperativePatients ................................................. 3 PasiLuukka 2 EfficientSupportVectorMachineMethodforSurvivalPrediction withSEERData ........................................................... 11 ZhenqiuLiu,DechangChen,GuoliangTian,Man-LaiTang, MingTan,andLiSheng 3 SearchingMaximalDegenerateMotifsGuidedbyaCompact SuffixTree ................................................................. 19 HongshanJiang,YingZhao,WenguangChen,andWeiminZheng 4 ExploringMotifCompositionofEukaryoticPromoterRegions ...... 27 NikolaStojanovicandAbanishSingh 5 Large-ScaleAnalysisofPhylogeneticSearchBehavior ................ 35 HyunJungPark,Seung-JinSul,andTiffaniL.Williams 6 SilicosectionandElucidationofthePlantCircadianClockUsing BayesianClassifiersandNewGeneminingAlgorithm ................. 43 SandraSmieszek,RainerRichter,BartlomiejPrzychodzen, andJaroslawMaciejewski 7 ChemBrowser:AFlexibleFrameworkforMining ChemicalDocuments ...................................................... 57 XianWu,LiZhang,YingChen,JamesRhodes,ThomasD.Griffin, StephenK.Boyer,AlfredoAlba,andKekeCai ix x Contents 8 ExperimentalStudyofModifiedVotingAlgorithmforPlanted (l,d)-MotifProblem ........................................................ 65 HazemM.Bahig,MostafaM.Abbas,andAshsafBhery 9 PredictionofSevereSepsisUsingSVMModel ......................... 75 Shu-LiWang,FanWu,andBo-HangWang 10 OnlineMulti-divisiveHierarchicalClusteringforOn-Body SensorData ............................................................... 83 IbrahimMusaIshagMusa,AnourF.A.Dafa-Alla,GyeongMinYi, DongGyuLee,Myeong-ChanCho,Jang-WhanBae,andKeunHoRyu 11 OnQualityAssuranceandAssessmentofBiologicalDatasets andRelatedStatistics .................................................... 89 MariaVardakiandHaralambosPapageorgiou 12 PatternRecognition-InformedFeedbackforNanoporeDetector Cheminformatics ......................................................... 99 A.MuratEren,IftekharAmin,AmandaAlba,EricMorales, AlexanderStoyanov,andStephenWinters-Hilt 13 AnMLPNeuralNetworkforECGNoiseRemovalBased onKalmanFilter ........................................................ 109 SaraMoein 14 DiscoveryofStructuralMotifsUsingProteinStructural Alphabetsand1DMotif-FindingMethods ........................... 117 Shih-YenKuandYuh-JyhHu 15 BiologicalDatabasesatDNADataBankofJapanintheEra ofNext-GenerationSequencingTechnologies ........................ 125 YuichiKodama,EliKaminuma,SatoshiSaruhashi,KazuhoIkeo, HideakiSugawara,YoshioTateno,andYasukazuNakamura PartII Microarray,GeneExpressionAnalysis,andGene RegulatoryNetworks 16 ComparisonofMicroarrayPreprocessingMethods ................. 139 K.Shakya,H.J.Ruskin,G.Kerr,M.Crane,andJ.Becker 17 ARobustEnsembleClassificationMethodAnalysis ................. 149 ZhongweiZhang,JiuyongLi,HongHu,andHongZhou
The list of books you might like
