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1、FoundationsofSystemsBiologyThispageintentionallyleftblankFoundationsofSystemsBiologyeditedbyHiroakiKitanoTheMITPressCambridge,MassachusettsLondon,Englandc2001MassachusettsInstituteofTechnologyAllrightsreserved.Nopartofthisbookmaybereproducedinanyformbyanyelectronicor
2、mechanicalmeans(includingphotocopying,recording,orinformationstorageandretrieval)withoutpermissioninwritingfromthepublisher.ThisbookwassetinPalatinobytheauthorusingtheLATEXdocumentpreparationsystem.PrintedonrecycledpaperandboundintheUnitedStatesofAmerica.LibraryofCong
3、ressCataloging-in-PublicationDataFoundationsofsystemsbiologyeditedbyHiroakiKitano.-1sted.p.cm.Includedbibliographicalreferences(p.).ISBN0-262-11266-3(hc.:alk.paper)1.Biologicalsystems-Research-Methodology2.Biologicalsystems-Research-Casestudies.I.Kitano,Hiroaki,1961-Q
4、H313.F662002573-dc212001042807ContentsContributorsixPrefacexiii1SystemsBiology:TowardSystem-levelUnderstandingofBiologicalSystems1HiroakiKitanoIADVANCEDMEASUREMENTSYSTEMS2AutomaticAcquisitionofCellLineagethrough4DMicroscopyandAnalysisofEarlyC.elegansEmbryogenesis39Shu
5、ichiOnami,ShugoHamahashi,MasaoNagasaki,SatoruMiyano,andHiroakiKitanoIIREVERSEENGINEERINGANDDATAMININGFROMGENEEXPRESSIONDATA3TheDBRFMethodforInferringaGeneNetworkfromLarge-ScaleSteady-StateGeneExpressionData59ShuichiOnami,KojiM.Kyoda,MineoMorohashi,andHiroakiKitano4The
6、AnalysisofCancerAssociatedGeneExpressionMatrices77MattiasWahdeandZoltanSzallasi5AutomatedReverseEngineeringofMetabolicPathwaysfromObservedDatabyMeansofGeneticProgramming95JohnR.Koza,WilliamMydlowec,GuidoLanza,JessenYu,andMartinA.KeaneIIISOFTWAREFORMODELINGANDSIMULATIO
7、N6TheERATOSystemsBiologyWorkbench:AnIntegratedEnvironmentforMultiscaleandMultitheoreticSimulationsinSystemsBiology125MichaelHucka,AndrewFinney,HerbertSauro,HamidBolouri,JohnDoyle,andHiroakiKitano7AutomaticModelGenerationforSignalTransductionwithApplicationstoMAP-Kinas
8、ePathways145BruceE.Shapiro,AndreLevchenko,andEricMjolsness8ModelingLargeBiologicalSystemsFromFunctionalGenomicData:Parameter
