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1、FoundationsofSystemsBiologyeditedbyHiroakiKitanoTheMITPressCambridge,MassachusettsLondon,Englandc2001MassachusettsInstituteofTechnologyAllrightsreserved.Nopartofthisbookmaybereproducedinanyformbyanyelectronicormechanicalmeans(includingphotocopying,recording,orinformationstoragean
2、dretrieval)withoutpermissioninwritingfromthepublisher.ThisbookwassetinPalatinobytheauthorusingtheLATEXdocumentpreparationsystem.PrintedonrecycledpaperandboundintheUnitedStatesofAmerica.LibraryofCongressCataloging-in-PublicationDataFoundationsofsystemsbiologyeditedbyHiroakiKitano.-
3、1sted.p.cm.Includedbibliographicalreferences(p.).ISBN0-262-11266-3(hc.:alk.paper)1.Biologicalsystems-Research-Methodology2.Biologicalsystems-Research-Casestudies.I.Kitano,Hiroaki,1961-QH313.F662002573-dc212001042807ContentsContributorsixPrefacexiii1SystemsBiology:TowardSystem-leve
4、lUnderstandingofBiologicalSystems1HiroakiKitanoIADVANCEDMEASUREMENTSYSTEMS2AutomaticAcquisitionofCellLineagethrough4DMicroscopyandAnalysisofEarlyC.elegansEmbryogenesis39ShuichiOnami,ShugoHamahashi,MasaoNagasaki,SatoruMiyano,andHiroakiKitanoIIREVERSEENGINEERINGANDDATAMININGFROMGENE
5、EXPRESSIONDATA3TheDBRFMethodforInferringaGeneNetworkfromLarge-ScaleSteady-StateGeneExpressionData59ShuichiOnami,KojiM.Kyoda,MineoMorohashi,andHiroakiKitano4TheAnalysisofCancerAssociatedGeneExpressionMatrices77MattiasWahdeandZoltanSzallasi5AutomatedReverseEngineeringofMetabolicPath
6、waysfromObservedDatabyMeansofGeneticProgramming95JohnR.Koza,WilliamMydlowec,GuidoLanza,JessenYu,andMartinA.KeaneIIISOFTWAREFORMODELINGANDSIMULATION6TheERATOSystemsBiologyWorkbench:AnIntegratedEnvironmentforMultiscaleandMultitheoreticSimulationsinSystemsBiology125MichaelHucka,Andre
7、wFinney,HerbertSauro,HamidBolouri,JohnDoyle,andHiroakiKitano7AutomaticModelGenerationforSignalTransductionwithApplicationstoMAP-KinasePathways145BruceE.Shapiro,AndreLevchenko,andEricMjolsness8ModelingLargeBiologicalSystemsFromFunctionalGenomicData:ParameterEstimation163PedroMendes
8、IVCELLULARSIMULATION9TowardsaVirt
