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1、ThisarticleispublishedinThePlantCellOnline,ThePlantCellPreviewSection,whichpublishesmanuscriptsacceptedforpublicationaftertheyhavebeeneditedandtheauthorshavecorrectedproofs,butbeforethe?nal,completeissueispublishedonline.Earlypostingofarticlesreducesno
2、rmaltimetopublicationbyseveralweeks.CURRENTPERSPECTIVEESSAYSPECIALSERIESONLARGE-SCALEBIOLOGYNetworkInference,Analysis,andModelinginSystemsBiologyCellsusesignalingandregulatorypathwaysconnectingnumer-nologiesbroughtanabundanceofdataonsystemelementsandou
3、sconstituents,suchasDNA,RNA,proteins,andsmallmol-interactions,leadingtoarevivalofsystemsbiology.ecules,tocoordinatemultiplefunctions,allowingthemtoadaptInsomecases,theorganizationofthenetworkofinteractionstochangingenvironments.High-throughputexperimen
4、talmeth-underlyingabiologicalsystemisstraightforward(e.g.,alinearodsenablethemeasurementofexpressionlevelsforthousandschainofinteractions),whileinothercasesamoreformalofgenesandthedeterminationofthousandsofproteinproteinrepresentation,offeredbymathemat
5、icalgraphtheory(Bolloba′s,orproteinDNAinteractions.Itisincreasinglyrecognizedthat1979),isrequired.Thesimplestpossiblegraphrepresentationtheoreticalmethods,suchasstatisticalinference,graphanal-reducesthesystemselementstographnodes(alsocalledysis,anddyna
6、micmodeling,areneededtomakesenseofthisvertices)andreducestheirpairwiserelationshipstoedges(alsoabundanceofinformation.Thisperspectivearguesthattheo-calledlinks)connectingpairsofnodes(Figure1).Thenodesofreticalmethodsandmodelsaremostusefuliftheyleadtono
7、vel(sub)cellularsystemsmaybegenesormRNA,protein,orotherbiologicalpredictionsandreviewsbiologicalpredictionsarisingmolecules.Directededges(alsocalledarcs)haveaspeci?edfromthreesystemsbiologytopics:graphinference(i.e.,recon-source(starting)nodeandtarget(
8、end)nodeandaremostsuitedstructingthenetworkofinteractionsamongasetofbiologicaltorepresentchemicaltransformationsandregulatoryrelation-entities),graphanalysis(i.e.,miningtheinformationcontentofships.Nondirectededgesaremostappropriateform
