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Dynamic Networks from Hierarchical Bayesian Graph Clustering 英文参考文献
DynamicNetworksfromHierarchicalBayesianGraph
Clustering
YongjinPark1,CristopherMoore2,3,JoelS.Bader1*
1DepartmentofBiomedicalEngineeringandHigh-ThroughputBiologyCenter,JohnsHopkinsUniversity,Baltimore,Maryland,UnitedStatesofAmerica,2Departmentof
ComputerScienceandDepartmentofPhysics,UniversityofNewMexico,Albuquerque,NewMexico,UnitedStatesofAmerica,3SantaFeInstitute,SantaFe,NewMexico,
UnitedStatesofAmerica
Abstract
Biological networks change dynamicallyas proteincomponents are synthesizedand degraded. Understanding thetime-
dependenceand,inamulticellularorganism,tissue-dependenceofanetworkleadstoinsightbeyondaviewthatcollapses
time-varyinginteractionsintoasinglestaticmap.Conventionalalgorithmsarelimitedtoanalyzingevolvingnetworksby
reducingthemtoaseriesofunrelatedsnapshots.Hereweintroduceanapproachthatgroupsproteinsaccordingtoshared
interactionpatternsthroughadynamicalhierarchicalstochasticblockmodel.Proteinmembershipinablockispermittedto
evolveasinteractionpatternsshiftovertimeandspace,representingthespatialorganizationofcelltypesinamulticellular
organism.Thespatiotemporalevolutionoftheproteincomponentsareinferredfromtranscriptprofiles,usingArabidopsis
rootdevelopment(5tissues,3temporalstages)asanexample.Thenewmodelrequiresessentiallynoparametertuning,
out-performs existing snapshot-based methods, identifies protein modules recruited to specific cell types and
developmentalstages,andcouldhavebroadapplicationtosocialnetworksandothersimilardynamicsystems.
Citation: Park Y, Moore C, Bader JS (2010) Dynamic Networks from Hierarchical Bayesian Graph Clustering. PLoS ONE 5(1): e8118. doi:10.1371/
journal.pone.0008118
Editor:MarkIsalan,CenterforGenomicRegulation,Spain
ReceivedSeptember17,2009;AcceptedSeptember25,2009;PublishedJanuary11,2010
Copyright:?2010Parketal.Thisisanopen-accessarticledistributedunderthetermsoftheCreativeCommonsAttributionLicense,whichpermitsunrestricted
use,distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited.
F
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