Effective Identification of Conserved Pathways in Biological Networks Using Hidden Markov Models 英文参考文献.docVIP

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Effective Identification of Conserved Pathways in Biological Networks Using Hidden Markov Models 英文参考文献.doc

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Effective Identification of Conserved Pathways in Biological Networks Using Hidden Markov Models 英文参考文献

EffectiveIdentificationofConservedPathwaysin BiologicalNetworksUsingHiddenMarkovModels XiaoningQian1,Byung-JunYoon2* 1Department of Computer Science and Engineering, University of South Florida, Tampa, Florida, United States ofAmerica, 2Department of Electrical and Computer Engineering,TexasAMUniversity,CollegeStation,Texas,UnitedStatesofAmerica Abstract Background: The advent of various high-throughput experimental techniques for measuring molecular interactions has enabled the systematic study of biological interactions on a global scale. Since biological processes are carried out by elaboratecollaborationsofnumerousmoleculesthatgiverisetoacomplexnetworkofmolecularinteractions,comparative analysis of these biological networks can bring important insights into the functional organization and regulatory mechanismsofbiologicalsystems. Methodology/Principal Findings: In this paper, we present an effective framework for identifying common interaction patterns in the biological networks of different organisms based on hidden Markov models (HMMs). Given two or more networks,ourmethodefficientlyfindsthetopkmatchingpathsintherespectivenetworks,wherethematchingpathsmay containaflexiblenumberofconsecutiveinsertionsanddeletions. Conclusions/Significance: Based on several protein-protein interaction (PPI) networks obtained from the Database of Interacting Proteins (DIP) and other public databases, we demonstrate that our method is able to detect biologically significantpathwaysthatareconservedacrossdifferentorganisms.Ouralgorithmhasapolynomialcomplexitythatgrows linearlywiththesizeofthealignedpaths.Thisenablesthesearchforverylongpathswithmorethan10nodeswithinafew minutesonadesktopcomputer.Thesoftwareprogramthatimplementsthisalgorithmisavailableuponrequestfromthe authors. Citation:QianX,YoonB-J(2009)EffectiveIdentificationofConservedPathwaysinBiologicalNetworksUsingHiddenMarkovModels.PLoSONE4(12):e8070. doi:10.1371/journal.pone.0008070 Editor:DiegoDiBernardo,FondazioneTeletho