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部分发表论文与专著：
2019年（*为通信作者）
[1]XiaokeMa*，DiDong,QuanWang.Communitydetectioninmulti-layernetworksusingjointnonnegativematrixfactorization.IEEETransactionsonKnowledegandDataEngineering.31(2):273-286.2019CCFA,IF=3.48
[2]XiaokeMa*,PenggangSun,Zhong-YuanZhang.Anintegrativeframeworkforproteininteractionandmethylationdatatodiscoverepigeneticmodules.IEEE/ACMTrans.Comp.Bio.andBioin.DOI:10.1109/TCBB.2018.281666,2018中科院II区，CCFB,IF=1.97
[3]JianbangZhao,XiaokeMa*.MultiplepartialregularizednonnegativematrixfactorizationforpredictingontologicalfunctionsoflncRNAs.FrontiersinGenetics.9:685.2019.中科院II区，IF=4.21
[4]XiaokeMa*，DongyuanLi,ShiyinTan,ZhihaoHuang.Detectingevolvingcommunitiesindynamicnetworksusinggraphregularizedevolutionarynonnegativematrixfactorization.PhysicaA.530:121279.中科院III区，IF=2.50
[5]XiaokeMa*,ShiyinTan,DongyuanLi,WenmingWu,PenggangSun,MaoguoGong.Anintegrativeframeworkofheterogeneousgenomicdataforcancerdynamicmodulesbasedonmatrixdecomposition.BMCGenomics.Accepted.中科院II区，IF=4.14
[6]DongyuanLi,XiaokeMa*.Nonnegativematrixfactorizationfordynamicmodulesincancertemporalnetworks.IEEEconferenceonBioinformaticsandBiomedicine(IEEEBIBM).accepted,2019.CCFB
[7]ZuhengXia,JingjingDeng,XianghuaXie,XiaokeMa*.Transferlearningforgeneprioritization.IEEEconferenceonBioinformaticsandBiomedicine(IEEEBIBM).accepted,2019.CCFB
[8]XiaokeMa*,BenhuiZhang,ZhiyuMa,ChangzhouMa,ZuhengXia.Co-regularizedNonnegativeMatrixFactorizationforEvolvingCommunityDetectioninDynamicNetworks.InformationSciences.Inrevision.
[9]TengtengYu,ChenxingDu,ZhenYu,LantingLiu,ZhaoLei,ZhongqingLi,JieXu,XiaojingWei,ShuhuiDeng,DehuiZou,GangAn,Yu-TzuTai,GuidoTricot,XiaokeMa*,LuguiQiu*,FenghuangZhan*,MuHao*.PHF19PromotesDrugResistanceviaIncreasedEZH2PhosphorylationinMultipleMyeloma.JournalofHematology&Oncology.Inrevision.
[10]XiaokeMa*,JingjingDeng.Jointnonnegativematrixfactorizationandnetworkembeddingforgraphco-clustering.Insubmission.
[11]DongyuanLi,XiaokeMa*.Dynamiccommunitydetectionbyfusingnetworkembeddingandnonnegativematrixfactorization.Insubmission.
[12]ZhihaoHuang,XiaoxiongZhong,MaoguoGong,XiaokeMa*.Communitydetectioninattributenetworksbydynamicallyjointnodeattributesandtopologicalstructure.Insubmission.
[13]ShiyinTan,XiaokeMa*.jointfeatureextractionandmulti-labellearningfortemporallinkprediction.Insubmission.
2018年
[1]LongGao,UzunYasin,PengGao,BingHe,XiaokeMa,JiahuiWang,JindongHan,KaiTan.Identifyingnoncodingriskvariantsusingdisease-relevantregulatorynetworks.NatureCommunications.8:702,2018中科院I区，IF=12.14
[2]XiaokeMa*,WanxinTang,etal.Extractingstage-specificanddynamicmodulesthroughanalyzingmultiplenetworksassociatedwithcancerprogression.IEEE/ACMTrans.Comp.Bio.andBioin.15(8):647--658,2018中科院II区，CCFB,IF=1.97
[3]XiaokeMa*,PenggangSun,GuiminQin.Identifyingcondition-specificmodulesbyclusteringmultiplenetworks.IEEE/ACMTrans.Comp.Bio.andBioinfo.15(5):1636-1648,2018中科院II区，CCFB,IF=1.97
[4]XiaokeMa*,BingboWang,LiangYu.Semi-supervisedspectralalgorithmsforcommunitydetectionincomplexnetworksbasedonequivalenceofclusteringmethods.PhysicaA.490(2018)786--802.中科院III区，IF=2.48
[5]XiaokeMa*,PenggangSun,YuWang.Graphregularizednonnegativematrixfactorizationfortemporallinkpredictionindynamicnetworks.PhysicaA.496(2018)121--136.中科院III区，IF=2.48
[6]XiaokeMa*,PenggangSun.Fusingheterogeneousgenomicdatatodiscovercancerprogressionrelateddynamicmodules.IEEEconferenceonBioinformaticsandBiomedicine(IEEEBIBM).pp.114-121,2018.CCFB
[7]EnliZhang,XiaokeMa*.Regularizedmulti-viewsubspaceclusteringforcommonmodulesacrosscancerstages.Molecules.23,1016.中科院III区，IF=3.42
[8]付立东，马小科*.进化谱分算法检测动态网络社团结构.西安电子科技大学学报.45(2):43-48.2018EI
2017年
[1]XiaokeMa*，DiDong.EvolutionaryNonnegativeMatrixFactorizationAlgorithmsforCommunityDetectioninDynamicNetworks.IEEETrans.Know.&Data.Eng.29(5)1045-1058CCFA,IF=3.48
[2]FengyinLi,BingHe,XiaokeMa,ShuyangYu,RupaliR.Bhave,StevenR.Lentz,KaiTan,MonicaL.Guzman,ChenZhao,Hai-HuiXue.ProstaglandinE1andItsAnalogMisoprostolInhibitHumanCMLStemCellSelf-RenewalviaEP4ReceptorActivationandRepressionofAP-1.CellStemCell.21(2017)1--15中科院I区，IF=23.96封面论文Cell出版社评价“最透明”与“最具同行评议”论文
[3]XiaokeMa*,PenggangSun,GuiminQin.Nonnegativematrixfactorizationalgorithmsforlinkpredictionintemporalnetworksusinggraphcommunicability.PatternRecognition.71(2017)361-374CCFB,IF=4.99
[4]PenggangSun,XiaokeMa*.Dominatingcommunitiesforhierarchicalcontrolofcomplexnetworks.InformationSciences.414(2017)247--259CCFB,IF=4.96
[5]WanxinTang，DongmeiZhang,XiaokeMa*.RNA-SequencingRevealsGenome-WideLongNon-codingRNAsProfilingAssociatedwithEarlyDevelopmentofDiabeticNephropathy.Oncotarget.8（62）105832--105847中科院I区，IF=5.96
[6]XiaokeMa,ZaiyiLiu,ZhongyuanZhang,XiaotaiHuang,WanxinTang*.Multiplenetworkalgorithmforepigeneticmodulesviatheintegrationofgenome-wideDNAmethylationandgeneexpressiondata.BMCBioinformatics.1:18中科院II区，IF=2.67
[7]PenggangSun,XiaokeMa*.Understandingthecontrollabilityofcomplexnetworksfromthemicrocosmictothemacrocosmic.NewJournalofPhysics.19:013022中科院II区，IF=3.69
[8]PenggangSun,XiaokeMa*.Controllabilityandobservabilityofcascadingfailurenetworks.JournalofStatisticalMechanics:TheoryandExperiment.2017:043404中科院II区，IF=2.49
[9]PeizhuoWang,LinGao,XiaokeMa*.Dynamiccommunitydetectionbasedonnetworkstructuralperturbationandtopologicalsimilarity.JournalofStatisticalMechanics:TheoryandExperiment.2017:013401中科院II区，IF=2.49
[10]PenggangSun,XiaokeMa*.Understandingcontrolofnetworkspreadingfromnetworkcontrollability.JournalofStatisticalMechanics:TheoryandExperiment.2017:093405中科院II区，IF=2.49
[11]XiaokeMa*,PeizhuoWang,LiangYu,XiaofeiYang.DiscoveringDNAmethylationpatternsforlongnon-codingRNAsassociatedwithcancersubtypes.ComputionalBiologyandChemistry.69:164--170中科院III区，IF=1.67APBC2017推荐
[12]PenggangSun,XiaokeMa*.Dominatingcomplexnetworksbyidentifyingminimumskeletons.Chaos,SolitonsandFractals.104:182--191.中科院IV区，IF=1.45
[13]XiaokeMa*,PenggangSun,JianbangZhao.Multi-objectiveoptimizationalgorithmtodiscovercondition-specificmodulesinmultiplenetworks.Molecules.22,2228.中科院III区，IF=3.40
2016-2013年
[1]XiaokeMa,LongGao,GeorgiosKaramanlidis,etal.RevealingPathwayDynamicsinHeartDiseasesbyAnalyzingMultipleDifferentialNetworks.PLoSComput.Biol.2015:e1003442CCFB,IF=6.32
[2]XiaokeMa,LongGao,KaiTan.Modelingdiseaseprogressionusingdynamicsofpathwayconnectivity.Bioinformatics.2014,30:2343--2350中科院I区，CCFB,IF=7.32
[3]XingliGuo,LinGao,QiLiao,HuiXiao,XiaokeMa,XiaofeiYang,HaitaoLuo,GuoguangZhao,DechaoBu,FeiJiao,QixiangShao,RunShengChen*andYiZhao.Longnon-codingRNAsfunctionannotation:aglobalpredictionmethodbasedonbi-colorednetworks.NuclearAcidsResearch.2013,41:e35.中科院I区，CCFB,IF=10.14
[4]FengLi,LinGao,XiaokeMa,XiaofeiYang.Detectionofdriverpathwaysusingmutatedgenenetworkincancer.MolecularBioSystem.2016,中科院III区，IF=3.29
[5]LiangYu,BingboWang,XiaokeMa,LinGao.Theextractionofdrug-diseasecorrelationsbasedonmoduledistanceinincompletehumaninteractome.BMCSystemsBiology,2016,10(Suppl4):111中科院II区，IF=2.33
[6]LiangYu,XiaokeMa,LongZhang,JingZhao,LinGao.Predictionofnewdrugindicationsbasedonclinicaldataandnetworkmodularity.ScientificReports.2016,6:32530中科院II区，IF=4.33
2012-2010年
[1]XiaokeMa*,LinGao.Predictingproteincomplexesinproteininteractionnetworksusingacore-attachmentalgorithmbasedongraphcommunicability.InformationSciences.2012,189:233--254.CCFB,IF=4.96
[2]XiaokeMa，LinGao*.Biologicalnetworkanalysis:insightsintostructureandfunctions.BriefingsinFunctionalGenomics.2012,6:434--442.中科院II区，IF=4.26
[3]XiaokeMa,LinGao*.Discoveringproteincomplexesinproteininteractionnetworksviaexploringtheweaktieseffect.BMCSystemsBiology.2012,6(Suppl1):S6.中科院II区，IF=2.33
[4]付立东，高琳，马小科.基于社团检测的复杂网络中心性方法.中国科学：信息科学，42（5）：550-560.2012.中科院II区，CCFB
[5]XiaokeMa*.LinGao.DetectingproteincomplexesinPPInetworks:Therolesofinteractions.IEEEInternationalConferenceonSystemsBiology.pp.52-592011.
[6]XiaokeMa*，LinGao.Non-traditionalspectralclusteringalgorithmsforthedetectionofcommunitystructureincomplexnetworks:acomparativeanalysis.JournalofStatisticalMechanics:TheoryandExperiment.2011:P05012中科院II区，IF=2.49
[7]XiaokeMa*,LinGao,XuerongYong,LidongFu.Semi-supervisedclusteringalgorithmforcommunitystructuredetectionincomplexnetworks.PhysicaA.2010,389:187--197.中科院III区，IF=2.48
[8]XiaokeMa*,LinGao,XuerongYong.Eigenspacesofnetworksrevealtheoverlappingandhierarchicalcommunitystructuremoreprecisely.JournalofStatisticalMechanics:TheoryandExperiment.2010:P08012中科院II区，IF=2.49
[9]LidongFu,LinGao,XiaokeMa.Acentralitymeasurebasedonthespectraloptimizationofmodularitydensity.SciencesinChinaSeriesF.2010,53:1727--1737CCFB，IF=1.37
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