姓名：刘琦
学位：博士
导师情况：硕士生导师
研究领域：生物信息学,药物信息学,机器学习及数据挖掘在生物及药物数据处理中的应用
E-mail：qiliu@tongji.edu.cn
联系电话：021-65980296
通讯地址：上海市四平路1239号，同济大学生命科学与技术学院（200092）


个人简介：
2008年浙江大学生物信息学博士,2006-2008年美国佐治亚大学系统生物学博士联合培养(导师:Prof.YingXu),2009年香港科技大学计算机应用博士后(导师:Prof.QiangYang).
主要研究方向为生物信息学及药物信息学,致力于应用不断发展的统计学习及机器学习技术来挖掘高通量生物数据及药物数据,解决具体问题.目前的研究兴趣偏重于小RNA分子及药物分子的筛选及活性预测,组合用药研究以及药物重定位研究等等.
已在主流的生物信息学及药物信息学期刊如BriefingsinBioinformatics,Plosone,JournalofComputationalChemistry,JournalofChemicalInformationandModeling,Bioinformatics,BMCBioinformatics等发表一系列论文,开发了相应的生物信息学分析软件平台并形成专利,承担及参与了国家及省部级科研项目.同时目前承担学院本科生“机器学习理论与方法”以及“生物信息学算法与实践”的专业必修课教学任务.

News:
@2012-9-14:Ournewintegrativepathwayrankinganalysisplatform,iPEAP,isready!Itisdevelopedforthefirsttimetohandlemulti-omicshigh-throughputdata,andcanbeusedasabenchmarktocomparevariouspathwayenrichmentalgorithms!Downloadhere

论文及著作：

BookChapter:
[1].DongshengChe,QiLiuandKhaledRasheed,DecisionTreeandEnsembleLearningAlgorithmswithTheirApplicationsinBioinformatics,SoftwareToolsandAlgorithmsforBiologicalSystems,Springer-Verlag,2011,696:191-9.

SelectpapersintheareaofBioinformatics:
2012
[1].QiLiu,HanZhou,KuiZhang,XiaoxiaoShi,WeiFan,PhilipYuandZhiweiCao,Insilicotarget-specificsiRNAdesignbasedondomaintransferinheterogeneousdata,Plosone,inpress,2012.
[2].QiLiu,HanZhou,RuixinZhu,YingXuandZhiweiCao,Reconsiderationofin-silicosiRNAdesignfromaperspectiveofheterogeneousdataintegration:problemsandsolutions,BriefingsinBioinformatics,inpress,2012.(TopJournalinBioinformaticsCommunity).
[3].HongKang,ZhenSheng,RuixinZhu,QiHuang,QiLiu#andZhiweiCao#,Avirtualdrugscreenschemabasedonmulti-viewsimilarityintegrationandrankingaggregation,inpress,J.Chem.Inf.Model.2012.(TopJournalinComputationalChemistryCommunity).
[4].TianleiXu,RuixinZhu,QiLiu#andZhiweiCao#,QuantitativelyIntegratingMolecularStructureandBioactivityProfileEvidenceintoDrug-TargetRelationshipAnalysis,BMCBioinformatics,inpress,2012.(DataandScript)
[5].YiSun,RuixinZhu,HaoYe,JingZhao,YujiaChen,QiLiu#andZhiweiCao#,Towardsabioinformaticsanalysisofanti-Alzheimer’sherbalmedicinesfromatargetnetworkperspective,BriefingsinBioinformatics,inpress,2012.(TopJournalinBioinformaticsCommunity).
[6].QiLiu,HanZhou,JuanCui,ZhiweiCaoandYingXu,ReconsiderationofIn-silicosiRNADesignBasedonFeatureSelection:ACross-platformDataIntegrationPerspective,Plosone,inpress,2012.
[7].JunGao,DongshengChe,VincentW.Zheng,RuixinZhu,QiLiu#，IntegratedQSARstudyforinhibitorsofHedgehogSignalPathwayagainstmultiplecelllines：acollaborativefilteringmethod,BMCBioinformatics,inpress,2012.
[8].JunGao#,QiLiu#,HongKang,ZhiweiCaoandRuixinZhu,Comparisonofdifferentrankingmethodsinprotein-ligandbindingsitesprediction,Int.J.Mol.Sci.,inpress,2012.

2011
[1].QiLiu,HanZhou,LinLiu,XiChen,RuixinZhuandZhiweiCao,Multi-targetQSARModellingintheAnalysisandDesignofHIV-HCVCo-InhibitorsAnIn-silicoStudy,BMCBioinformatics,201112:294.
[2].GaoJun,ZhuRuixinLiu,QiLiu#,CaoZhiwei#,PetriNetbasedMetabolicNetworkParametersFittingwithGPUAcceleration,Chin.J.Chem.,2011,29(9),1805-1810.
[3].ZhuRuixin,WangFei,LiuQi#,KangTingguo#,QuantitativeStructure-ActivityRelationshipofIOPY/ISPYAnaloguesasHIV-1Non-NucleosideReverseTranscriptaseInhibitors,ACTACHIMICASINICA,Vol,69,2011,No.15,1731-1736.
[4].RuixinZhu#,QiLiu#,JianTang,HuiliangandZhiweiCao,InvestigationsonInhibitorsofHedgehogSignalPathway:AQSARStudy,Int.J.Mol.Sci.,12,3018-3033,2011.

2010
[1].ShengZhen,KongHong,DaiTianli,LiuQi#,ZhuRuixin#,Complementarystudyofstructurefeaturesandgeneprofilefeaturesforchemicalcompounds,ACTACHIMICASINICA,2010,68(23),2395-2400.
[2].LiuQi,CheDongsheng,HuangQi,CaoZhiwei,ZhuRuixin,Multi-targetQSARStudyintheAnalysisandDesignofHIV-1Inhibitors,Chin.J.Chem.1587-1592,2010.
[3].QiLiu,JuanCui,QiangYangandYingXu,In-silicopredictionofblood-secretoryhumanproteinsusingarankingalgorithm,BMCBioinformatics,11:250,2010.(Manifoldrankingframeworkforbloodysecretedproteinprediction)
[4].QiLiu,QianXu,WenchengZhen,HongXue,ZhiWeiCao,QiangYang,Multi-tasklearningforcross-platformsiRNAefficacyprediction,anin-silicostudy.BMCBioinformatics,11:181,2010.(Multi-tasklearningframeworkforsiRNAefficacyprediction)
[5].HaoYe,LiYe,HongKang,DuanfengZhang,LinTao,KailinTang,XuepingLiu,RuixinZhu,QiLiu,Y.Z.Chen,YixueLiandZhiweiCao,HIT:linkingherbalactiveingredientstotargets,NucleicAcidsResearch.2010,1-5.(HITDatabase)

2009
[1].QiLiu,JinlingHuang,HuiqingLiu,PingWan,XiuziYe,YingXu,AnalysesofDomainsandDomainFusionsinHumanProto-Oncogenes,BMCBioinformatics,2009,10:88.(Taxdom)

2008
[1].QiLiu,YinZhang,YingXu,XiuziYe,FuzzykernelclusteringofRNAsecondarystructureensembleusinganovelsimilaritymetric.JournalofBiomolecularStructureandDynamics,25(6):685-696,2008.(RNAsscc:softwareuponrequest)
[2].QiLiu,YuYang,ChunChen,JiajunBu,YingZhang,XiuziYe,RNACompress:Grammar-basedcompressionandinformationalcomplexitymeasurementofRNAsecondarystructure.BMCBioinformatics,9:176,2008.(RNACompress)
[3].QiLiu,V.Olman,HuiqingLiu,XiuziYe,ShilunQiu,YingXu,RNACluster:anintegratedtoolforRNAsecondarystructurecomparisonandclustering.JournalofComputationalChemistry,26(9),1517-1526,2008.(TopJournalinComputationalChemistryCommunity)(RNACluster)
[4].JuanCui,QiLiu,DavidPuett,YingXu,Computationalpredictionofhumanproteinsthatcanbesecretedintothebloodstream,Bioinformatics,24(20),2370-2375,2008.(ComputationalWebserverforbloodysecretedproteinprediction)
[5].QiLiu,YingZhang,MingyiWang,RongdongYuandXiuziYe,Progressofnormalizationmethodsforhigh-densityoligonucleotidemicroarraydata,JournalofZhejiangUniversity(EngineeringScience),2008,42(9),1653-1660.
[6].QiLiu,YinZhang,XiuziYe,RongdongYu,ADiscreteHopfieldNeuralNetworkbasedMISfindingalgorithmforstemsselectinganditsapplicationinRNAsecondarystructureprediction,ChineseJournalofComputers,2008(1),51-58.

SelectpapersintheareaofMachineLearning:
2011
[1].XiaoxiaoShi,QiLiu,WeiFan,andPhilipS.Yu,TransferacrossCompletelyDifferentFeatureSpacesviaSpectralEmbedding,IEEETransactionsonKnowledgeandDataEngineering(TKDE),Inpress,2011.(TopJournalinMachineLearningCommunity)

2010
[1].XiaoxiaoShi,QiLiu,WeiFan,PhilipYu,andRuixinZhu,TrainingDataExtractionfromCompletelyDifferentFeatureSpacesviaSpectralTransformation,IEEEInternationalConferenceonDataMining(ICDM2010),1049-1054,2010.(TopConferenceinMachineLearningCommunity)
[2].XiaoXiaoshi,QiLiu,WeiFan,QiangYang,PhilipS.Yu.PredictiveModelingwithheterogeneousSources,the2010SIAMInternationalConferenceonDataMining(SDM’2010),814-825,2010.(TopConferenceinMachineLearningCommunity)

LastUpdated:2012-3-1
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