李园园
生物化工专业：硕士生导师

女，1975年生。1996年本科毕业于南开大学微生物系；1999年硕士毕业于中国医学科学院协和医科大学肿瘤研究所分子病毒学实验室；2003年博士毕业于中科院上海生化所。上海生物信息技术研究中心系统生物学课题组长，研究员。在PLoSComputationalBiology、Bioinformatics、MolecularSystemsBiology等权威专业期刊上发表论文三十余篇，总影响因子超过100。获得软件著作权6项，申请专利1项。作为项目负责人已完成或正在承担自然科学基金面上项目两项、973一项、863一项，科技部传染病重大专项一项、上海市重大基础一项。2006年当选上海市科技启明星。


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研究方向和领域：
生物学假说驱动的数据挖掘和系统建模，通过基于组学数据和先验知识的生物学网络分析，揭示生物系统特定状态下的调控机制。（生物信息学，系统生物学。）
发表论文：
1.YangJ,LiYY,LiYX,YeZQ.PartitionDatasetaccordingtoAminoAcidTypeImprovesthePredictionofDeleteriousNon-synonymousSNPs.BBRC.2012,419(1):99-103
2.HuSN,YuH,ZhangYB,WuZL,YanYC,LiYX,LiYY,LiYP.Spliceblockingofzygoticsox31leadstodevelopmentalarrestshortlyafterMid-BlastulaTransitionandinducesapoptosisinzebrafish.FEBSletters.2011.
3.ChangX,LiY,PingJ,XingXB,SunH,JiaP,WangC,LiYY*,LiYX*.EcoBrowser:aweb-basedtoolforvisualizingtranscriptomedataofEscherichiacoli.BMCResearchNotes.2011,4:405.(Co-correspondingauthor)
4.YuH,LiuBH,YeZQ,LiC,LiYX*,LiYY*.Link-basedQuantitativeMethodstoIdentifyDifferentiallyCoexpressedGenesandGenePairs.BMCBioinformatics.2011,12:315.
5.LiRD,LiYY,LuLY,RenC,LiYX,LiuL*.AnImprovedKineticModelforAcetone-Butanol-EthanolPathwayofClostridiumacetobutylicumandModel-BasedPerturbationAnalysis.BMCSystemsBiology2011,5(Suppl1):S12.(co-firstauthor)
6.YiZhong,XiaoChang,Xing-JunCao,YanZhang,Hua-JunZheng,Yong-ZhangZhu,Cheng-SongCai,Yuan-YuanLi,Guo-Ping,Zhao,Sheng-YueWang,Yi-XueLi,RongZeng,XuanLi*,Xiao-KuiGuo*.ComparativeProteogenomicAnalysisoftheLeptospirainterrogansVirulenceAttenuatedStrainIPAVagainstthePathogenicStrain56601.CellResearch2011Mar22[Epubaheadofprint].doi:10.1038/cr.2011.46.PMID:21423275
7.YeZQ,NiuS,YuY,YuH,LiRX,XiaoHS,ZengR,LiYX,WuJR*,LiYY*.AnalysesofCopyNumberVariationofGKRatRevealNewPutativeType2DiabetesSusceptibilityLoci.PLoSOne.2010.5(11):e14077.
8.ShiYX,LiYY*.LargeNumberofPhosphotransferaseIIGenesintheClostridiumbeijerinckiiNCIMB8052GenomeandtheStudyonTheirEvolution.BMCBioinformatics.2010.11(Suppl11):S9.
9.ChenYQ,YuH,LiYX*,LiYY*.SortingOutInherentFeaturesofHead-to-HeadGenePairsbyEvolutionaryConservation.BMCBioinformatics.2010.11(Suppl11):S16.
10.YuH,TuK,XieL*,LiYY*.DigOUT:viewingdifferentialexpressiongenesasoutliers.JournalofBioinformaticsandComputationalBiology2010.8(Suppl1):161-175.
11.LiuBH,YuH,TuK,LiC,LiYX*,LiYY*.DCGL:anRpackageforidentifyingdifferentiallycoexpressedgenesandlinksfromgeneexpressionmicroarraydata.Bioinformatics.2010;26(20):2637-8.
12.ChangX,CaoXJ,LiYY*.EvolutionaryrateanalysisofdifferentiallyexpressedproteinsbetweenStaphylococcusepidermidisRP62AandATCC12228.ChineseScienceBulletin.2010.55:3297-3301.
13.ChangX,LiuS,YuYT,LiYX*,LiYY*.IdentifyingmodulesofcoexpressedtranscriptunitsandtheirorganizationofSaccharopolysporaerythraeafromtimeseriesgeneexpressionprofiles.PLoSONE.2010;5(8):e12126.
14.ChangX,WangZ,HaoP,LiYY*,LiYX*.Exploringmitochondrialevolutionandmetabolismorganizationprinciplesbycomparativeanalysisofmetabolicnetworks.Genomics.2010;95:339-344.(Co-correspondingauthor)
15.YeBC*,ZhangY,YuH,YuWB,LiuBH,YinBH,YinCY,LiYY*,ChuJ,ZhangSL.Time-ResolvedTranscriptomeAnalysisofBacillussubtilisRespondingtoValine,Glutamate,andGlutamine.PLoSOne.2009;4(9):e7073.doi:10.1371/journal.pone.0007073(Co-correspondingauthor)
16.ZhangY,WeiZ,LiYY,ChenY,ShenW,LuC*.TranscriptionlevelofmRNApergenecopydeterminedwithdual-spike-instrategy.AnalyticalBiochemistry.2009;394:202-208.(Co-firstauthor)
17.TuK,YuH,HuaYJ,LiYY,LiuL*,XieL*,LiYX*.CombinatorialnetworkofprimaryandsecondarymicroRNA-drivenregulatorymechanisms.NucleicAcidsResearch.2009:1-12.doi:10.1093/nar/gkp638
18.HuiYu,Fu-DongYu,Guo-QingZhang,XiangShen,Yun-QinChen,Yuan-YuanLi*,Yi-XueLi*.DBH2H:vertebratehead-to-headgenepairsannotatedatgenomicandpost-genomiclevels.Database:TheJournalofBiologicalDatabasesandCuration.2009:bap006-bap006.(Co-correspondingauthor)
19.YuH,LiYY*.Recoveringcontext-specificgenenetworkmodulesfromexpressiondata:abriefreview.FrontiersofBiologyinChina.2009.(Correspondingauthor)
20.LuoR,WeiH,YeL,WangK,ChenF,LuoL,LiuL,LiY,CrabbeMJ,JinL,LiY,ZhongY.PhotosyntheticmetabolismofC3plantsshowshighlycooperativeregulationtomaintainfunctionunderchangingenvironmentalconditions:asystemsbiologicalanalysisofrobustness.ProcNatlAcadSciUSA.2009;106(3):847-52.
21.BinKang,Yuan-YuanLi,XiaoChang,LeiLiu,Yi-XueLi.ModelingtheEffectsofCellCycleM-phaseTranscriptionalInhibitiononCircadianOscillation.PLoSComputationalBiology.2008;4(3)
22.Fu-DongYu,Yi-XueLi,LeiLiu*,Yuan-YuanLi*.Comparativegenomicsofhuman-likeSchistosomajaponicumgenesindicatesaputativemechanismforhost-parasiterelationship.Genomics.2008;91:152-157.(Co-correspondingauthor)
23.Fu-DongYu,BinKang,Yuan-YuanLi*,Yi-XueLi*.FunctionalanalysisofschistosomesEF-handdomain-containingtegumentproteins.ChineseScienceBulletin.2007;52(15):2100-2107.(Co-correspondingauthor)
24.HuiYu,FengWang,KangTu,LuXie,Yuan-YuanLi*,Yi-XueLi*.Transcript-levelannotationofAffymetrixprobesetsimprovestheinterpretationofgeneexpressiondata.BMCBioinformatics.2007Jun11;8:194.(QualifiedasHighlyaccessed)(Co-correspondingauthor)
25.Yuan-YuanLi,HuiYu,Zong-MingGuo,Ting-QingGuo,KangTu,Yi-XueLi.Systematicanalysisofhead-to-headgeneorganization:evolutionaryconservationandpotentialbiologicalrelevance.PLOSComputationalBiology.2006Jul7;2(7):687-697.
26.Yuan-YuanLi,LeiQin,Zong-MingGuo,LeiLiu,HaoXu,PeiHao,JiongSu,YixiangShi,Wei-ZhongHe,Yi-XueLi.Insilicodiscoveryofhumannaturalantisensetranscripts.BMCBioinformatics.2006Jan13,7(1):18.(PMID:16409644)(QualifiedasHighlyaccessed)
27.LiliWang,ZhongYang,YuanyuanLi,FudongYu,PaulJ.Brindley,DonaldP.McManus,DongzhiWei,ZeguangHan,ZhengFeng,YixueLi,WeiHu.ReconstructionandinsilicoanalysisoftheMAPKsignalingpathwaysinthehumanbloodfluke,Schistosomajaponicum.FEBSletters.2006Jun26;580(15):3677-86.
28.RuoyuLuo,ShaLiao,GuanyangTao,YuanyuanLi,YixueLi,QingmingLuo.Dynamicanalysisofoptimalityinmyocardialenergymetabolismundernormalandischemicconditions.MolecularSystemsBiology.2006;2:2006.0031.Epub2006Jun6.
29.ZhuoWang,Xin-guangZhu,YazhuChen,YuanyuanLi,JingHou,YixueLi,LeiLiu.Dynamicanalysisofoptimalityinmyocardialenergymetabolismundernormalandischemicconditions.BMCGenomics.2006Apr30;7:100.
30.LIRong,CAOShunliang,LIYuanyuan,TANHao,ZHUYangyong,ZHONGYangandLIYixue.AMeasureofSemanticSimilaritybetweenGeneOntologyTermsBasedonSemanticPathwayCovering.ProgressinNaturalScience.2006;16(7):721-726.
31.QiangLu,PeiHao,VasaCurcin,WeizhongHe,Yuan-YuanLi,Qing-MingLuo,Yi-KeGuoandYi-XueLi.KDEBioscience:Platformforbioinformaticsanalysisworkflows.JournalofBiomedicalInformatics.2006.
32.LiY,WangL,LiS,GuoT,GuoX,YanP,ChenY,WangL,LuC.P53proteinactivatesthetranscriptionofhumanproliferatingcellnuclearantigeninresponseto4-nitroquinolineN-oxidetreatment.InternationalJournalofBiochemistryandCellBiology.2005Feb,37(2):416-426.
33.LiYY,WangL,LuCD.AnE2Fsiteinthe5-promoterregioncontributestoserum-dependentup-regulationofthehumanproliferatingcellnuclearantigengene.FEBSLetters.2003Jun5,544(1-3):112-118.
联系方式：
E-mail:yyli@scbit.org