在岗研究生导师情况介绍
所系名称系统生物学实验室
性别男
专业名称生物信息学
技术职务研究员
行政职务生物信息中心主任
Mail地址yxli@sibs.ac.cn
指导博士
生总数35指导硕士
生总数10已毕业学生通讯地址岳阳路320，系统生物学重点实验室
目前博士
生数20目前硕士
生数3目前在校生邮政编码200031
研究方向生物学数据整合和挖掘，生物系统建模与功能研究，功能基因组信息学，药物基因组信息学
研究工作
研究方向：生物信息学，系统生物学
研究内容：生物学数据挖掘方法，生物学数据整合和数据库构建，生物学理论建模，生物学数据分析工作流设计和软件开发。通过大力与实验室和合作，近年来的研究工作主要涉及在如下方面：
1、基因组信息学，主要是基因组功能注释方面的数据整合，分析方法研究等。
2、转录组学，EST数据分析，电子克隆，基因调控网络分析和理论建模，基因芯片数据分析等。
3、蛋白质组学，蛋白质组学数据标准研究，数据整合，蛋白质相互作用网络研究，亚细胞定位分析等。
4、代谢组学，代谢网络建模、拓扑结构分析和动力学分析，基于整合的代谢组数据的蛋白质功能分析方法研究。
5、小分子调控和药物基因组学
6、其它，如SNP数据分析与疾病基因定位，小RNA分析，反义RNA分析以及基因和蛋白质功能预测分析算法研究等。
获奖情况2003年上海市劳动模范，2003年上海市优秀学科带头人，上海市科教兴市领军人才，全国五一国际劳动奖章获得者，享受国务院特殊津贴，曾获教育部自然科学一等奖，上海市自然科学二等奖
指导研究
生情况指导博士研究生35名，多名研究生获得科学院院长奖、明治乳业科学奖等奖项，十几名博士和硕士毕业生在国外如EMBL、HeidelbergUniversity，MunichUniversity，DukeUniversity等研究所和大学继续科研工作。
个人简介李亦学Tel：021-54920089；Email：yxli@sibs.ac.cn
研究员，博士生导师。上海生物信息学会理事长，曾任国家中长期发展规划第十五专题组副组长，上海市科学预见专家，国家“十五”863计划生物和农业技术领域生物信息技术主题专家组组长，国家“十一五”863计划生物医药技术领域专家组专家。
1996年10月获德国海德堡大学理论物理研究所理论物理博士学位。1996年11月至1997年3月在德国斯图加特大学第三计算机应用研究所从事计算数学博士后研究。1997年4月至2000年6月在欧洲分子生物学实验室（EMBL）从事生物物理博士后研究。2000年7月回国到中科院上海生命科学研究院生物信息中心工作，任常务副主任，2002年任主任，2002年7月任上海生物信息技术研究中心主任，2007年兼任上海交通大学生物信息学和生物统计学系系主任，2007年1月任中科院系统生物学重点实验室副主任。
2000年回国后，先后主持和承担了国家“九五”863计划生物技术领域《生物信息学数据库开发和建设》重大项目。作为首席科学家主持了中科院《生物信息学重大基础理论与应用》重大研究项目；国家973《重大疾病相关蛋白质组学生物信息学》课题；中科院上海生科院《生物信息技术平台建设》项目,国家中长期科学规划基础科学重大专项蛋白质科学研究《模式生物和细胞等功能系统的系统生物学研究》专项等，现为德国JournalofIntegrativeBioinformatics杂志编辑，英国BMCBioinformatics杂志责任编辑,国内《科学通报》特邀编辑，生物物理和生物化学学报、中国生物工程杂志以及Genomics,ProteomicsandBioinformatics等杂志编委。
回国以来带共发表100余篇SCI收录科学论文，包括Science,Nature,NatureGenetics,NatureBiotechnology,PNAS,Oncogene,MolecularSystemsBiology,MolecularCelluleProteomics,PlosComputationalBiology,PlosOne,NuclearAcidResearch,Bioinformatics，BMCBioinfomatics,BMCGenomics,BBRC,FEBSLatter等,其中以第一和通讯作者发表的SCI科学论文超过80篇，论文他人引用超过1000次。
近期论文2004年来发表的主要论文
1.HongLi,GuohuiDing,LuXie,YixueLi,2009,dbDEPC:aDatabaseofDifferentiallyExpressedProteinsinHumanCancer.acceptedbyNucleicAcidsResearch.
2.TaoHuang,WeirenCui,Zhi-SongS.He,LeleHu,FangLiu,TieqiaoWen,YixueLi*,YudongCai*,2009,FunctionalassociationbetweeninfluenzaA(H1N1)virusandhuman.Export.AcceptedbyBiochemicalandbiophysicalresearchommunications.
3.TaoHuang,WeiRenCui,LeLeHu,KaiYanFeng,Yi-XueLi,Yu-DongCai,2009,PredictionofPharmacologicalandXenobioticResponsestoDrugsBasedonTimeCourseGeneExpressionProfiles.AcceptedbyPlosOne.
4.HuiYu,Fu-DongYu,Guo-QingZhang,XiangShen,Yun-QinChen,Yuan-YuanLi,*andYi-XueLi*,DBH2H:vertebratehead-to-headgenepairsannotatedatgenomicandpost-genomiclevels.Database,2009,doi:10.1093/database/bap006.
5.YaoYu，KangTu,SiyuanZheng,YunLi,GuohuiDing,JiePing,PeiHaoandYixueLi，GEOGLE:contextminingtoolforthecorrelationbetweengeneexpressionandthephenotypicdistinction.BMCBioinformatics2009,10:264doi:10.1186/1471-2105-10-264.
6.Tu,Kang;Yu,Hui;Hua,Youjia;Li,Yuanyuan;Liu,Lei,Xie,Lu,YixueLi*,CombinatorialnetworkofprimaryandsecondarymicroRNA-drivenregulatorymechanisms,acceptedbyNucleicAcidsResearch.2009，37(18):5969-80.
7.JingSun,DiWu,TianleiXu,XiaojingWang,XiaolianXu,LinTao,Y.X.Li*andZ.W.Cao*，SEPPA:acomputationalserverforspatialepitopepredictionofproteinantigens，NucleicAcidsResearch.2009，W612–W616.
8.HongLi,GuohuiDing,LuXie*andYixueLi*,PAnnBuilder:anRpackageforassemblingproteomicannotationdata,Bioinformatics,2009,25(8):1094-1095.
9.HongLi,XiaobingXing,GuohuiDinproteomicg,LuXie*,RongZeng*,YixueLi*,SysPTM-asystematicresourceforresearchofpost-translationalmodifications,MolecularandCellularProteomics.2009,8(8):1839-49.
10.ZhenWang,GuohuiDing,ZhonghaoYu,LeiLiu*,YixueLi*,CHSMiner:aGUItooltoidentifychromosomalhomologoussegments.AlgorithmsMol.Biol.,2009,4(1):2.
11.SonglingLi,HongLi,MinfaLi,LuXie*,YixueLi*.2009，Improvedpredictionoflysineacetylationbysupportvectormachines.AcceptedbyProteinandPeptideLetters.
12.PeiHao,SiyuanZheng,JiePing,KangTu,ChristianGieger,RuiWang-Sattler,YangZhong*,YixueLi*，Humangeneexpressionsensitivityaccordingtolargescalemeta-analysis，BMCBioinformatics.2009,10(Suppl1):S56.
13.HongSun,GeirSkogerbo,XiaohuiZheng,WeiLiu*andYixueLi*,Genomicregionswithdistinctgenomicdistanceconservationinvertebrategenomes,BMCGenomics,2009,10:133.
14.HongXi,…,YixueLi*,SysPIMP:theweb-basedsystematicalplatformforidentifyinghumandisease-relatedmutatedsequencesfrommassspectrometry,NucleicAcidsResearch.200937:D913-D920.
15.SujunLi,HongLi,YixueLi*,RongZeng,Sys-BodyFluid:aSystematicalDatabaseforHumanBodyFluidProteomeResearch,NucleicAcidsResearch.2009Jan;37:D907-12.
16.GuohuiDing,…,YixueLi*,H.J.Thiesen*,SysZNF:theC2H2ZincFingerGenedatabase,NucleicAcidsResearch.200937:D267-D273.
17.ZhenWang,GuohuiDing,ZhonghaoYu,LeiLiu*,YixueLi*,Modelingtheagedistributionofgeneduplicationsinvertebrategenomeusingmixturedensity.Genomics.2009;93(2):146-51.
18.Ruo-YuLuo,Hai-BinWei,LinYe,KankanWang,LeiLiu,Yuan-YuanLi,Yi-XueLi*andYangZhong*,PhotosyntheticmetabolismofC3plantsshowshighlycooperativeregulationtomaintainfunctionunderchangingenvironmentalconditions:asystemsbiologicalanalysisofrobustness,PNAS.2009,vol.106no.3847-852.
19.HongSun,…,Wei,Liu*,YixueLi*,StructuralRelationshipsbetweenHighlyConservedElementsandGenesinVertebrateGenomes,PlosOne.2008,Vol.3,No.11,e3727.
20.GuohuiDing,…,YixueLi*,TreeofLifeBasedonGenomeContextNetworks,PlosOne.2008,Vol.3,No.10,e3357.
21.YunLi,PeiHao,SiyuanZgeng,KangTu,LeiLiu*,YixueLi*,2008,GeneExpressionModulebasedChemicalFunctionSimilaritySearch,NucleicAcidsResearch，2008,Vol.36,No.20e137.
22.GuangyongZheng,KangTu,…,YixueLi*,ITFP:anintegratedplatformofmammaliantranscriptionfactors,Bioinformatics.WLi,LXie,XHe,JLi,KTu,LWei,JWu,YGuo,WenxiLi,LuXie,XianghuoHe,JinjunLi,KangTu,…,YixueLi*,JianrenGu*,2008,DiagnosticandprognosticimplicationsofmicroRNAsinhumanhepatocellularcarcinoma,Int.J.Cancer,123,1616–1622.
23.SiyuanZheng,…,PeiHao*,LeiLiu*,YixueLi*,2008,MPSQ:Awebtoolforproteinstatesearching,Bioinformatics.200824(20):2412-2413.
24.TaoHuang,KangTu,YuShyr,Chao-ChunWei,LuXie*andYi-XueLi*,Thepredictionofinterferontreatmenteffectsbasedontimeseriesmicroarraygeneexpressionprofiles,JournalofTranslationalMedicine,2008Aug9;6(1):44.
25.GuangyongZheng,ZiliangQian,QingYang,ChaochunWei,LuXie,YangyongZhu*andYixueLi*,2008,ThecombinationapproachofSVMandECOCforpowerfulidentificationandclassificationoftranscriptionfactor,BMCBioinformatics,9:282.
26.HuaYJ,TuK.,TangZY,LiYX*,XiaoHS*,2008,ComparisonofnormalizationmethodswithmicroRNAmicroarray.Genomics,doi:10.1016/j.ygeno.2008.04.002.
27.QingweiXu,YixiangShi,QiangLu,GuoqingZhang,QingmingLuo*andYixueLi*，2008，GORouter:anRDFmodelforprovidingsemanticqueryandinferenceservicesforGeneOntologyanditsassociations，BMCBioinformatics,9(Suppl1):S6.
28.CBin,Kang,LieLiu*,YixueLi*,2008,ModelingEffectsofCellCycleM-phaseTranscriptionalInhibitiononCircadianOscillator,PloscomputationalBiology,V.4,Issue3.
29.PeilinJia,ZiliangQian,KaiyanFeng,WencongLu,YixueLi*,YudongCai*,2008,Predictionofmembraneproteintypesinahybridspace,JProteomeResearch,7(3),1131–1137.
30.ChangzhenDong,…,YixueLi*,Gene-centricCharacteristicsofGenome-wideAssociationStudies,PlosOne,2007;2(12):e1262.
31.JingLi,ZijingLiu,YuchunPan,QiLiu,XingFu,NigelG.F.Cooper,YixueLi*,MengshengQiu*andTieliuShi*,RegulatoryModuleNetworkofbHLHTranscriptionFactorsinMouseBrain,GenomeBiology2007,8:R244.
32.GuohuiDing,YanSun,HongLi,ZhenWang,HaiweiFan,ChuanWang,DanYangandYixueLi*,2007,EPGD:acomprehensivewebresourceforintegratinganddisplayingeukaryoticparalog/paralogoninformation.NucleicAcidsResearch,v.36(Databaseissue):D255–D262.
33.JianCui,PengLi,GuangLi,FengXu,ChenZhao,YuhuaLi,ZhongnanYang,GuangWang,QingboYu,YixueLi*andTieliuShi*,AtPID:Arabidopsisthalianaproteininteractomedatabase—anintegrativeplatformforplantsystemsbiology,2007,NucleicAcidsResearch,36:D999-D1008.
34.PeilinJia,ZiliangQian，ZhenBinZeng,YudongCai*,andYixueLi*,Predictionofsubcellularproteinlocalizationbasedonfunctionaldomaincomposition,BiochemicalandBiophysicalResearchCommunications，Volume357,Issue2,1June2007,Pages366-370.
35.ZiliangQian,LingyiLu,XiaoJunLiu,Yu-DongCai*,andYixueLi*，2007,AnApproachtoPredictTranscriptionFactorDNABindingSiteSpecificityBaseduponGeneandTranscriptionFactorFunctionalCategorization,Bioinformatics,23(18):2449-2454.
36.BoshuLiu,SujunLi,YinglinWang,LinLu,YixueLi*andYudongCai*，PredictingtheproteinSUMOmodificationsitesbasedonPropertiesSequentialForwardSelection(PSFS)，BiochemicalandBiophysicalResearchCommunications，2007，Volume358,Issue1,22June2007,Pages136-139.
37.LLu,ZQian,YDCai*,YLi*，Softwarenote:ECS:Anautomaticenzymeclassifierbasedonfunctionaldomaincomposition，2007，ComputationalBiologyandChemistry,Volume31，226-232.
38.JingZhao,Guo-HuiDing,LinTao,HongYu,Zhong-HaoYu,Jian-HuaLuo,Zhi-WeiCao*andYi-XueLi*，2007，Modularco-evolutionofmetabolicnetworks，BMCBioinformatics,8:311,doi:10.1186/1471-2105-8-311.
39.HuiYu,FengWang,KangTu,LuXie,Yuan-YuanLi*andYi-XueLi*，2007，Transcript-levelannotationofAffymetrixprobesetsimprovestheinterpretationofgeneexpressiondata，BMCBioinformatics,8:194,doi:10.1186/1471-2105-8-194.
40.ChangzhengDong，XunChu，YingWang，YiWang，LiJin，TieliuShi，WeiHuang*，YixueLi*，2007,ExplorationofGene-GeneInteractionEffectsUsingEntropy-BasedMethods，EuropeanJournalofHumanGenetics,16(2):229-35.
41.WuWei,…,YixueLi,LarsSteinmetz*,2007,"GenomesequencingandcomparativeanalysisofSaccharomyces,PNAS,vol.104,no.31,12825-12830.
42.SujunLi,…,YixueLi*,2007,PredictionProteinN-glycosylationbyCombiningFunctionalDomanandSecretionInformation,J.BiomolecularStructure&Dynamics,Vol.25,49-54.
43.QuanhuSheng,…,YixueLi,RongZeng*,JiaruiWu*,2006,ComparisonofProteomicApproachtoMicroarray-basedApproachforDetectingExonsofMouseGenome.NatureGenetics,38,1223–1224.
44.GuohuiDing,JiuhongKang,QiLiu,TieliuShi,GangPei,andYixueLi*,2006,Insightsintothecouplingofduplicationeventsandmacroevolutionfromanagedistributionofanimaltransmembranegenefamilies,PlosComputationalBiology,Vol.2,issue8,e102.
45.JingZhao,HongYu,Jian-HuaLuo,Zhi-WeiCao,Yi-XueLi*，2006,Hierarchicalmodularityofnestedbow-tiesinmetabolicnetworks，BMCBioinformatics,7:386.
46.ZiliangQian,YudongCai,YixueLi*,2006,AutomaticTranscriptionFactorClassifierbasedonFunctionalDomainComposition,BiochemicalandBiophysicalResearchCommunications，18;347(1):141-4.
47.PLJia,TLShi*,YDCai*.andYXLi*,2006,DemonstrationoftwonovelmethodsforpredictingfunctionalsiRNAefficiency,BMCBioinformatics,7:271,doi:10.1186/471-2105-7-271.
48.PeiHao,…,YixueLi*,2006,“BioinformaticsResearchontheSARSCoronavirusinChina”,Curr.Pharm.Design.Vol.12,Nr.35.
49.ZiliangQian，YanbinYin，YongZhang,LingyiLu,YixueLiandYingJiang*，2006,GenomiccharacterizationofribitolteichoicacidsynthesisinStaphylococcusaureus:genes,genomicorganizationandgeneduplication,BMCGenomics,7:74.
50.WuWei,ZiweiCao,…,YixueLi*，2006,Thepathfromcommensalismtopathogenicity:comparativephylogeneticprofilesofStaphylococcusepidermidisRP62AandATCC12228,BMCGenomics,7:112，doi:10.1186/1471-2164-7-112.
51.XiaojingYu,…,YixueLi*,2006,Classificationofproteinquaternarystructurebyfunctionaldomaincomposition,BMCBioinformatics,7:187.
52.YuanyuanLi,…,YixueLi*,2006,"Insilicodiscoveryofhumannaturalantisensetranscripts",BMCBioinformatics.13;7:18.
53.SujunLi,…,YixueLi*,2006,PredictingO-glycosylationsitesinmammalianproteinsbyusingSVMs,ComputBiolChem.30(3):203-208.
54.KangTu,…,YixueLi*,2006,CombiningGeneExpressionProfilesandProtein-ProteinInteractiondatatoinferGeneFunctionsBioinformatics:microarrayanalysis&PPInetworkanalysis,JournalofBiotechnology,124,475-485.
55.YuX,CaoJ,CaiY,ShiT,YixueLi*.2006,PredictingrRNA-,RNA-,andDNA-bindingproteinsfromprimarystructurewithsupportvectormachines.JTheor.Biol.21;240(2):175-84.
56.ZhuoWang,Xin-GuangZhu,…,YuanyuanLi,YixueLi*,LeiLiu*,2006,Exploringphotosynthesisevolutionbycomparativeanalysisofmetabolicnetworksbetweenchloroplastsandphotosyntheticbacteria,BMCGenomics.,7:100,doi:10.1186/1471-2164-7-100.
57.RuoyuLuo,ShaLiao,GuanyangTao,YuanyuanLi,YixueLi*,QingmingLuo*.2006,Dynamicanalysisofoptimalityinmyocardialmetabolicnetworkundernormalandischemicconditions,MolecularSystemsBiology,2:2006.0031.
58.Yuan-YuanLi,HuiYu,Zong-MingGuo,Ting-QingGuo,KangTu,WeiLin,Yi-XueLi*,2006,Systematicanalysisofhead-to-headgeneorganization:evolutionaryconservationandpotentialbiologicalrelevance,PlosComputationalBiology,Vol.2,issue7,e74.
59.Guo-qingZhang,Zhi-weiCao,Qing-mingLuoa,Yu-DongCai,YixueLi*，2006,OperonpredictionbasedonSVM，ComputBiolChem,30,233-240.
60.LiliWang,ZhongYang,…,YixueLi*,WeiHu*,2006,ReconstructionandinsilicoanalysisofMAPKsignallingpathwaysinthehumanbloodfluke,Schistosomajaponicum,FEBSLetters580,3677-3686.
61.ZhuoFang,JiongYang,YixueLi,2006,QingmingLuoandLeiLiu*,Knowledgeguidedanalysisofmicroarraydata,JBiomedInform,Volume39,Issue4,p:401-411.
62.JingLi,QiLiu,MengshengQiu,YuchunPan,YixueLiandTieliuShi,2006,Identificationandanalysisofthemousebasic/Helix-Loop-Helixtranscriptionfactorfamily,BiochemicalandBiophysicalResearchCommunications,Volume350,Issue3,24November2006,Pages648-656.
63.LuQ,HaoP,CurcinV,HeW,LiYY,LuoQM,GuoYK,LiYX.2005,KDEBioscience:Platformforbioinformaticsanalysisworkflows.JBiomedInform,Volume39,Issue4,August2006,Pages440-450.
64.PeiHao,…,YixueLi*，GuopingZhao*,2005,Cross-hostevolutionofSARScoronavirusinpalmcivetandhuman,PNAS.102(7)，2430–2435.
65.JingchunSun,…,YixueLi*,2005,Refinedphylogeneticprofilesmethodforpredictingprotein-proteininteractions,Bioinformatics,15;21(16):3409-15.
66.PeiHao,…,YixueLi*&YangZhong*,2005,“MPSS:anintegrateddatabasesystemforsurveyingasetofproteins”，Bioinformatics.Vol.21no.9,2142–2143.
67.LuW,WuXD,…,LiYX,…,PeiG,WuJR,SunB,etal.,2005,SyntheticpeptidesderivedfromSARScoronavirusSproteinwithdiagnosticandtherapeuticpotential.FEBSLett.11;579(10):2130-6.
68.PeiHao,……,YixueLi,……,GuopingZhao,et.al.,2004,‘MolecularevolutionoftheSARS-coronavirusduringthecourseoftheSARSepidemicinChina’,Science,12March,303:1666-1669.
69.HenningHermjakob，……,YixueLi,……,ChrisHogue&RolfApweiler,2004,TheHUPOPSI'sMolecularInteractionformat—acommunitystandardfortherepresentationofproteininteractiondata,NatureBiotechnology,22，pp177–183.
70.LijianHui,……,YixueLi*，etal.,2004,“IdentificationofAlternativelySplicedmRNAVariantsRelatedtoCancersbyGenome-wideESTsAlignment.”,Oncogene，1-11.
71.ChengLuo,……,YixueLi,XuShe,andHualiangJiang,2004,NucleocapsidproteinofSARScoronavirustightlybindstohumancyclophilinA,BiochemBiophysResCommun.Aug27;321(3):557-65.
72.DengX,QiuL,YixueL*,2004,ScoringhiddenMarkovmodelstodiscriminatebeta-barrelmembraneproteins.ComputBiolChem,Jul;28(3):189-94.
*Correspondingauthor.
