在岗研究生导师情况介绍
所系名称计算生物学研究所
性别男
专业名称计算生物学
技术职务研究员
行政职务无
Mail地址khaitovich@eva.mpg.de
指导博士
生总数11指导硕士
生总数10已毕业学生通讯地址岳阳路320号计算生物学研究所
目前博士
生数10目前硕士
生数0目前在校生邮政编码200031
研究方向比较生物学
研究工作我的研究工作主要包括研究灵长类动物基因表达的一般模式和寻找对人类独特表型特征作出贡献的基因。寻找在人类进化历程中正选择的基因对研究人类潜在特殊能力,尤其是人类感知能力方面的分子机制有重要启示。
具体研究方向:
1.人类大脑在一生中尤其是童年时代经历的变化对人类感知能力的形成起了至关重要的作用。目前,我们正在研究取自从新生婴儿到完全成年的八个生命阶段的人类大脑样本所有基因的基因表达方式,及相应年龄组的黑猩猩和猕猴同样的大脑区域的基因表达方式。决定这种作用的基因将是了解人类感知能力发展的分子机制的关键所在。
2.研究人脑从发育到衰老过程中转录组(包含mRNA,miRNA,ncRNA),代谢组,蛋白组的变化以及变化调控机制。从转录组水平上建立人脑从发育到衰老的主要变化模型。通过测量并比较多组学数据,建立人脑发育衰老过程的分子变化基准图,并通过调控网络研究鉴定发育衰老过程中的关键调控因子。
3.人类疾病的表型是可得到的功能表型信息的唯一来源。为了进一步了解人类独特疾病特征的进化,将结合进化数据和临床数据,研究人类独特疾病的基因和在人类世系中正选择的标记之间的关系。
4.比较人类、黑猩猩和猕猴不同脑部区域发育衰老全过程中的转录组,代谢组,蛋白组等多种分子水平的变化,鉴定人脑特有的分子变化特征并据此探索人脑特有功能进化的机制。已发现人类大脑皮质在代谢组和转录组水平上的加速进化现象,并首次提出了人脑进化可能起源于皮质突触发育延迟。进一步将鉴定并比较人类更多脑部区域的特有分子变化特征,并通过比对认知能力紊乱相关疾病患者脑部中的多组学数据,全面解析作用于人脑发达认知能力形成下的进化机制。
5.结合已有的人类DNA序列多态数据和表达变异数据,在个体基因水平上检测正选择的标记。
获奖情况
2011年荣获青年科学家国际合作奖
指导研究
生情况
近五年来,中科院计算所生物学研究院指导研究生共11名(含已毕业和在培)
个人简介1990-1994莫斯科州立大学学生
1991-1993莫斯科州立大学交叉学科学生
1994-1995莫斯科州立大学研究助理
1994-1995俄罗斯蛋白质研究中心研究助理
1995-1999美国伊利诺州立大学研究生
1996-1999美国伊利诺州立大学研究助理
1999-2000美国伊利诺州立大学博士后
2000-2003德国马普学会进化所博士后
2001-2006德国莱比锡大学讲师
2006--计算生物学研究所课题组长
近期论文SelectedPublications:
2012:
LiuX,SomelM,TangL,YanZ,JiangX,GuoS,YuanY,HeL,OleksiakA,ZhangY,LiN,HuY,ChenW,QiuZ,PääboS,KhaitovichP.Extensionofcorticalsynapticdevelopmentdistinguisheshumansfromchimpanzeesandmacaques.GenomeRes,2012,
2011:
SomelM,LiuX,TangL,YanZ,HuH,GuoS,JiangX,ZhangX,XuG,XieG,LiN,HuY,ChenW,PääboS,KhaitovichP.MicroRNA-drivendevelopmentalremodelinginthebraindistinguisheshumansfromotherprimates.PLoSBiol.2011Dec;9(12):e1001214.Epub2011Dec6.PubMedPMID:22162950;PubMedCentralPMCID:PMC3232219.
HuHY,GuoS,XiJ,YanZ,FuN,ZhangX,MenzelC,LiangH,YangH,ZhaoM,ZengR,ChenW,PääboS,KhaitovichP.MicroRNAexpressionandregulationinhuman,chimpanzee,andmacaquebrains.PLoSGenet.2011Oct;7(10):e1002327.Epub2011Oct13.PubMedPMID:22022286;PubMedCentralPMCID:PMC3192836.
BrawandD,SoumillonM,NecsuleaA,JulienP,CsárdiG,HarriganP,WeierM,LiechtiA,Aximu-PetriA,KircherM,AlbertFW,ZellerU,KhaitovichP,GrütznerF,BergmannS,NielsenR,PääboS,KaessmannH.Theevolutionofgeneexpressionlevelsinmammalianorgans.Nature.2011Oct19;478(7369):343-8.doi:10.1038/nature10532.PubMedPMID:22012392.
YuanY,ChenYP,NiS,XuAG,TangL,VingronM,SomelM,KhaitovichP.Developmentandapplicationofamodifieddynamictimewarpingalgorithm(DTW-S)toanalysesofprimatebrainexpressiontimeseries.BMCBioinformatics.2011Aug18;12:347.PubMedPMID:21851598;PubMedCentralPMCID:PMC3180390.
JinC,LiJ,GreenCD,YuX,TangX,HanD,XianB,WangD,HuangX,CaoX,YanZ,HouL,LiuJ,ShukeirN,KhaitovichP,ChenCD,ZhangH,JenuweinT,HanJD.HistonedemethylaseUTX-1regulatesC.eleganslifespanbytargetingtheinsulin/IGF-1signalingpathway.CellMetab.2011Aug3;14(2):161-72.PubMedPMID:21803287.
YanZ,HuHY,JiangX,MaierhoferV,NebE,HeL,HuY,HuH,LiN,ChenW,KhaitovichP.WidespreadexpressionofpiRNA-likemoleculesinsomatictissues.NucleicAcidsRes.2011Aug;39(15):6596-607.Epub2011May5.PubMedPMID:21546553;PubMedCentralPMCID:PMC3159465.
FuX,GiavaliscoP,LiuX,CatchpoleG,FuN,NingZB,GuoS,YanZ,SomelM,PääboS,ZengR,WillmitzerL,KhaitovichP.Rapidmetabolicevolutioninhumanprefrontalcortex.ProcNatlAcadSciUSA.2011Apr12;108(15):6181-6.Epub2011Mar28.PubMedPMID:21444806;PubMedCentralPMCID:PMC3076848.
LiuY,HanD,HanY,YanZ,XieB,LiJ,QiaoN,HuH,KhaitovichP,GaoY,HanJD.AbinitioidentificationoftranscriptionstartsitesintheRhesusmacaquegenomebyhistonemodificationandRNA-Seq.NucleicAcidsRes.2011Mar;39(4):1408-18.Epub2010Oct14.PubMedPMID:20952408;PubMedCentralPMCID:PMC3045608.
2010:
SomelM,GuoS,FuN,YanZ,HuHY,XuY,YuanY,NingZ,HuY,MenzelC,HuH,LachmannM,ZengR,ChenW,KhaitovichP.MicroRNA,mRNA,andproteinexpressionlinkdevelopmentandaginginhumanandmacaquebrain.GenomeRes.2010Sep;20(9):1207-18.Epub2010Jul20.PubMedPMID:20647238;PubMedCentralPMCID:PMC2928499.
GigerT,KhaitovichP,SomelM,LorencA,LizanoE,HarrisLW,RyanMM,LanM,WaylandMT,BahnS,PääboS.Evolutionofneuronalandendothelialtranscriptomesinprimates.GenomeBiolEvol.2010Jul12;2:284-92.Print2010.PubMedPMID:20624733;PubMedCentralPMCID:PMC2998193.
KhaitovichP.Annotatingconservedandnovelfeaturesofprimatetranscriptomesusingsequencing.GenomeBiol.2010;11(7):125.Epub2010Jul23.PubMedPMID:20624272;PubMedCentralPMCID:PMC2926776.
XuAG,HeL,LiZ,XuY,LiM,FuX,YanZ,YuanY,MenzelC,LiN,SomelM,HuH,ChenW,PääboS,KhaitovichP.Intergenicandrepeattranscriptioninhuman,chimpanzeeandmacaquebrainsmeasuredbyRNA-Seq.PLoSComputBiol.2010Jul1;6:e1000843.PubMedPMID:20617162;PubMedCentralPMCID:PMC2895644.
ShaoNY,HuHY,YanZ,XuY,HuH,MenzelC,LiN,ChenW,KhaitovichP.ComprehensivesurveyofhumanbrainmicroRNAbydeepsequencing.BMCGenomics.2010Jun30;11:409.PubMedPMID:20591156;PubMedCentralPMCID:PMC2996937.
LiuY,HuW,WangH,LuM,ShaoC,MenzelC,YanZ,LiY,ZhaoS,KhaitovichP,LiuM,ChenW,BarnesBM,YanJ.GenomicanalysisofmiRNAsinanextrememammalianhibernator,theArcticgroundsquirrel.PhysiolGenomics.2010Sep;42A(1):39-51.Epub2010May4.PubMedPMID:20442247.
2009:
HoffmannS,OttoC,KurtzS,SharmaCM,KhaitovichP,VogelJ,StadlerPF,HackermüllerJ.Fastmappingofshortsequenceswithmismatches,insertionsanddeletionsusingindexstructures.PLoSComputBiol.2009Sep;5(9):e1000502.Epub2009Sep11.PubMedPMID:19750212;PubMedCentralPMCID:PMC2730575.
HuHY,YanZ,XuY,HuH,MenzelC,ZhouYH,ChenW,KhaitovichP.SequencefeaturesassociatedwithmicroRNAstrandselectioninhumansandflies.BMCGenomics.2009Sep4;10:413.PubMedPMID:19732433;PubMedCentralPMCID:PMC2751786.
DannemannM,LorencA,HellmannI,KhaitovichP,LachmannM.Theeffectsofprobebindingaffinitydifferencesongeneexpressionmeasurementsandhowtodealwiththem.Bioinformatics.2009Nov1;25(21):2772-9.Epub2009Aug18.PubMedPMID:19689957.
LangenbergerD,Bermudez-SantanaC,HertelJ,HoffmannS,KhaitovichP,StadlerPF.EvidenceforhumanmicroRNA-offsetRNAsinsmallRNAsequencingdata.Bioinformatics.2009Sep15;25(18):2298-301.Epub2009Jul6.PubMedPMID:19584066.
StadlerPF,ChenJJ,HackermüllerJ,HoffmannS,HornF,KhaitovichP,KretzschmarAK,MosigA,ProhaskaSJ,QiX,SchuttK,UllmannK.EvolutionofvaultRNAs.MolBiolEvol.2009Sep;26(9):1975-91.Epub2009Jun2.PubMedPMID:19491402.
HarrisLW,LockstoneHE,KhaitovichP,WeickertCS,WebsterMJ,BahnS.Geneexpressionintheprefrontalcortexduringadolescence:implicationsfortheonsetofschizophrenia.BMCMedGenomics.2009May20;2:28.PubMedPMID:19457239;PubMedCentralPMCID:PMC2694209.
WeickertCS,ElashoffM,RichardsAB,SinclairD,BahnS,PaaboS,KhaitovichP,WebsterMJ.Transcriptomeanalysisofmale-femaledifferencesinprefrontalcorticaldevelopment.MolPsychiatry.2009Jun;14(6):558-61.PubMedPMID:19455171.
FuX,FuN,GuoS,YanZ,XuY,HuH,MenzelC,ChenW,LiY,ZengR,KhaitovichP.EstimatingaccuracyofRNA-Seqandmicroarrayswithproteomics.BMCGenomics.2009Apr16;10:161.PubMedPMID:19371429;PubMedCentralPMCID:PMC2676304.
SomelM,FranzH,YanZ,LorencA,GuoS,GigerT,KelsoJ,NickelB,DannemannM,BahnS,WebsterMJ,WeickertCS,LachmannM,PääboS,KhaitovichP.Transcriptionalneotenyinthehumanbrain.ProcNatlAcadSciUSA.2009Apr7;106(14):5743-8.Epub2009Mar23.PubMedPMID:19307592;PubMedCentralPMCID:PMC2659716.
2008:
FarkasLM,HaffnerC,GigerT,KhaitovichP,NowickK,BirchmeierC,PääboS,HuttnerWB.(2008)Insulinoma-associated1hasapanneurogenicroleandpromotesthegenerationandexpansionofbasalprogenitorsinthedevelopingmouseneocortex.Neuron9;60(1):40-55
ChaixR,SomelM,KreilDP,KhaitovichP,LunterGA.(2008)Evolutionofprimategeneexpression:driftandcorrectivesweeps?Genetics180(3):1379-89
KhaitovichP,LockstoneHE,WaylandMT,TsangTM,JayatilakaSD,GuoAJ,ZhouJ,SomelM,HarrisLW,HolmesE,PääboS,BahnS.(2008)Metabolicchangesinschizophreniaandhumanbrainevolution.GenomeBiol.9(8):R124.
BonnefontJ,NikolaevSI,PerrierAL,GuoS,CartierL,SorceS,LaforgeT,AubryL,KhaitovichP,PeschanskiM,AntonarakisSE,KrauseKH.(2008)EvolutionaryforcesshapethehumanRFPL1,2,3genestowardaroleinneocortexdevelopment.AmJHumGenet.83(2):208-18.
SomelM,CreelyH,FranzH,MuellerU,LachmannM,KhaitovichP,PääboS.(2008)Humanandchimpanzeegeneexpressiondifferencesreplicatedinmicefeddifferentdiets.PLoSONE3(1):e1504.
2007:
KhaitovichP.(2007)Brainexpression--isitallinourSNPs?MolSystBiol.3:155
Fu,N.,Drinnenberg,I.,Kelso,J.,Wu,J.R.,Paabo,S.,Zeng,R.,andKhaitovich,P.(2007).ComparisonofproteinandmRNAexpressionevolutioninhumansandchimpanzees.PLoSONE2,e216.
Prufer,K.,Muetzel,B.,Do,H.H.,Weiss,G.,Khaitovich,P.,Rahm,E.,Paabo,S.,Lachmann,M.,andEnard,W.(2007).FUNC:apackagefordetectingsignificantassociationsbetweengenesetsandontologicalannotations.BMCBioinformatics8,41.
2006:
Somel,M.,Khaitovich,P.,Bahn,S.,Paabo,S.,andLachmann,M.(2006).Geneexpressionbecomesheterogeneouswithage.CurrBiol16,R359-360.
Khaitovich,P.,Tang,K.,Franz,H.,Kelso,J.,Hellmann,I.,Enard,W.,Lachmann,M.,andPaabo,S.(2006).Positiveselectionongeneexpressioninthehumanbrain.CurrBiol16,R356-358.
Khaitovich,P.,Kelso,J.,Franz,H.,Visagie,J.,Giger,T.,Joerchel,S.,Petzold,E.,Green,R.E.,Lachmann,M.,andPaabo,S.(2006).Functionalityofintergenictranscription:anevolutionarycomparison.PLoSGenet2,e171.
Khaitovich,P.,Enard,W.,Lachmann,M.,andPaabo,S.(2006).Evolutionofprimategeneexpression.NatRevGenet7,693-702.
Creely,H.,andKhaitovich,P.(2006).Humanbrainevolution.ProgBrainRes158,295-309.
2005:
Yohn,C.T.,Jiang,Z.,McGrath,S.D.,Hayden,K.E.,Khaitovich,P.,Johnson,M.E.,Eichler,M.Y.,McPherson,J.D.,Zhao,S.,Paabo,S.,etal.(2005).Lineage-SpecificExpansionsofRetroviralInsertionswithintheGenomesofAfricanGreatApesbutNotHumansandOrangutans.PLoSBiol3,1-11.
Khaitovich,P.,Paabo,S.,andWeiss,G.(2005).Towardaneutralevolutionarymodelofgeneexpression.Genetics170,929-939.
Khaitovich,P.,Hellmann,I.,Enard,W.,Nowick,K.,Leinweber,M.,Franz,H.,Weiss,G.,Lachmann,M.,andPaabo,S.(2005).Parallelpatternsofevolutioninthegenomesandtranscriptomesofhumansandchimpanzees.Science309,1850-1854.
Heissig,F.,Krause,J.,Bryk,J.,Khaitovich,P.,Enard,W.,andPaabo,S.(2005).Functionalanalysisofhumanandchimpanzeepromoters.GenomeBiol6,R57.
Fraser,H.B.,Khaitovich,P.,Plotkin,J.B.,Paabo,S.,andEisen,M.B.(2005).AgingandGeneExpressioninthePrimateBrain.PLoSBiol3,e274.
Franz,H.,Ullmann,C.,Becker,A.,Ryan,M.,Bahn,S.,Arendt,T.,Simon,M.,Paabo,S.,andKhaitovich,P.(2005).Systematicanalysisofgeneexpressioninhumanbrainsbeforeandafterdeath.GenomeBiol6,R112.
Cheng,Z.,Ventura,M.,She,X.,Khaitovich,P.,Graves,T.,Osoegawa,K.,Church,D.,DeJong,P.,Wilson,R.K.,Paabo,S.,etal.(2005).Agenome-widecomparisonofrecentchimpanzeeandhumansegmentalduplications.Nature437,88-93.