個人基本情況介紹---教育及工作經轉錄和轉錄調控研究:水稻雜種優(yōu)勢分子機理的究

RNARNA

1999--

2003--

2008--助理研究員副研究員個人基本情況介紹---科研工（一）RNA-omics生物信息學方法的研RNA表觀遺傳數(shù)據(jù)（RIP-seq）分析方法的建mRNA-seq的等 表達分析方法的建mRNA-seq的可變剪 的檢測及分植物miRNA數(shù)據(jù)分析軟件的開 （2010年EST、SAGE轉錄組數(shù)據(jù)分析方法的改（2007年

RNA-據(jù)通 1998---1998---2009---個人基本情況介紹---科研（二）水稻雜種優(yōu)勢中生殖優(yōu)勢的系統(tǒng)生物學(2010雜種優(yōu)勢相 數(shù)據(jù)共享平臺的構建(2009年 片轉錄組的研究(2009 花序-根-葉片主 、專利

SongS.H.,QuH.Z.,ChenC.,HuS.N.,YuJ.Differentialgeneexpressioninanelitehybridricecultivar(Oryzasativa,L)anditsparentallinesbasedonSAGEdata.BMC ntBiology2007Sep19;7(1):49.IF：3.23SongS.H.,HuangY.F.,WangX.,WeiG.,QuH.Z.,WangW.W.,GeX.M.,HuGuozhenLiu1,LiangY.C.,J.HRGD:aDatabaseforminingpotentialheterosis-relatedgenesinnts.ntMolecularBiology.10.1007/s11103-008-9421-6,IF:3.847ZhaoD.X.SongS.H.*WangQ.ZhangX.W.HuS.NChenL.QDiscoveryofimmune-relatedgenesinmittencrab(EriocheirsinensisbyexpressedsequencetagysisofhaemocytesAquacultureIF1.735（并列第一作者）XuX.Q.,SongS.H,WangQ.,QinF.,LiuK.,ZhangX.W.,HuS.N.,ZhaoY.L.ysisandcomparisonofasetofexpressedsequencetagsoftheparthenogeneticwaterfleaDaphniacarinataMolecularGeneticsand IF:2.978（并列第一作者ZhuJ.,HeF.H.,SongS.H.,WangJ.,YuJ.Howmanyhumangenescanbedefinedashousekee withcurrentexpressiondata?BMCGenomics2008,9:172.IF:4.18WangW.W.,MengB.,GeX.M.,SongS.S.,YangY.,YuX.M.,WangL.G.,HuLiuS.Q.,YuJ.ProteomicProfilingofRiceEmbryosfromaHybridRiceCultivarandItsParentalLines.Proteomics，2008,8(22):4808-4821.IF:5.479GeX.M.,ChenW.H.,SongS.H.,WangW.W.,HuS.N.,YuJ.Transcriptomicprofilingofmatureembryofromanelitesuper-hybridriceLYP9anditsparentallinesBMC ntBiology.2008,8:114.IF：3.23YangM.,SongS.H.,LiuG.M.,ChenK.F.,TianX.J.,ZhaoZ.Z.J,HuYuJ.A ysisofproteinphosphatasesinriceand

團隊人田東陳婷田東陳婷李翠李語王西姚富2009

2012

2012

2012

2010

2014 ThePast,PresentandFutureofRNATeamWhatdowewanttodo?RNAOmics------>Informatics----- DNAmechanismofmechanismofRNA-

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ng mRNA-seqtechnologyanddata BIGTranscriptome&smallRNAData SpecialTopicandCaseOtheravailable轉錄組有轉錄產物的總和，轉錄組研究是功能組研究的一項重要內容。轉錄組是連接組遺傳信息與生物功能RNAmRNA,tRNA,rRNA,siRNA,miRNA,snoRNA,snRNAetAbout5%ofgenomeSmallNon-coding轉錄組轉錄組（transcriptome）andRNA-隨著第二代技術的迅猛發(fā)展，其高通量、快速、低成時的首選，尤其在轉錄組(RNA-seq)方面更顯示出極大的潛力。尤其相對于真核生物全組來說，轉錄組得到的序列不含有內含子及其它非編碼序列，因此轉錄組有著無可比擬的高性價比優(yōu)勢。 RNAcSNP的鑒定、可變剪接的研究、融 鑒定、RNA-RNA-seqdataOverviewofRNA-seqtranscriptome RNA‐seqdataSequenceAlignment GO KEGG SamplesandExpression ysis(>3ExpressionFusionShortReadsUnsplicedMaq,ZOOM,RMAP,SeqMap,SOAP2,SplicedHMMSplicer,MapSplice,SOAPsplice,SpliceMap,SplitSeek, t,TopHatGene/isoform KnownALEXA-Seq,htseq,IsoInfer,MISO,NovelandKnownGene/IsoformCufflinks,Scripture,MMSEQDifferentialExpressionParametricbaySeq,Cuffdiff,DEGseq,Deseq,EdgeR,GPSeq,Myrna,ASC,GENE-CounterNon-parametricapproaches ysisCumulativeCumulativeRepeatUnmappedErrorRatErrorRatQ20135 Unique and resultSoftware:Software: MappedReadsMap UniquemappedReadsExonMappedReadsIntronMappedReads AnnotationandGenomeregionstat.ofuniquemappedRNAspeciesstat.ofuniquemappedRNA ficationofgeneexpressionRPKM,ReadsPerKilobaseofexonmodelperMillionmappedreads,isdefinedinthisway[Mortazavietal.,2008]:ficationofgeneexpression(1)CalculateexpressReadsnumber>Minimum(1)CalculateexpressRPKM>MinimumRPKMRamskoldD,WangET,BurgeCB,SandbergR:Anabundanceofubiquitouslyexpressedgenesrevealedbytissuetranscriptomesequencedata.PLoSComputBiol2009,5(12):e

HeG,ZhuX,EllingAA,ChenL,WangX,GuoL,LiangM,HeH,ZhangH,ChenFetal:Globalepigeneticandtranscriptionaltrendsamongtworicesubspeciesandtheirreciprocal ntCell2010,22(1):17-33.ficationofgeneexpression(2)(2)SaturationPearson ysisbetweenDetectionofdifferentiallyexpressedSoftware:Software:KEGGpathwayannotationand KEGGpathwayannotationand NnMmPKEGGChemokinesignalingUbiquitinmediatedLong-termAlzheimer'sN-GlycanNOD-likereceptorsignalingWntsignalingTcellreceptorsignalingCellFocalFcgR-mediatedCelladhesionmoleculesHuntington'sGeneGOAnnotationGo entKEGGPathway mRNA-seqtechnologyand ysismRNA-seqmRNA-seqQuality andAnnotationandficationofgeneexpressionDetectionofdifferentiallyexpressedKEGGpathwayannotationand mRNA-seqtechnologyanddata BIGTranscriptome&smallRNAData SpecialOtheravailableRNAdata ysispipelineMapped

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ysisQualitydistribution ysiswapRNA wapRNA wapRNA 累計獨立IP累計頁 累計請求累 量mRNA-seqtechnologyand ysisBIGTranscriptome&smallRNA ysisSpecial– ysismethodsOtheravailableAdvancedtopicsinAlternativesplicing Hierarchical K-means模糊聚c=16,m=樣本300017timeCluster

Hierarchical應用舉例（二Ourrice(un-publishedCo-expressionRegulation/RegulationGeneticsregulationCo-expressionUsingUsingAlternativeMethodsandIsoformbasdtranscriptexpression DifferentiateexpressedNewisoformVariationofisoformbetweenIsoformDifferentiallyIsoformexpressedinisoformexpressionExpressedtranscriptFusetrans- ntmRNA-seqtechnologyanddata BIGTranscriptome&smallRNAData SpecialOtheravailablemRNA-Seq ysis andAssemblyBWA-BWAisafastlight-weightedtoolthatalignsrelativelyshortsequences(queries)toasequencedatabase(targe),suchasthehumanreferencegenomeSeqMap-AToolForMap MillionsOfShortSequencesToTheGenome.MAQ-standsforMap andAssemblywithQualityItbuildsassemblybymapshortreadstoreferencesequences.ERANGE-Map fyingM lianTranscriptomesbyRNA-SeqCufflinks-assemblestranscripts,estimatestheirabundances,andtestsfordifferentialexpressionandregulationinRNA-Seqsamples.iAssembler–astandalonepackagetoassembleESTsgeneratedusingSangerand/orRoche-454pyrosequencing intocontigs.Supportsplice TopHat-isafastsplicejunctionmapperforRNA-SeqSpliceMap-SpliceMapisadenovosplicejunctiondiscoverytool.ItoffershighsensitivityandsupportforarbitrarilylongRNA-seqreadlengths.MapSplice-SpliceJunction TrinityRNA-SeqAssembly–softwaresolutionstargetedtothereconstructionoffull-lengthtranscriptsandalternativelysplicedisoformsfromIlluminaRNA-SeqdataPALMapper-acombinationofthesplicedalignmentmethodQPALMAwiththeshortreadalignmenttoolGenomeMapper.Web-basedrQuant.web-isawebservicetoprovideconvenientaccesstotoolsforthe ysisofRNA-Seqdata.Galaxy-Map pipelineforIllumina,454,andSOLiDsequencingdata.UCSCGenomeBrowser-Thissitecontainsthereferencesequenceandworkingdraftassembliesforalargecollectionofgenomes.ItalsoprovidesportalstotheENCODEandNeandertalprojects.Bioconductor-Bioconductorisanopensourceandopendevelopmentsoftwareprojectforthe ysisandcomprehensionofgenomicdata.ExpEdit-isawebapplicationforassessingRNAeditinginhumanatknownoruserspecifiedsitessupportedbytranscriptdataobtainedbyRNA-Seqexperiments.Myrna-acloudcomputingtoolforRNAGenePattern-isapowerfulgenomicysistformthatprovidesaccesstomorethan100toolsforgeneexpressionysis,proteomics,SNPysisandcommondataprocessingtasks.Oqtans: tativeTranscriptomeTopHat-isafastsplicejunctionmapperforRNA-SeqScripture-isamethodfortranscriptomereconstructionthatreliessolelyonRNA-Seqreadsandanassembledgenometobuildatran