阮珏(JueRuan)
硕士生导师，副研究员
E-Mail：ruanj@big.ac.cn
研究领域：生物信息学
导师简介：学习经历：
2000年9月-2004年6月南开大学生物科学本科2004年9月-2009年6月中国科学院北京基因组研究所生物信息学博士
工作经历：
2009年7月-2011年12月中国科学院北京基因组研究所助理研究员2012年1月-至今中国科学院北京基因组研究所副研究员
学术兼职：
获奖及荣誉：
1.生物信息学(Bioinformatics)序列比对，关注于短序列与参考基因组比对以及短序列之间的联配；基因组组装，早期主要从事短序列的大基因组组装开发，目前关注于复杂基因组的解决；序列聚类，主要研究RAD序列的高效聚类及组装；基因的系统发生关系。2.DNA测序技术相关研发(DNASequencingtechnology)低频突变检测、大片段序列全长测序、单细胞基因组扩增。
近期主要学术成果：
1.Gong,Qiang,YongTao,Jian-RongYang,JunCai,YunfeiYuan,JueRuan,JinYang,HailiangLiu,WanghuaLi,andXuemeiLu.“IdentificationofMedium-sizedGenomicDeletionswithLowCoverage,Mate-pairedRestrictedTags.”BMCGenomics14,no.1(2013):51.2.Chong,Zechen,JueRuan#,andChung-IWu.“Rainbow:AnIntegratedToolforEfficientClusteringandAssemblingRAD-seqReads.”Bioinformatics28,no.21(2012):2732–2737.3.Kua,Chai-Shian,JueRuan,JohnHarting,Cheng-XiYe,MatthewRHelmus,JunYu,andCharlesHCannon.“Reference-FreeComparativeGenomicsof174Chloroplasts.”PloSOne7,no.11(2012):e48995.4.Zhou,Qi,Hong-meiZhu,Quan-feiHuang,LiZhao,Guo-jieZhang,ScottWRoy,BeatrizVicoso,Zhao-linXuan,JueRuan,andYueZhang.“DecipheringNeo-sexandBChromosomeEvolutionbytheDraftGenomeofDrosophilaAlbomicans.”BMCGenomics13,no.1(2012):109.5.Tao,Yong,JueRuan*,Shiou-HweiYeh,XuemeiLu,YuWang,WeiweiZhai,JunCai,ShaopingLing,QiangGong,andZechengChong.“RapidGrowthofaHepatocellularCarcinomaandtheDrivingMutationsRevealedbyCell-populationGeneticAnalysisofWhole-genomeData.”ProceedingsoftheNationalAcademyofSciences108,no.29(2011):12042.6.Li,Ruiqiang,HongmeiZhu,JueRuan*,WubinQian,XiaodongFang,ZhongbinShi,YingruiLi,etal.“DeNovoAssemblyofHumanGenomeswithMassivelyParallelShortReadSequencing.”GenomeResearch20,no.2(2010):265–72.doi:10.1101/gr.097261.109.7.Li,Ruiqiang,WeiFan,GengTian,HongmeiZhu,LinHe,JingCai,QuanfeiHuang,QingleCai,BoLi,andYinqiBai.“TheSequenceanddeNovoAssemblyoftheGiantPandaGenome.”Nature463,no.7279(2009):311–317.8.Huang,Sanwen,RuiqiangLi,ZhonghuaZhang,LiLi,XingfangGu,WeiFan,WilliamJLucas,XiaowuWang,BingyanXie,andPeixiangNi.“TheGenomeoftheCucumber,CucumisSativusL.”NatureGenetics41,no.12(2009):1275–1281.9.Li,Heng,BobHandsaker,AlecWysoker,TimFennell,JueRuan,NilsHomer,GaborMarth,GoncaloAbecasis,andRichardDurbin.“TheSequenceAlignment/MapFormatandSAMtools.”Bioinformatics(Oxford,England)25,no.16(2009):2078–9.doi:10.1093/bioinformatics/btp352.10.Li,Heng,JueRuan,andRichardDurbin.“MappingShortDNASequencingReadsandCallingVariantsUsingMappingQualityScores.”GenomeResearch18,no.11(2008):1851–1858.11.Wang,Jun,WeiWang,RuiqiangLi,YingruiLi,GengTian,LaurieGoodman,WeiFan,JunqingZhang,JunLi,andJuanbinZhang.“TheDiploidGenomeSequenceofanAsianIndividual.”Nature456,no.7218(2008):60–65.12.Ruan,Jue*,HengLi,ZhongzhongChen,AvrilCoghlan,LachlanJamesMCoin,YiranGuo,Jean-KarimHériché,YafengHu,KarstenKristiansen,andRuiqiangLi.“TreeFam:2008Update.”NucleicAcidsResearch36,no.suppl1(2008):D735–D740.13.Ruan,Jue*,YiranGuo,HengLi,YafengHu,FeiSong,XinHuang,KarstenKristiensen,LarsBolund,andJunWang.“PigGIS:PigGenomicInformaticsSystem.”NucleicAcidsResearch35,no.Databaseissue(2007):D654–7.doi:10.1093/nar/gkl808.14.Li,Heng,AvrilCoghlan,JueRuan*,LachlanJamesCoin,Jean-KarimHériché,LaraOsmotherly,RuiqiangLi,TaoLiu,ZhangZhang,andLarsBolund.“TreeFam:aCuratedDatabaseofPhylogeneticTreesofAnimalGeneFamilies.”NucleicAcidsResearch34,no.suppl1(2006):D572–D580.15.Wang,Jing,QingyouXia,XimiaoHe,MingtaoDai,JueRuan,JieChen,GuoYu,etal.“SilkDB:aKnowledgebaseforSilkwormBiologyandGenomics.”NucleicAcidsResearch33,no.Databaseissue(2005):D399–402.doi:10.1093/nar/gki116.16.Wang,Jing,XimiaoHe,JueRuan,MingtaoDai,JieChen,YongZhang,YafengHu,etal.“ChickVD:aSequenceVariationDatabasefortheChickenGenome.”NucleicAcidsResearch33,no.Databaseissue(2005):D438–41.doi:10.1093/nar/gki092.17.Wong,GaneKa-Shu,BinLiu,JunWang,YongZhang,XuYang,ZengjinZhang,QingshunMeng,etal.“AGeneticVariationMapforChickenwith2.8MillionSingle-nucleotidePolymorphisms.”Nature432,no.7018(December2004):717–22.doi:10.1038/nature03156.
1、国家自然科学基金青年科学基金项目，31000588，二代测序技术下转录组组装软件，2010-10-012014-12-31，在研，课题组长2、国家自然科学基金重大研究计划微进化过程中的多基因作用机制重点项目，91131904，金丝猴属物种高海拔和食性适应，2012-01-012016-12-31，在研，参与
欢迎熟悉分子生物学实验技术的生物专业或者具有较好编程能力的计算机专业的学生报考。
工作经历：
2009年7月-2011年12月中国科学院北京基因组研究所助理研究员2012年1月-至今中国科学院北京基因组研究所副研究员
主要研究领域：
1.生物信息学(Bioinformatics)序列比对，关注于短序列与参考基因组比对以及短序列之间的联配；基因组组装，早期主要从事短序列的大基因组组装开发，目前关注于复杂基因组的解决；序列聚类，主要研究RAD序列的高效聚类及组装；基因的系统发生关系。2.DNA测序技术相关研发(DNASequencingtechnology)低频突变检测、大片段序列全长测序、单细胞基因组扩增。
承担科研项目情况：
1、国家自然科学基金青年科学基金项目，31000588，二代测序技术下转录组组装软件，2010-10-012014-12-31，在研，课题组长2、国家自然科学基金重大研究计划微进化过程中的多基因作用机制重点项目，91131904，金丝猴属物种高海拔和食性适应，2012-01-012016-12-31，在研，参与
代表论著：
1.Gong,Qiang,YongTao,Jian-RongYang,JunCai,YunfeiYuan,JueRuan,JinYang,HailiangLiu,WanghuaLi,andXuemeiLu.“IdentificationofMedium-sizedGenomicDeletionswithLowCoverage,Mate-pairedRestrictedTags.”BMCGenomics14,no.1(2013):51.2.Chong,Zechen,JueRuan#,andChung-IWu.“Rainbow:AnIntegratedToolforEfficientClusteringandAssemblingRAD-seqReads.”Bioinformatics28,no.21(2012):2732–2737.3.Kua,Chai-Shian,JueRuan,JohnHarting,Cheng-XiYe,MatthewRHelmus,JunYu,andCharlesHCannon.“Reference-FreeComparativeGenomicsof174Chloroplasts.”PloSOne7,no.11(2012):e48995.4.Zhou,Qi,Hong-meiZhu,Quan-feiHuang,LiZhao,Guo-jieZhang,ScottWRoy,BeatrizVicoso,Zhao-linXuan,JueRuan,andYueZhang.“DecipheringNeo-sexandBChromosomeEvolutionbytheDraftGenomeofDrosophilaAlbomicans.”BMCGenomics13,no.1(2012):109.5.Tao,Yong,JueRuan*,Shiou-HweiYeh,XuemeiLu,YuWang,WeiweiZhai,JunCai,ShaopingLing,QiangGong,andZechengChong.“RapidGrowthofaHepatocellularCarcinomaandtheDrivingMutationsRevealedbyCell-populationGeneticAnalysisofWhole-genomeData.”ProceedingsoftheNationalAcademyofSciences108,no.29(2011):12042.6.Li,Ruiqiang,HongmeiZhu,JueRuan*,WubinQian,XiaodongFang,ZhongbinShi,YingruiLi,etal.“DeNovoAssemblyofHumanGenomeswithMassivelyParallelShortReadSequencing.”GenomeResearch20,no.2(2010):265–72.doi:10.1101/gr.097261.109.7.Li,Ruiqiang,WeiFan,GengTian,HongmeiZhu,LinHe,JingCai,QuanfeiHuang,QingleCai,BoLi,andYinqiBai.“TheSequenceanddeNovoAssemblyoftheGiantPandaGenome.”Nature463,no.7279(2009):311–317.8.Huang,Sanwen,RuiqiangLi,ZhonghuaZhang,LiLi,XingfangGu,WeiFan,WilliamJLucas,XiaowuWang,BingyanXie,andPeixiangNi.“TheGenomeoftheCucumber,CucumisSativusL.”NatureGenetics41,no.12(2009):1275–1281.9.Li,Heng,BobHandsaker,AlecWysoker,TimFennell,JueRuan,NilsHomer,GaborMarth,GoncaloAbecasis,andRichardDurbin.“TheSequenceAlignment/MapFormatandSAMtools.”Bioinformatics(Oxford,England)25,no.16(2009):2078–9.doi:10.1093/bioinformatics/btp352.10.Li,Heng,JueRuan,andRichardDurbin.“MappingShortDNASequencingReadsandCallingVariantsUsingMappingQualityScores.”GenomeResearch18,no.11(2008):1851–1858.11.Wang,Jun,WeiWang,RuiqiangLi,YingruiLi,GengTian,LaurieGoodman,WeiFan,JunqingZhang,JunLi,andJuanbinZhang.“TheDiploidGenomeSequenceofanAsianIndividual.”Nature456,no.7218(2008):60–65.12.Ruan,Jue*,HengLi,ZhongzhongChen,AvrilCoghlan,LachlanJamesMCoin,YiranGuo,Jean-KarimHériché,YafengHu,KarstenKristiansen,andRuiqiangLi.“TreeFam:2008Update.”NucleicAcidsResearch36,no.suppl1(2008):D735–D740.13.Ruan,Jue*,YiranGuo,HengLi,YafengHu,FeiSong,XinHuang,KarstenKristiensen,LarsBolund,andJunWang.“PigGIS:PigGenomicInformaticsSystem.”NucleicAcidsResearch35,no.Databaseissue(2007):D654–7.doi:10.1093/nar/gkl808.14.Li,Heng,AvrilCoghlan,JueRuan*,LachlanJamesCoin,Jean-KarimHériché,LaraOsmotherly,RuiqiangLi,TaoLiu,ZhangZhang,andLarsBolund.“TreeFam:aCuratedDatabaseofPhylogeneticTreesofAnimalGeneFamilies.”NucleicAcidsResearch34,no.suppl1(2006):D572–D580.15.Wang,Jing,QingyouXia,XimiaoHe,MingtaoDai,JueRuan,JieChen,GuoYu,etal.“SilkDB:aKnowledgebaseforSilkwormBiologyandGenomics.”NucleicAcidsResearch33,no.Databaseissue(2005):D399–402.doi:10.1093/nar/gki116.16.Wang,Jing,XimiaoHe,JueRuan,MingtaoDai,JieChen,YongZhang,YafengHu,etal.“ChickVD:aSequenceVariationDatabasefortheChickenGenome.”NucleicAcidsResearch33,no.Databaseissue(2005):D438–41.doi:10.1093/nar/gki092.17.Wong,GaneKa-Shu,BinLiu,JunWang,YongZhang,XuYang,ZengjinZhang,QingshunMeng,etal.“AGeneticVariationMapforChickenwith2.8MillionSingle-nucleotidePolymorphisms.”Nature432,no.7018(December2004):717–22.doi:10.1038/nature03156.
社会任职：
获奖及荣誉：
