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阮珏课题组

来源: 发布者: 时间:2020年02月10日

  阮珏课题组

  课题组长

  阮珏,研究员,博士生导师,组学技术研究中心主任,农业基因组学技术研发与应用创新团队首席科学家。主要从事基因组领域的方法学研发。针对序列组装、序列比对和体细胞变异检测等基因组学基础问题,进行系统的方法学研究。在Nature、Nature Methods、Nature Genetics、Nature Communications、National Science Reviews等期刊以一作或通讯作者(含并列)发表16篇学术论文,所有学术论文累计他引14000多次。获得4项发明专利授权。国家优秀青年基金获得者,中国农科院“青年英才”,2016年荣获“中国专利优秀奖”,2018年获评农业农村部“杰出青年农业科学家”,2019年荣获“广东青年五四奖章”。

 

  工作经历

  2017.5至今                      中国农业科学院农业基因组研究所                        研究员

  2014.5 至 2017.4            中国农业科学院深圳农业基因组研究所                  研究员

  2012.1 至 2014.4            中国科学院北京基因组研究所                               副研究员

  2009.7 至 2011.12          中国科学院北京基因组研究所                               助理研究员

 

  教育经历

  中国科学院北京基因组研究所           生物信息学        博士             2004.9 - 2009.7

  南开大学                                         生物科学            学士             2000.9 - 2004.7

 

  团队成员

  研究人员:秦茂、艾成、李阿伦、伍世刚、侯志浩、谢欣(助理)、刘海琳(博士后)

  研究生:赵凤利(已博士毕业)、冯虎(博士)、王晓波(博士)、丁璐璐(博士)、张勇(硕士)

  课题组联系方式: 阮珏 <ruanjue@caas.cn>、谢欣<xiexin01@caas.cn>

 

  团队研究方向:

  团队研究方向主要包括全基因组组装算法、极低频点突变检测、基因组结构变异检测、DNA存储技术、以及基因组分析技术开发。1)研发计算效率极高的三代长序列组装算法,以降低大型复杂基因组组装对计算资源的巨大需求;2)为提高结构变异的检测准确性和敏感性,开发高效算法;3)为针对性提高基因组极低频突变测序的检测效率与数据利用率,开发新型高效测序检测技术;4)实现产学研结合,将基因组学技术应用到科研项目,辅助解决重大科研问题。

 

  研究进展:

  团队针对最新的测序技术,以序列比对与基因组组装技术为重点,展开了多个重难点算法与软件的开发与应用,推动了数项重大合作研究的顺利进行。

  重要进展成果1:率先提出了将256个连续碱基合并为一个基本比对单元的长序列比对思路(kmer-bin-mapping),显著提高了测序数据的比对速度,并开发了三代长序列组装算法WTDBG,在保证组装结果的连续性和准确性下,极大地提高了第三代数据的组装速度,首次将数据分析时间降低到少于数据产出时间;

  重要进展成果2:开发的NovoBreak算法有效地提高结构变异的检测准确性和敏感性,在领域内权威的国际体细胞突变检测挑战赛上,连续取得最佳平衡准确度;开发了基因组极低频突变测序检测方法O2N-Seq,不仅极大地降低了第二代测序技术的碱基错误率,且数据有效利用率较传统标签法高出10-30倍;

  重要进展成果3:先后与多个科研院所及高校进行了以基因组学技术为支撑的项目合作,在Nature、Nature Genetics、Nature Methods、Nature Communications、National Science Review、Genome Research等期刊上发表一系列文章,在领域内均有较高的引用率。

 

  PI

  Jue Ruan, Research Professor, Doctoral Advisor, Director of the Omics Technology Research Center, Chief scientist of Agricultural Genomics Technology Innovation & Application Innovative Group, His research focuses on the Methodology in the Genome Field, which mainly on  genome  sequence alignment, genome assemble, variation detection of somatic cell, etc. He has published 16 SCI papers (the first author or corresponding author) in journals including Nature, Nature Methods, Nature Genetics, Genome Research, PNAS, Nature Communications. All publications have  total citations of 14000 times to date. He obtained 4 patents for innovation. He is the winner of National Excellent Youth Fund, selected as the "Young Talents" of Chinese Academy of Agricultural Sciences, owner of the 18th Chinese Outstanding Patent Invention & Industrial Design in 2016, awarded with “the Excellent Youth Agricultural Scientist” in 2018 by Ministry of Agriculture and Rural Affairs, China,and obtained Guangdong Province's Youth Award In 2019.

  

  Working Experience

  Agricultural Genomics Institute at Shenzhen-CAAS             

  research Professor                                                                   2017.5 – Present

  Shenzhen Agricultural Genomics Institute at Shenzhen-CAAS   

  research Professor                                                                   2014.5 – 2017.4

  Chinese Academy of Sciences      

  associate professo                                                                   2012.1 – 2014.4

  Chinese Academy of Sciences      

  research associate                                                                   2009.7 – 2011.12

  

  Education Experience

  Chinese Academy of Sciences Bioinformatics    Ph.D                    2004.1–2009.7

  Nankai University                   Science of Life  Master                 2000.9–2004.7

  

  Research Interest

  Our team focuses on the development of novel genomic technologies on genome assembly, ultra-low frequency mutation detections, genomic structure variation detections, digital DNA data storage, and genome analysis. Specifically, we work on 1)developing efficient algorithms of assembling long sequencing reads in order to reduce computational burden under heavy workloads; 2) increasing the accuracy and sensitivity of detecting structural variations in genomics; 3) optimizing the technology of detecting and tracking extremely low-frequency mutations; 4) applying the technologies and methods in genomics to other scientific research with aims to better understand and help solve important scientific problems.

 

  Major Achievements

  We developed multiple lines of approaches in solving important problems in genomics. Specifically

  We proposed a novel approach of analyzing the continuous 256 bases as a mapping unit (kmer-bin-mapping, KBM) in computing to increase the speed of reads, developed software WTDBG for long reads assembly with high efficiency, and reduced of data analysis time to less than data output time for the first time. We designed novel algorithms, NovoBreak and O2N-Seq, which significantly improved the accuracy and sensitivity in detecting structural variations and extremely low-frequency mutations, and increased the usability of collected data by 10-30 times compared to traditional approaches; We collaborated with several academic institutes on the genomics research, and published papers in high-impact journals including Nature、Nature Genetics、Nature Methods、Nature Communications、National Science Review、Genome Research.

  

  Selected Publication

  1.Jue Ruan and Heng Li.“Fast and accurate long-read assembly with wtdbg2.”Nature Methods,2019.12.10

        2.Mao Qin, Shigang Wu, Alun Li, Fengli Zhao, Hu Feng, Lulu Ding and Jue Ruan.“LRScaf: improving draft genomes using long noisy reads.”BMC Genomics,2019.20(1)955.

        3.WenSheng Wang, Ramil Mauleon, ZhiQiang Hu, Dmytro Chebotarov, ShuaiShuai Tai, ZhiChao Wu, Min Li, TianQing Zheng, Roven Rommel Fuentes, Fan Zhang, Locedie Mansueto, Dario Copetti,...Ruaraidh Sackville Hamilton; , Rod A. Wing  ,Jue Ruan. ,Gengyun Zhang,Chaochun Wei, Nickolai Alexandrov, Kenneth L. McNally, Zhikang Li& Hei Leung."Genomic variation in 3,010 diverse accessions of Asian cultivated rice." Nature,2018.557 (7703): 43-49.(Jue Ruan is the co-corresponding author)

  4.Guo-Dong Wang, Xiu-Juan Shao, Bing Bai, Junlong Wang,Xiaobo Wang, Xue Cao, Yan-Hu Liu, Xuan Wang1, Ting-Ting Yin,Shao-Jie Zhang, Yan Lu, Zechong Wang, Lu Wang, Wenming Zhao,Bing Zhang, Jue Ruan and Ya-Ping Zhang,Structural variation during dog domestication: insights from gray wolf and dhole genomes.National Science Review,2018,6,19.

  5.Kaile Wang, Shujuan Lai, Xiaoxu Yang, Tianqi Zhu, Xuemei Lu, Chung-I Wu, and Jue Ruan. Ultrasensitive and High-Efficiency Screen of de Novo Low-Frequency Mutations by O2n-Seq.Nature Communications, 2017,5,15335.

  6.Zechen Chong, Jue Ruan, Min Gao, et al. novoBreak: local assembly for breakpoint detection in cancer genomes. Nature Methods, 2016, 11: 65-67.

  7.Li Yu, Guodong Wang, Jue Ruan, Yongbin Chen, et al. Genomic analysis of snub-nosed monkeys (Rhinopithecus) identifies genes and processes related to high-altitude adaptation. Nature Genetics, 2016, 48:947-952.

  8.Kaile,Wang Qin Ma, Lan Jiang , Shujuan Lai, Xuemei Lu, Yali Hou, Chung-I Wu, Jue Ruan. Ultra-precise detection of mutations by droplet-based amplification of circularized DNA.BMC Genomics, 2016, 17: 214-214.

 

  Selected Patent

  1. ZL201410448968.0,改进的测序文库及其制备和应用,王开乐;阮珏;吕雪梅;吴仲义

        2. ZL201410448896.X,一种DNA扩增方法,阮珏;王开乐;沈栩吕;雪梅;吴仲义

        3. CN201310651462.5,测序文库及其制备和应用,阮珏;王开乐;吕雪梅;吴仲义 

        4. ZL200810218338.9,一种短序列组装中构建图的方法及系统,李瑞强;阮珏;朱红梅;李松岗;王俊;杨焕明;汪建

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