阮珏课题组

Ruan Jue Lab

课题组长

阮珏，研究员，博士生导师，农业基因组学技术研发与应用创新团队首席科学家，长期专注于基因组组装问题，主导开发的三代测序数据组装与序列比对算法SMARTdenovo、wtdbg和bsalign，突破了三代数据组装速度落后于测序速度的领域难题，成为三代测序组装的主流算法。以第一/通讯作者（含并列）在Nature、Cell、Nature Methods、National Science Review、Nature Communications等国际学术期刊上发表论文30余篇，所有论文累计被引4万余次（Scopus）。

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

 

课题组成员

研究方向	学生	科研助理
基因组算法开发	王晓波、张妍、宗培玉、邓文鹏、张勇、李新慧、刘帆波	伍世刚、刘海琳、于洋
表型组算法开发	常建业、刘秉文、潘禹辰、董林森、候登峰、程豪（客座）
DNA存储技术	丁璐璐、许亚苹
测序方法研发	侯志浩、张娅、关欣悦
生物信息分析	周红玲、吴越（客座）	艾成、李阿伦、宋艳妮

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

研究方向:

课题组主要从事组学算法研发：1）开发快速精准的序列比对与组装算法开发；2）开发高效的图基因组构建与分析流程；3）制备图像表型标准数据集，搭建共享平台，开发植物表型图像识别算法；4）开发具有高纠错能力的DNA数字存储算法；5）拓展测序方法研发：如低频突变检测，宏基因组测序等；6）在组学算法研发的基础上，进一步开展生物信息学研究，为组学算法的深入利用提供支撑。

研究进展：

课题组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：提出被广泛使用的同聚碱基压缩方法SMARTdenovo，实现了高效率三代长序列组装，该算法能够在3,000 核心小时（CPU * hours）内完成人类基因组组装，效率较早期算法HGAP提高100多倍。2015年起SMARTdenovo供领域开源使用，是早期纳米孔测序组装的首选组装算法；

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、Cell、Cell Research、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。

 

代表论文:

(1) Chentao Yang#, Yang Zhou#, Yanni Song#, Dongya Wu#, Yan Zeng#, Lei Nie, Panhong, Liu,Shilong Zhang, Guangji Chen, Jinjin Xu, Hongling Zhou, Long Zhou, Xiaobo Qian, Chenlu Liu, Shangjin Tan,Chengran Zhou, Wei Dai, Mengyang Xu, Yanwei Qi, Xiaobo Wang, Lidong Guo, Guangyi Fan, Aijun Wang, Yuan Deng, Yong Zhang, Jiazheng Jin, Yunqiu He, Chunxue Guo, Guoji Guo, Qing Zhou, Xun Xu, Huanming Yang, Jian Wang, Shuhua Xu, Yafei Mao,Xin Jin, Jue Ruan*and Guojie Zhang*. "The complete and fully-phased diploid genome of a male Han Chinese."Cell Research. 2023,0:1–17.

(2) Yong Zhang#, Hong-Wei Lu#, Jue Ruan*. "GAEP: a comprehensive genome assembly evaluating pipeline."Journal of Genetics and Genomics.2023,0:1-8.

(3) Lianguang Shang#, Xiaoxia Li#, Huiying He#, Qiaoling Yuan#, Yanni Song#, Zhaoran Wei#, Hai Lin#, Min Hu#, Fengli Zhao#,Chao Zhang, Yuhua Li, Hongsheng Gao, Tianyi Wang, Xiangpei Liu, Hong Zhang, Ya Zhang, Shuaimin Cao, Xiaoman Yu, Bintao Zhang, Yong Zhang, Yiqing Tan, Mao Qin, Cheng Ai, Yingxue Yang, Bin Zhang, Zhiqiang Hu, Hongru Wang, Yang Lv, Yuexing Wang, Jie Ma, Quan Wang, Hongwei Lu, Zhe Wu, Shanlin Liu, Zongyi Sun, Hongliang Zhang, Longbiao Guo, Zichao Li, Yongfeng Zhou ,Jiayang Li,Zuofeng Zhu*, Guosheng Xiong*, Jue Ruan*,Qian Qian*."A super pan-genomic landscape of rice."Cell Research. 2022,32(10): 878-896.

(4) Dingyu Yan*, Xier Luo#, Jiabin Tang#, Shanghua Xu, Kongwei Huang, Xiaobo Wang, Tong Feng, Tengcheng Que, Miaomiao Jia, Xiaobing Guo, Saif ur Rehman, Zhipeng Li, Yufeng Yang, Kaixiang Li, Kuiqing Cui, Jue Ruan*, and Qingyou Liu*. "High-Quality Genomes of Pangolins: Insights into the Molecular Basis of Scale Formation and Adaption to Myrmecophagous Diet."Molecular Biology and Evolution, 2022,40(1):1-15.

(5) Yong Shao*, Xiao-Bo Wang#, Mei-Ling Zhang#, Yan Liu#, Sheng Wang, Bao-Lin Zhang, Min-Min Yang, Ming-Hai Yang, Ting Jia, Tian-Chun Pu, Yan Lu, He Liu, Zhe Xu, Bo Li, Ning Liu, Violet Magoma Onsongo, Dong-Dong Wu, Cheng-Lin Zhang*, Jue Ruan*, and Yan Li*. "Long-Read Genome Sequencing Provides Molecular Insights into Scavenging and Societal Complexity in Spotted Hyena Crocuta crocuta. "Molecular Biology and Evolution, 2022,39(3):1-13.

(6) Xiumei Xing*, Cheng Ai#, Tianjiao Wang#, Yang Li#, Huitao Liu#, Pengfei Hu#, Guiwu Wang#, Huamiao Liu, Hongliang Wang, Ranran Zhang, Junjun Zheng, Xiaobo Wang, Lei Wang, Yuxiao Chang, Qian Qian, Jinghua Yu, Lixin Tang, Shigang Wu, Xiujuan Shao, Alun Li, Peng Cui, Wei Zhan, Sheng Zhao, Zhichao Wu, Xiqun Shao, Yimeng Dong, Min Rong, Yihong Tan, Xuezhe Cui, Shuzhuo Chang, Xingchao Song, Tongao Yang, Limin Sun, Yan Ju, Pei Zhao, Huanhuan Fan, Ying Liu, Xinhui Wang, Wanyun Yang, Min Yang, Tao Wei, Shanshan Song, Jiaping Xu, Zhigang Yue, Qiqi Liang*, Chunyi Li*, Jue Ruan*, and Fuhe Yang*. "The first high-quality reference genome of sika deer provides insights for high-tannin adaptation."Genomics, Proteomics & Bioinformatics, 2022,21(1):203-215.

(7) Weihua Pan#*, and Jue Ruan#*. "En Route to Completion: What Is An Ideal Reference Genome?"Genomics Proteomics & Bioinformatics, 2022,20(1), 1-3.

(8) Rui Ruan#, Tong Feng#, Ying Li, Huamei Yue, Huan Ye, Hao Du, Qingyou Liu, Jue Ruan*, Chuangju Li*, and Qiwei Wei*. "Screening and identification of female-specific DNA sequences in octaploid sturgeon using comparative genomics with high-throughput sequencing."Genomics, 2021,113(6).

(9) Xier Luo#, Kuiqing Cui#, Zhiqiang Wang#, Zhipeng Li, Zhengjiao Wu, Weiyi Huang, Xing-Quan Zhu, Jue Ruan*, Weiyu Zhang*, and Qingyou Liu*. "High-quality reference genome of Fasciola gigantica: Insights into the genomic signatures of transposon-mediated evolution and specific parasitic adaption in tropical regions."PLoS Neglected Tropical Diseases, 2021,15(10):1-24.

(10) Hailin Liu#, Xin Han#, Jue Ruan#, Lian Xu#, and Bing He#*. "Transcriptome Analysis of Ginkgo biloba L. Leaves across Late Developmental Stages Based on RNA-Seq and Co-Expression Network."Forests, 2021,12(3):1-16.

(11) Hailin Liu#, Xiaobo Wang#, Guibin Wang#, Peng Cui#, Shigang Wu, Cheng Ai, Nan Hu, Alun Li, Bing He, Xiujuan Shao, Zhichao Wu, Hu Feng, Yuxiao Chang, Desheng Mu, Jing Hou, Xiaogang Dai, Tongming Yin*, Jue Ruan*, and Fuliang Cao*. "The nearly complete genome of Ginkgo biloba illuminates gymnosperm evolution."Nature Plants, 2021, 7 (6): 748-+..

(12) Hailin Liu#, Shigang Wu#, Alun Li#, and Jue Ruan*. "SMARTdenovo: a de novo assembler using long noisy reads."Gigabyte, 2021,2021:15.

(13) Kun Wang#, Jun Wang#, Chenglong Zhu#, Liandong Yang#, Yandong Ren#, Jue Ruan#, Guangyi Fan#, Jiang Hu#, Wenjie Xu, Xupeng Bi, Youan Zhu, Yue Song, Huatao Chen, Tiantian Ma, Ruoping Zhao, Haifeng Jiang, Bin Zhang, Chenguang Feng, Yuan Yuan, Xiaoni Gan, Yongxin Li, Honghui Zeng, Qun Liu, Yaolei Zhang, Feng Shao, Shijie Hao, He Zhang, Xun Xu, Xin Liu, Depeng Wang, Min Zhu, Guojie Zhang, Wenming Zhao*, Qiang Qiu*, Shunping He*, and Wen Wang*. "African lungfish genome sheds light on the vertebrate water-to-land transition."Cell, 2021,184(5), 1362-1376.

(14) Fengli Zhao#, Yuexing Wang#, Jianshu Zheng#, Yanling Wen, Minghao Qu, Shujing Kang, Shigang Wu, Xiaojuan Deng, Kai Hong, Sanfeng Li, Xing Qin, Zhichao Wu, Xiaobo Wang, Cheng Ai, Alun Li, Longjun Zeng ,Jiang Hu, Dali Zeng, Lianguang Shang, Quan Wang, Qian Qian, Jue Ruan* and Guosheng Xiong*. "A Genome-Wide Survey of Copy Number Variations Reveals an Asymmetric Evolution of Duplicated Genes in Rice."BMC Biology， 2020.26;18(1):73.

(15) Xinchao Wang#, Hu Feng#, Yuxiao Chang#, Chunlei Ma#, Liyuan Wang#, Xinyuan Hao#, A lun Li, Hao Cheng, Lu Wang, Peng Cui, Jiqiang Jin, Xiaobo Wang, Kang Wei, Cheng Ai, Sheng Zhao, Zhichao Wu, Youyong Li, Benying Liu, Guo-Dong Wang*, Liang Chen*, Jue Ruan* and Yajun Yang*. "Population sequencing enhances understanding of tea plant evolution."Nature Communications，2020,7;11(1):4447.

(16) Jing Luo #, Jing Chai#, Yanling Wen#, Min Tao#, Guoliang Lin#, Xiaochuan Liu, Li Ren, Zeyu Chen, Shigang Wu, Shengnan Li, Yude Wang, Qinbo Qin, Shi Wang, Yun Gao, Feng Huang, Lu Wang, Cheng Ai, Xiaobo Wang, Lianwei Li, Chengxi Ye, Huimin Yang, Mi Luo, Jie Chen, Hong Hu, Liujiao Yuan, Li Zhong, Jing Wang, Jian Xu, Zhenglin Du, Zhanshan Sam Ma,  Robert W.Murphy, Axel Meyer, Jianfang Gui, Peng Xu*, Jue Ruan*, Z.Jeffrey Chen*, Shaojun Liu*, Xuemei Lu*, Ya-ping Zhang*. "From asymmetrical to balanced genomic diversification during rediploidization: subgenomic evolution in allotetraploid fish."Science Advance. 2020.6,22:7677.

(17) Yong Shao#, Xiaobo Wang#, Jinjin Zhang#, Mingli Li#, Shousong Wu, Xiyao Ma, Xue Wang, Huifang Zhao, Yuan Li, Helenhe Zhu, David M. Irwin, Depeng Wang, Guojie Zhang*, Jue Ruan*, Dongdong Wu*."Genome and single-cell RNA-sequencing of the earthworm Eisenia andrei identifies cellular mechanisms underlying regeneration."Nature Communications. 2020,11(1):2656.

(18) Xier Luo#, Yu Zhou#, Bing Zhang#, Yi Zhang#, Xiaobo Wang, Tong Feng , Zhipeng Li, Kuiqing Cui, Zhiqiang Wang, Chan Luo, Hui Li, Yanfei Deng, Fenghua Lu, Jianlin Han, Yongwang Miao, Huaming Mao, Xiaoyan Yi, Cheng Ai, Shigang Wu, Alun Li, Zhichao Wu, Zijun Zhuo, Do DaGiang, Bikash Mitra, Mohammad Farhad Vahidi, Shahid Mansoor, Sahar Ahmed Al-Bayatti, Eka Meutia Sari, Neena Amatya Gorkhali, Sigit Prastowo, Laiba Shafique, Guoyou Ye, Qian Qian, Baoshan Chen, Deshun Shi*, Jue Ruan* and Qingyou Liu*. “Understanding divergent domestication traits from the whole-genome sequencing of swamp and river buffalo populations."National Science Review, 2020.7,3:686-701.

(19) Jue Ruan?* and Heng Li*."Fast and accurate long-read assembly with wtdbg2."Nature Methods, 2020.17:155–158.

(20) 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, 2019.201:955.

(21) 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#, Millicent Sanciangco, Kevin Christian Palis, Jianlong Xu, Chen Sun, Binying Fu, Hongliang Zhang, Yongming Gao, Xiuqin Zhao, Fei Shen, Xiao Cui, Hong Yu, Zichao Li, Miaolin Chen, Jeffrey Detras, Yongli Zhou, Xinyuan Zhang, Yue Zhao, Dave Kudrna, Chunchao Wang, Rui Li, Ben Jia, Jinyuan Lu, Xianchang He, Zhaotong Dong, Jiabao Xu, Yanhong Li, Miao Wang, Jianxin Shi, Jing Li, Dabing Zhang, Seunghee Lee, Wushu Hu, Alexander Poliakov, Inna Dubchak, Victor Jun Ulat, Frances Nikki Borja, John Robert Mendoza, Jauhar Ali, Jing Li, Qiang Gao, Yongchao Niu, Zhen Yue, Ma. Elizabeth B. Naredo, Jayson Talag, Xueqiang Wang, Jinjie Li, Xiaodong Fang, Ye Yin, Jean-Christophe Glaszmann, Jianwei Zhang, Jiayang Li, Ruaraidh Sackville Hamilton, Rod A. Wing*, Jue Ruan*, Gengyun Zhang*, Chaochun Wei*, Nickolai Alexandrov*, Kenneth. McNally*, Zhikang Li*, Hei Leung. "Genomic variation in 3,010 diverse accessions of Asian cultivated rice."Nature, 2018.557(7703): 43-49.

(22) Guodong Wang#, Xiujuan Shao#, Bing Bai#, Junlong Wang, Xiaobo Wang, Xue Cao, Yanhu Liu, Xuan Wang, Tingting Yin, Shaojie Zhang, Yan Lu, Zechong Wang, Lu Wang, Wenming Zhao, Bing Zhang, Jue Ruan*, Yaping Zhang*. "Structural variation during dog domestication: insights from grey wolf and dhole genomes."National Science Review, 2018.6,（1）:110–122.

(23) Tao Lin#, Xia Xu#, Jue Ruan#, Shizhong Liu, Shigang Wu, Xiujuan Shao, Xiaobo Wang, Lin Gan, Bi Qin, Yushuang Yang, Zhukuan Cheng, Suhua Yang, Zhonghua Zhang, Guosheng Xiong, Sanwen Huang, Hong Yu* and Jiayang Li *. “Genome Analysis of Taraxacum Kok-Saghyz Rodin Provides New Insights into Rubber Biosynthesis.”National Science Review, 2018.5(1):78–87.

(24) KaiLe Wang#, Shujuan Lai, Xiaoxu Yang, Tianqi Zhu, Xuemei Lu, Chung-I. Wu*, Jue Ruan*."Ultrasensitive and high-efficiency screen of de novo low-frequency mutations by o2n-seq."Nature Communications, 2017,8:

(25) Zechen Chong#, Jue Ruan#, Min Gao#, Wanding Zhou, Tenghui Chen, Xian Fan, Li Ding, Anna Y Lee, Paul Boutros, JunJie Chen, Ken Chen*. "novoBreak: local assembly for breakpoint detection in cancer genomes."Nature Methods, 2017. 14(1): 65-67.

(26) Li Yu#, Guodong Wang#, Jue Ruan#, Yongbin Chen#, Cuiping Yang#, Xue Cao#, Hong Wu#, Yanhu Liu#, Zhenglin Du#, Xiaoping Wang#, Jing Yang#, Shaochen Cheng#, Li Zhong, Lu Wang, Xuan Wang, Jingyang Hu, Lu Fang, Bing Bai, Kaile Wang, Na Yuan, Shifang Wu, Baoguo Li, Jinguo Zhang, Yeqin Yang, Chenglin Zhang, Yongcheng Long, Haishu Li, Jingyuan Yang, David M Irwin, Oliver A Ryder, Ying Li*, Chung-I Wu*, Yaping Zhang*. "Genomic analysis of snub-nosed monkeys Rhinopithecus identifies genes and processes related to high-altitude adaptation."Nature Genetics, 2016.48(8):947-952.

(27) 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

(28) Kaile Wang#, Xiaolu Ma#, Xue Zhang, Dafei Wu, Chenyi Sun, Yazhou Sun, Xuemei Lu, Chung-I. Wu*, Caixia Guo*, Jue Ruan*. "Using ultra-sensitive next generation sequencing to dissect DNA damage-induced mutagenesis."Scientific Reports, 2016.6: 25310.

代表专利：

(1) 李瑞强;阮珏;朱红梅;李松岗;王俊;杨焕明;汪健.一种组装基因组的方法,2011-6-29，中国，CN200810218338.9（授权）,获国家优秀专利奖

(2) 阮珏;王开乐;吕雪梅;吴仲义.测序文库及其制备和应用,2017-10-20,中国，CN201310651462.5（授权）（国际专利同号）

(3) 阮珏;王开乐;沈栩;吕雪梅;吴仲义.一种DNA扩增方法,2019-5-17，中国，

CN201410448896.X（授权）

(4) 王开乐;阮珏;吕雪梅;吴仲义.改进的测序文库及其制备和应用，2019-10-15，中国，CN201410448968.0（授权）

(5) 阮珏;王开乐.测序文库及其制备和应用，2020-4-21，中国，CN201510638417.5（授权）

(6) 阮珏;王开乐;吴仲义;吕雪梅.测序文库及其制备和应用，2020-7-21，US10718015B2（国际专利）

(7) 刘庆友;罗西尔;阮珏;石德顺;周宇;崔奎青;李志鹏;李辉;冯彤;王晓波.一种基于全基因组SNP信息追溯水牛血统来源以及进行基因组选配的方法，2022-12-06，中国，CN202010198365.5（授权）

(8) 阮珏;王开乐.测序文库及其制备和应用，2023-7-18，US11702690（国际专利）

(9) 阮珏;侯志浩;王开乐;常玉晓;李阿伦.核酸检测试剂盒、反应体系及方法，2021-09-15，中国，CN202111081033.X（申请）

(10) 阮珏;丁璐璐;伍世刚.DNA存储的软判决信息译码方法及编码方法，2022-09-14，CN202211116662.6（申请）

(11) 阮珏;陈鹏;常玉晓;郭建飞.一种简化基因组测序的方法与相关应用，2022-11-01，CN202211356595.5（申请）

(12) 阮珏;来昊政;常建业;王盼盼.基于单目深度估计的农作物株高测量方法，2023-02-09，CN202310152950.5（申请）

奖励：

1. 2023年获第八届中国农业科学院“十佳青年”；

2. 2022获“中国农业农村重大科技新成果”；

3. 2022获“中国农业科学重大进展”；

4. 2021年获“十大重大科学发现”；

5. 2021年获“中国生命科学十大进展”；

6. 2021年获中国百篇最具影响国际学术论文；

7. 2020获中国生物信息学十大进展；

8. 2020年获中国农业科学院“8项重大科学发现”；

9. 2020年获中国农业科学院“2020年十大科技进展”；

10. 2019年获中国农业科学院“2019年十大科技进展”；

11. 2018年获“杰出青年农业科学家”；

12. 2016年获“中国专利优秀奖”。

 

阮珏课题组更新于2023年8月