J
Jue Ruan
Researcher at Civil Aviation Authority of Singapore
Publications - Â 96
Citations - Â 61838
Jue Ruan is an academic researcher from Civil Aviation Authority of Singapore. The author has contributed to research in topics: Genome & Sequence assembly. The author has an hindex of 29, co-authored 82 publications receiving 48854 citations. Previous affiliations of Jue Ruan include Beijing Genomics Institute & Chinese Academy of Sciences.
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Journal ArticleDOI
The Sequence Alignment/Map format and SAMtools
Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
Journal ArticleDOI
Mapping short DNA sequencing reads and calling variants using mapping quality scores
Heng Li,Jue Ruan,Richard Durbin +2 more
TL;DR: This work describes the software MAQ, software that can build assemblies by mapping shotgun short reads to a reference genome, using quality scores to derive genotype calls of the consensus sequence of a diploid genome, e.g., from a human sample.
Journal ArticleDOI
De novo assembly of human genomes with massively parallel short read sequencing
Ruiqiang Li,Hongmei Zhu,Jue Ruan,Wubin Qian,Xiaodong Fang,Zhongbin Shi,Yingrui Li,Shengting Li,Gao Shan,Karsten Kristiansen,Songgang Li,Huanming Yang,Jing Wang,Jun Wang +13 more
TL;DR: The development of this de novo short read assembly method creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost-effective way.
Journal ArticleDOI
The genome of the cucumber, Cucumis sativus L.
Sanwen Huang,Ruiqiang Li,Zhonghua Zhang,Li Li,Xingfang Gu,Wei Fan,William J. Lucas,Xiaowu Wang,Bingyan Xie,Peixiang Ni,Yuanyuan Ren,Hongmei Zhu,Jun Li,Kui Lin,Weiwei Jin,Zhangjun Fei,Guangcun Li,Jack E. Staub,Andrzej Kilian,Edwin A. G. van der Vossen,Yang Wu,Jie Guo,Jun He,Zhiqi Jia,Yi Ren,Geng Tian,Yao Lu,Jue Ruan,Wubin Qian,Mingwei Wang,Quanfei Huang,Bo Li,Zhaoling Xuan,Jianjun Cao,Asan,Zhigang Wu,Juanbin Zhang,Qingle Cai,Yinqi Bai,Bowen Zhao,Yonghua Han,Ying Li,Xuefeng Li,Shenhao Wang,Qiuxiang Shi,Shiqiang Liu,Won Kyong Cho,Jae-Yean Kim,Yong Xu,Katarzyna Heller-Uszynska,Han Miao,Zhouchao Cheng,Shengping Zhang,Jian Wu,Yuhong Yang,Houxiang Kang,Man Li,Huiqing Liang,Xiaoli Ren,Zhongbin Shi,Ming Wen,Min Jian,Hailong Yang,Guojie Zhang,Zhentao Yang,Rui Chen,Shifang Liu,Jianwen Li,Lijia Ma,Hui Liu,Yan Zhou,Jing Zhao,Xiaodong Fang,Guoqing Li,Lin Fang,Yingrui Li,Dongyuan Liu,Hongkun Zheng,Yong Zhang,Nan Qin,Zhuo Li,Guohua Yang,Shuang Yang,Lars Bolund,Karsten Kristiansen,Hancheng Zheng,Shaochuan Li,Xiuqing Zhang,Huanming Yang,Jing Wang,Rifei Sun,Zhang Baoxi,Shuzhi Jiang,Jun Wang,Yongchen Du,Songgang Li +95 more
TL;DR: This study establishes that five of the cucumber's seven chromosomes arose from fusions of ten ancestral chromosomes after divergence from Cucumis melo, and identifies 686 gene clusters related to phloem function.
Journal ArticleDOI
The sequence and de novo assembly of the giant panda genome
Ruiqiang Li,Wei Fan,Geng Tian,Hongmei Zhu,Lin He,Lin He,Jing Cai,Jing Cai,Quanfei Huang,Qingle Cai,Bo Li,Yinqi Bai,Zhihe Zhang,Ya-Ping Zhang,Wen Wang,Jun Li,Fuwen Wei,Heng Li,Min Jian,Jianwen Li,Zhaolei Zhang,Rasmus Nielsen,Dawei Li,Wanjun Gu,Zhentao Yang,Zhaoling Xuan,Oliver A. Ryder,Frederick C. Leung,Yan Zhou,Jianjun Cao,Xiao Sun,Yonggui Fu,Xiaodong Fang,Xiaosen Guo,Bo Wang,Rong Hou,Fujun Shen,Bo Mu,Peixiang Ni,Runmao Lin,Wubin Qian,Guo-Dong Wang,Guo-Dong Wang,Chang Yu,Wenhui Nie,Jinhuan Wang,Zhigang Wu,Huiqing Liang,Jiumeng Min,Qi Wu,Shifeng Cheng,Jue Ruan,Mingwei Wang,Zhongbin Shi,Ming Wen,Binghang Liu,Xiaoli Ren,Huisong Zheng,Dong Dong,Kathleen Cook,Gao Shan,Hao Zhang,Carolin Kosiol,Xueying Xie,Zuhong Lu,Hancheng Zheng,Yingrui Li,Cynthia C. Steiner,Tommy Tsan-Yuk Lam,Siyuan Lin,Qinghui Zhang,Guoqing Li,Jing Tian,Timing Gong,Hongde Liu,Dejin Zhang,Lin Fang,Chen Ye,Juanbin Zhang,Wenbo Hu,Anlong Xu,Yuanyuan Ren,Guojie Zhang,Guojie Zhang,Michael William Bruford,Qibin Li,Lijia Ma,Yiran Guo,Na An,Yujie Hu,Yang Zheng,Yongyong Shi,Zhiqiang Li,Qing Liu,Yanling Chen,Jing Zhao,Ning Qu,Shancen Zhao,Feng Tian,Xiaoling Wang,Haiyin Wang,Lizhi Xu,Xiao Liu,Tomas Vinar,Yajun Wang,Tak-Wah Lam,Siu-Ming Yiu,Shiping Liu,Hemin Zhang,Desheng Li,Yan Huang,Xia Wang,Guohua Yang,Zhi Jiang,Junyi Wang,Nan Qin,Li Li,Jingxiang Li,Lars Bolund,Karsten Kristiansen,Gane Ka-Shu Wong,Maynard V. Olson,Xiuqing Zhang,Songgang Li,Huanming Yang,Jing Wang,Jun Wang +126 more
TL;DR: Using next-generation sequencing technology alone, a draft sequence of the giant panda genome is generated and assembled, indicating that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition.