J
Jia Ye
Researcher at Zhejiang University
Publications - 20
Citations - 7551
Jia Ye is an academic researcher from Zhejiang University. The author has contributed to research in topics: Genome & Sequence analysis. The author has an hindex of 15, co-authored 18 publications receiving 6593 citations. Previous affiliations of Jia Ye include Beijing Institute of Genomics & Chinese Academy of Sciences.
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Journal ArticleDOI
WEGO: a web tool for plotting GO annotations
Jia Ye,Lin Fang,Hongkun Zheng,Yong Zhang,Jie Chen,Zengjin Zhang,Jing Wang,Shengting Li,Ruiqiang Li,Lars Bolund,Jun Wang +10 more
TL;DR: WEGO (Web Gene Ontology Annotation Plot) is a simple but useful tool for visualizing, comparing and plotting GO annotation results, designed to deal with the directed acyclic graph structure of GO to facilitate histogram creation of Go annotation results.
Journal ArticleDOI
SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data.
Chen Yuxin,Yongsheng Chen,Chunmei Shi,Huang Zhibo,Zhang Yong,Li Shengkang,Yan Li,Jia Ye,Chang Yu,Zhuo Li,Xiuqing Zhang,Jian Wang,Huanming Yang,Fang Lin,Qiang Chen +14 more
TL;DR: SOAPnuke is demonstrated as a tool with abundant functions for a “QC-Preprocess-QC” workflow and MapReduce acceleration framework that enables large scalability to distribute all the processing works to an entire compute cluster.
Journal ArticleDOI
A draft sequence for the genome of the domesticated silkworm (Bombyx mori).
Qingyou Xia,Zeyang Zhou,Cheng Lu,Daojun Cheng,Fangyin Dai,Bin Li,Ping Zhao,Xingfu Zha,Tingcai Cheng,Chunli Chai,Guoqing Pan,Jinshan Xu,Chun Liu,Ying Lin,Ji-Feng Qian,Yong Hou,Zhengli Wu,Guanrong Li,Minhui Pan,Chunfeng Li,Yihong Shen,Xiqian Lan,Lianwei Yuan,Tian Li,Hanfu Xu,Guangwei Yang,Yongji Wan,Yong Zhu,Maode Yu,Weide Shen,Dayang Wu,Zhonghuai Xiang,Jun Yu,Jun Yu,Jun Wang,Jun Wang,Ruiqiang Li,Jianping Shi,Heng Li,Guangyuan Li,Jianning Su,Xiaoling Wang,Guoqing Li,Zengjin Zhang,Qingfa Wu,Jun Li,Qingpeng Zhang,Ning Wei,Jianzhe Xu,Haibo Sun,Le Dong,Dongyuan Liu,Shengli Zhao,Xiaolan Zhao,Qingshun Meng,Fengdi Lan,Xiangang Huang,Yuanzhe Li,Lin Fang,Changfeng Li,Dawei Li,Yongqiao Sun,Zhenpeng Zhang,Zheng Yang,Yanqing Huang,Yan Xi,Qiuhui Qi,Dandan He,Haiyan Huang,Xiaowei Zhang,Zhiqiang Wang,Wenjie Li,Yuzhu Cao,Yingpu Yu,Hong Yu,Jinhong Li,Jiehua Ye,Huan Chen,Yan Zhou,Bin Liu,Jing Wang,Jia Ye,Hai Ji,Shengting Li,Peixiang Ni,Jianguo Zhang,Yong Zhang,Hongkun Zheng,Bingyu Mao,Wen Wang,Chen Ye,Songgang Li,Jian Wang,Jian Wang,Gane Ka-Shu Wong,Gane Ka-Shu Wong,Gane Ka-Shu Wong,Huanming Yang,Huanming Yang +98 more
TL;DR: A draft sequence for the genome of the domesticated silkworm (Bombyx mori), covering 90.9% of all known silkworm genes is reported, which exceeds the estimated gene count for Drosophila melanogaster.
Journal ArticleDOI
The diploid genome sequence of an Asian individual.
Jun Wang,Wei Wang,Ruiqiang Li,Ruiqiang Li,Yingrui Li,Yingrui Li,Yingrui Li,Geng Tian,Geng Tian,Laurie Goodman,Wei Fan,Junqing Zhang,Jun Li,Juanbin Zhang,Yiran Guo,Yiran Guo,Binxiao Feng,Heng Li,Heng Li,Yao Lu,Xiaodong Fang,Huiqing Liang,Zhenglin Du,Dong Li,Yiqing Zhao,Yiqing Zhao,Yujie Hu,Yujie Hu,Zhenzhen Yang,Hancheng Zheng,Ines Hellmann,Michael Inouye,John E. Pool,Xin Yi,Xin Yi,Jing Zhao,Jinjie Duan,Yan Zhou,Junjie Qin,Junjie Qin,Lijia Ma,Lijia Ma,Guoqing Li,Zhentao Yang,Guojie Zhang,Guojie Zhang,Bin Yang,Chang Yu,Fang Liang,Fang Liang,Wenjie Li,Shaochuan Li,Dawei Li,Peixiang Ni,Jue Ruan,Jue Ruan,Qibin Li,Qibin Li,Hongmei Zhu,Dongyuan Liu,Zhike Lu,Ning Li,Ning Li,Guangwu Guo,Guangwu Guo,Jianguo Zhang,Jia Ye,Lin Fang,Qin Hao,Qin Hao,Quan Chen,Quan Chen,Yu Liang,Yu Liang,Yeyang Su,Yeyang Su,A. san,A. san,Cuo Ping,Cuo Ping,Shuang Yang,Fang Chen,Fang Chen,Li Li,Ke Zhou,Hongkun Zheng,Hongkun Zheng,Yuanyuan Ren,Ling Yang,Yang Gao,Yang Gao,Guohua Yang,Guohua Yang,Zhuo Li,Xiaoli Feng,Karsten Kristiansen,Gane Ka-Shu Wong,Gane Ka-Shu Wong,Rasmus Nielsen,Richard Durbin,Lars Bolund,Lars Bolund,Xiuqing Zhang,Xiuqing Zhang,Songgang Li,Songgang Li,Songgang Li,Huanming Yang,Huanming Yang,Jian Wang,Jian Wang +110 more
TL;DR: Genotyping analysis showed that SNP identification had high accuracy and consistency, indicating the high sequence quality of this assembly, and the potential usefulness of next-generation sequencing technologies for personal genomics.
Journal ArticleDOI
The Genomes of Oryza sativa: a history of duplications.
Jun Yu,Jun Yu,Jun Wang,Jun Wang,Wei Lin,Songgang Li,Songgang Li,Heng Li,Heng Li,Jun Zhou,Peixiang Ni,Wei Dong,Songnian Hu,Changqing Zeng,Jianguo Zhang,Yong Zhang,Yong Zhang,Ruiqiang Li,Zuyuan Xu,Shengting Li,Xianran Li,Hongkun Zheng,Lijuan Cong,Liang Lin,Jianning Yin,Jianing Geng,Guangyuan Li,Jianping Shi,Juan Liu,Hong Lv,Jun Li,Jing Wang,Jing Wang,Yajun Deng,Longhua Ran,Xiaoli Shi,Xiaoli Shi,Xiyin Wang,Xiyin Wang,Qingfa Wu,Changfeng Li,Xiaoyu Ren,Jingqiang Wang,Xiaoling Wang,Dawei Li,Dongyuan Liu,Xiaowei Zhang,Zhendong Ji,Wenming Zhao,Yongqiao Sun,Zhenpeng Zhang,Jingyue Bao,Yujun Han,Lingli Dong,Jia Ji,Peng Chen,Shuming Wu,Jinsong Liu,Ying Xiao,Dongbo Bu,Jianlong Tan,Li Yang,Chen Ye,Jingfen Zhang,Jingyi Xu,Yan Zhou,Yingpu Yu,Bing Zhang,Shulin Zhuang,Haibin Wei,Bin Liu,Meng Lei,Hong Yu,Yuanzhe Li,Hao Xu,Shulin Wei,Ximiao He,Lijun Fang,Zengjin Zhang,Yunze Zhang,Xiangang Huang,Zhixi Su,Wei Tong,Jinhong Li,Zongzhong Tong,Shuangli Li,Jia Ye,Lishun Wang,Lin Fang,Tingting Lei,Chen Chen,Huan Chen,Zhao Xu,Haihong Li,Haiyan Huang,Feng Zhang,Huayong Xu,Na Li,Caifeng Zhao,Shuting Li,Lijun Dong,Yanqing Huang,Long Li,Yan Xi,Qiuhui Qi,Wenjie Li,Bo Zhang,Wei Hu,Yanling Zhang,Xiangjun Tian,Yongzhi Jiao,Xiaohu Liang,Jiao Jin,Jiao Jin,Lei Gao,Lei Gao,Wei-Mou Zheng,Wei-Mou Zheng,Bailin Hao,Bailin Hao,Siqi Liu,Siqi Liu,Wen Wang,Wen Wang,Longping Yuan,Mengliang Cao,Jason E. McDermott,Ram Samudrala,Jian Wang,Jian Wang,Gane Ka-Shu Wong,Gane Ka-Shu Wong,Gane Ka-Shu Wong,Huanming Yang,Huanming Yang +134 more
TL;DR: A more inclusive new approach for analyzing duplication history is introduced here, which reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications.