Bioinplant Lab

Bioinplant Lab of Zhejiang University

本实验室为浙江大学作物科学研究所、生物信息学研究所、IBM生物计算实验室、空气污染与健康研究中心重要组成部分。利用生物信息学和基因组等组学技术优势，我们主要开展（1）作物基因组及大数据育种技术研究；（2）非编码RNA鉴定与分析；（3）健康医疗与作物安全评价研究。具体包括作物及其野生植物基因组解析、基因组为导向的大数据育种技术、非编码RNA生物信息学鉴定方法及其在复杂性状/疾病发生的遗传机制、基于组学数据的烟草制品等安全评价、精准医疗的生物信息学相关方法等研究。

The Bioinplant lab is a part of Institute of Crop Sciences, Institute of Bioinformatics, IBM Biocomputing Laboratory and Research Center for Air Pollution and Health, Zhejiang University. Our purpose is to further knowledge of genes and genomes for crop breeding and complex traits/diseases, particularly through approaches of bioinformatics, genomics and genetics. Our current research interests focus on (1) genomes of crops and their relatives; (2) approaches to bridge the gap between genomics and crop improvement, such as genomic big data-based breeding techniques; (3) non-coding RNA basis for a complex trait/disease and bioinformatic methods for identification of epigenetic elements; (4) omic data-based approaches for evaluation of crop safety; (5) development of bioinformatic tools for precision medicine.[PPT1] [PPT2]

最新消息（News）

Ø 博士生沈一飞第十九届国际植物学大会做专题报告（2017-8-11）

Ø 隆平高科高管来访讨论作物育种与生物信息学领域合作（2017-8-10）

Ø 陈曦讲师参加“农业健康与环境”组学大数据整合生物信息学研讨会并做大会报告（2017-8-10）

Ø Michael Timko教授来访进行学术合作和交流（2017-8-3）

Ø 日本京都大学Iwakami博士来访进行学术交流（2017-8-2）

Ø 实验室组团赴深圳参加第十九届国际植物学大会（IBC2017）（2017-8-1）

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教学材料（Courses）

Ø 《生物信息学札记（第 4 版）》（《生物信息学》，樊龙江主编，2017）

Ø Classical Articles in Bioinformatics and Genomics

Ø History of Bioinformatics

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数据库与生物信息学工具（Databases and Tools）

PlantcircBase

PcircRNA-finder

eTM_finder

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近期发表论文（Recent Publications）

Echinochloa crus-galli genome analysis provides insight into its adaptation and invasiveness as a weed. Guo Longbiao#, Jie Qiu#, Chuyu Ye, Gulei Jin, Lingfeng Mao,Haiqiang Zhang, Xuefang Yang, Qiong Peng, Yingying Wang, Lei Jia, Zhangxiang Lin, Gengmi Li, Fei Fu, Chen Liu, Li Chen, Enhui Shen, Weidi Wang, Sanling Wu, Chenyang Xia, Yongfei Zhang,Xiaomao Zhou, Lifeng Wang, Lamei Wu, Weijie Song, Yunfei Wang, Qingyao Shu, Daisuke Aoki, Emi Yumoto, Takao Yokota, Koji Miyamoto, Kazunori Okada, Do-Soon Kim, Daguang Cai, Chulong Zhang, Yonggen Lou, Qian Qian, Hirofumi Yamaguchi, Hisakazu Yamane, Chui-Hua Kong, Michael P. Timko, Lianyang Bai*, Longjiang Fan*. Nature Communications, 2017. In press.

Comparative whole-genome analysis reveals artificial selection effects on Ustilago esculenta genome. Zihong Ye, Yao Pan, Yafen Zhang, Haifeng Cui, Gulei Jin, Alice C. McHardy, Longjiang Fan*, and Xiaoping Yu*. DNA Research, 2017. doi: 10.1093/dnares/dsx031 [PDF]

Genomic variation associated with local adaptation of weedy rice during de-domestication. Jie Qiu, Yongjun Zhou, Lingfeng Mao, Chuyu Ye, Weidi Wang, Jianping Zhang, Yongyi Yu, Fei Fu, Yunfei Wang, Feijian Qian, Ting Qi, Sanling Wu, Most. Sultana, Ya-Nan Cao, Yu Wang, Michael Timko, Song Ge, Longjiang Fan*, and Yongliang Lu*. Nature Communications, 2017. doi: 10.1038/ncomms15323 [PDF] [News]

Analysis of transcriptional and epigenetic changes in hybrid vigor of allopolyploid Brassica napus uncovers key roles for small RNAs. Shen, Yifei; Sun, Shuo; Hua, Shuijin; Shen, Enhui; Ye, Chuyu; Cai, Daguang; Timko, Michael; Zhu, Qian-Hao; Fan, Longjiang*. The Plant Journal, 2017. doi: 10.1111/tpj.13605 [PDF]

PlantcircBase: a database for plant circular RNAs. Qinjie Chu, Xingchen Zhang, Xintian Zhu, Chen Liu, Lingfeng Mao, Chuyu Ye, Qian-Hao Zhu, Longjiang Fan*. Molecular Plant, 2017. doi: http://dx.doi.org/10.1016/j.molp.2017.03.003 [PDF]

Accumulation of high OPDA level correlates with reduced ROS and elevated GSH benefiting white cell survival in variegated leaves. Ying-Hsuan Sun, Chiu-Yueh Hung, Jie Qiu, Jianjun Chen, Farooqahmed S. Kittur, Carla E. Oldham, Richard J. Henny, Kent O. Burkey, Longjiang Fan & Jiahua Xie. Scientific Reports, 2017. doi: 10.1038/srep44158 [PDF]

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重要链接（Links）

u Important databases and Bioinformatics Homepages

u Crop Genomes