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发生的遗传机制、基于组学数据的烟草制品等安全评价、健康风险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 and bioinformatic methods for identification of epigenetic elements; (4) omic data-based approaches/bioinformatic tools for evaluation of crop safety and health.[PPT1] [PPT2]


最新消息News

Ø 我实验室植物环化RNA论文获评Web of Science“热点论文” (2017-12-5)
Ø 樊龙江教授应邀第十届长三角作物学博士论坛大会报告,博士生毛凌峰荣获优秀报告二等奖 (2017-11-28)
Ø 喜讯!本实验室研究生获国家奖学金等多项奖项 (2017-11-14)
Ø 樊龙江教授应邀赴长沙全国植保大会报告 (2017-11-13)
Ø 樊龙江教授团队Nature Communications稻田稗草基因组论文获F1000推荐 (2017-10-28)
Ø 樊龙江教授应邀第四届全国功能基因组大会报告 (2017-10-25)
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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】【郝柏林院士序言

   [生信大讲堂留言][【亚马逊在线购买】BIOINFORMATICS book (in Chinese by Prof. Fan) at Amazon ]

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:a database for plant circular RNAs
PcircRNA-finder:a program to identify circular RNAs in plants
eTM_finder:a tool to predict eTMs (endogenous target mimics) of miRNAs in plants
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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. doi: 10.1038/s41467-017-01067-5 [PDF][Media Coverage][F1000 Recommended]

A naive Bayes algorithm for tissue origin diagnosis (TOD-Bayes) of synchronous multifocal tumors in the hepatobiliary and pancreatic system. Weiqin Jiang, Yifei Shen, Yongfeng Ding, Chuyu Ye, Yi Zheng, Peng Zhao,Lulu Liu, Zhou Tong,Linfu Zhou, Shuo Sun, Xingchen Zhang, Lisong Teng, Michael P. Timko, Longjiang Fan*, Weijia Fang*. International Journal of Cancer, 2017. doi: 10.1002/ijc.31054 [PDF][Cover story]

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] [Media Coverage]

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]

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重要链接Links)

Important Databases and Bioinformatics Portals

{NCBI

{EMBL

{Expasy

{JCVI

{CBI-PU (Applied Bioinformatics Course)

Crop and Relatives Genomes

{Rice [MSU][RAP-DB][RIGW]

{Weedy rice [Weedomes]

{Barnyardgrass (Echinochloa) [Weedomes]

{Oilseed rape [BRAD][GENOSCOPE]

{Gu/Jiaobai (Zizania) [Link]

{Tobacco [Sol Genomics]

Links at ZJU

{作物科学研究所(Institute of Crop Science)

{生物信息学研究所(Institute of Bioinformatics)

{IBM生物计算实验室(IBM Biocomputational Laboratory)

{中美作物分子育种联合实验室(Sino-US Crop Molecular Breeding Joint Laboratory)

{沃森基因组研究院(James D. Watson Institute of Genome Sciences)


实验室成员Staff)

Staff of Bioinplant
实验室照片Photos)
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Genome and Bioinformatics Cartoons

联系我们Contact Us
Professor Fan 樊龙江Email: fanlj@zju.edu.cn

bioinplant@zju.edu.cn  (实验室)Tel86-571-88982730


Last updated: December 5, 2017, bioinplant@zju.edu.cn