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. [Poster] [Family]

Ø 樊龙江教授“数字农业”西湖学术论坛做“农业大数据及其育种利用”报告（2019-06-19）

Ø 浙江大学“生物信息与农业大数据”创新团队青年教师招聘启事（2019-05-10）

Ø 实验室合作发表亚洲油菜系谱基因组分析论文（2019-04-05）

Ø 樊龙江教授任《Frontiers in Genetics》副主编（Associate Editor）（2019-04-04）

Ø 邱杰博士后访问美国圣路易斯华盛顿大学（2019-03-29）

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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]；[亚马逊在线购买]

Ø 实验室公众号生信入门好文推荐

Ø 友情链接：基因课（张旭东）

Ø 经典论文翻译

Ø Classical Articles in Bioinformatics and Genomics

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数据库与生物信息学工具（Databases and Tools）

BnPedigome: a genomic database for the pedigrees and breeding of Brassica napus

RiceRelativesGD: a database of rice relatives for rice breeding

PlantcircBase：a database for plant circular RNAs

PcircRNA-finder：a program to identify circular RNAs in plants

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近期发表论文（Recent Publications）

Elimination of a retrotransposon for quenching genome instability in modern rice. Yu Peng#, Yingying Zhang#, Yijie Gui, Dong An, Junzhong Liu, Xun Xu, Qun Li, Junmin Wang, Wen Wang, Chunhai Shi, Longjiang Fan, Baorong Lu, Yiwen Deng*, Sheng Teng*, Zuhua He*. Molecular Plant, 2019. doi: https://doi.org/10.1016/j.molp.2019.06.004 [PDF]

Genome-wide selection footprints and deleterious variations in young Asian allotetraploid rapeseed. Jun Zou#, Lingfeng Mao#, Jie Qiu#, Meng Wang, Lei Jia, Dongya Wu, Zhesi He, Meihong Chen, Yifei Shen, Enhui Shen, Yongji Huang, Ruiyuan Li, Dandan Hu, Lei Shi, Kai Wang, Qian-Hao Zhu, Chuyu Ye, Ian Bancroft, Graham J King, Jinling Meng, Longjiang Fan*. Plant Biotechnology Journal, 2019. doi: https://onlinelibrary.wiley.com/doi/10.1111/pbi.13115 [PDF]

Bi-directional selection in upland rice leads to its adaptive differentiation from lowland rice on drought resistance and productivity. Hui Xia, Zhi Luo, Jie Xiong, Xiaosong Ma, Qiaojun Lou, Haibin Wei, Jie Qiu, Hua Yang, Guolan Liu, Longjiang Fan, Liang Chen, Lijun Luo*. Molecular Plant, 2018. doi: https://doi.org/10.1016/j.molp.2018.12.011 [PDF]

Characteristics of Plant Circular RNAs. Chu Qinjie, Bai Panpan, Zhu Xintian, Zhang Xingchen, Mao Lingfeng, Zhu Qian-Hao, Fan Longjiang, Ye Chuyu*. Briefings in Bioinformatics, 2018. doi: 10.1093/bib/bby111 [PDF]

Genome-wide identification of oil biosynthesis-related long non-coding RNAs in allopolyploid Brassica napus. Enhui Shen#, Xintian Zhu#, Shuijin Hua, Hongyu Chen, Chuyu Ye, Longhua Zhou, Qing Liu, Qian-Hao Zhu, Longjiang Fan and Xi Chen*. BMC Genomics, 2018. doi: https://doi.org/10.1186/s12864-018-5117-8 [PDF]

Genomic clues for crop-weed interactions and evolution. Guo Longbiao#, Jie Qiu#, Lin-Feng Li, Baorong Lu, Kenneth Olsen and Longjiang Fan*. Trends in Plant Science, 2018. doi: https://doi.org/10.1016/j.tplants.2018.09.009 [PDF]

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重要链接（Links）

Important Databases and Bioinformatics Portals

✽ NCBI

✽ EMBL

✽ Expasy

✽ JCVI

✽ CBI-PU

Crop and Relatives Genomes

✽ Rice [MSU][RAP-DB][RIGW][RiceRelativesGD][PlantcircBase]

✽ Weedy rice [RiceRelativesGD]

✽ Barnyardgrass (Echinochloa) [RiceRelativesGD]