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 德国基尔大学博士生Markus Schemmel来访进行学术交流（2019-11-06）

Ø 博士生吴东亚获中国作物学会2019年学术年会优秀学术报告奖（2019-10-30）

Ø 我实验室作物拟态研究论文获F1000最高星级推荐（2019-10-16）

Ø 樊龙江教授应邀在中科院遗传发育所和南京农大报告作物拟态研究进展（2019-10-14）

Ø 樊龙江教授团队Nature Ecology & Evolution发表论文揭示作物拟态遗传机制!（2019-09-17）【国内外新闻报道】【BEHIND THE PAPER】【《影响世界的中国植物》纪录片《水稻》一集】【F1000Prime推荐】【Nature Plants Highlights】【中文翻译版】

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教学材料（Courses）

Ø 《植物基因组学》（樊龙江主编，2019）；[韩斌院士序言]

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 [韩斌院士谈作物学学科发展方向]； [韩斌院士谈农学专业]

Ø 大型记录片《影响世界的中国植物》第二集《水稻》 [新闻链接]

Ø 实验室公众号生信入门好文推荐

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数据库与生物信息学工具（Databases and Tools）

RiceRelativesGD: a database of rice relatives for rice breeding

PlantcircBase：a database for plant circular RNAs

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

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

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近期发表论文（Recent Publications）

A transcriptomic profile of topping responsive non-coding RNAs in tobacco roots (Nicotiana tabacum). Xi Chen, Shuo Sun, Fangjie Liu, Enhui Shen, Lu Liu, Chuyu Ye, Bingguang Xiao, Michael P. Timko, Qian-Hao Zhu, Longjiang Fan* & Peijian Cao*. BMC Genomics, 2019. doi:https://doi.org/10.1186/s12864-019-6236-6 [PDF]

AKR, a novel mechanism involved in glyphosate metabolism and resistance in Echinochloa colona. Pan Lang, Qin Yu*, Heping Han, Lingfeng Mao, Alex Nyporko, Longjiang Fan*, Lianyang Bai*, and Stephen Powles. Plant Physiology, 2019. doi:https://doi.org/10.1104/pp.19.00979 [PDF]

Genomic evidence of human selection on Vavilovian mimicry. Ye Chu-Yu, Wei Tang, Dongya Wu, Lei Jia, Jie Qiu, Meihong Chen, Lingfeng Mao, Feng Lin, Haiming Xu, Xiaoyue Yu, Yongliang Lu, Yonghong Wang, Kenneth M Olsen, Michael P. Timko, Longjiang Fan*. Nature Ecology & Evolution, 2019. doi: https://doi.org/10.1038/s41559-019-0976-1 [PDF] [Behind The Paper]] [Newswise Report] [F1000Prime] [Nature Plants Highlights]

RiceRelativesGD: a genomic database of rice relatives for rice research. Mao Lingfeng, Chen Meihong, Chu Qinjie, Jia Lei, Most. Humaira Sultana, Wu Dongya, Kong X, Qiu Jie, Ye Chu-Yu, Chen Xi*, and Fan Longjiang. Database, 2019. doi:https://doi.org/10.1093/database/baz110 [PDF]

Characterization and evolution of gene clusters for terpenoid phytoalexin biosynthesis in tobacco. Chen Xi, Fangjie Liu, Lu Liu, Jie Qiu, Dunhuang Fang, Weidi Wang, Xingcheng Zhang, Chuyu Ye, Michael Paul Timko, Qian-Hao Zhu, Longjiang Fan, Bingguang Xiao*. Planta, 2019. doi: https://doi.org/10.1007/s00425-019-03255-7 [PDF]

Gene modules co-regulated with biosynthetic gene clusters for allelopathy between rice and barnyardgrass. Sultana Most. Humaira, Fangjie Liu, Md. Alamin, Lingfeng Mao, Lei Jia, Hongyu Chen, Dongya Wu, Yingying Wang, Fei Fu, Sanling Wu, Weidi Wang, Chuyu Ye, Qian-hao Zhu, Jie Qiu *, Longjiang Fan. International Journal of Molecular Sciences, 2019. doi: https://www.mdpi.com/1422-0067/20/16/3846 [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]