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.[PPT1] [PPT2]

Ø 澳大利亚联邦科学院朱乾浩研究员来访（2018-10-11）

Ø 祝贺！实验室《Trends Plant Sci》发表作物与杂草互作与进化基因组学综述（2018-10-8）

Ø 美国俄克拉荷马大学健康科学中心主任李师博教授等一行访问实验室（2018-9-30）

Ø 江苏省农科院植保所李永丰研究员来访（2018-9-29）

Ø 莫纳什大学马来西亚分校Song Beng Kah博士来访（2018-9-29）

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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】

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

Ø 经典论文翻译

Ø Classical Articles in Bioinformatics and Genomics

Ø History of Early 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）

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. In press.

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]

Genome-wide selection footprints and deleterious variations in young Asian allotetraploid rapeseed. Jun Zou#, Lingfeng Mao#, Jie Qiu#, Meng Wang, Zhesi He, Lei Jia, Dongya Wu, Yongji Huang, Meihong Chen, Yifei Shen, Enhui Shen, Ruiyuan Li, Dandan Hu, Kai Wang, LeiShi, Chuyu Ye, Ian Bancroft, Graham King, Jinling Meng and Longjiang Fan*. bioRxiv, 2018. doi: https://doi.org/10.1101/412551 [PDF]

The red bayberry genome and genetic basis of sex determination. Hui-Min Jia#, Hui-Juan Jia#, Qing-Le Cai#, Yan Wang, Hai-Bo Zhao, Wei-Fei Yang, Guo-Yun Wang, Ying-Hui Li, Dong-Liang Zhan, Yu-Tong Shen, Qing-Feng Niu, Le Chang, Jie Qiu, Lan Zhao, Han-Bing Xie, Wan-Yi Fu, Jing Jin, Xiong-Wei Li, Yun Jiao, Chao-Chao Zhou, Ting Tu, Chun-Yan Chai, Jing-Long Gao, Long-Jiang Fan, Eric van de Weg, Jun-Yi Wang* and Zhong-Shan Gao*. Plant Biotechnology Journal, 2018. doi: 10.1111/pbi.12985 [PDF]

The power and potential of genomics in weed biology and management. Karl Ravet, Eric L. Patterson, Hansjörg Krähmer, Kateřina Hamouzová, Longjiang Fan, Marie Jasieniuk, Amy Lawton-Rauh, Jenna M. Malone, J. Scott McElroy, Aldo Merotto Jr, Philip Westra, Christopher Preston, Martin M. Vila-Aiub, Roberto Busi, Patrick J. Tranel, Carl Reinhardt, Christopher Saski, Roland Beffa, Paul Neve* and Todd A. Gaines*. Pest Management Science, 2018. doi: 10.1002/ps.5048 [PDF]

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重要链接（Links）

Important Databases and Bioinformatics Portals

Crop and Relatives Genomes

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

{Weedy rice [RiceRelativesGD]

{Barnyardgrass (Echinochloa) [RiceRelativesGD]