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]


最新消息(News)
Ø 樊龙江教授参加岳麓山种业创新论坛暨生物种业超算中心首届创新论坛(2020-10-16)
Ø 樊龙江教授参加2020全国植物生物学大会 (2020-10-14)
Ø 樊龙江教授参加第九届全国生物信息学与系统生物学学术大会(2020-09-29)
Ø Molecular Plant 撰文评价樊龙江教授团队作物和杂草多倍化适应性进化机制研究成果! (2020-09-20)
Ø 生物信息与数量遗传方向暑期团建 (2020-08-14)
Ø 浙江大学樊龙江教授应 Molecular Plant 和Plant Communications联合邀请 在线讲解杂草基因组与作物起源进化 (2020-07-31)
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教学材料(Courses)
Ø 《植物基因组学》,樊龙江主编,2020重磅!《植物基因组学》出版[韩斌院士序] ;[《植物基因组学》后记]
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]
Ø “生物信息学”(樊龙江,2002)(《破译生命密码——基因工程》,浙江大学出版社)
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)

The genomes of the allohexaploid Echinochloa crus-galli and its progenitors provide insights into polyploidization-driven adaptation. Chu-Yu Ye; Dongya Wu; Lingfeng Mao; Lei Jia; Jie Qiu; Sangting Lao; Meihong Chen; Bowen Jiang; Wei Tang; Qiong Peng; Lang Pan; Lifeng Wang; Xiaoxiao Feng; Longbiao Guo; Chulong Zhang; Elizabeth Kellogg; Kenneth Olsen; Lianyang Bai; Longjiang Fan*. Molecular Plant, 2020. doi:https://doi.org/10.1016/j.molp.2020.07.001 [PDF] [MP Spotlight]

Expansion of MIR482/2118 by a Class II transposable element in cotton. Enhui Shen, Tianzhi Chen, Xintian Zhu, Longjiang Fan, Jie Sun, Danny Llewellyn, Iain Wilson, Qian-Hao Zhu*. The Plant Journal, 2020. doi:https://onlinelibrary.wiley.com/doi/10.1111/tpj.14885 [PDF]

Genomic evidence for convergent evolution of gene clusters for momilactone biosynthesis in land plants. Lingfeng Mao, Hiroshi Kawaide, Sho Miyazaki, Meihong Chen, Yoshiki Hirata, Honoka Kimura, Toshiya Higuchi, Miyu Teruya, Kaoru Fujiwara, Keisuke Tomita, Koji Miyamoto, Hisakazu Yamane, Ken-ichiro Hayashi, Hideaki Nojiri, Lei Jia, Jie Qiu, Chuyu Ye,Michael P. Timko, Longjiang Fan* and Kazunori Okada*. PNAS, 2020. doi:https://doi.org/10.1073/pnas.1914373117 [PDF] [PNAS Commentary][ Nature Plants Highlight]

Diverse genetic mechanisms underlie worldwide convergent rice feralization. Jie Qiu, Lei Jia, Dongya Wu, Xifang Weng, Lijuan Chen, Jian Sun, Meihong Chen, Lingfeng Mao, Bowen Jiang, Chuyu Ye, Guilherme Turra, Longbiao Guo, Guoyou Ye, Qianhao Zhu, Toshiyuki Imaizumi, Beng-Kah Song, Laura Scarabel, Aldo Merotto, Kenneth Olsen*, Longjiang Fan*. Genome Biology, 2020. doi:https://doi.org/10.1186/s13059-020-01980-x [PDF]

TOD-CUP: A gene expression rank-based majority vote algorithm for tissue origin diagnosis of cancers of unknown primary. Shen Yifei, Qinjie Chu, Xinxin Yin, Yinjun He, Panpan Bai, Yunfei Wang, Weijia Fang, Michael P. Timko, Longjiang Fan*, Weiqin Jiang*. Briefings in Bioinformatics, 2020. doi:doi:https://doi.org/10.1093/bib/bbaa031 [PDF]

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]

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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]
✽ Red rice / weedy rice [RiceRelativesGD]
✽ Barnyard millet / barnyardgrass (Echinochloa) [RiceRelativesGD]
✽ Oilseed rape [BnPedigome][BRAD][GENOSCOPE]
✽ Gu/Jiaobai (Zizania) [RiceRelativesGD]
✽ Tobacco [Sol Genomics]
✽ Bryophyte (Calohypnum, formely Hypnum ) [BIGD]
Links at ZJU
✽ 中美植物与健康医学联合研究中心 (Sino-US Plant and Health Medicine Joint Reasearch Center)
✽ 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)
Pictures
Genome and Bioinformatics Cartoons

实验室视频 (Videos)
生物信息与大数据技术创新中心暑期夏令营宣传视频

联系我们Contact Us
Professor Fan 樊龙江 Email: fanlj@zju.edu.cn
bioinplant@zju.edu.cn (实验室Tel:  86-571-88982730

Last updated: August, 2019, bioinplant@zju.edu.cn