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、中美植物与医学健康联合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）植物基因组及大数据育种技术；（2）组学大数据分析方法、数据库与工具；（3）转化医学与健康。具体包括作物及其相关植物基因组解析、基因组数据为导向的大数据育种技术、单细胞组学数据生物信息学分析方法与工具、健康与医学相关内容（如跨界调控、单细胞组学技术应用）等。[简介] [全家福][公众号]

The Bioinplant lab is a part of Institute of Crop Sciences, Institute of Bioinformatics, IBM Biocomputing Laboratory and Sino-US Plant and Health Medicine Joint Reasearch Center, Zhejiang University. Our purpose is to further knowledge of genomes for crop breeding and complex traits/diseases, particularly through approaches of bioinformatics and omics. Our current research interests focus on (1) genomes of crops and their relatives and approaches to bridge the gap between genomics and crop improvement, such as genome-based breeding techniques; (2) Algorithms, databases, bioinformatic tools for omic data from single-cells, 3D genomes, etc.; (3) plant comparative medicine and health, such as comparative studies on diseases (tumors, scar, etc) in both plant and human, cross-talk of plant genetic elements (miRNA) in human, omic data-based approaches for safety evaluation of agricultural products.

Ø 褚琴洁研究员第二届植物单细胞生物学国际研讨会大会报告（2022-08-15）

Ø 博士生孙砚青赴长三角作物学博士论坛荣获报告二等奖（2022-07-14）

Ø 纪念哈兰（Harlan）——“One man's weed is another man's crop”（2022-07-06）

Ø 祝贺！博士生吴东亚入选2022年度博士后创新人才支持计划（2022-07-01）

Ø 祝贺！博士生孙砚青获得2022年浙江大学争创优秀博士学位论文资助（2022-07-01）

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教学材料（Courses）

Ø 《生物信息学》（第二版），樊龙江主编，2021; 致敬经典：《生物信息学》（第二版）出版！ [后记——纪念郝柏林院士] [视频简介]

Ø 《植物基因组学》，樊龙江主编，2020；图片下载；重磅！《植物基因组学》出版；[韩斌院士序] ；[后记] ；[植物基因组测序20周年回顾与展望] [视频简介]

Ø 《生物信息学札记》（樊龙江，2001，2005，2010）

Ø 本实验室公众号：生信大讲堂

Ø 韩斌院士谈作物学学科发展方向与农学专业

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数据库与生物信息学工具（Databases and Tools）

PlantscRNAdb: A database for plant single-cell RNA analysis

RiceRelativesGD: A database of rice relatives for rice research

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）

When domestication bottleneck meets weed. Yanqing Sun; Longbiao Guo; Qian-Hao Zhu; Longjiang Fan*. Molecular Plant, 2022.doi:https://doi.org/10.1016/j.molp.2022.08.002

Lateral transfers lead to the birth of momilactone biosynthetic gene clusters in grass. Dongya Wu, Yiyu Hu, Akashi Shota, Nojiri Hideaki, Longbiao Guo, Chuyu Ye, Qianhao Zhu, Okada Kazunori, Longjiang Fan*. The Plant Journal, 2022.doi: https://doi.org/10.1111/tpj.15893

Multi-Omic Molecular Biomarkers and database of Osteoarthritis. Jianhua Li, Xiaotian Yang, Qiejie Chu, Lingjuan Xie, Yuwen Ding, Xiaoxu Xu, Michael P. Timko, Longjiang Fan*. DATABASE, 2022.doi:https://doi.org/10.1093/database/baac052

The complete chloroplast genome of weedy rye Secale cereale subsp. segetale. Tianyu Du, Yiyu Hu, Yanqing Sun, Chuyu Ye, Enhui Shen*. Mitochondrial DNA Part B, 2022.doi:https://doi.org/10.1080/23802359.2022.2080600

PlantcircBase 7.0: full-length transcripts and conservation of plant circRNAs. Xiaoxu Xu, Tianyu Du, Weihua Mao, Xiaohan Li, Chu-Yu Ye, Qian-Hao Zhu, Longjiang Fan, Qinjie Chu*. Plant Communications, 2022.doi:https://doi.org/10.1016/j.xplc.2022.100343

Horizontal transfer and evolution of the biosynthetic gene cluster for benzoxazinoid in plants. Dongya Wu, Bowen Jiang, Chuyu Ye, Michael P.Timko, Longjiang Fan*. Plant Communications, 2022.doi:https://doi.org/10.1016/j.xplc.2022.100320

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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]