 Bioinplant Group |
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生物信息与植物基因组学（bioinformatics and plant genomics）团队（Bioinplant）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、中美作物分子育种联合实验室、中美植物与医学健康联合研究中心、海南研究院、新农村发展研究院等重要组成部分。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) 植物基因组及其演化和育种利用技术；(2) 组学大数据分析、数据库与方法工具；(3) 单细胞组学技术及其应用；(4) 植物转化医学与健康。团队承担了《生物信息学》、《植物基因组学》、《单细胞组学》和《组学数据分析》等课程教学任务，本网站提供了有关教学相关资源。[简介] [全家福][公众号] 团队研究组（PI）：樊龙江教授；叶楚玉教授；褚琴洁研究员；陈露研究员 |
The Bioinplant (bioinformatics and plant genomics) group is a part of Institute of Crop Sciences, Institute of Bioinformatics, IBM Biocomputing Laboratory, Sino-US Molecular Breeding Joint Lab, Sino-US Plant and Health Medicine Joint Reasearch Center, Hainan Institute, 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 and analysis of multiple omic data, including single-cell omic data; (3) plant translational medicine and health. Our group undertakes the teaching tasks for courses such as "Bioinformatics," "Plant Genomics," "Single-cell Omics," and "Genomic Data Analysis." This website provides teaching-related resources. |
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| 最新消息（News） |
| Ø Plant Communications | 浙江大学樊龙江团队构建作物基因组-表型成对数据库（2024-4-3） |
| Ø Nature Plants | 浙江大学樊龙江团队开展植物基因组测序与组装技术分析并建立N3数据库（2024-3-20） |
| Ø GigaScience | 鸭跖草目第一个参考基因组——水葫芦基因组演化及其全球传播（2024-3-17） |
| Ø 博士生谢玲娟赴第二届浙江省作物学会研究生国际学术论坛作报告（2023-12-12） |
| Ø Plant Communications | 浙江大学樊龙江团队大规模群体基因组分析揭示红米演化历史（2023-12-6） |
| Ø 博士生姚洁荣获“学术新星培养计划”，赴斯坦福大学进行联合培养（2023-12-2） |
| Ø 祝贺！吴东亚和陈洪瑜两位博士获得博士后基金资助（2023-11-21） |
| Ø 吴东亚博士Plant Communications论文获得该刊2022年度最佳论文（2023-08-24） |
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| 教学材料（Courses） |
| Ø 《生物信息学》（Bioinformatics）（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] |
| Ø 《生物信息学实验指导》，樊龙江、叶楚玉主编，2022 |
| Ø 《植物基因组学》(Plant Genomics)，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] |
| Ø 《生物信息学札记》（樊龙江，2001，2005，2010） |
| Ø 本团队公众号：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） |
| The database of N3: plants,genomes,technologies |
| 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 |
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| 近期发表论文 （Recent Publications） |
Spatiotemporal transcriptomic landscape of rice embryonic cells during seed germination. Jie Yao, Qinjie Chu, Xing Guo, Wenwen Shao, Nianmin Shang, Kang Luo, Xiaohan Li, Hongyu Chen, Qing Cheng1, Fangyu Mo, Dihuai Zheng, Fan Xu, Fu Guo, Qian-Hao Zhu, Shuiguang Deng, Chengcai Chu, Xun Xu, Huan Liu*, Longjiang Fan*. Developmental Cell, 2024. in press |
BreedingAIDB: a database integrating crop genome-to-phenotype paired data with machine learning tools applicable in breeding. Zijie Shen, Enhui Shen, Kun Yang, Zuoqian Fan, Qian-Hao Zhu, Longjiang Fan, Chu-Yu Ye* . Plant Communications, 2024. doi:https://doi.org/10.1016/j.xplc.2024.100894 |
Technology-enabled great leap in deciphering plant genomes. Lingjuan Xie, Xiaojiao Gong, Kun Yang, Yujie Huang, Shiyu Zhang, Leti Shen, Yanqing Sun, Dongya Wu, Chuyu Ye, Qian-Hao Zhu, Longjiang Fan*. Nature Plants, 2024. doi:https://www.nature.com/articles/s41477-024-01655-6 |
A reference genome of Commelinales provides insights into the commelinids evolution and global spread of water hyacinth (Pontederia crassipes). Yujie Huang, Longbiao Guo, Lingjuan Xie, Nianmin Shang, Dongya Wu, Chuyu Ye, Eduardo Carlos Rudell, Kazunori Okada, Qian-Hao Zhu, Beng-Kah Song, Daguang Cai, Aldo Merotto Junior, Lianyang Bai*, Longjiang Fan*. GigaScience, 2024. doi:https://doi.org/10.1093/gigascience/giae006 |
Multidimensional assessment of the biological effects of electronic cigarettes on lung bronchial epithelial cells. Meng Wang, Qing Cheng, Zehong Wu, Longjiang Fan, Linghui Zeng, Hongyu Chen* Scientific Reports, 2024. doi:https://www.nature.com/articles/s41598-024-55140-3 |
Population genomic analysis unravels the evolutionary roadmap of pericarp color in rice. Lingjuan Xie, Dongya Wu, Yu Fang, Chuyu Ye, Qianhao Zhu, Xinghua Wei, Longjiang Fan*. Plant Communications, 2023. doi:https://doi.org/10.1016/j.xplc.2023.100778 |
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重要链接 （Links） |
| Important Databases and Bioinformatics Portals |
| ✽ CNCB（中国国家生物信息中心） |
| ✽ NCBI |
| ✽ EMBL |
| ✽ ExPASy |
| ✽ JCVI |
| ✽ CBI-PU |
| Plant genomes by us |
| ✽ Rice / cultivated red rice [NGDC(Wu)][NGDC(Xie)][RiceRelativesGD]（Wu et al., 2023; Xie et al., 2023） |
| ✽ Weedy rice (red rice) [RiceRelativesGD] (Qiu et al., 2014;Qiu et al., 2017; Qiu et al., 2020; Wu et al., 2023) |
| ✽ Barnyard millet / barnyardgrass (Echinochloa) [RiceRelativesGD] (Guo et al., 2017; Ye et al., 2019; Ye et al., 2021; Wu et al., 2022) |
| ✽ Oilseed rape [BnPedigome] (Zou et al., 2019) |
| ✽ Gu/Jiaobai (Zizania) [RiceRelativesGD] (Guo et al., 2016) |
| ✽ Bryophyte (Calohypnum, formely Hypnum ) [BIGD] [RiceRelativesGD] (Mao et al., 2020) |
| ✽ Water hyacinth (Pontederia crassipes) [GigaDB] (Huang et al., 2024) |
| 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) |
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| 团队成员 （Group member） |
| 照片 （Photos） |
| Pictures |
| Genome and Bioinformatics Cartoons |
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| 视频与海报 （Video & Poster） |
| Video |
| Poster |
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| 联系我们 （Contact Us） |
| bioinplant@zju.edu.cn |
Last updated: July, 2023, bioinplant@zju.edu.cn