 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《组学与大数据分析》等课程教学任务，本网站提供了有关教学相关资源。 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 Trends Plant Sci | 中美学者系统总结植物空间多组学研究趋势及其数据分析策略（2025-10-30） |
| Ø 博士生黄毓杰和Babatunde Kehinde第9届国际杂草科学大会作口头报告（2025-10-24） |
| Ø Nature Genetics | 浙江大学樊龙江/吴东亚团队揭示水稻基因组着丝粒遗传多样性与演化规律（2025-10-21） |
| Ø 喜报！博士生许继伟获得2024-2025学年先正达齐尔顿研究生奖学金 (2025-10-18) |
| Ø 喜讯！博士生黄毓杰荣获袁隆平追梦奖学金博士生科研创新青年奖 (2025-10-14) |
| Ø 中科荃银与浙江大学等合作开发杂交水稻不育系基因组选择育种技术（2025-9-19） |
| Ø 祝贺！博士生莫钫宇获批海南省教育厅博士研究生科研创新基金项目（2025-8-31） |
| Ø 实验室发表Nature Genetics观点综述（我国第一篇）（2025-7-16） |
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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] 《生物信息学实验指导》（2022） |
| Ø 《植物基因组学》(Plant Genomics)（第二版），樊龙江主编，2025； 基因组学研究新标杆|《植物基因组学（第二版）》焕新出版 |
| Ø 《单细胞组学基础》（Single-Cell Omics），樊龙江主编，2024； 解锁细胞、洞见微观 | 《单细胞组学基础》重磅发布！ |
| Ø 组学与大数据分析相关经典教材 |
| Ø 《生物信息学札记》（樊龙江，2001，2005，2010） |
| Ø 生信大讲堂公众号 |
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| 数据库与生物信息学工具 （Databases and Tools） |
| BreedingAIDB: A database integrating crop genome-to-phenotype paired data with machine learning tools applicable in breeding |
| PscLncRNA: A database for plant single-cell lncRNA analysis |
| 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 |
| planTrichome: A database of glandular trichome cells in plants |
| VarietyFace: A platform for crop variety genomes and breeding |
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| 近期发表论文 （Recent Publications） |
Genetic diversity and evolution of rice centromeres. Xie Lingjuan, Yujie Huang, Wei Huang, Lianguang Shang, Yanqing Sun, Quanyu Chen, Shuangtian Bi, Mingyu Suo, Shiyu Zhang, Chentao Yang, Xiaoming Zheng, Weiwei Jin, Qian Qian, Longjiang Fan*, Dongya Wu*. Nature Genetics, 2025. doi:https://doi.org/10.1038/s41588-025-02365-1 |
Weeds provide genomic resources for climate-adapted crops. Babatunde O. Kehinde, Yujie Huang, Qian Qian, Jian Sun*, Longjiang Fan*. Science Bulletin, 2025. doi:https://doi.org/10.1016/j.scib.2025.10.047 |
Advances in plant spatial multi-omics data analysis. Jie Yao, Alexandre P. Marand, Yinqi Bai, Robert J. Schmitz, Longjiang Fan*. Trends in Plant Science, 2025. doi:https://doi.org/10.1016/j.tplants.2025.10.005 |
Genome-assisted breeding of an elite sterile line from restorer line for hybrid rice. Yu Fang, Qianlong Li, Qi Feng , Ahong Wang, Hui Wang, Yunhu Zhang, Guoli Zheng, Yunhai Kang, Dilin Liu, Huijiang Xie, Guixiang Zhou, Jing Yang, Conghe Zhang* and Longjiang Fan*. Plant Biotechnology Journal, 2025. doi:https://doi.org/10.1111/pbi.70367 |
Toward improving multiomic research in understudied cereals. Fanjing Yang, Xiaojiao Gong, Pan Zhao, Lingtong Cheng, Yujie Zhang, Yingting Luo, Qian-Hao Zhu, Chu-Yu Ye*.Nature Genetics, 2025. doi:https://doi.org/10.1038/s41588-025-02245-8 |
mKmer: An unbiased K-mer embedding of microbiomic single-microbe RNA sequencing data. Fangyu Mo, Qinghong Qian, Dihuai Zheng, Wenjie Cai, Xiaolin Lu, Jie Yao, Hongyu Chen, Yujie Huang, Xiang Zhang, Sanling Wu, Yifei Shen, Yingqi Bai, Yongcheng Wang*, Weiqin Jiang*, Longjiang Fan*. Briefings in Bioinformatics, 2025. doi:https://doi.org/10.1093/bib/bbaf227 |
A long road ahead to reliable and complete medicinal plant genomes. Lingtong Cheng, Zilong Wang, Qianhao Zhu, Min Ye, Chuyu Ye*. Nature communications, 2025. doi:https://doi.org/10.1038/s41467-025-57448-8 |
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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; Xie et al., 2025） |
| ✽ 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: October, 2025, bioinplant@zju.edu.cn