 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 实验室发表Nature Genetics观点综述（我国第一篇）（2025-7-16） |
| Ø 基因组学研究新标杆|《植物基因组学（第二版）》焕新出版（2025-7-10） |
| Ø 祝贺本实验室2位博士和4位硕士顺利完成论文答辩！（2025-6-4） |
| Ø 樊龙江团队开发基于K-mer微生物组单细胞数据分析新算法（2025-5-26） |
| Ø 樊龙江教授应邀国际单细胞与空间组学大会（TICSSO）报告（2025-3-31） |
| Ø 实验室发表NC综述，阐述药用植物基因组研究进展（2025-3-5） |
| Ø Bioinplant团队获得基因组育种算法国际竞赛优胜奖（2025-1-9） |
| Ø 喜报！博士生黄毓杰入选浙江大学“博士研究生求是新星培养计划”（2025-1-8） |
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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)，樊龙江主编，2020； 重磅！《植物基因组学》出版；[韩斌院士序] ；[后记] |
| 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） |
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 |
The DNA methylomes of Echinochloa species provide insights into polyploidization-driven adaptation and orphan crop domestication. Qinjie Chu, Xiaojiao Gong, Yiyu Hu, Qianhao Zhu, Longjiang Fan, Chuyu Ye*. The Plant journal, 2025. doi: https://doi.org/10.1111/tpj.70033 |
Identification of cell‐type specificity, trans‐ and cis‐acting functions of plant lincRNAs from single‐cell transcriptomes. Jiwei Xu#, Enhui Shen#, Fu Guo, Kaiqiang Wang, Yurong Hu, Leti Shen, Hongyu Chen, Xiaohan Li, Qian-Hao Zhu, Longjiang Fan, Qinjie Chu*. New Phytologist, 2024. doi: https://doi.org/10.1111/nph.20269 |
The Dynamic Transcriptome Reveals Response Patterns to Black Shank Disease in Tobacco (Nicotiana tabacum L.). Zhijun Tong#, Zuoqian Fan#, Tianyu Du, Dunhuang Fang, Xueyi Sui, Chuyu Ye, Qian-Hao Zhu, Longjiang Fan, Bingguang Xiao* and Enhui Shen*. Plant Stress, 2024. doi: https://doi.org/10.1016/j.stress.2024.100676 |
Assembling a reference-quality genome and resequencing diverse accessions of Beckmannia syzigachne provide insights into population structure and gene family evolution. Yang Han, Jianxiang Wu, Qian-Hao Zhu, Chu-Yu Ye*, Xinxin Li*. Plant Communications, 2024. doi: https://doi.org/10.1016/j.xplc.2024.101174 |
Retrospect and Prospect of Nicotiana Tabacum Genome Sequencing. Zhijun Tong, Yujie Huang, Qian-Hao Zhu, Longjiang Fan, Bingguang Xiao*, Enhui Shen*. Frontiers in Plant Science, 2024. doi: 10.3389/fpls.2024.1474658. |
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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