 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 祝贺！博士生谢玲娟获得2024年浙江大学争创优秀博士学位论文资助（2024-6-27） |
| Ø Dev Cell | 浙江大学樊龙江团队牵头绘制水稻种胚单细胞时空图谱（2024-6-7） |
| Ø 实验室单细胞小组成员赴深圳参加2024植物时空组学国际研讨会（2024-6-4） |
| Ø Protein & Cell | 王永成/樊龙江团队合作开发微生物组单细胞转录组测序技术（2024-5-27） |
| 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） |
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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年 |
| 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） |
| 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） |
Single-cell landscape of long and short glandular trichomes in Nicotiana tabacum leaves. Hongyu Chen, Xiaohan Li, Qing Cheng, Nianmin Shang, Zhijun Tong, Qinjie Chu, Chuyu Ye, Xiner Shen, Qian-Hao Zhu, Bingguang Xiao*, Longjiang Fan*.iScience, 2024. in press |
Are miRNAs applicable for balancing crop growth and defense trade-off? Enhui Shen*, Tianlun Zhao, Qian-Hao Zhu*. New Phytologist, 2024. doi: https://doi.org/10.1111/nph.19939 |
Current status of community resources and priorities for weed genomics research. Montgomery J, Morran S, MacGregor DR, McElroy JS, Neve P, Neto C, Vila-Aiub MM, Sandoval MV, Menéndez AI, Kreiner JM, Fan L, Caicedo AL, Maughan PJ, Martins BAB, Mika J, Collavo A, Merotto A Jr, Subramanian NK, Bagavathiannan MV, Cutti L, Islam MM, Gill BS, Cicchillo R, Gast R, Soni N, Wright TR, Zastrow-Hayes G, May G, Malone JM, Sehgal D, Kaundun SS, Dale RP, Vorster BJ, Peters B, Lerchl J, Tranel PJ, Beffa R, Fournier-Level A, Jugulam M, Fengler K, Llaca V, Patterson EL, Gaines TA*. Genome Biology, 2024.doi:10.1186/s13059-024-03274-y |
High-throughput single-microbe RNA sequencing reveals adaptive state heterogeneity and host-phage activity associations in human gut microbiome. Yifei Shen, Qinghong Qian, Liguo Ding, Wenxin Qu, Tianyu Zhang, Mengdi Song, Yingjuan Huang, Mengting Wang, Ziye Xu, Jiaye Chen, Ling Dong,Hongyu Chen, Enhui Shen, Shufa Zheng, Yu Chen, Jiong Liu, Longjiang Fan*, Yongcheng Wang*. Protein & Cell, 2024. doi:https://doi.org/10.1093/procel/pwae027 |
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. doi:https://doi.org/10.1016/j.devcel.2024.05.016 |
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 |
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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