Bioinplant Group of Zhejiang University
 

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.


最新消息(News)
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)
Ø 博士生谢玲娟赴第二十二届全国植物基因组学大会作报告(2023-08-23)
Ø Crop Design | 植物单细胞转录组学研究进展(2023-08-15)
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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)

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. in press

A reference genome of Commelinales provides insights into the commelinids evolution and global spread of water hyacinth (Pontederia crassipes). Huang Y; Guo l; Xie l; Shang N; Wu D; Ye C; Rudell EC; Okada K; Zhu Q; Song B; Cai D; Junior AM; Bai L*; Fan L*. GigaScience, 2024. in press

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

GSCtool: a novel descriptor that characterizes the genome for applying machine learning in genomics. Zijie Shen, Enhui Shen, Qianhao Zhu, Longjiang Fan, Quan Zou*, Chuyu Ye*. Advanced Intelligent Systems, 2023. doi:https://onlinelibrary.wiley.com/doi/10.1002/aisy.202300426

Editorial: The Application of Population Genomics in Crop Research. Fanjing Yang, Wei Ma, and Chuyu Ye. Agronomy, 2023.doi:https://doi.org/10.3390/agronomy13102480

Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision. Marieke Vromman, Jasper Anckaert, Stefania Bortoluzzi, Alessia Buratin, Chia-Ying Chen, Qinjie Chu, Chuyu Ye, et al. Nature Methods, 2023.doi: :https://www.nature.com/articles/s41592-023-01944-6

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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)

团队成员 (Group member)

PI及其他教职工(staff)和学生(student)

照片 (Photos)
Pictures
Genome and Bioinformatics Cartoons

视频与海报 (Video & Poster)
Video
Poster

联系我们Contact Us
bioinplant@zju.edu.cn

Last updated: July, 2023, bioinplant@zju.edu.cn