Bioinplant Lab

Bioinplant Lab of Zhejiang University

本实验室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、中美植物与医学健康联合研究中心重要组成部分。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）植物基因组及大数据育种技术；（2）组学大数据分析方法、数据库与工具；（3）转化医学与健康。具体包括作物及其相关植物基因组解析、基因组数据为导向的大数据育种技术、单细胞组学数据生物信息学分析方法与工具、健康与医学相关内容（如跨界调控、单细胞组学技术应用）等。[简介] [全家福][公众号]

The Bioinplant lab is a part of Institute of Crop Sciences, Institute of Bioinformatics, IBM Biocomputing Laboratory and Sino-US Plant and Health Medicine Joint Reasearch Center, 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 for omic data from single-cells, 3D genomes, etc.; (3) plant comparative medicine and health, such as comparative studies on diseases (tumors, scar, etc) in both plant and human, cross-talk of plant genetic elements (miRNA) in human, omic data-based approaches for safety evaluation of agricultural products.

Ø 《植物基因组学》（第二版）编写组第一次会议顺利召开（2023-05-16）

Ø 樊龙江教授参加国家水稻商业化分子育种技术创新联盟2023年南繁成果展示会（2023-04-20）

Ø 博士生姚洁在首届长三角生物信息学大会青年学者论坛上作报告（2023-04-18）

Ø 樊龙江教授主编《生物信息学》（第二版）入选农业农村部“十四五”规划教材（2023-04-07）

Ø 吴东亚荣获浙江大学2022年度优秀博士学位论文（2023-03-10）

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教学材料（Courses）

Ø 《生物信息学》（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] [视频简介]

Ø 《植物基因组学》，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] [视频简介]

Ø 《生物信息学札记》（樊龙江，2001，2005，2010）

Ø 本实验室公众号：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）

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

PcircRNA-finder: A program to identify circular RNAs in plants

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近期发表论文（Recent Publications）

Asymmetric variation of DNA methylation during domestication and de-domestication of rice. Shuai Cao, Kai Chen, Kening Lu, Shiting Chen, Xiyu Zhang, Congcong Shen, Shuangbin Zhu, Yanan Niu, Longjiang Fan, Z. Jeffrey Chen*, Jianlong Xu*, Qingxin Song*. Plant Cell, 2023. in press

Genome-wide dissection of Quan9311A breeding and application. Qianlong Li, Qi Feng, Heqin Wang, Yunhai Kang, Conghe Zhang, Ming Du, Yunhu Zhang, Hui Wang, Jinjie Chen, Bin Han, Yu Fang, Ahong Wang. Rice Science, 2023. doi: https://doi.org/10.21203/rs.3.rs-1727782/v1

High-throughput single nucleus total RNA sequencing of formalin-fixed paraffin-embedded tissues by snRandom-seq. Ziye Xu, Tianyu Zhang, Hongyu Chen, Yuyi Zhu, Yuexiao Lv, Shunji Zhang, Jiaye Chen, Haide Chen, Lili Yang, Weiqin Jiang, Shengyu Ni, Fangru Lu, Zhaolun Wang, Hao Yang, Ling Dong, Feng Chen, Hong Zhang, Yu Chen, Jiong Liu, Dandan Zhang, Longjiang Fan*, Guoji Gu* and Yongcheng Wang*. Nature Communications, 2023. doi:https://www.nature.com/articles/s41467-023-38409-5

A syntelog-based pan-genome provides insights into rice domestication and de-domestication. Dongya Wu, Lingjuan Xie, Yanqing Sun, Yujie Huang, Lei Jia, Chenfeng Dong, Enhui Shen, Chuyu Ye, Qian Qian*, Longjiang Fan*. bioRxiv, 2023. doi:https://www.biorxiv.org/content/10.1101/2023.03.17.533115v1

Editorial: The roles of ncRNAs in the genome evolution and cross-kingdom regulation. Enhui Shen*, Jun Zou, Jiandong Bao, Qianhao Zhu*. Frontiers in Plant Science, 2023.doi: https://doi.org/10.3389/fpls.2023.1133096

Weed genomics: Yielding insights into the genetics of weedy traits for crop improvement. Yujie Huang, Dongya Wu, Zhaofeng Huang, Xiangyu Li, Aldo Merotto Jr, Lianyang Bai*, Longjiang Fan*. aBIOTECH , 2022.doi: https://doi.org/10.1007/s42994-022-00090-5

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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

Crop and Relatives Genomes

✽ Rice [MSU][RAP-DB][RIGW][RiceRelativesGD][PlantcircBase]

✽ Red rice / weedy rice [RiceRelativesGD]