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.

最新消息（News）

Ø 本实验室合作发表杂草基因组及其育种利用研究进展（2023-01-11）

Ø 喜讯！本实验室学生获2021-2022学年国家奖学金等多项奖项（2022-10-19）

Ø 褚琴洁研究员在CSPB全国学术年会作专题报告（2022-10-17）

Ø 吴东亚博士荣获先正达奇尔顿研究生奖学金（2022-10-13）

Ø Mol Plant │ 观点——无意识选择使驯化瓶颈效应复杂化（2022-08-17）

Ø 褚琴洁研究员第二届植物单细胞生物学国际研讨会大会报告（2022-08-15）

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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）

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

Poaceae chloroplast genome sequencing: great leap forward in recent ten years. Yiyu Hu, Yanqing Sun, Qianhao Zhu, Longjiang Fan, Jianhua Li*. Current Genomics , 2022. doi: https://doi.org/10.2174/1389202924666221201140603

A Manually curated database and analysis platform of cell markers of scars. Yan Zheng, Jie Yao, Xiner Shen, Haijun Cheng, Yinbo Peng, Weiqiang Tan, Michael P. Timko, Longjiang Fan*. Journal of Investigative Dermatology , 2022. doi: https://www.sciencedirect.com/science/article/abs/pii/S0022202X2202663X

Identification of plant-derived microRNAs in human kidney. Xi Chen, Xishao Xie, Lu Liu, Hongyu Chen, Bo Wang, Zheng Li, Linghui Zeng, Micheal Timko, Jianhua Chen*, Weiqiang Lin*, Longjiang Fan* bioRxiv , 2022. doi: https://doi.org/10.1101/2022.10.25.513797

Single-cell transcriptome of Nepeta tenuifolia leaves reveal differentiation trajectories in glandular trichomes. Peina Zhou, Hongyu Chen, Jingjie Dang, Zunrui Shi, Yongfang Shao, Chanchan Liu, Longjiang Fan*, Qinan Wu*. Frontiers in Plant Science, 2022. doi:https://doi.org/10.3389/fpls.2022.988594

EMLI-ICC: An ensemble machine learning-based integration algorithm for metastasis prediction and risk-stratification in intrahepatic cholangiocarcinoma. Jian Ruan, Shuaishuai Xu, Ruyin Chen, Qiong Li, Chanqi Ye, Wei Wu, Qi Jiang, Feifei Yan, ..., Michael P. Timko, Peng Zhao*, Longjiang Fan*, Yifei Shen*. Briefings in Bioinformatics, 2022. doi:https://doi.org/10.1093/bib/bbac450

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重要链接（Links）

Important Databases and Bioinformatics Portals

✽ NCBI

✽ EMBL

✽ ExPASy

✽ JCVI

✽ CBI-PU

Crop and Relatives Genomes

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

✽ Red rice / weedy rice [RiceRelativesGD]

✽ Barnyard millet / barnyardgrass (Echinochloa) [RiceRelativesGD]