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）植物比较医学与健康。具体包括作物及其野生植物基因组解析、基因组为导向的大数据育种技术、单细胞、三维基因组非编码RNA等生物信息学分析方法及其工具、基于组学数据的农产品制品安全评价、动植物肿瘤发生等保守遗传机制、植物跨界调控等研究。[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 浙江大学2021年招生宣传片——《新生》（本实验室参与拍摄）（2021-06-13）

Ø 祝贺本实验室5位学生顺利完成论文答辩！（2021-06-10）

Ø 生信大讲堂：追根溯源——生物统计（2021-06-03）

Ø 博士生吴东亚参加第三届江浙生物信息学学术交流会（2021-05-29）

Ø 博士生吴东亚获得浙江大学农学院博士生创新论坛学术报告一等奖（2021-05-28）

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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]

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]

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）

scDetect: A rank-based ensemble learning algorithm for cell type identification of single-cell RNA sequencing in cancer. Yifei Shen*, Qinjie Chu, Micheal Timko, Longjiang Fan*. Bioinformatics, 2021. in press

PlantscRNAdb: A database for plant single-cell RNA analysis. Hongyu Chen, Xinxin Yin, Longbiao Guo, Jie Yao, Yuwen Ding, Xiaoxu Xu, Lu Liu, Zhu Qian-Hao, Qinjie Chu*, Longjiang Fan*. Molecular Plant, 2021. doi:https://doi.org/10.1016/j.molp.2021.05.002

Rice bioinformatics in the genomic era: status and perspectives. Lei Jia, Lingjuan Xie, Sangting Lao, Qian-Hao Zhu, Longjiang Fan*. The Crop Journal, 2021. doi:https://doi.org/10.1016/j.cj.2021.03.003

An ABCC-type transporter endowing glyphosate resistance in plants. Lang Pan, Qin Yu*, Junzhi Wang, Heping Han, Lingfeng Mao, Alex Nyporko, Anna Maguza, Longjiang Fan, Lianyang Bai*, Stephen Powles*. PNAS, 2021. doi:https://doi.org/10.1073/pnas.2100136118

Decoding genomes changed our understanding and approaches for plant breeding.(TrendsTalk). Longjiang Fan*. Trends in Plant Science, 2021. doi:https://doi.org/10.1016/j.tplants.2021.03.013

De-domestication: an extension of crop evolution. Dongya Wu, Sangting Lao, Longjiang Fan*. Trends in Plant Science, 2021. doi:https://doi.org/10.1016/j.tplants.2021.02.003

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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]