 Bioinplant Lab |
The Bioinplant lab is a part of Institute of Crop Sciences, Institute of Bioinformatics, IBM Biocomputing Laboratory and Research Center for Air Pollution and Health, Zhejiang University. Our purpose is to further knowledge of genes and genomes for crop breeding and complex traits/diseases, particularly through approaches of bioinformatics, genomics and genetics. Our current research interests focus on (1) genomes of crops and their relatives; (2) approaches to bridge the gap between genomics and crop improvement, such as genomic big data-based breeding techniques; (3) non-coding RNA basis for a complex trait and bioinformatic methods for identification of epigenetic elements; (4) omic data-based approaches/bioinformatic tools for evaluation of crop safety and health. [Poster] [Family] |
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| 最新消息（News） |
| Ø 农学院褚琴洁博士入选2020年度“中国博士后创新人才支持计划” （2020-07-06） |
| Ø 浙江大学樊龙江团队揭示作物和杂草多倍化适应性进化机制差异 （2020-07-03） |
| Ø 深圳雾芯科技吴泽宏博士一行来访参观烟气安全生物评价平台 （2020-06-23） |
| Ø Nature Plants和 PNAS 撰文评价樊龙江教授团队稻壳素基因簇研究成果 （2020-06-09） |
| Ø 浙江大学樊龙江团队揭示稻壳素合成相关基因成簇进化规律 （2020-05-15）【浙大新闻】 【PNAS Commentary】 【Nature Plants Highlight】 |
| Ø 浙江大学樊龙江团队搭建水稻相关物种基因组数据库，助力水稻分子设计育种！（2020-05-01） |
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| 教学材料（Courses） |
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《植物基因组学》，樊龙江主编，2020；重磅！《植物基因组学》出版；[韩斌院士序] ；[《植物基因组学》后记]
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《生物信息学札记（第4版）》；《生物信息学》，樊龙江主编，2017；[郝柏林院士序言]
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| Ø [韩斌院士谈作物学学科发展方向]； [韩斌院士谈农学专业] |
| Ø 大型记录片《影响世界的中国植物》第二集《水稻》 [新闻链接] |
| Ø 实验室公众号生信入门好文推荐 |
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| 数据库与生物信息学工具 （Databases and Tools） |
| RiceRelativesGD: a database of rice relatives for rice breeding |
| PlantcircBase：a database for plant circular RNAs |
| BnPedigome: a genomic database for the pedigrees and breeding of Brassica napus |
| PcircRNA-finder：a program to identify circular RNAs in plants |
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| 近期发表论文 （Recent Publications） |
The genomes of the allohexaploid Echinochloa crus-galli and its progenitors provide insights into polyploidization-driven adaptation. Chu-Yu Ye; Dongya Wu; Lingfeng Mao; Lei Jia; Jie Qiu; Sangting Lao; Meihong Chen; Bowen Jiang; Wei Tang; Qiong Peng; Lang Pan; Lifeng Wang; Xiaoxiao Feng; Longbiao Guo; Chulong Zhang; Elizabeth Kellogg; Kenneth Olsen; Lianyang Bai; Longjiang Fan*. Molecular Plant, 2020. doi:https://doi.org/10.1016/j.molp.2020.07.001 [PDF] |
Expansion of MIR482/2118 by a Class II transposable element in cotton. Enhui Shen, Tianzhi Chen, Xintian Zhu, Longjiang Fan, Jie Sun, Danny Llewellyn, Iain Wilson, Qian-Hao Zhu*. The Plant Journal, 2020. doi:https://onlinelibrary.wiley.com/doi/10.1111/tpj.14885 [PDF] |
Genomic evidence for convergent evolution of gene clusters for momilactone biosynthesis in land plants. Lingfeng Mao, Hiroshi Kawaide, Sho Miyazaki, Meihong Chen, Yoshiki Hirata, Honoka Kimura, Toshiya Higuchi, Miyu Teruya, Kaoru Fujiwara, Keisuke Tomita, Koji Miyamoto, Hisakazu Yamane, Ken-ichiro Hayashi, Hideaki Nojiri, Lei Jia, Jie Qiu, Chuyu Ye,Michael P. Timko, Longjiang Fan* and Kazunori Okada*. PNAS, 2020. doi:https://doi.org/10.1073/pnas.1914373117 [PDF] [PNAS Commentary][ Nature Plants Highlight] |
Diverse genetic mechanisms underlie worldwide convergent rice feralization. Jie Qiu, Lei Jia, Dongya Wu, Xifang Weng, Lijuan Chen, Jian Sun, Meihong Chen, Lingfeng Mao, Bowen Jiang, Chuyu Ye, Guilherme Turra, Longbiao Guo, Guoyou Ye, Qianhao Zhu, Toshiyuki Imaizumi, Beng-Kah Song, Laura Scarabel, Aldo Merotto, Kenneth Olsen*, Longjiang Fan*. Genome Biology, 2020. doi:https://doi.org/10.1186/s13059-020-01980-x [PDF] |
TOD-CUP: A gene expression rank-based majority vote algorithm for tissue origin diagnosis of cancers of unknown primary. Shen Yifei, Qinjie Chu, Xinxin Yin, Yinjun He, Panpan Bai, Yunfei Wang, Weijia Fang, Michael P. Timko, Longjiang Fan*, Weiqin Jiang*. Briefings in Bioinformatics, 2020. doi:doi:https://doi.org/10.1093/bib/bbaa031 [PDF] |
A transcriptomic profile of topping responsive non-coding RNAs in tobacco roots (Nicotiana tabacum). Xi Chen, Shuo Sun, Fangjie Liu, Enhui Shen, Lu Liu, Chuyu Ye, Bingguang Xiao, Michael P. Timko, Qian-Hao Zhu, Longjiang Fan* & Peijian Cao*. BMC Genomics, 2019. doi:https://doi.org/10.1186/s12864-019-6236-6 [PDF] |
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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] |
| ✽ Oilseed rape [BnPedigome][BRAD][GENOSCOPE] |
| ✽ Gu/Jiaobai (Zizania) [RiceRelativesGD] |
| ✽ Tobacco [Sol Genomics] |
| ✽ Bryophyte (Calohypnum, formely Hypnum ) [BIGD] |
| 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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| 实验室成员 （Staff） |
| Staff of Bioinplant |
| 实验室照片 （Photos） |
| Pictures |
| Genome and Bioinformatics Cartoons |
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| 联系我们 （Contact Us） |
| Professor Fan （樊龙江） Email: fanlj@zju.edu.cn |
| bioinplant@zju.edu.cn (实验室）Tel: 86-571-88982730 |
Last updated: August, 2019, bioinplant@zju.edu.cn