樊伟课题组

Fan Wei Lab

　　课题组长

　　樊伟，研究员，博士生导师，入选中国农科院“青年英才”，深圳市国家级领军人才。致力于基因组学和生物信息学研究，主要学术成果包括：首次利用第二代测序技术完成大熊猫基因组研究，首次利用单细胞测序技术完成人类精子和卵子细胞基因组研究，首次在国际上完成了鸡肠道宏基因组系统研究。研究成果发表于Nature、Science、Cell、Bioinformatics、Microbiome等国际期刊，累计他引3000次以上。(联系方式：[email protected])

　　

　　工作经历

　　2015.7-至今             首席科学家，中国农业科学院深圳农业基因组研究所

　　2005.7-2011.2         科研项目负责人，华大基因研究院

　　

　　教育经历

　　2001.9-2005.6           理学学士           南开大学

　　2012.9-2015.6           理学硕士           北京大学

　　

　　研究方向

　　团队研究方向包括与基因组紧密相关的生命科学问题研究，有显著农业应用价值物种的基因组学研究，以及开发解决基因组学前沿问题的生物信息学算法软件。利用基因组学与生物信息学技术推动生物育种和病虫害防治等领域的重大变革。

　　

　　研究进展

　　1. 基因组学研究：已经完成生殖细胞精子和卵子单细胞基因组研究，揭示了个体水平上的减数分裂重组规律和非整倍体的发生规律，该成果将促进生殖细胞的筛选、优生优育和生物育种领域的发展；已经完成大熊猫、薇甘菊、多头带绦虫、福寿螺、非洲大蜗牛、绿盲蝽等多种生物的基因组学研究，揭示了这些物种的独特表型背后的基因组遗传机制，为这些物种的持续开发利用奠定基础。已经完成鸡肠道微生物、沼气微生物等宏基因组学研究，构建了核心微生物的基因组和基因集，为进一步选育有益菌铺平道路。

　　

　　2. 生物信息学研究：已经开发测序数据特征分析与精准模拟算法 （PIRS）、基于Kmer的基因组特征估计算法（GCE）、二代短序列组装算法（DBG）、单细胞变异检测和重组位点检测算法(SPERMSNP)、同源基因定位算法(FGF)等多个生物信息学算法软件。这些算法软件在生物信息学领域具有一定的影响，促进了一系列基因组研究项目的开展，软件代码开源在Github (https://github.com/fanagislab)。

　　

　　PI

　　Wei Fan, a Research professor and doctoral advisor, was honored as " Outstanding Young Talent" of CAAS and " Shenzhen High-level Talent". He focus on genomics and bioinformatics research, the major research results include: the genomic analysis of giant panda by using the second generation sequencing technology, genome of sperm and ovum in human by using single cell sequencing technology, the chicken gut metagenomic system research. These researches were published in International journals such as Nature, Science, Cell, Bioinformatics and Microbiome, with more than 3,000 citations. (Email：[email protected])

　　

　　Working Experience

　　Agriculture Genomics Institute at shenzhen – CAAS               Chief scientist                                 2015.7-present

　　Beijing Genomics Institute                                                       Scientific project leader                   2005.7-2011.12

　　

　　Education Experience

　　Nankai University          bachelor             2001.9-2005.6

　　Peking University           master                2012.9-2015.6

　　

　　Research Interest

　　Our team focuses on the key biological questions that closely related with the genome, genomics researches for agriculture valuable species, and developing bioinformatics algorithms to resolve the cutting-edge genomics applications. Using the genomics and bioinformatics technologies to promote the revolution in biotechnology breeding and prevention of worms and diseases.

　　

　　Major Achievements　

　　In genomics, we have completed single-cell genomics studies on the sperm and oocyte cells, reveals the individual-level meiosis crossover and aneuploidy distributions, which will promote the selection of germ cells and biotechnology breeding. We have completed genomics studies on Giant panda, Mikania micrantha, Taenia multiceps, golden apple snail, giant African snail, and Apolygus lucorμm, reveals the genetic basis of special phenotypes of these species; We have also completed metagenomics studies on the chicken gut and biogas production, and constructed the core microbial genomes and gene sets, which will facilitate selecting and engineering of the beneficial microorganisms.　　

　　In bioinformatics, we have developed several algorithms for cutting-edge genomic data analysis, such as illumina-reads simulator pIRS (published on Bioinformatics), genomic characters estimation with K-mer frequency GCE (arXiv: 1308.2012), De bruijn graph short-reads assembly DBG_assembly (published on Briefings in Functional Genomics), single-cell meiosis crossover and aneuploidy detection software Probing_Meiotic_Recombination (published on Science), and Fishing gene family FGF (published on Nucleic Acids Research). These software have been successfully applied in many genomics projects, and the codes are free accessible at GitHub ( https://github.com/fanagislab ). 

　　

　　Selected Publication　　

　　1. Conghui Liu, Yuwei Ren, Zaiyuan Li, Qi Hu, Lijuan Yin, et al, Fanghao Wan, Wanqiang Qian?, Wei Fan?. Giant african snail genomes provide insights into molluscan whole-genome duplication and aquatic-terrestrial transition. Molecular Ecology Resources. 2020;00:1–17.  (2020)

　　2. Yang Liu, Hangwei Liu, Hengchao Wang, Tianyu Huang, et al, Kongming Wu?, Wei Fan?, Guirong Wang?. Apolygus lucorum genome provides insights into omnivorousness and mesophyll feeding. Molecular Ecology Resources. Mol Ecol Resour. 2021;21:287–300. (2020)

　　3. Lei Zhang, Bo Liu, Weigang Zheng, Conghui Liu, et al. Wei Fan?, Wanqiang Qian?, Kongming Wu?, Yutao Xiao?. Genetic structure and insecticide resistance characteristics of fall armyworm populations invading China. Molecular Ecology Resources. 2020;20:1682–1696. doi: 10.1111/1755-0998.13219 (2020)　　

　　4. Bo Liu*, Jian Yan*, Weihua Li*, Lijuan Yin*, Ping Li*, et al. Changlian Peng, Wanqiang Qian, Wei Fan* & Fanghao Wan*. (2020) Mikania micrantha genome provides insights into the molecular mechanism of rapid growth. Nature communications .　

　　5. Li W*, Liu B*, Yang Y*, Ren Y*, Wang S*, Liu C*, Zhang N, Qu Z, Yang W, Zhang Y, Yan H, Jiang F, Li L, Li S, Jia W, Yin H, Cai X, Liu T, Donald P. McManus?, Fan W?, and Fu B?.(2018). The genome of tapeworm Taenia multiceps sheds light on understanding parasitic mechanism and control of coenurosis disease. DNA Research . 25(5): 499-510

　　6. Liu C*, Zhang Y*, Ren Y*, Wang H, Li S, Jiang F, Yin L, Qiao X, Zhang G, Qian W, Liu B? and Fan W?.(2018).The genome of the golden apple snail Pomacea canaliculata provides insight into stress tolerance and invasive adaptation. GigaScience . 7: 1-13

　　7. Huang P*, Zhang Y*, Xiao K*, Jiang F*, Wang H, Tang D, Liu D,Liu B, Liu Y, He X,…Guo Y?, Fan W? and Zeng J?.(2018).The chicken gut metagenome and the modulatory effects of plant-derived benzylisoquinoline alkaloids. Microbiome .6:211

　　8. Yu Hou*, Wei Fan*, Liying Yan*, et al. (2013) Genome Analyses of Single Human Oocytes. Cell 155, 1492–1506

　　9. Zhenyu Li, Yanxiang chen, Desheng Mu, et al. Bicheng Yang? and Wei Fan?. (2012) Comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph. Briefings in Functional Genomics . VOL 11. NO 1. 25-37

　　10. Xuesong Hu, Jianying Yuan, Yujian Shi, et al. and Wei Fan?. (2012) pIRS: Profile based Illumina pair-end Reads Simulator. Bioinformatics Vol. 28 no. 11, 1533–1535

　　11. Wei Fan* & Ruiqiang Li. (2012) Test driving genome assemblers. Nature biotechnology , volume 30 number 4.

　　12. Sijia Lu*, Chenghang Zong*, Wei Fan*, Mingyu Yang*, et al. (2012) Probing Meiotic Recombination and Aneuploidy of Single Sperm Cells by Whole Genome Sequencing. Science 338, 1627

　　13. Ruiqiang Li*, Wei Fan*, Geng Tian*, Hongmei Zhu*, Lin He*, Jing Cai*, et.al. (2010) The sequence and de novo assembly of the giant panda genome. Nature 463, 311-317

　　14. Sanwen Huang*, Zhonghua Zhang*, Xingfang Gu*, William J. Lucas*, Ruiqiang Li*, Li Li*, Wei Fan*, William J Lucas*, et.al. (2009) The genome of the cucumber, Cucumis sativus L. Nature Genetics . 41, 1275 - 1281

　　樊伟课题组更新于2021年1月