樊偉課題組

Fan Wei Lab

　　課題組長

　　樊偉，研究員，博士生導師。致力于基因組學和生物信息學研究，主要學術成果包括：首次利用第二代測序技術完成大熊貓基因組研究，首次利用單細胞測序技術完成人類精子和卵子細胞基因組研究，首次在國際上完成了雞腸道宏基因組系統研究。研究成果發(fā)表于Nature、Science、Cell、Bioinformatics、Microbiome等國際期刊，累計他引3000次以上。(聯系方式：[email protected])

　　

　　工作經歷

　　2015.7-至今             首席科學家，中國農業(yè)科學院深圳農業(yè)基因組研究所

　　2005.7-2011.2         科研項目負責人，華大基因研究院

　　

　　教育經歷

　　2001.9-2005.6           理學學士           南開大學

　　2012.9-2015.6           理學碩士           北京大學

　　

　　研究方向

　　團隊研究方向包括與基因組緊密相關的生命科學問題研究，有顯著農業(yè)應用價值物種的基因組學研究，以及開發(fā)解決基因組學前沿問題的生物信息學算法軟件。利用基因組學與生物信息學技術推動生物育種和病蟲害防治等領域的重大變革。

　　

　　研究進展

　　1. 基因組學研究：已經完成生殖細胞精子和卵子單細胞基因組研究，揭示了個體水平上的減數分裂重組規(guī)律和非整倍體的發(fā)生規(guī)律，該成果將促進生殖細胞的篩選、優(yōu)生優(yōu)育和生物育種領域的發(fā)展；已經完成大熊貓、薇甘菊、多頭帶絳蟲、福壽螺、非洲大蝸牛、綠盲蝽等多種生物的基因組學研究，揭示了這些物種的獨特表型背后的基因組遺傳機制，為這些物種的持續(xù)開發(fā)利用奠定基礎。已經完成雞腸道微生物、沼氣微生物等宏基因組學研究，構建了核心微生物的基因組和基因集，為進一步選育有益菌鋪平道路。

　　

　　2. 生物信息學研究：已經開發(fā)測序數據特征分析與精準模擬算法 （PIRS）、基于Kmer的基因組特征估計算法（GCE）、二代短序列組裝算法（DBG）、單細胞變異檢測和重組位點檢測算法(SPERMSNP)、同源基因定位算法(FGF)等多個生物信息學算法軟件。這些算法軟件在生物信息學領域具有一定的影響，促進了一系列基因組研究項目的開展，軟件代碼開源在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

　　樊偉課題組更新于2021年1月