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。

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）、基于HiC数据的完整染色体组装算法(EndHiC)、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)。

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　　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