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: fanwei@caas.cn)

Working Experience

Agriculturl 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 Publications

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. Giga Science. 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