长期致力于解析生物性状进化的遗传创新（genetic innovation）机制，提出了一系列新方法、新思路，在新基因起源进化和动物重要性状进化的遗传创新基础研究等方面取得了重要成果。以第一或通讯作者（含共同通讯）发表论文160余篇，其中Science 6篇，Cell 2篇、Nature Genetics 3篇、Nature Biotechnology 4篇、Nature Ecology and Evolution 7篇、Nature Communications 7篇、《中国科学》和《科学通报》7 篇。目前论文被引用超2.57万次。相关结果先后两次获得国家自然科学二等奖（均排名第一）、教育部自然科学一等奖（排名第一）和“全国创新争先奖”，两次入选“中国生命科学十大进展”。

王文教授曾主持国家杰出青年基金项目，担任某项目首席科学家（两次）、国家创新研究群体首席科学家，入选首批“新基石研究员”。

1.新基因在生物表型适应进化过程中的作用机制

　　一方面我们以经典模式生物果蝇、酵母为材料，基于前期在新基因起源进化机制方面的研究积累，进一步利用分子生物学研究手段深入探讨新基因、新pathway的分子调控机制，并侧重于从头起源新基因（denovo genes）；另一方面，我们将以表型多样性著称的鳞翅目蝴蝶作为研究材料，结合多组学与基因组编辑技术，建立研究evo-devo的新模式，揭示新基因、新pathway起源进化和维持调整的机制，开辟一条认知遗传、发育和进化统一的新道路。  

2.人工选择下基因组进化的模式及基因资源的规模化挖掘  

　　开展家养物种及其野生种基因组、表观组等开展大规模比较分析，并基于多组学大数据资源进行人工选择下基因组变异规律跨物种的分析，阐明人工选择机制，挖掘重要性状相关基因资源，为遗传和基因工程育种提供重要的理论指导和基因及品系资源。 

Li XY, Fan DD, Zhang W, Liu GC, Zhang L, Zhao L, Fang X, Chen L, Dong Y, Chen Y, Ding Y, Zhao RP, Feng MJ, Zhu Y, Feng Y, Jiang XT, Zhu DY, Xiang H, Feng XK, Li SC, Wang J*, Zhang GJ*, Kronforst MR* &Wang W*. 2015. Outbred genome sequencing and CRISPR/Cas9 gene editing in butterflies.Nature Communications. 6:8212. 

2. Zhou ZK, Jiang Y, Wang Z, Gou ZH, Lyu J, Li WY, Yu Y, Shu LP, Zhao YJ, Ma YM, Fang C, Shen YT, Liu TF, Li CC, Li Q, Wu M, Wang M, Wu YS, Dong Y, Wan WT, Wang X, Ding ZL, Gao YD, Xiang H, Zhu BG, Lee SK,Wang W*& Tian ZX*. 2015. Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean.Nature biotechnology.33(4):408-414.

3.Jiang Y,Xie M,Chen WB,Talbot R,Maddox JF,Faraut T,Wu CH,Muzny DM,Li YX,Zhang WG,Stanton JA,Brauning R,Barris WC,Hourlier T,Aken BL,Searle SM,Adelson DL,Bian C,Cam GR,Chen YL,Cheng SF,DeSilva U,Dixen K,DongY,Fan GY,Franklin IR,Fu SY,Guan R,Highland MA,Holder ME,Huang GD,Ingham AB,Jhangiani SN,Kalra D,Kovar CL,Lee SL,Liu WQ,Liu X,Lu CX,Lv T,Mathew T,McWilliam S,Menzies M,Pan SK,Robelin D,Servin B,Townley D,Wang WL,Wei B,White SN,Yang XH,Ye C,Yue YJ,Zeng P,Zhou Q,Hansen JB,Kristiansen K,Gibbs RA,Flicek P,Warkup CC,Jones HE,Oddy VH,Nicholas FW,McEwan JC,Kijas J,Wang J,Worley KC*,Archibald AL*,Cockett N*,Xu X*,Wang W*& Dalrymple BP*.2014. The sheep genome illuminates biology of the rumen and lipid metabolism.Science. 344(6188):1168-1173.

4. Chen L, Tang LY, Xiang H, Jin LJ, Li QY, Dong Y,Wang W*and Zhang GJ*. 2014. Advances in genome editing technology and its promising application in evolutionary and ecological studies.GigaScience. (2015，IF= 7.463, 5year-IF= 11.660 ) 3:24.

5.Lyu J,Zhang S,Dong Y,He W,Zhang J,Deng X,Zhang Y,Li X,Li B,Huang W,Wan W,Yu Y,Li Q,Li J,Liu X,Wang B,Tao D,Zhang G,Wang J,Xu X,Hu F* &Wang W*. 2013. Analysis of elite variety tag SNPs reveals an important allele in upland rice.Nature Communications. 4: 2138.

6. Dong Y, Xie M, Jiang Y, Xiao NQ, Du XY, Zhang WG, Tosser-Klopp G, Wang JH, Yang S, Liang J, Chen WB, Chen J, Zeng P, Hou Y, Bian C, Pan SK, Li YX, Liu X, Wang WL, Servin B, Sayre B, Zhu B, Sweeney D, Moore R, Nei WH, Shen YY, Zhao RP, Zhang GJ, Li JQ, Faraut T, Womack J, Zhang YP, Kijas J, Cockett N, Xu X*, Zhao SH*, Wang J* &Wang W*.2013.Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus).Nature biotechnology.31, 135-141.

7. Ding Y, Zhou Q,Wang W*. 2012.Origins of New Genes and Evolution of their Novel Functions.Annual Review of Ecology and Systematics. 43：345-363.

8. Zhan ZB, Ding Y,Zhao RP,Zhang Y,Yu HJ,Zhou Q, Yang S, Xiang H*,Wang W*. 2012. Rapid functional divergence of a newly evolved polyubiquitin gene inDrosophilaand its role in the trade-off between male fecundity and lifespan.Molecular biology and Evolution. 29(5):1407-1416.

9. Xu X, Liu X, Ge S, Jensen D J, Hu FY, Li X, Dong Y, Gutenkunst NR, Fang L, Huang Li, Li JX, He WM, Zhang GJ, Zheng XM, Zhang FM, Li YR, Yu C, Kristiansen K, Zhang XQ, Wang J, Wright M, McCouch S, Nielsen R*, Wang J*,Wang W*.2012. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes.Nature Biotechnology.30:105-111.

10. Ding Y, Zhao L, Yang S, Jiang Y, Chen Y, Zhao RP, Zhang Y, Zhang GJ, Dong Y, Yu HJ, Zhou Q,Wang W*. 2010. A YoungDrosophilaDuplicate Gene Plays Essential Roles in Spermatogenesis by Regulating Several Y-Linked Male Fertility Genes.PLoS Genetics.6(12):e1001255.

11. Xiang H, Zhu JD, Chen Q, Dai FY, Li X, Li MW, Zhang HY, Zhang GJ, Li D, Dong Y, Zhao L, Lin Y, Cheng DJ, Yu J, Sun JF, Zhou XY, Ma KL, He YH, Zhao YX, Guo SC, Ye MZ, Guo GW, Li YR, Li RQ, Zhang XQ, Ma LJ, Kristiansen K, Guo QH, Jiang JH, Beck S, Xia QY*,Wang W*, Wang J*. 2010. Single base–resolution methylome of the silkworm reveals a sparse epigenomic map.Nature Biotechnology. 28:516-520.

12. Li D, Dong Y, Jiang Y, Jiang HF, Cai J,Wang W*.2010. A de novo originated gene depresses budding yeast mating pathway and is repressed by the protein encoded by its antisense strand.Cell Research. 20:408-420.

13. Zhou Q, Zhang GJ, Zhang Y, Xu SY, Zhao RP, Zhan ZB, Li X, Ding Y, Yang S,Wang W*.2008. On the origin of new genes inDrosophila.Genome Research. 18(9):1446-1455. 

14.Jiang HF, Guan WJ, Pinney D,Wang W*, Gu ZL*. 2008. Relaxation of yeast mitochondrial functions after whole genome duplication.Genome Research.18(9):1466-1471.

15. Li XY, Liang J, Yu HJ, Su B, Xiao C, Shang YF* &Wang W*.2007. Functional consequence of new exon acquisition in mammalian CDYL genes.Trends in Genetics. 23:427-431.