2012年，中国科学院百篇优秀博士论文奖，个人奖。2013年，云南省自然科学奖特等奖（基因组多样性与亚洲人群的演化），排名第三。2013年，云南省自然科学奖一等奖（动物适应性进化的分子机制），排名第五。2013年，入选中国科学院青年创新促进会。2014年，中国科学院卢嘉锡青年人才奖，个人奖。2015年，国家自然科学奖二等奖（基因组多样性与亚洲人群的演化），排名第三。

    1.灵长类动物基因组进化 

利用灵长类动物资源，借助基因组测序技术，整合分子进化学、系统生物学、生物信息学等分析手段，通过多学科交叉，解析灵长类动物复杂性状进化发育的遗传机制。 

2.家养动物环境适应的遗传机制 

基于大规模组学数据，综合利用各种生物学方法，解析家养动物适应不同自然环境的遗传机制。 

1.Wu DD*, Ding XD, Wang S, Wójcik JM, Zhang Y, Tokarska M, Li Y, Wang MS, Faruque O, Nielsen R*, Zhang Q*, Zhang YP*. Pervasive introgression facilitated domestication and adaptation in the Bos species complex.Nature Ecol Evol.2018 2(7):1139-1145. 

2. Zeng L, Ming C, …,Wu DD* Zhang YP *. Out of Southern East Asia of the Brown Rat Revealed by Large-Scale Genome Sequencing.Molecular Biology and Evolution22018 1:149–158. (cover) 

3. Zeng L, Ming C, …,Wu DD, * and Zhang YP *. Rapid Evolution of Genes Involved in Learning and Energy Metabolism for Domestication of the Laboratory Rat.Molecular Biology and Evolution2017, 34(12):3148-3153. 

4.  Li Y, Wang MS, Otecko N, Wang W, Shi P,Wu DD*, Zhang YP*. Hypoxia Potentially Promotes Tibetan Longevity.Cell Research2017 27(2):302-305. 

5. Wang MS, Yang HC, Otecko N,Wu DD*, Zhang YP*. Olfactory genes in Tibetan wild boar.Nature Genetics2016 48(9):972-973. 

6.  Wang MS, Su LY, Li Y, Peng MS, Liu HQ, Zeng L, Irwin DM, Yao YG, Wu DD*, and Zhang YP *. Positive selection rather than relaxation of functional constraint drives the evolution of vision during chicken domestication.Cell Research2016 26(5):556-573 

7.  Wang MS*, Li Y*, Peng MS*, Zhong L, Wang ZJ, Li QY, Tu XL, Dong Y, Zhu CL, Wang L, Yang MM, Wu SF, Miao YW, Liu JP, Irwin DM, Wang W,Wu DD*, Zhang YP*. Genomic Analyses Reveal Potential Independent Adaptation to High Altitude in Tibetan Chickens. Molecular Biology and Evolution2015 32(7):1880-1889. 

8. Li Y, Wu DD *, Boyko AR, Wang GD, Wu SF, Irwin DM, Zhang YP*. Population variation revealed high-altitude adaptation of Tibetan mastiffs. Molecular Biology and Evolution2014 31(5):1200-1205.  

9. Li Y, vonHoldt BM, Reynolds A, Boyko AR, Wayne RK,Wu DD*, Zhang YP*. Artificial selection on brain expressed genes during the domestication of dog.Molecular Biology and Evolution2013 30(8):1867-76.  

10. Jin W,Wu DD*, Zhang X, Irwin DM, Zhang YP*. Positive Selection on the Gene RNASEL: Correlation between Patterns of Evolution and Function.Molecular Biology and Evolution2012 29(10):3161-8. 

11.Wu DD, Irwin DM, Zhang YP. De novo origin of human protein coding genes.PLoS Genetics2011 7(11):e1002379 

12.Wu DD, Wang GD, Irwin DM, Zhang YP. A profound role for the expansion of trypsin-like serine protease family in the evolution of hematophagy in mosquito.Molecular Biology and Evolution2009 26(10):2333-2341