主持国家、省部级课题近30项，包括国家自然科学基金重大研究计划、重点项目、杰出青年基金、中科院先导专项项目负责人、国家基础科学中心骨干等。

【代表性论文】（*通讯作者）

1. Yang Gao#, Xiaofei Yang#, Hao Chen#, Xinjiang Tan#, Zhaoqing Yang#, Lian Deng#, Baonan Wang, Shuang Kong, Songyang Li, Yuhang Cui, Chang Lei, Yimin Wang, Yuwen Pan, Sen Ma, Hao Sun, Xiaohan Zhao, Yingbing Shi, Ziyi Yang, Dongdong Wu, Shaoyuan Wu, Xingming Zhao, Binyin Shi, Li Jin, Zhibin Hu, Chinese Pangenome Consortium (CPC), Yan Lu*, Jiayou Chu*, Kai Ye* & Shuhua Xu*. A pangenome reference of 36 Chinese populations. Nature. 2023. 619:112–121.

2. Zhilin Ning#, Xinjiang Tan#, Yuan Yuan#, Ke Huang, Yuwen Pan, Lei Tian, Yan Lu, Xiaoji Wang, Ruicheng Qi, Dongsheng Lu, Yajun Yang, Yaqun Guan, Dolikun Mamatyusupu, Shuhua Xu*. Expression profiles of East-West highly differentiated genes in Uyghur genomes. National Science Review. 2023. doi:10.1093/nsr/nwad077.

3. Yuwen Pan, Jia Wen, Zhilin Ning, Yuan Yuan, Xubing Liu, Yajun Yang, Yaqun Guan, Yan Lu, Dolikun Mamatyusupu, Shuhua Xu*. Comparative genomic and transcriptomic analyses reveal the impacts of genetic admixture in Kazaks, Uyghurs, and Huis. Molecular Biology and Evolution. 2023. 40(3):msad054.

4. Xiaohan Zhao, Shuhua Xu, Sen Ma, Baonan Wang, Xuetong Jiang, Shuhua Xu*. PGG.MHC: Toward understanding the diversity of major histocompatibility complexes in human populations. Nucleic Acids Research. 2022. 51(D1):D1102-D1108.

5. Yimin Wang, Yunchao Ling, Jiao Gong, Xiaohan Zhao, Hanwen Zhou, Bo Xie, Haiyi Lou, Xinhao Zhuang, Li Jin, Shaohua Fan*, Guo-Qing Zhang*, Shuhua Xu*. PGG.SV: a whole-genome-sequencing-based structural variant resource and data analysis platform. Nucleic Acids Research. 2022. 51(D1):D1109–D1116.

6. Yuwen Pan, Panhong Liu, Fang Wang, Peng Wu, Fanjun Cheng, Xin Jin, Shuhua Xu*. Lineage-specific positive selection on ACE2 contributes to the genetic susceptibility of COVID-19. National Science Review. 2022. 9(9):nwac118.

7.Haiyi Lou#*, Bo Xie#, Yimin Wang#, Yang Gao, Shuhua Xu*. Improved NGS variant calling tool for the PRSS1–PRSS2 locus. Gut. 2022. 72(1):210-212.

8.Haiyi Lou#*, Yang Gao#, Bo Xie#, Yimin Wang#, Haikuan Zhang, Miao Shi, Sen Ma, Xiaoxi Zhang, Chang Liu, Shuhua Xu*. Haplotype-resolved de novo assembly of a Tujia genome suggests the necessity for high-quality population-specific genome references. Cell Systems. 2022. 13(4):321-333.

9.Lian Deng#, Yuwen Pan#, Yinan Wang, Hao Chen, Kai Yuan, Sihan Chen, Dongsheng Lu, Yan Lu, Siti Shuhada Mokhtar, Thuhairah Abdul Rahman, Boon-Peng Hoh, Shuhua Xu*. Genetic connections and convergent evolution of tropical indigenous peoples in Asia. Molecular Biology and Evolution. 2022. 39(2):msab361.

10. Kai Yuan#, Xumin Ni#, Chang Liu#, Yuwen Pan#, Lian Deng#, Rui Zhang#, Yang Gao, Xueling Ge, Jiaojiao Liu, Xixian Ma, Haiyi Lou, Taoyang Wu and Shuhua Xu*. Refining models of archaic–modern human admixture in Eurasia with ArchaicSeeker 2.0. Nature Communications. 2021. 12:6232.

11. Xixian Ma#, Wenjun Yang#, Yang Gao, Yuwen Pan, Yan Lu, Hao Chen, Dongsheng Lu, Shuhua Xu*. Genetic origins and sex-biased admixture of the Huis. Molecular Biology and Evolution. 2021. 38(9):3804-3819.

12. Lan-Tao Gou, Yang Gao, Jun-Yan Kang, Xin Wang, Hao Chen, Min-Min Hua, Zheng Li, Dangsheng Li, Xiang-Dong Fu, Hui-Juan Shi*, Shuhua Xu* and Mo-Fang Liu*. Reply to Lack of evidence for a role of PIWIL1 variants in human male infertility. Cell. 2021. 184(8):1943-1944.

13. Yang Gao#, Chao Zhang#, Liyun Yuan#, YunChao Ling, Xiaoji Wang, Chang Liu, Yuwen Pan, Xiaoxi Zhang, Xixian Ma, Yuchen Wang, Yan Lu, Kai Yuan, Wei Ye, Jiaqiang Qian, Huidan Chang, Ruifang Cao, Xiao Yang, Ling Ma, Yuanhu Ju, Long Dai, Yuanyuan Tang, The Han100K Initiative, Guoqing Zhang, Shuhua Xu*.  PGG.Han: The Han Chinese Genome Database and Analysis Platform. Nucleic Acids Research. 2020, 48(D1):D971-D976.

14. Chao Zhang#, Yang Gao#, Zhilin Ning#, Yan Lu#, Xiaoxi Zhang, Jiaojiao Liu, Bo Xie, Zhe Xue, Xiaoji Wang, Kai Yuan, Xueling Ge, Yuwen Pan, Chang Liu, Lei Tian, Yuchen Wang, Dongsheng Lu, Boon-Peng Hoh, Shuhua Xu*.  PGG.SNV: Understanding the evolutionary and medical implications of human single nucleotide variations in diverse populations. Genome Biology. 2019, 20:215.

15. Chao Zhang#, Yang Gao#, Jiaojiao Liu, Zhe Xue, Yan Lu, Lian Deng, Lei Tian, Qidi Feng, Shuhua Xu*.  PGG.Population: a database for understanding the genomic diversity and genetic ancestry of human populations. Nucleic Acids Research. 2018, 46:D984–D993.

16. Chao Zhang#, Yan Lu#, Qidi Feng#, Xiaoji Wang#, Haiyi Lou, Jiaojiao Liu, Zhilin Ning, Kai Yuan, Yuchen Wang, Ying Zhou, Lian Deng, Lijun Liu, Yajun Yang, Shilin Li, Lifeng Ma, Zhiying Zhang, Li Jin, Bing Su, Longli Kang, Shuhua Xu*. Differentiated demographic histories and local adaptations between Sherpas and Tibetans. Genome Biology. 2017, 18:115.

17. Dongsheng Lu, Haiyi Lou, Kai Yuan, Xiaoji Wang, Yuchen Wang, Chao Zhang, Yan Lu, Xiong Yang, Lian Deng, Ying Zhou, Qidi Feng, Ya Hu, Qiliang Ding, Yajun Yang, Shilin Li, Li Jin, Yaqun Guan, Bing Su, Longli Kang, and Shuhua Xu*. Ancestral Origins and Genetic History of Tibetan Highlanders. Am.J.Hum.Genet. 2016, 99:580-594.

18. Haiyi Lou, Yan Lu, Dongsheng Lu, Ruiqing Fu, Xiaoji Wang, Qidi Feng, Sijie Wu, Yajun Yang, Shilin Li, Longli Kang, Yaqun Guan, Boon-Peng Hoh, Yeun-Jun Chung, Li Jin, Bing Su, Shuhua Xu*. A 3.4-kb Copy-Number Deletion near EPAS1 Is Significantly Enriched in High-Altitude Tibetans but Absent from the Denisovan Sequence. Am.J.Hum.Genet. 2015, 97(1):54-66.

19. Shuhua Xu*, Irina Pugach, Mark Stoneking, Manfred Kayser, Li Jin, The HUGO Pan-Asian SNP Consortium. Genetic Dating Indicates that the Asian-Papuan Admixture through Eastern Indonesia Corresponds to the Austronesian Expansion. Proceedings of the National Academy of Sciences. 2012, 109(12):4574-4579.

20. The HUGO Pan-Asian SNP Consortium (Li Jin*, Edison T. Liu*, Mark Seielstad*, Shuhua Xu*; 93 authors from 10 countries). Mapping Genetic Diversity in Asia. Science. 2009, 326:1541-1545.