Home >> People >> Faculty
XU Shuhua

Ph.D.

Professor, Principal Investigator

Laboratory of Population Genomics

Lab Page Link: http://www.picb.ac.cn/PGG

Email: xushua@picb.ac.cn

Tel: 86-21-54920479

Research Areas: 

Human Population Genomics and Microevolution 

  • Modeling linkage disequilibrium and recombination  

  • Inference of human population admixture and migration history  

  • Detection of footprints of natural selection in the human genome (focusing on Asian populations, but including as well investigation of human microbiomes)  

  • Exploring the medical and evolutionary impact of genetic admixture  

 

Brief Biography: 

Dr. Shuhua Xu is professor of human population genetics and Principal Investigator of Population Genomics Group at the CAS-MPG Partner Institute for Computational Biology. He is currently holding the position of Max-Planck Independent Research Group Leader and a Distinguished Adjunct Professorship at ShanghaiTech University. He received his PhD at Fudan University, China. His scientific research has focused on population genomics research of human admixture history and biological adaptation to local environment. The ultimate goal of his research is to understand microevolution mechanisms in human, while genetic admixture was taken as a cut-in point to pursue this ambition. The Population Genomics Group led by Dr. Xu is using computational approaches and developing new methods to dissect genetic architecture of human populations, quantitatively characterize their admixture features, and reveal their migration history and adaptive divergence. Dr. Xu has authored many scientific papers published in Science, PNAS, The American Journal of Human Genetics, Genome Research, Molecular Biology and Evolution, Human Molecular Genetics, European Journal of Human Genetics, the PLoS and the BMC series. Dr. Xu serves as Editorial Board member of several international peer-reviewed journals such as Human Genomics, Frontier in Genetics, Hereditas, Molecular Genetics and Genomics, Scientific Reports, BMC Genetics (Section Editor). 

 

Selected Publications:*Corresponding Author 

  1. Xumin Ni, Kai Yuan, Xiong Yang, Qidi Feng, Wei Guo, Zhiming Ma* & Shuhua Xu*. 2018. Inference of multiple-wave admixtures by length distribution of ancestral tracks. Heredity. doi:10.1038/s41437-017-0041-2. 

  2. Lei Tian, Asifullah Khan, Zhilin Ning, Kai Yuan, Chao Zhang, Haiyi Lou, Yuan Yuan, Shuhua Xu*. 2018. Genome-wide comparison of allele-specific gene expression between African and European populations. Human Molecular Genetics. 27(6):1067-1077. 

  3. Jing Li#*, Ruiqing Fu#, Yajun Yang, Hans-Peter Horz, Yaqun Guan, Yan Lu, Haiyi Lou, Lei Tian, Shijie Zheng, Hongjiao Liu, Meng Shi, Kun Tang, Sijia Wang, Shuhua Xu*. 2017. A metagenomic approach to dissect the genetic composition of enterotypes in Han Chinese and two Muslim groups. Systematic and Applied Microbiology. 41(1):1-12. 

  4. Chao Zhang#, Jiaojiao Liu#, Furhan Iqbal, Yan Lu, Saima Mustafa, Firdous Bukhari, Haiyi Lou, Ruiqing Fu, Zhendong Wu, Xiong Yang, Ihtisham Bukhari, Muhammad Aslam & Shuhua Xu*. 2017. A missense point mutation in COL10A1 identified with whole-genome deep seqencing in a 7-generation Pakistan dwarf family. Heredity. 120(1):83-89. 

  5. Chao Zhang#, Yang Gao#, Jiaojiao Liu, Zhe Xue, Yan Lu, Lian Deng, Lei Tian, Qidi Feng, Shuhua Xu*. 2017. PGG.Population: a database for understanding the genomic diversity and genetic ancestry of human populations. Nucleic Acids Research46(D1):D984-D993. 

  6. Jianqi Lu#, Haiyi Lou#, Ruiqing Fu#, Dongsheng Lu#, Feng Zhang#, Zhendong Wu, Xi Zhang, Changhua Li, Baijun Fang, Fangfang Pu, Jingning Wei, Qian Wei, Chao Zhang, Xiaoji Wang, Yan lu, Shi Yan, Yajun Yang, Li Jin*, Shuhua Xu*. 2017. Assessing genome-wide copy number variation in the Han Chinese population. Journal of Medical Genetics. 54(10):685. 

  7. 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 and Shuhua Xu*. 2017. Differentiated demographic histories and local adaptations between Sherpas and Tibetans. Genome Biology. 18:115. 

  8. Qidi Feng#, Yan Lu#, Xumin Ni#, Kai Yuan#, Yajun Yang#, Xiong Yang, Chang Liu, Haiyi Lou, Zhilin Ning, Yuchen Wang, Dongsheng Lu, Chao Zhang, Ying Zhou, Meng Shi, Lei Tian, Xiaoji Wang, Xi Zhang, Jing Li, Asifullah Khan, Yaqun Guan, Kun Tang*, Sijia Wang*, Shuhua Xu*. 2017. Genetic history of Xinjiang’s Uyghurs suggests Bronze Age multiple-way contacts in Eurasia. Molecular Biology and Evolution. 34(10):2572-2582. 

  9. Ying Zhou, Kai Yuan, Yaoliang Yu, Xumin Ni, Pengtao Xie, Eric P. Xing, Shuhua Xu*. 2017. Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with polynomial functions. Heredity. 118(5):503-510. 

  10. 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*. 2016. Ancestral Origins and Genetic History of Tibetan Highlanders. Am.J.Hum.Genet. 99:580-594. 

  11. 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*. 2015. 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. 97(1):54-66. 

  12. Lian Deng, Hoh Boon Peng, Dongsheng Lu, Ruiqing Fu, Maude E. Phipps, Shilin Li, Ab Rajab Nur-Shafawati, Wan Isa Hatin, Endom Ismail, Siti Shuhada Mokhtar, Li Jin, Bin Alwi Zilfalil, Christian R Marsha, Stephen W Scherer, Fahd Al-Mulla, Shuhua Xu*. 2014. The Population Genomic Landscape of Human Genetic Structure, Admixture History and Local Adaptation in Peninsular Malaysia. Human Genetics. 133:1169–1185. 

  13. Jing Li, Haiyi Lou, Xiong Yang, Dongsheng Lu, Shilin Li, Li Jin, Xinwei Pan, Wenjun Yang, Manshu Song, Dolikun Mamatyusupu, Shuhua Xu*. 2014. Genetic Architectures of ADME Genes in Five Eurasian Admixed Populations and Implications for Drug Safety and Efficacy. Journal of Medical Genetics. 51:614-622. 

  14. Wenfei Jin, Ran Li, Ying Zhou, Shuhua Xu*. 2014. Distribution of Ancestral Chromosomal Segments in Admixed Genomes and Its Implications for Inferring Population History and Admixture Mapping. European Journal of Human Genetics. 22:930-937.  

  15. Ying Wang, Ying Zhou, Linfeng Li, Xian Chen, Yuting Liu, Zhi-Ming Ma, Shuhua Xu*. 2014. A new method for modeling coalescent processes with recombination. BMC Bioinformatics. 15:273.  

  16. Dongsheng Lu, Shuhua Xu*. 2013. Principal component analysis reveals the 1000 Genomes Project does not sufficiently cover the human genetic diversity in Asia. Frontiers in Genetics. 4:127.  

  17. Yuan Yuan, Ling Yang, Meng Shi, Dongsheng Lu, Haiyi Lou, Yi-Ping Phoebe Chen, Li Jin, Shuhua Xu*. 2013. Identification of well-differentiated gene expressions between Han Chinese and Japanese using genome-wide microarray data analysis. Journal of Medical Genetics. 50:534-542.  

  18. Shuhua Xu*. 2012. Human Population Admixture in Asia. Genomics & Informatics 10(3):133-144. (Invited Review). 

  19. Shuhua Xu* Wenfei Jin. 2012. Population Genetics in the Genomic Era (Book Chapter in Population Genetics, Book edited by Dr. Stuart Raleigh, University of Northampton, UK), InTech, Rijeka, Croatia (ISBN 979-953-307-446-6). Page: 137-168.  

  20. Wenfei Jin, Sijia Wang, Haifeng Wang, Li Jin, Shuhua Xu*. 2012. Exploring Population Admixture Dynamics Using Empirical and Simulated Genome-Wide Distribution of Ancestral Chromosomal Segments. American Journal of Human Genetics. 91:849-862.  

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

  22. Wenfei Jin, Pengfei Qin, Haiyi Lou, Li Jin*, Shuhua Xu*. 2012. A Systematic Characterization of Genes Underlying both Complex and Mendelian Diseases. Human Molecular Genetics. 21(7):1611-1624.  

  23. Wenfei Jin, Shuhua Xu*, Haifeng Wang, Yongguo Li, Yiping Shen, Bailin Wu, Li Jin*. 2012. Genome-Wide Detection of Natural Selection in African Americans Pre-and Post-Admixture. Genome Research. 22(3):519-527.  

  24. Shuhua Xu*, Shilin Li, Yajun Yang, Jingze Tan, Haiyi Lou, Wenfei Jin, Ling Yang, Xuedong Pan, Jiucun Wang, Yiping Shen, Bailin Wu, Hongyan Wang, Li Jin*. 2011. A Genome-Wide Search for Signals of High Altitude Adaptation in Tibetans. Molecular Biology and Evolution. 28:1003-1011.  

  25. Shuhua Xu*, Sanchit Guputa and Li Jin*. 2010. PEAS V1.0: A Package for Elementary Analysis of SNP Data. Molecular Ecology Resources. 10:1085-1088.  

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

  27. Shuhua Xu, Xianyong Yin, Shilin Li, Wenfei Jin, Haiyi Lou, Ling Yang, Xiaohong Gong, Xuejun Zhang, Xianyong Yin, Yungang He, Yajun Yang , Yi Wang, Wenqing Fu, Yu An, Jingze Tan, Jiucun Wang, Ji Qian, Xin Zhang, Yangfei Sun, Hongyan Wang ,Bailin Wu , Li Jin*. 2009. Genomic Dissection of Population Substructure of Han Chinese and Its Implication in Association Studies. American Journal of Human Genetics. 85:762-774. 

  28. Shuhua Xu, Wenfei Jin, Li Jin*. 2009. Haplotype Sharing Analysis Showing Uyghurs Are Unlikely Genetic Donors. Molecular Biology and Evolution. 26:2197-2206.  

  29. Shuhua Xu, Li Jin*. 2008. A Genome-wide Analysis of Admixture in Uyghurs and a High-Density Admixture Map for Disease-Gene Discovery. American Journal of Human Genetics. 83:322-336.  

  30. Shuhua Xu, Wei Huang, Ji Qian, Li Jin*. 2008. Analysis of Genomic Admixture in Uyghur and Its Implication in Mapping Strategy. American Journal of Human Genetics. 82:883-894.