Publications
- Boon-Peng Hoh#, Xiaoxi Zhang#, Lian Deng#, Kai Yuan, Chee-Wei Yew, Woei-Yuh Saw, Mohammad Zahirul Hoque, Farhang Aghakhanian, Maude E Phipps, Yik-Ying Teo, Vijay Kumar Subbiah*, Shuhua Xu*. 2020. Shared Signature of Recent Positive Selection on the TSBP1 – BTNL2 – HLA-DRA Genes in Five Native Populations from North Borneo. Genome Biology and Evolution. doi: 10.1093/gbe/evaa207.
- Shuhua Xu. Population genomics study of ethnic minorities in Xinjiang and Tibet. Science (KEXUE). 2020. 72(2):11-16.
- Jin Sun#, Lanhai Wei#, Lingxiang Wang#, Yunzhi Huang, Shi Yan, Huizhen Cheng, Rick Twee-Hee Ong, Woei-Yuh Saw, Zhiquan Fan, Xiaohua Deng, Yan Lu, Chao Zhang, Shuhua Xu, Li Jin, Yik-Ying Teo*, Hui Li*. Paternal gene pool of Malays in Southeast Asia and its applications for the early expansion of Austronesians. American Journal of Human Biology. 2020. e23486.
- Lian Deng#, Haiyi Lou#, Xiaoxi Zhang#, Thiruvahindrapuram Bhooma, Dongsheng Lu, Christian R Marshall, Chang Liu, Bo Xie, Wanxing Xu, Lai-Ping Wong, Chee-Wei Yew, Aghakhanian Farhang, Rick Twee-Hee Ong, Mohammad Zahirul Hoque, Abdul Rahman Thuhairah, Bhak Jong, Maude E Phipps, Stephen W Scherer, Yik-Ying Teo, Subbiah Vijay Kumar*, Boon-Peng Hoh*, Shuhua Xu*. 2019. Analysis of Five Deep-sequenced Trio-genomes of the Peninsular Malaysia Orang Asli and North Borneo Populations. BMC Genomics. 20:842.
- Ouzhuluobu#, Yaoxi He#, Haiyi Lou#, Chaoying Cui#, Lian Deng#, Yang Gao, Wangshan, Zheng, Yongbo Guo, Xiaoji Wang, Zhilin Ning, Jun Li, Bin Li, Caijuan Bai，Baimakangzhuo，Gonggalanzi, Dejiquzong, Bianba, Duojizhuoma, Shiming Liu, Tianyi Wu, Shuhua Xu*, Xuebin Qi*, Bing Su*. 2019. De novo assembly of a Tibetan genome and identification of novel structural variants associated with high altitude adaptation. National Science Review. 7(2):391-402.
- Lian Deng#, Chao Zhang#, Kai Yuan#, Yang Gao#, Yuwen Pan,Xueling Ge, Yaoxi He, Yuan Yuan, Yan Lu, Xiaoxi Zhang, Hao Chen, Haiyi Lou, Xiaoji Wang, Dongsheng Lu, Jiaojiao Liu, Lei Tian, Qidi Feng, Asifullah Khan, Yajun Yang, Zi-Bing Jin, Jian Yang, Fan Lu, Jia Qu, Longli Kang, Bing Su, Shuhua Xu*. 2019. Prioritizing natural selection signals from the deep-sequencing genomic data suggests multi-variant adaptation in Tibetan highlanders. National Science Review. 6(6):1201–1222.
- Qidi Feng#, Dongsheng Lu#, Shuhua Xu*. 2018. AncestryPainter: A Graphic Program for Displaying Ancestry Composition of Populations and Individuals. Genomics Proteomics Bioinformatics. 16(5):382-385.
- Shuhua Xu*. 2018. Commentary: A Mechanism of Nitric Oxide Regulation in High-altitude Tibetans. National Science Review. 5:516–629.
- Lingxiang Wang, Yan Lu, Chao Zhang, Lanhai Wei, Shi Yan, Yunzhi Huang, Chuanchao Wang, Swapan Mallick, Shaoqing Wen, Li Jin, Shuhua Xu*, Hui Li. 2018. Reconstruction of Y-chromosome phylogeny reveals two neolithic expansions of Tibeto-Burman populations. Molecular Genetics and Genomics. 293(5):1293-1300.
- Yuchen Wang, Dongsheng Lu, Yeun-Jun Chung, Shuhua Xu*. 2018. Genetic Structure, Divergence and Admixture of Han Chinese, Japanese and Korean Populations. Hereditas. 155:19.
- Chee Wei Yew, Mohd Zahirul Hoque, Jacqueline Pugh-Kitingan, Alexander Minsong, Christopher Lok Yung Voo, Julian Ransangan, Sophia Tiek Ying Lau, Xu Wang, Woei Yuh Saw, Rick Twee-Hee Ong, Yik-Ying Teo, Shuhua Xu, Boon-Peng Hoh, Maude E. Phipps, S. Vijay Kumar*. 2018. Genetic relatedness of indigenous ethnic groups in northern Borneo to neighboring populations from Southeast Asia, as inferred from genome-wide SNP data. Annals of Human Genetics. 82(4):216-226.
- Ruiqing Fu, Siti Shuhada Mokhtar, Maude Elvira Phipps, Boon-Peng Hoh, Shuhua Xu*. 2018. A genome-wide characterization of copy number variations in native populations of Peninsular Malaysia. European Journal of Human Genetics. 26:247-257.
- Chee-Wei Yew#, Dongsheng Lu#, Lian Deng#, Lai-Ping Wong#, Rick Twee-Hee Ong, Yan Lu, Xiaoji Wang, Yushimah Yunus, Farhang Aghakhanian, Siti Shuhada Mokhtar, Mohammad Zahirul Hoque, Christopher Lok-Yung Voo, Thuhairah Abdul Rahman, Jong Bhak, Maude E. Phipps, Shuhua Xu, Yik-Ying Teo, Subbiah Vijay Kumar*, Boon-Peng Hoh*. 2018. Genomic structure of the native inhabitants of Peninsular Malaysia and North Borneo suggests complex human population history in Southeast Asia. Human Genetics. 137(2):161-173.
- 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*. 2018. A missense point mutation in COL10A1 identified with whole-genome deep seqencing in a 7-generation Pakistan dwarf family. Heredity. 120(1):83-89.
- 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.
- 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.
- 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.
- Lian Deng, Boon-Peng Hoh, Dongsheng Lu, Woei-Yuh Saw, Rick Twee-Hee Ong, Anuradhani Kasturiratne, H. Janaka de Silva, Bin Alwi Zilfalil, Norihiro Kato, Ananda R. Wickremasinghe, Yik-Ying Teo & Shuhua Xu*. 2015. Dissecting the genetic structure and admixture of four geographical Malay populations. Scientific Reports. 5:14375.
- Boon-Peng Hoh*, Lian Deng, Mat Jusoh Julia-Ashazila, Zakaria Zuraihan, Ma’amor Nur-Hasnah, Ab Rajab Nur-Shafawati, Wan Isa Hatin, Ismail Endom, Bin Alwi Zilfalil, Yusoff Khalid and Shuhua Xu*. 2015. Fine-scale population structure of Malays in Peninsular Malaysia and Singapore and implications for association studies. Human Genomics. 9:16.
- 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.
- Haiyi Lou, Shilin Li, Wenfei Jin, Ruiqing Fu, Dongsheng Lu, Xinwei Pan, Huaigu Zhou, Yuan Ping, Li Jin and Shuhua Xu*. 2015. Copy number variations and genetic admixtures in three Xinjiang ethnic minority groups. European Journal of Human Genetics. 23:536-542.
- Xuanyao Liu, Yushimah Yunus, Dongsheng Lu, Farhang Aghakhanian, Woei-Yuh Saw, Lian Deng, Mohammad Ali, Xu Wang, Fadzilah Ghazali, Thuhairah Abdul Rahman, Shahrul Azlin Shaari, Mohd Zaki Salleh, Maude E. Phipps, Rick Twee-Hee Ong, Shuhua Xu, Yik-Ying Teo, Boon-Peng Hoh*. 2015. Differential positive selection of malaria resistance genes in three indigenous populations of Peninsular Malaysia. Human Genetics. 134(4):375-392.
- Xiong Yang, Suzanne Al-Bustan, Qidi Feng, Wei Guo, Zhiming Ma, Makia Marafie, Sindhu Jacob, Fahd Al-Mulla and Shuhua Xu*. 2014. The influence of admixture and consanguinity on population genetic diversity in Middle East. Journal of Human Genetics. 59:615-622.
- 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(9):614-22.
- Lian Deng, Boon Peng Hoh, 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. Marshall, 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(9):1169-1185
- Shuhua Xu*. 2012. Human Population Admixture in Asia. Genomics & Informatics 10(2):133-144.
- Shuhua Xu*, Irina Pugach, Mark Stoneking, Manfred Kayser, Li Jin, and The HUGO Pan-Asian SNP Consortium. 2012. Genetic Dating Indicates that the Asian-Papuan Admixture Through Eastern Indonesia Corresponds to the Austronesian Expansion. PNAS. 109(12):4574-4579.
- Xiong Yang, Shuhua Xu*, The HUGO Pan-Asian SNP Consortium. 2011. Identification of Close Relatives in the HUGO Pan-Asian SNP Database. PLoS One 6(12):e29502.
- 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. Mol.Biol.Evol. 28(2):1003-1011.
- Chumpol Ngamphiw, Anunchai Assawamakin, Shuhua Xu, Philip J. Shaw, Jin Ok Yang, Ho Ghang, Jong Bhak, Edison Liu, Sissades Tongsima*, The HUGO Pan-Asian SNP Consortium. 2011. PanSNPdb: The Pan-Asian SNP Genotyping Database. PLoS One 6(6):e21451.
- Wan Isa Hatin, Ab Rajab Nur-Shafawati, Mohd-Khairi Zahri, Shuhua Xu, Li Jin, Soon-Guan Tan, Mohammed Rizman-Idid, Bin Alwi Zilfalil, The HUGO Pan-Asian SNP Consortium. 2011. Population Genetic Structure of Peninsular Malaysia Malay Sub-Ethnic Groups. PLoS One 6(4):e18312.
- Frederick Delfin, Jazelyn M Salvador, Gayvelline C Calacal, Henry B Perdigon, Kristina A Tabbada, Lilian P Villamor, Saturnina C Halos, Ellen Gunnarsdo´ ttir, Sean Myles, David A Hughes, Shuhua Xu, Li Jin, Oscar Lao, Manfred Kayser, Matthew E Hurles, Mark Stoneking and Maria Corazon A De Ungria*. 2011. The Y-chromosome landscape of the Philippines: extensive heterogeneity and varying genetic affinities of Negrito and non-Negrito groups. Eur.J.Hum.Genet. 19:224-230.
- Shuhua Xu, Daoroong Kangwanpong, Mark Seielstad, Metawee Srikummool, Jatupol Kampuansai, Li Jin*, The HUGO Pan-Asian SNP Consortium. 2010. Genetic Evidence Supports Linguistic Affinity of Mlabri — a Hunter-Gatherer Group in Thailand. BMC Genet. 11:18.
- 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.
- Shuhua Xu, Wenfei Jin, Li Jin*. 2009. Haplotype Sharing Analysis Showing Uyghurs Are Unlikely Genetic Donors. Mol.Biol.Evol. 26(10): 2197-2206.
- Shuhua Xu, Li Jin*. 2008. A Genome-wide Analysis of Admixture in Uyghur and a High-Density Admixture Map for Disease-Gene Discovery. Am.J.Hum.Genet. 83:322-336.
- Shuhua Xu, Wei Huang, Ji Qian, Li Jin*. 2008. Analysis of Genomic Admixture in Uyghur and Its Implication in Mapping Strategy. Am.J.Hum.Genet. 82:883-894.