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论文发表

[109] Qidi Feng#, Dongsheng Lu#, Shuhua Xu*. 2018. AncestryPainter: A Graphic Program for Displaying Ancestry Composition of Populations and Individuals. Genomics Proteomics Bioinformatics16(5):382-385.

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[108] Sijie Wu#, Manfei Zhang#, Xinzhou Yang#, Fuduan Peng, Juan Zhang, Jingze Tan, Yajun Yang, Lina Wang, Yanan Hu, Qianqian Peng, Jinxi Li, Yu Liu, Yaqun Guan, Chen Chen, Merel A. Hamer, Tamar Nijsten, Changqing Zeng, Kaustubh Adhikari, Carla Gallo, Giovanni Poletti, Lavinia Schuler-Faccini, Maria-Cátira Bortolini, Samuel Canizales-Quinteros, Francisco Rothhammer,Gabriel Bedoya, Rolando González-José, Hui Li, Jean Krutmann, Fan Liu, Manfred Kayser, Andres Ruiz-Linares, Kun Tang, Shuhua Xu, Liang Zhang*, Li Jin*, Sijia Wang*. 2018. Genome-wide association studies and CRISPR/Cas9-mediated gene editing identify regulatory variants influencing eyebrow thickness in humans. PLoS Genetics. 14(9):e1007640.

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[107] Ewelina Pośpiech, Yan Chen, Magdalena Kukla-Bartoszek, Krystal Breslin, Anastasia Aliferi, Jeppe D. Andersen, David Ballard, Lakshmi Chaitanya, Ana Freire-Aradas, Kristiaan J.van der Gaag, Lorena Girón-Santamaría, Theresa E. Gross, Mario Gysi, Gabriela Huber, Ana Mosquera-Miguel, Charanya Muralidharan, Małgorzata Skowron, Ángel Carracedo, Cordula Haas, Niels Morling, Walther Parson, Christopher Phillips, Peter M. Schneider, Titia Sijen, Denise Syndercombe-Court, Marielle Vennemann, Sijie Wu, Shuhua Xu, Li Jin, Sijia Wang, Ghu Zhu, Nick G. Martin, Sarah E. Medland, EUROFORGEN NoE Consortium, Wojciech Branicki, Susan Walsh, Fan Liu, Manfred Kayser*. 2018. Towards broadening Forensic DNA Phenotyping beyond pigmentation: Improving the prediction of head hair shape from DNA. Forensic Science International: Genetics. 37(2018):241-251.

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[106] Xumin Ni, Kai Yuan, Chang Liu, Qidi Feng, Lei Tian, Zhiming Ma*, Shuhua Xu*. 2018. MultiWaver 2.0: modeling discrete and continuous gene flow to reconstruct complex population admixtures. European Journal of Human Genetics. 27:133-139.

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[105] Lu Qiao, Yajun Yang, Pengcheng Fu, Sile Hu, Hang Zhou, Shouneng Peng, Jingze Tan, Yan Lu, Haiyi Lou, Dongsheng Lu, Sijie Wu, Jing Guo, Li Jin, Yaqun Guan, Sijia Wang*, Shuhua Xu*, Kun Tang*. 2018. Genome-wide variants of Eurasian facial shape differentiation and a prospective model of DNA based face prediction. Journal of Genetics and Genomics45(8):419-432.

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[104] Shuhua Xu*. 2018. Commentary: A Mechanism of Nitric Oxide Regulation in High-altitude Tibetans. National Science Review5:516–629.

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[103] Lan-Hai Wei, Ling-Xiang Wang, Shao-Qing Wen, Shi Yan, Rebekah Canada, Vladimir Gurianov, Yun-Zhi Huang, Swapan Mallick, Alessandro Biondo, Amy O’Leary, Chuan-Chao Wang, Yan Lu, Chao Zhang, Li Jin, Shuhua Xu* & Hui Li*. 2018. Paternal origin of Paleo-Indians in Siberia: insights from Y-chromosome sequences. European Journal of Human Genetics. 26:1687-1696.

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[102] 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.

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[101] 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.

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[100] 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.

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[99] 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 Genetics26:247-257.

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[98] 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. Heredity121:52-63.

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[97] 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.

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[96] 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.

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[95] 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*.2018. A metagenomic approach to dissect the genetic composition of enterotypes in Han Chinese and two Muslim groups. Systematic and Applied Microbiology41(1):1-12.

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[94] Fan Liu#,*, Yan Chen#, Gu Zhu, Pirro G. Hysi, Sijie Wu, Kaustubh Adhikari, Krystal Breslin, Ewelina Pośpiech, Merel A. Hamer, Fuduan Peng, Charanya Muralidharan, Victor Acuna-Alonzo, Samuel Canizales-Quinteros, Gabriel Bedoya, Carla Gallo, Giovanni Poletti, Francisco Rothhammer, Maria Catira Bortolini, Rolando Gonzalez-Jose, Changqing Zeng, Shuhua Xu, Li Jin, André G. Uitterlinden, M. Arfan Ikram, Cornelia M. van Duijn, Tamar Nijsten, Susan Walsh, Wojciech Branicki, Sijia Wang, Andrés Ruiz-Linares, Timothy D. Spector, Nicholas G. Martin, Sarah E. Medland* and Manfred Kayser*. 2018. Meta-analysis of genome-wide association studies identifies 8 novel loci involved in shape variation of human head hair. Human Molecular Genetics. 27(3):559-575.

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[93] 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.

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[92] Chao Zhang#, Yang Gao#, Jiaojiao Liu, Zhe Xue, Yan Lu, Lian Deng, Lei Tian, Qidi Feng, Shuhua Xu*. 2018PGG.Population: a database for understanding the genomic diversity and genetic ancestry of human populations. Nucleic Acids Research. 46(D1):D984-D993.

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[91] Cheng Zhang, Jianqi Lu, Haiyi Lou, Renqian Du, Shuhua Xu, Yiping Shen, Feng Zhang*, Li Jin*. 2017. CNVbase: Batch identification of novel and rare copy number variations based on multi-ethnic population data. Journal of Genetics and Genomics44(7):367-370.

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[90] Ruihong Liu#, Chuming Chen#, Xuefeng Xia#, Qijun Liao#, Qiong Wang, Paul J. Newcombe, Shuhua Xu, Minghui Chen, Yue Ding, Xiaoying Li, Zhihong Liao, Fucheng Li, Minlian Du, Huaiqiu Huang, Ruimin Dong, Weiping Deng, Ye Wang, Binghui Zeng, Qihao Pan, Danhua Jiang, Hao Zeng, Pak Sham, Yingnan Cao, Patrick H. Maxwell, Zhi-liang Gao*, Liang Peng* & Yiming Wang*. 2017. Homozygous p.Ser267Phe in SLC10A1 is associated with a new type of hypercholanemia and implications for personalized medicine. Scientific Reports7:9214.

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[89] Kai Yuan#, Ying Zhou#, Xumin Ni#, Yuchen Wang, Chang Liu and Shuhua Xu*. 2017. Models, methods and tools for ancestry inference and admixture analysis. Quantitative Biology. 5(3):236-250.

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[88] Yong-Bo Guo#, Yao-Xi He#, Chao-Ying Cui#, Ouzhuluobu, Baimakangzhuo, Duojizhuoma, Dejiquzong, Bianba, Yi Peng, Cai-juan Bai, Gonggalanzi, Yong-Yue Pan, Qula, Kangmin, Cirenyangji, Baimayangji, Wei Guo, Yangla, Hui Zhang, Xiao-Ming Zhang, Wang-Shan Zheng, Shu-Hua Xu, Hua Chen, Sheng-Guo Zhao, Yuan Cai, Shi-Ming Liu, Tian-Yi Wu, Xue-Bin Qi*, Bing Su*. 2017GCH1 plays a role in the high-altitude adaptation of Tibetans. Zoological Research38(3): 155-162.

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[87] Wang-Shan Zheng#, Yao-Xi He#, Chao-Ying Cui#, Ouzhuluobu, Dejiquzong, Yi Peng, Cai-Juan Bai, Duojizhuoma, Gonggalanzi, Bianba, Baimakangzhuo, Yong-Yue Pan, Qula, Kangmin, Cirenyangji, Baimayangji, Wei Guo, Yangla, Hui Zhang, Xiao-Ming Zhang, Yong-Bo Guo, Shu-Hua Xu, Hua Chen, Sheng-Guo Zhao, Yuan Cai, Shi-Ming Liu, Tian-Yi Wu, Xue-Bin Qi*, Bing Su*. 2017EP300 contributes to high-altitude adaptation in Tibetans by regulating nitric oxide production.Zoological Research38(3):163-170.

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[86] Lian Deng and Shuhua Xu*. 2017. Adaptation of human skin color in various populations. Hereditas155:1.

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[85] 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.

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[84] 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 Biology18:115.

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[83] 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.

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[82] Lanhai Wei#, Shi Yan#, Yik-Ying Teo, Yunzhi Huang, Lingxiang Wang, Ge Yu, Woei-Yuh Saw, Rick Twee-Hee Ong, Yan Lu, Chao Zhang, Shuhua Xu, Li Jin, Hui Li*. 2017. Phylogeography of Y-chromosome haplogroup O3a2b2-N6 reveals patrilineal traces of Austronesian populations on the eastern coastal regions of Asia. PLoS One12(4):e0175080.

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[81] Ying Zhou, Hongxiang Qiu & Shuhua Xu*. 2017. Modeling Continuous Admixture Using Admixture-Induced Linkage Disequilibrium. Scientific Reports7:43054.

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[80] 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.

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[79] Yi Peng, Chaoying Cui, Yaoxi He, Ouzhuluobu, Hui Zhang, Deying Yang, Qu Zhang, Bianbazhuoma, Lixin Yang, Yibo He, Kun Xiang, Xiaoming Zhang, Sushil Bhandari, Peng Shi, Yangla, Dejiquzong, Baimakangzhuo, Duojizhuoma, Yongyue Pan, Cirenyangji, Baimayangji, Gonggalanzi, Caijuan Bai, Bianba, Basang, Ciwangsangbu, Shuhua Xu, Hua Chen, Shimin Liu, Tianyi Wu*, Xuebin Qi* and Bing Su*. 2017. Down-regulation of EPAS1 Transcription and Genetic Adaptation of Tibetans to High-altitude Hypoxia. Mol.Biol.Evol. doi: 10.1093/molbev/msw280.

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[78] Xuanyao Liu, Dongsheng Lu, Woei-Yuh Saw, Philip J Shaw, Pongsakorn Wangkumhang, Chumpol Ngamphiw, Suthat Fucharoen, Worachart Lert-itthiporn, Kwanrutai Chin-inmanu, Tran Nguyen Bich Chau, Katie Anders, Anuradhani Kasturiratne, H Janaka de Silva, Tomohiro Katsuya, Ryosuke Kimura, Toru Nabika, Takayoshi Ohkubo, Yasuharu Tabara, Fumihiko Takeuchi, Ken Yamamoto, Mitsuhiro Yokota, Dolikun Mamatyusupu, Wenjun Yang, Yeun-Jun Chung, Li Jin, Boon-Peng Hoh, Ananda R Wickremasinghe, RickTwee-Hee Ong, Chiea-Chuen Khor, Sarah J Dunstan, Cameron Simmons, Sissades Tongsima, Prapat Suriyaphol, Norihiro Kato, Shuhua Xu and Yik-Ying Teo*. 2017. Characterising private and shared signatures of positive selection in 37 Asian populations. European Journal of Human Genetics. doi: 10.1038/ejhg.2016.181.

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[77] Manfei Zhang, Sijie Wu, Juan Zhang, Yajun Yang, Jingze Tan, Haijuan Guan, Yu Liu, Kun Tang, Jean Krutmann, Shuhua Xu, Li Jin, Yaqun Guan*, Hui Li*, Sijia Wang*. 2017. Large-scale genome-wide scans do not support petaloid toenail as a Mendelian trait. Journal of Genetics and Genomics43(12):702-704.

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[76] Sijie Wu, Jingze Tan, Yajun Yang, Qianqian Peng, Manfei Zhang, Jinxi Li, Dongsheng Lu, Yu Liu, Haiyi Lou, Qidi Feng, Yan Lu, Yaqun Guan, Zhaoxia Zhang, Yi Jiao, Pardis Sabeti, Jean Krutmann, Kun Tang, Li Jin*, Shuhua Xu*, Sijia Wang*. 2016. Genome-wide scans reveal variants at EDAR predominantly affecting hair straightness in Han Chinese and Uyghur populations. Human Genetics135(11):1279-1286.

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[75] Yu Xue, Eric-Wubbo Lameijer, Kai Ye, Kunlin Zhang, Suhua Chang, Xiaoyue Wang, Jianmin Wu, Ge Gao, Fangqing Zhao, Jian Li, Chunsheng Han, Shuhua Xu, Jingfa Xiao, Xuerui Yang, Xiaomin Ying, Xuegong Zhang, Wei-Hua Chen, Yun Liu, Zhang Zhang, Kun Huang, Jun Yu*. 2016. Precision Medicine: What Challenges Are We Facing? Genomics, Proteomics & Bioinformatics14(5):253-261.

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[74] Dan Chen*, Stefan Enroth, Han Liu, Yang Sun, Huibo Wang, Min Yu, Lian Deng, Shuhua Xu, Ulf Gyllensten. 2016. Pooled analysis of genome-wide association studies of cervical intraepithelial neoplasia 3 (CIN3) identifies a new susceptibility locus. Oncotarget7:42216-42224 (Article No.27).

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[73] Qianqian Peng, Jinxi Li, Jingze Tan, Yajun Yang, Manfei Zhang, Sijie Wu, Yu Liu, Juan Zhang, Pengfei Qin, Yaqun Guan, Yi Jiao, Zhaoxia Zhang, Pardis C Sabeti, Kun Tang, Shuhua Xu, Li Jin, Sijia Wang*. 2016. EDARV370A associated facial characteristics in Uyghur population revealing further pleiotropic effects. Human Genetics135: 99-108.

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[72] 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.

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[71] Xian Gong, Chao Zhang, Aisa Yiliyasi, Ying Shi, Xuewei Yang, Aosiman Nuersimanguli, Yaqun Guan*, Shuhua Xu*. 2016. Comparative Analysis of Type 2 Diabetes Susceptibility Candidate Genes Diversity in World Wide Populations. Hereditas (Beijing)38:1-21.

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[70] Lian Deng, Andres Ruiz-Linares, Shuhua Xu* & Sijia Wang*. 2016. Ancestry variation and footprints of natural selection along the genome in Latin American populations. Scientific Reports6:21766.

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[69] Xumin Ni, Xiong Yang, Wei Guo, Kai Yuan, Ying Zhou, Zhiming Ma* & Shuhua Xu*. 2016. Length Distribution of Ancestral Tracks under a General Admixture Model and Its Applications in Population History Inference. Scientific Reports6:20048.

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[68] Zhaohui Yang*, Hua Zhong*, Jing Chen*, Xiaoming Zhang*, Hui Zhang, Xin Luo, Shuhua Xu, Hua Chen, Dongsheng Lu, Yinglun Han, Jinkun Li, Lijie Fu, Xuebin Qi, Yi Peng, Kun Xiang, Qiang Lin, Yan Guo, Ming Li, Xiangyu Cao, Yanfeng Zhang, Shiyu Liao, Yingmei Peng, Lin Zhang, Xiaosen Guo, Shanshan Dong, Fan Liang, Jun Wang, Andrew Willden, Hong Seang Aun, Bun Serey, Tuot Sovannary, Long Bunnath, Ham Samnom, Graeme Mardon, Qingwei Li, Anming Meng, Hong Shi and Bing Su. 2016. A genetic mechanism for convergent skin lightening during recent human evolution. Molecular Biology and Evolution. 33(5):1177-1187.

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[67] Asifullah Khan, Lei Tian, Chao Zhang, Kai Yuan & Shuhua Xu*. 2016. Genetic diversity and natural selection footprints of the glycine amidinotransferase gene in various human populations. Scientific Reports6:18755.

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[66] Xia Liu, Bo Zhao, Hua-Jun Zheng, Yan Hu, Gang Lu, Chang-Qing Yang, Jie-Dan Chen, Jun-Jian Chen, Dian-Yang Chen, Liang Zhang, Yan Zhou, Ling-Jian Wang, Wang-Zhen Guo, Yu-Lin Bai, Ju-Xin Ruan, Xiao-Xia Shangguan, Ying-Bo Mao, Chun-Min Shan, Jian-Ping Jiang, Yong-Qiang Zhu, Lei Jin, Hui Kang, Shu-Ting Chen, Xu-Lin He, Rui Wang, Yue-Zhu Wang, Jie Chen, Li-Jun Wang, Shu-Ting Yu, Bi-Yun Wang, Jia Wei, Si-Chao Song, Xin-Yan Lu, Zheng-Chao Gao, Wen-Yi Gu, Xiao Deng, Dan Ma, Sen Wang, Wen-Hua Liang, Lei Fang, Cai-Ping Cai, Xie-Fei Zhu, Bao-Liang Zhou, Z. Jeffrey Chen, Shu-Hua Xu, Yu-Gao Zhang*, Sheng-Yue Wang, Tian-Zhen Zhang*, Guo-Ping Zhao & Xiao-Ya Chen*. 2015.  Gossypium barbadense genome sequence provides insight into the evolution of extra-long staple fiber and specialized metabolites. Scientific Reports5:14139.

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[65] Xumin Ni, Wei Guo, Kai Yuan, Xiong Yang, Zhiming Ma, Shuhua Xu, Shihua Zhang*. 2015. A Probabilistic Method for Estimating the Sharing of Identity by Descent for Populations with Migration. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 13(2):281-90.

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[64] Zhuoma Basang, Boyang Wang, Lei Li, La Yang, Lan Liu, Chaoying Cui, Gongga Lanzi, Nima Yuzhen, Ji Duo, Hongxiang Zheng, Yi Wang, Shuhua Xu, Li Jin*, Xiaofeng Wang*. 2015. HIF2A Variants Were Associated with Different Levels of High-Altitude Hypoxia among Native Tibetans. PLoS One10(9):e0137956.

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[63] 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 Reports5:14375.

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[62] 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 Genomics9:16.

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[61] Yungang He*, Minxian Wang, Xin Huang, Ran Li, Hongyang Xu, Shuhua Xu and Li Jin.2015. A probabilistic method for testing and estimating selection differences between populations. Genome Research25:1903-1909.

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[60] 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.

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[59] Pankaj Jha, Dongsheng Lu, Shuhua Xu*. 2015. Natural Selection and Functional Potentials of Human Noncoding Elements Revealed by Analysis of Next Generation Sequencing Data. PLoS One. 10(6):e0129023

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[58] Chao Zhang, Jing Li, Dongsheng Lu, Kai Yuan, Yuan Yuan, Shuhua Xu*. 2015. Differential Natural Selection of Human Zinc Transporter Genes between African and Non-African Populations. Scientific Reports5:9658.

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[57] Pankaj Jha, Dongsheng Lu, Yuan Yuan, Shuhua Xu*. 2015. Signature of positive selection of PTK6 gene in East Asian populations: a cross talk for Helicobacter pylori invasion and gastric cancer endemicity. Molecular Genetics and Genomics. 290(5):1741-1752.

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[56] 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 Genetics23:536-542.

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[55] Pengfei Qin, Ying Zhou, Haiyi Lou, Dongsheng Lu, Xiong Yang, Yuchen Wang, Li Jin, Yeun-Jun Chung, Shuhua Xu*. 2015. Quantitating and Dating Recent Gene Flow between European and East Asian Populations. Scientific Reports5:9500.

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[54] 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. Hum Genet. 134(4):375-392.

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[53] Yuan Yuan, Lei Tian, Dongsheng Lu, Shuhua Xu*. 2015. Analysis of Genome-Wide RNA-Sequencing Data Suggests Age of the CEPH/Utah (CEU) Lymphoblastoid Cell Lines Systematically Biases Gene Expression Profiles. Scientific Reports5:7960.

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[52] Qiliang Ding, Ya Hu, Shuhua Xu, Chuanchao Wang, Hui Li, Ruyue Zhang, Shi Yan, Jiucun Wang, Li Jin*. 2014. Neanderthal Origin of the Haplotypes Carrying the Functional Variant Val92Met in the MC1R in Modern Humans. Molecular Biology and Evolution.31(8):1994-2003.

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[51] Jing Guo, Jingze Tan, Yajun Yang, Hang Zhou, Sile Hu, Agu Hashan, Nurmamat Bahaxar, Shuhua Xu, Timothy D. Weaver, Li Jin, Mark Stoneking, Kun Tang*. 2014. Variation and signatures of selection on the human face. J.Hum.Evol. 75:143-152.

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[50] Liang Peng; Qiang Zhao, Qibin Li, Miaoxin Li, Caixia Li,Tingting Xu,Xiangyi Jing, Xiang Zhu, Ye Wang, Fucheng Li, Ruihong Liu, Cheng Zhong, Qihao Pan, Binghui Zeng, Qijun Liao, Bin Hu, Zhao-xia Hu, Yang-su Huang, Pak Sham, Jinsong Liu, Shuhua Xu, Jun Wang, Zhi-liang Gao, Yiming Wang. 2014. The p.Ser267Phe variant in SLC10A1 is associated with resistance to chronic hepatitis B. Hepatology. 61(4):1251-1260.

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[49] Wan Isa Hatin, Ab Rajab Nur-Shafawati, Ali Etemad, Wenfei Jin, Pengfei Qin, Shuhua Xu, Li Jin,Soon-Guan Tan, Pornprot Limprasert, Merican Amir Feisal, Mohammed Rizman-Idid, Bin Alwi Zilfalil* and The HUGO Pan-Asian SNP Consortium. 2014. A genome wide pattern of population structure and admixture in peninsular Malaysia Malays. The HUGO Journal8:5.

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[48] 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

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[47] Ying Wang, Ying Zhou, Linfeng Li, Xian Chen, Yuting Liu, Zhi-Ming Ma* and Shuhua Xu*. 2014. A new method for modeling coalescent processes with recombination. BMC Bioinformatics15:273

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[46] 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.

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[45] 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. Hum Genet. 133(9):1169-1185

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[44] Jing Li, Xingzhen Lao, Chao Zhang, Lei Tian, Dongsheng Lu and Shuhua Xu*. 2014. Increased genetic diversity of ADME genes in African Americans compared with their putative ancestral source populations and implications for Pharmacogenomics. BMC Genetics15:52

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[43] Pengfei Qin, Zhiqiang Li, Wenfei Jin, Dongsheng Lu, Haiyi Lou, Jiawei Shen, Li Jin*, Yongyong Shi* and Shuhua Xu*. 2014. A panel of ancestry informative markers to estimate and correct potential effects of population stratification in Han Chinese. European Journal of Human Genetics. 22:248-253

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[42] Wenfei Jin, Ran Li, Ying Zhou and 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 Genetics22:930-937

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[41] Yang Liu, Liangliang Zhang, Shuhua Xu, Landian Hu, Laurence D. Hurst, Xiangyin Kong*.2013. Identification of Two Maternal Transmission Ratio Distortion Loci in Pedigrees of the Framingham Heart Study. Scientific Reports3. Article No. 2147.

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[40] Erli Wang, Shuna Sun, Bin Qiao, Wenyuan Duan, Guoying Huang, Yu An, Shuhua Xu, Yufang Zheng, Zhixi Su, Xun Gu, Li Jin*, Hongyan Wang*. 2013. Identification of Functional Mutations in GATA4 in Patients with Congenital Heart Disease. PLoS One. 8(4): e62138

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[39] Qiliang Ding, Ya Hu, Shuhua Xu. Jiucun Wang, Li Jin*. 2013. Neanderthal Introgression at Chromosome 3p21.31 was Under Positive Natural Selection in East Asians. Molecular Biology and Evolution. 31(3):683-95.

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[38] Jun Rong*, Shuhua Xu, Patrick G. Meirmans and Klaas Vrieling. 2013. Dissimilarity of contemporary and historical gene flow in a wild carrot (Daucus carota) metapopulation under contrasting levels of human disturbance: implications for risk assessment and management of transgene introgression. Annals of Botany.112(7):1361-1370

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[37] Dongsheng Lu and Shuhua Xu*. 2013. Principal component analysis reveals the 1000 Genomes Project does not sufficiently cover the human genetic diversity in Asia. Frontiers in Genetics. 4:1-9. Article No. 127.

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[36] Sathiya Maran, Yeong Yeh Lee*, Shuhua Xu, Nur-Shafawati Rajab, Norhazrini Hasan, Syed Hassan Syed Abdul Aziz, Noorizan Abdul Majid, Bin Alwi Zilfalil. 2013. Gastric precancerous lesions are associated with gene variants in Helicobacter pylori -susceptible ethnic Malays. World Journal of Gastroenterology. 19(23):3615-3622

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[35] 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

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[34] Sathiya Maran, Yeong Yeh Lee*, Shuhua Xu, Mahendra Raj Sundramoorthy, Noorizan Abdul Majid, Keng Ee Choo, Zilfalil Alwi, David Y Graham. 2013. Toward understanding the low prevalence of Helicobacter pylori (H. pylori) in Malays: Genetic variants differ among H. pylori negative ethnic Malays in the north-eastern region of Peninsular Malaysia and Han Chinese and South Indians. Journal of Digestive Diseases. 14:196-202

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[33] Wei Qian, Lian Deng, Dongsheng Lu, Shuhua Xu*. 2013. Genome-Wide Landscapes of Human Local Adaptation in Asia. PLoS One 8(1): e54224

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[32] Shuhua Xu*. 2013. Admixture population genomics of modern human. Science (KEXUE). 65(1):14-18

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[31] 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. Am.J.Hum.Genet. 91(5):849-862

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[30] Shuhua Xu*. 2012. Human Population Admixture in Asia. Genomics & Informatics 10(2):133-144.

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[29] 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.

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[28] Shuhua Xu* and Mark Stoneking. 2012. Reply to Denham and Donohue: Asian-Papuan genetic admixture is in excellent agreement with Austronesian dispersal in eastern Indonesia. PNAS. 109:39

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[27] Sathiya Maran, Yeong Yeh Lee*, Shuhua Xu, Nur-Shafawati Rajab, Norhazrini Hasan, Nazri Mustaffa, Noorizan Abdul Majid and Zilfalil Alwi. 2012. Deleted in Colorectal Cancer (DCC) Gene Polymorphism is Associated with H. pylori Infection among Susceptible Malays from the North-Eastern Region of Peninsular Malaysia. Hepato-Gastroenterology 60(121):124-128.

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[26] Hui-Qi Qu*, Quan Li, Shuhua Xu, Joseph B. McCormick, Susan P. Fisher-Hoch, Momiao Xiong, Jin Qian, and Li Jin*. 2012. Ancestry Informative Marker Set for Han Chinese Population. G3: Genes, Genomes, Genetics. 2(3):339-41.

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[25] Yungang He*, Wei R. Wang, Shuhua Xu, Li Jin, and The HUGO Pan-Asian SNP Consortium. 2012. Paleolithic Contingent in Modern Japanese: Estimation and Inference using Genome-wide Data. Scientific Reports. 2:355

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[24] 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

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[23] Wenfei Jin, Pengfei Qin, Haiyi Lou, Li Jin*, Shuhua Xu*. 2012. A Systematic Characterization of Genes Underlying both Complex and Mendelian Diseases. Hum.Mol.Genet. 21(7): 1611-1624.

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[22] 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 Res. 22(3): 519-527.

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[21] 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

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[20] Haiyi Lou, Shilin Li, Yajun Yang, Longli Kang, Xin Zhang, Wenfei Jin, Bailin Wu , Li Jin*, Shuhua Xu*. 2011. A Map of Copy Number Variations in Chinese Populations. PLoS One 6(11): e27341.

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[19] Shuhua Xu*, Li Jin. 2011. Chromosome-Wide Haplotype Sharing: A Measure Integrating Recombination Information to Reconstruct the Phylogeny of Human Populations. Ann.Hum.Genet. 75(6): 694-706.

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[18] 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: 1003-1011.

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[17] 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.

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[16] Pankaj Jha, Swapnil Sinha, Kanika Kanchan, Tabish Qidwai, Ankita Narang, Prashant Kumar Singh, Sudhanshu S. Pati, Sanjib Mohanty, Saroj K. Mishra, Surya K. Sharma, Shally Awasthi, Vimala Venkatesh, Sanjeev Jain, Analabha Basu, Shuhua Xu, Indian Genome Variation ConsortiumMitali Mukerji, Saman Habib. 2011. Deletion of the APOBEC3B gene strongly impacts susceptibility to falciparum malaria. Infection, Genetics and Evolution 12: 142-148 (10.1016/j.meegid.2011.11.001).

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[15] Xiaoyun Cai, Zhendong Qin, Bo Wen, Shuhua Xu, Yi Wang, Yan Lu, Lanhai Wei, Chuanchao Wang, Shilin Li, Xingqiu Huang, Li Jin, Hui Li*, the Genographic Consortium. 2011. Human Migration through Bottlenecks from Southeast Asia into East Asia during Last Glacial Maximum Revealed by Y Chromosomes. PLoS One 6(8): e24282.

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[14] 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.

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[13] 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 Lao4, 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.

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[12] Shuhua Xu*, Sanchit Guputa and Li Jin*. 2010. PEAS V1.0: A Package for Elementary Analysis of SNP Data. Mol.Ecol.Res. 10:1085-1088.

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[11] 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.

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[10] 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.

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[9] Shuhua Xu, Xianyong Yin, Shilin Li, Wenfei Jin, Haiyi Lou, Ling Yang, Xiaohong Gong, Hongyan Wang, Yiping shen, Xuedong Pan, Yungang He, Yajun Yang, Yi Wang, Wenqing Fu, Yu An, Jiucun Wang, Jingze Tan, Ji Qian, Xiaoli Chen, Xin Zhang, Yangfei Sun, Xuejun Zhang, Bailin Wu, Li Jin*. 2009. Genomic Dissection of Population Substructure of Han Chinese and Its Implication in Association Studies. Am.J.Hum.Genet. 85:762-774.

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[8] Shuhua Xu and Li Jin*. 2009. Genetic Landscape of Eurasia and ‘‘Admixture’’ in Uyghurs Response. Am.J.Hum.Genet. 85(6):937-939.

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[7] Shuhua Xu, Wenfei Jin, Li Jin*. 2009. Haplotype Sharing Analysis Showing Uyghurs Are Unlikely Genetic Donors. Mol.Biol.Evol. 26(10): 2197-2206.

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[6] Shuhua Xu, Li Jin. 2009. Computational Biology—Review and Prospects. Science (KEXUE). 61(4):34-37.

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[5] Yungang He, Shuhua Xu, Chuan Jia, Li Jin*. 2009. A design of multi-source samples as a shared control for association studies in genetically stratified populations. Cell Research 19:913-915.

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[4] 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.

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[3] 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.

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[2] Fuzhong Xue, Yi Wang, Shuhua Xu, Feng Zhang, Bo Wen, Xuesen Wu, Ming Lu, Ranjan Deka, Ji Qian, and Li Jin*. 2008. A spatial analysis of genetic structure of human populations in China reveals distinct difference between maternal and paternal lineages. Eur.J.Hum.Genet. 16:705-717.

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[1] Shuhua Xu, Wei Huang, Haifeng Wang, Yungang He, Ying Wang, Yi Wang, Ji Qian, Momiao Xiong, Li Jin*. 2007. Dissecting Linkage Disequilibrium in African American Genomes: Roles of Markers and Individuals. Mol.Biol.Evol. 24:2049-2058.

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