Population Genomics Group (PGG) (since 2010)

Max Planck Independent Research Group on Population Genomics (since 2012)

Recent Publications

 

[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.

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[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.

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

 

[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.

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[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.

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[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.

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[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.

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[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 Evolution31(8):1994-2003.

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[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.

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[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. Hepatology61(4):1251-1260.

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[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.

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[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 Genetics59:615-622.

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[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.

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[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 Genetics51(9):614-22.

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[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

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[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

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[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 Genetics22:248-253

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[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

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[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.

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[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 One8(4): e62138

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[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 Evolution31(3):683-95.

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[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 Botany112(7):1361-1370

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[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.

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[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 Gastroenterology19(23):3615-3622

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[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

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[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 Diseases14:196-202

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[33] Wei Qian, Lian Deng, Dongsheng Lu, Shuhua Xu*. 2013. Genome-Wide Landscapes of Human Local Adaptation in Asia. PLoS One8(1):e54224.

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

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

[link]

[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.

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[30] Shuhua Xu*. 2012. Human Population Admixture in Asia. Genomics & Informatics10(2):133-144.

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

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

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[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.PNAS109:39.

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[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-Gastroenterology60(121):124-128.

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[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, Genetics2(3):339-41.

[Abstract]       [Full text]       [PDF]      [Supplementary Material]       [Cited Times]

[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 Reports2:355.

[Abstract]       [Full text]       [PDF]      [Supplementary Material]       [Cited Times]

[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. PNAS109(12):4574-4579.

[Abstract]       [Full text]       [PDF]      [Supplementary Material]       [Cited Times]

[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.

[Abstract]       [Full text]       [PDF]      [Supplementary Material]       [Cited Times]

[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.

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[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.

[Abstract]       [Full text]       [PDF]       [Cited Times]

[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 One6(11):e27341.

[Abstract]       [Full text]       [PDF]       [Cited Times]

[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.

[Abstract]       [Full text]       [PDF]       [Supplementary Material]    [Cover]       [Cited Times]

[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(2):1003-1011.

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[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.

[Abstract]       [Full text]       [PDF]       [Cited Times]

[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).

[Abstract]       [Full text]       [PDF]       [Cited Times]

[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.

[Abstract]       [Full text]       [PDF]       [Cited Times]

[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 One6(4):e18312.

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[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 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.

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[12] Shuhua Xu*, Sanchit Guputa and Li Jin*. 2010. PEAS V1.0: A Package for Elementary Analysis of SNP Data. Mol.Ecol.Res. 10(6):1085-1088.

[Abstract]       [Full text]       [PDF]       [Software download]       [Cited Times]

[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.

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[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. Science326:1541-1545.

[Abstract]       [Full text]       [PDF]       [Supplementary Material]      [News]       [Cited Times]

[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.

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

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

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

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

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

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

[Link]       [PDF]

[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 Research19:913-915.

[Abstract]       [Full text]       [PDF]       [Cited Times]

[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.

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[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.

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[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.

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]

[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.

[Abstract]       [Full text]       [PDF]       [Supplementary Material]       [Cited Times]