Shuhua Xu

Summary

Affiliation: CAS-MPG Partner Institute for Computational Biology
Country: China

Publications

  1. ncbi request reprint Dissecting linkage disequilibrium in African-American genomes: roles of markers and individuals
    Shuhua Xu
    MOE Key Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
    Mol Biol Evol 24:2049-58. 2007
  2. ncbi request reprint A design of multi-source samples as a shared control for association studies in genetically stratified populations
    Yungang He
    1 CAS MPG Partner Institute for Computational Biology, SIBS, CAS, Shanghai 200031, China 2 Key laboratory of Computational Biology at CAS MPG Partner Institute for Computational Biology, SIBS, CAS, Shanghai 200031, China
    Cell Res 19:913-5. 2009
  3. pmc Genome-wide landscapes of human local adaptation in Asia
    Wei Qian
    Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society CAS MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    PLoS ONE 8:e54224. 2013
  4. pmc Increased genetic diversity of ADME genes in African Americans compared with their putative ancestral source populations and implications for pharmacogenomics
    Jing Li
    Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society CAS MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
    BMC Genet 15:52. 2014
  5. pmc A map of copy number variations in Chinese populations
    Haiyi Lou
    Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences and Max Planck Society CAS MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
    PLoS ONE 6:e27341. 2011
  6. pmc Identification of close relatives in the HUGO Pan-Asian SNP database
    Xiong Yang
    Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences and Max Planck Society CAS MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    PLoS ONE 6:e29502. 2011
  7. pmc Genetic evidence supports linguistic affinity of Mlabri--a hunter-gatherer group in Thailand
    Shuhua Xu
    Chinese Academy of Sciences and Max Planck Society CAS MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
    BMC Genet 11:18. 2010
  8. pmc Human population admixture in Asia
    Shuhua Xu
    Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society CAS MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
    Genomics Inform 10:133-44. 2012
  9. doi request reprint A genome-wide search for signals of high-altitude adaptation in Tibetans
    Shuhua Xu
    Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    Mol Biol Evol 28:1003-11. 2011
  10. doi request reprint Chromosome-wide haplotype sharing: a measure integrating recombination information to reconstruct the phylogeny of human populations
    Shuhua Xu
    Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology, Key laboratory of Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
    Ann Hum Genet 75:694-706. 2011

Detail Information

Publications29

  1. ncbi request reprint Dissecting linkage disequilibrium in African-American genomes: roles of markers and individuals
    Shuhua Xu
    MOE Key Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
    Mol Biol Evol 24:2049-58. 2007
    ....
  2. ncbi request reprint A design of multi-source samples as a shared control for association studies in genetically stratified populations
    Yungang He
    1 CAS MPG Partner Institute for Computational Biology, SIBS, CAS, Shanghai 200031, China 2 Key laboratory of Computational Biology at CAS MPG Partner Institute for Computational Biology, SIBS, CAS, Shanghai 200031, China
    Cell Res 19:913-5. 2009
    ..Cell Research (2009) 19:913-915. doi: 10.1038/cr.2009.75; published online 23 June 2009...
  3. pmc Genome-wide landscapes of human local adaptation in Asia
    Wei Qian
    Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society CAS MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    PLoS ONE 8:e54224. 2013
    ..In summary, this study contributes to the overall understanding of human local adaptation in Asia and has identified both known and novel signatures of natural selection in the human genome...
  4. pmc Increased genetic diversity of ADME genes in African Americans compared with their putative ancestral source populations and implications for pharmacogenomics
    Jing Li
    Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society CAS MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
    BMC Genet 15:52. 2014
    ..In particular, the genetic admixture influences the genomic diversity of drug metabolism-related genes, and may cause high heterogeneity of drug responses in admixed populations such as African Americans...
  5. pmc A map of copy number variations in Chinese populations
    Haiyi Lou
    Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences and Max Planck Society CAS MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
    PLoS ONE 6:e27341. 2011
    ..Our results suggest the necessity of a full characterization of CNVs in Chinese populations, and the CNV map we constructed serves as a useful resource in further evolutionary and medical studies...
  6. pmc Identification of close relatives in the HUGO Pan-Asian SNP database
    Xiong Yang
    Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences and Max Planck Society CAS MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    PLoS ONE 6:e29502. 2011
    ..In addition, we provided gender information for PASNP samples, which were not included in the original dataset, based on analysis of X chromosome data...
  7. pmc Genetic evidence supports linguistic affinity of Mlabri--a hunter-gatherer group in Thailand
    Shuhua Xu
    Chinese Academy of Sciences and Max Planck Society CAS MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
    BMC Genet 11:18. 2010
    ..This study aims to examine whether the genetic affinity of the Mlabri is consistent with this linguistic relationship, and to further explore the origins of this enigmatic population...
  8. pmc Human population admixture in Asia
    Shuhua Xu
    Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society CAS MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
    Genomics Inform 10:133-44. 2012
    ..Here, I will provide an overview of population genomic studies that have been published to date on human admixture in Asia, focusing on population structure and population history...
  9. doi request reprint A genome-wide search for signals of high-altitude adaptation in Tibetans
    Shuhua Xu
    Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    Mol Biol Evol 28:1003-11. 2011
    ..Our results also suggest limitations of extended haplotype homozygosity-based method due to its compromised power in case the natural selection initiated long time ago and particularly in genomic regions with recombination hotspots...
  10. doi request reprint Chromosome-wide haplotype sharing: a measure integrating recombination information to reconstruct the phylogeny of human populations
    Shuhua Xu
    Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology, Key laboratory of Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
    Ann Hum Genet 75:694-706. 2011
    ..The advantage of CHS is rooted in its integration of both drift and recombination information, therefore providing additional resolution especially for populations separated recently...
  11. pmc Analysis of genomic admixture in Uyghur and its implication in mapping strategy
    Shuhua Xu
    Chinese Academy of Sciences and Max Planck Society CAS MPG, Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
    Am J Hum Genet 82:883-94. 2008
    ....
  12. pmc Genomic dissection of population substructure of Han Chinese and its implication in association studies
    Shuhua Xu
    Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, PR China
    Am J Hum Genet 85:762-74. 2009
    ..These signals indicating significant differences among Han Chinese subpopulations should be carefully explained in case they are also detected in association studies, especially when sample sources are diverse...
  13. pmc Genome-wide detection of natural selection in African Americans pre- and post-admixture
    Wenfei Jin
    Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences and Max Planck Society CAS MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    Genome Res 22:519-27. 2012
    ..We suggest that the new approach is reasonably powerful and can also be applied to other admixed populations such as Latinos and Uyghurs...
  14. doi request reprint Identification of well-differentiated gene expressions between Han Chinese and Japanese using genome-wide microarray data analysis
    Yuan Yuan
    Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society CAS MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    J Med Genet 50:534-42. 2013
    ..Several previous studies have examined and compared variations in gene expression between continental populations. However, differences in gene expression variation between closely related populations have not been studied yet...
  15. pmc Exploring population admixture dynamics via empirical and simulated genome-wide distribution of ancestral chromosomal segments
    Wenfei Jin
    Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society CAS MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    Am J Hum Genet 91:849-62. 2012
    ..In summary, this study not only provides approaches to explore population admixture dynamics, but also advances our understanding on population history of African Americans, Mexicans, and Middle Eastern populations...
  16. pmc Genetic dating indicates that the Asian-Papuan admixture through Eastern Indonesia corresponds to the Austronesian expansion
    Shuhua Xu
    Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences and Max Planck Society, CAS MPG, Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
    Proc Natl Acad Sci U S A 109:4574-9. 2012
    ....
  17. doi request reprint Haplotype-sharing analysis showing Uyghurs are unlikely genetic donors
    Shuhua Xu
    Chinese Academy of Sciences and Max Planck Society CAS MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    Mol Biol Evol 26:2197-206. 2009
    ..We concluded that the gene pool of modern UIGs is more likely a sole recipient with contribution from both EAS and EUR...
  18. pmc A genome-wide analysis of admixture in Uyghurs and a high-density admixture map for disease-gene discovery
    Shuhua Xu
    Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
    Am J Hum Genet 83:322-36. 2008
    ..To our knowledge, our map constitutes the first practical resource for admixture mapping in Uyghurs, and it will enable studies of diseases showing differences in genetic risk between EUR and EAS populations...
  19. pmc A panel of ancestry informative markers to estimate and correct potential effects of population stratification in Han Chinese
    Pengfei Qin
    1 Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Shanghai, China 2 Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    Eur J Hum Genet 22:248-53. 2014
    ....
  20. pmc Human migration through bottlenecks from Southeast Asia into East Asia during Last Glacial Maximum revealed by Y chromosomes
    Xiaoyun Cai
    Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
    PLoS ONE 6:e24282. 2011
    ..The ages of O3a3b-M7 and O3a3c1-M117 were estimated to be approximately 19 thousand years, followed by the emergence of the ancestors of HM lineages out of MK and the unidirectional northward migrations into East Asia...
  21. ncbi request reprint Neanderthal Origin of the Haplotypes Carrying the Functional Variant Val92Met in the MC1R in Modern Humans
    Qiliang Ding
    State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
    Mol Biol Evol 31:1994-2003. 2014
    ....
  22. doi request reprint A spatial analysis of genetic structure of human populations in China reveals distinct difference between maternal and paternal lineages
    Fuzhong Xue
    MOE Key Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, School of Life Sciences, Fudan University, 220 Handan Road, Shanghai, China
    Eur J Hum Genet 16:705-17. 2008
    ..On the paternal side, however, no obvious genetic differentiation between northern and southern populations is revealed...
  23. pmc Identification of two maternal transmission ratio distortion loci in pedigrees of the Framingham heart study
    Yang Liu
    The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200025, China
    Sci Rep 3:2147. 2013
    ..7~1.8:1. Genotyping validation and further replication is still necessary to confirm the TRD. This study shows that there may be large-effect maternal-specific TRD loci of common SNPs in the human genome but that these are rare. ..
  24. doi request reprint A systematic characterization of genes underlying both complex and Mendelian diseases
    Wenfei Jin
    Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China
    Hum Mol Genet 21:1611-24. 2012
    ..In brief, our study not only revealed the characteristics of MC genes, but also provided new insights into the other four gene categories...
  25. doi request reprint Neanderthal introgression at chromosome 3p21.31 was under positive natural selection in East Asians
    Qiliang Ding
    State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
    Mol Biol Evol 31:683-95. 2014
    ..Interestingly, the distribution of rs35455589-G suggests that this allele was lost during the exodus of ancestors of modern Eurasians from Africa and reintroduced to Eurasians from Neanderthals...
  26. pmc Identification of functional mutations in GATA4 in patients with congenital heart disease
    Erli Wang
    Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences and Max Planck Society CAS MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    PLoS ONE 8:e62138. 2013
    ..Together with the newly reported mutations, approximately 110 non-synonymous mutations have currently been identified in GATA4. Our future analysis will explore why the evolutionarily conserved GATA4 appears to be hypermutable...
  27. pmc Distribution of ancestral chromosomal segments in admixed genomes and its implications for inferring population history and admixture mapping
    Wenfei Jin
    Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society CAS MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    Eur J Hum Genet 22:930-7. 2014
    ..Therefore, we suggest using a case-control approach rather than a case-only approach to conduct admixture mapping to retain the statistics power in recently admixed populations. ..
  28. doi request reprint PEAS V1.0: a package for elementary analysis of SNP data
    Shuhua Xu
    Chinese Academy of Sciences and Max Planck Society CAS MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
    Mol Ecol Resour 10:1085-8. 2010
    ..To our knowledge, these analyses are not available in any other computer program. PEAS for Windows is freely available for academic users from http://www.picb.ac.cn/~xushua/index.files/Download_PEAS.htm...