Yali Xue

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. pmc An Exceptional Gene: Evolution of the TSPY Gene Family in Humans and Other Great Apes
    Yali Xue
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, UK
    Genes (Basel) 2:36-47. 2011
  2. pmc Contrasting signals of positive selection in genes involved in human skin-color variation from tests based on SNP scans and resequencing
    Johanna Maria de Gruijter
    Department of Forensic Molecular Biology, Erasmus MC University Medical Center, PO Box 2040, Rotterdam, 3000 CA, The Netherlands
    Investig Genet 2:24. 2011
  3. pmc The functional spectrum of low-frequency coding variation
    Gabor T Marth
    Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA
    Genome Biol 12:R84. 2011
  4. pmc Human Y chromosome base-substitution mutation rate measured by direct sequencing in a deep-rooting pedigree
    Yali Xue
    The Wellcome Trust Sanger Institute, Hinxton, Cambs CB10 1SA, UK
    Curr Biol 19:1453-7. 2009
  5. pmc Revisiting the thrifty gene hypothesis via 65 loci associated with susceptibility to type 2 diabetes
    Qasim Ayub
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1HH, UK
    Am J Hum Genet 94:176-85. 2014
  6. pmc Population differentiation as an indicator of recent positive selection in humans: an empirical evaluation
    Yali Xue
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, United Kingdom
    Genetics 183:1065-77. 2009
  7. pmc FOXP2 targets show evidence of positive selection in European populations
    Qasim Ayub
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Am J Hum Genet 92:696-706. 2013
  8. pmc Genetic basis of Y-linked hearing impairment
    Qiuju Wang
    Department of Otolaryngology, Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
    Am J Hum Genet 92:301-6. 2013
  9. pmc A worldwide survey of human male demographic history based on Y-SNP and Y-STR data from the HGDP-CEPH populations
    Wentao Shi
    The Wellcome Trust Sanger Institute, Hinxton, Cambs, United Kingdom
    Mol Biol Evol 27:385-93. 2010
  10. pmc A calibrated human Y-chromosomal phylogeny based on resequencing
    Wei Wei
    The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
    Genome Res 23:388-95. 2013

Collaborators

Detail Information

Publications48

  1. pmc An Exceptional Gene: Evolution of the TSPY Gene Family in Humans and Other Great Apes
    Yali Xue
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, UK
    Genes (Basel) 2:36-47. 2011
    ....
  2. pmc Contrasting signals of positive selection in genes involved in human skin-color variation from tests based on SNP scans and resequencing
    Johanna Maria de Gruijter
    Department of Forensic Molecular Biology, Erasmus MC University Medical Center, PO Box 2040, Rotterdam, 3000 CA, The Netherlands
    Investig Genet 2:24. 2011
    ..In the current study, we resequenced 4.7 to 6.7 kb of DNA from each of these genes in Africans, Europeans, East Asians, and South Asians...
  3. pmc The functional spectrum of low-frequency coding variation
    Gabor T Marth
    Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA
    Genome Biol 12:R84. 2011
    ....
  4. pmc Human Y chromosome base-substitution mutation rate measured by direct sequencing in a deep-rooting pedigree
    Yali Xue
    The Wellcome Trust Sanger Institute, Hinxton, Cambs CB10 1SA, UK
    Curr Biol 19:1453-7. 2009
    ..0 x 10(-8)), consistent with estimates of 2.3 x 10(-8)-6.3 x 10(-8) mutations/nucleotide/generation for the same Y-chromosomal region from published human-chimpanzee comparisons depending on the generation and split times assumed...
  5. pmc Revisiting the thrifty gene hypothesis via 65 loci associated with susceptibility to type 2 diabetes
    Qasim Ayub
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1HH, UK
    Am J Hum Genet 94:176-85. 2014
    ..Overall, we conclude that past positive selection has not been a powerful influence driving the prevalence of T2D risk alleles...
  6. pmc Population differentiation as an indicator of recent positive selection in humans: an empirical evaluation
    Yali Xue
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, United Kingdom
    Genetics 183:1065-77. 2009
    ....
  7. pmc FOXP2 targets show evidence of positive selection in European populations
    Qasim Ayub
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Am J Hum Genet 92:696-706. 2013
    ....
  8. pmc Genetic basis of Y-linked hearing impairment
    Qiuju Wang
    Department of Otolaryngology, Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
    Am J Hum Genet 92:301-6. 2013
    ..We suggest that a third copy of one or more genes from the shared segment of chromosome 1 might be responsible for the hearing-loss phenotype...
  9. pmc A worldwide survey of human male demographic history based on Y-SNP and Y-STR data from the HGDP-CEPH populations
    Wentao Shi
    The Wellcome Trust Sanger Institute, Hinxton, Cambs, United Kingdom
    Mol Biol Evol 27:385-93. 2010
    ..However, some unexpected demographic histories were also found, including low growth rates in the Hazara and Kalash from Pakistan and recent expansion of the Mozabites in North Africa...
  10. pmc A calibrated human Y-chromosomal phylogeny based on resequencing
    Wei Wei
    The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
    Genome Res 23:388-95. 2013
    ..In all, we provide a nearly 10-fold increase in the number of Y markers with phylogenetic information, and novel historical insights derived from placing them on a calibrated phylogenetic tree...
  11. pmc A map of human genome variation from population-scale sequencing
    Richard M Durbin
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
    Nature 467:1061-73. 2010
    ..These methods and public data will support the next phase of human genetic research...
  12. pmc A comparison of Y-chromosomal lineage dating using either resequencing or Y-SNP plus Y-STR genotyping
    Wei Wei
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Forensic Sci Int Genet 7:568-72. 2013
    ..In principle, systematic comparisons of this kind can in future studies be used to identify the combinations of Y-SNP and Y-STR markers, and time estimation methodologies, that correspond best to resequencing data...
  13. pmc Wide distribution and altitude correlation of an archaic high-altitude-adaptive EPAS1 haplotype in the Himalayas
    Sophie Hackinger
    The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
    Hum Genet 135:393-402. 2016
    ....
  14. pmc A genome-wide survey of genetic variation in gorillas using reduced representation sequencing
    Aylwyn Scally
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
    PLoS ONE 8:e65066. 2013
    ....
  15. pmc Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding
    Yali Xue
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
    Science 348:242-5. 2015
    ..We discuss the causes of their decline and the consequences for their future survival. ..
  16. pmc Tracing the route of modern humans out of Africa by using 225 human genome sequences from Ethiopians and Egyptians
    Luca Pagani
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK Department of Archaeology and Anthropology, University of Cambridge, Cambridge CB2 1QH, UK Department of Biological, Geological, and Environmental Sciences, University of Bologna, 40126 Bologna, Italy Electronic address
    Am J Hum Genet 96:986-91. 2015
    ..Both the haplotype and MSMC analyses thus suggest a predominant northern route out of Africa via Egypt...
  17. pmc High altitude adaptation in Daghestani populations from the Caucasus
    Luca Pagani
    The Wellcome Trust Sanger Institute, Hinxton, UK
    Hum Genet 131:423-33. 2012
    ..These variants illustrate both the common pathways of adaptation to high altitude in different populations and features specific to the Daghestani populations, showing how even a mildly hypoxic environment can lead to genetic adaptation...
  18. pmc Deleterious- and disease-allele prevalence in healthy individuals: insights from current predictions, mutation databases, and population-scale resequencing
    Yali Xue
    The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
    Am J Hum Genet 91:1022-32. 2012
    ....
  19. pmc Genes Regulated by Vitamin D in Bone Cells Are Positively Selected in East Asians
    Elena Arciero
    The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, United Kingdom
    PLoS ONE 10:e0146072. 2015
    ..We also observed haplotype sharing between East Asians, Finns and an extinct archaic human (Denisovan) sample at the CXXC1 locus, which is best explained by incomplete lineage sorting. ..
  20. pmc Geographical affinities of the HapMap samples
    Miao He
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
    PLoS ONE 4:e4684. 2009
    ..What effects could this non-standard ascertainment have on the interpretation of HapMap results?..
  21. pmc Exploration of signals of positive selection derived from genotype-based human genome scans using re-sequencing data
    Min Hu
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
    Hum Genet 131:665-74. 2012
    ....
  22. pmc Insights into hominid evolution from the gorilla genome sequence
    Aylwyn Scally
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
    Nature 483:169-75. 2012
    ..The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution...
  23. pmc The hare and the tortoise: one small step for four SNPs, one giant leap for SNP-kind
    Yali Xue
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, UK
    Forensic Sci Int Genet 4:59-61. 2010
    ..Y-SNPs therefore now offer the best resolution of Y haplotypes and promise to distinguish almost every Y chromosome. This work illustrates the promise of current sequencing technology for forensically relevant applications...
  24. pmc Ancient DNA and the rewriting of human history: be sparing with Occam's razor
    Marc Haber
    The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
    Genome Biol 17:1. 2016
    ..Here, we review some of the key events in the peopling of the world in the light of the findings of work on ancient DNA. ..
  25. pmc Association of a germline copy number polymorphism of APOBEC3A and APOBEC3B with burden of putative APOBEC-dependent mutations in breast cancer
    Serena Nik-Zainal
    1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK 2 Department of Medical Genetics, Addenbrooke s Hospital National Health Service NHS Trust, Cambridge, UK
    Nat Genet 46:487-91. 2014
    ....
  26. pmc Genetic evidence for an origin of the Armenians from Bronze Age mixing of multiple populations
    Marc Haber
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
    Eur J Hum Genet 24:931-6. 2016
    ....
  27. pmc Structural variation on the human Y chromosome from population-scale resequencing
    Jose Rodrigo Flores Espinosa
    Chris Tyler Smith, The Wellcome Trust Sanger Institute, Hinxton, Cambs CB10 1SA, UK
    Croat Med J 56:194-207. 2015
    ..To investigate the information about Y-structural variants (SVs) in the general population that could be obtained by low-coverage whole-genome sequencing...
  28. pmc A genome-wide survey of the prevalence and evolutionary forces acting on human nonsense SNPs
    Bryndis Yngvadottir
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, UK
    Am J Hum Genet 84:224-34. 2009
    ..This study underlines the extent of variation in gene content within humans and emphasizes the importance of understanding this type of variation...
  29. pmc Adaptive evolution of UGT2B17 copy-number variation
    Yali Xue
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
    Am J Hum Genet 83:337-46. 2008
    ..In contrast, diversity was low in East Asia where a single haplotype predominated, suggesting positive selection for the deletion in this part of the world...
  30. pmc A world in a grain of sand: human history from genetic data
    Vincenza Colonna
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
    Genome Biol 12:234. 2011
    ..To see a world in a grain of sand ...William Blake, Auguries of Innocence...
  31. pmc A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation
    Patrick S Tarpey
    Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
    Nat Genet 41:535-43. 2009
    ..The study has, however, also highlighted issues confronting whole-genome sequencing screens, including the observation that loss of function of 1% or more of X-chromosome genes is compatible with apparently normal existence...
  32. pmc Modeling the contrasting Neolithic male lineage expansions in Europe and Africa
    Michael J Sikora
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Investig Genet 4:25. 2013
    ..This revealed contrasting bifurcating and starlike phylogenies for the major lineages associated with the Neolithic expansions in sub-Saharan Africa and Western Europe, respectively...
  33. pmc Variation of the oxytocin/neurophysin I (OXT) gene in four human populations
    Yang Xu
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs, CB10 1SA, UK
    J Hum Genet 53:637-43. 2008
    ....
  34. pmc A systematic survey of loss-of-function variants in human protein-coding genes
    Daniel G MacArthur
    Wellcome Trust Sanger Institute, Hinxton, UK
    Science 335:823-8. 2012
    ..We describe functional and evolutionary differences between LoF-tolerant and recessive disease genes and a method for using these differences to prioritize candidate genes found in clinical sequencing studies...
  35. pmc Deep Roots for Aboriginal Australian Y Chromosomes
    Anders Bergström
    The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Curr Biol 26:809-13. 2016
    ..We find divergence times dating back to ∼50 kya, thus excluding the Y chromosome as providing evidence for recent gene flow from India into Australia...
  36. ncbi request reprint The population history of the Xibe in northern China: a comparison of autosomal, mtDNA and Y-chromosomal analyses of migration and gene flow
    Gareth T Powell
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Forensic Sci Int Genet 1:115-9. 2007
    ..In the Chinese samples examined, the combination of a northeastern autosomal background with a northwestern Y chromosome is indicative of a Xibe individual...
  37. pmc Variation of 52 new Y-STR loci in the Y Chromosome Consortium worldwide panel of 76 diverse individuals
    Si Keun Lim
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Int J Legal Med 121:124-7. 2007
    ..Ten loci showed occasional missing alleles, duplicated peaks or intermediate-sized alleles...
  38. pmc Variation in genome-wide mutation rates within and between human families
    Donald F Conrad
    Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
    Nat Genet 43:712-4. 2011
    ..These observations suggest considerable variation in mutation rates within and between families...
  39. pmc A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium
    Nicole Soranzo
    Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
    Nat Genet 41:1182-90. 2009
    ....
  40. pmc The variant call format and VCFtools
    Petr Danecek
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
    Bioinformatics 27:2156-8. 2011
    ..VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API...
  41. pmc Human Knockout Carriers: Dead, Diseased, Healthy, or Improved?
    Vagheesh M Narasimhan
    Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
    Trends Mol Med 22:341-51. 2016
    ..We examine their relevance to studying gene function, population genetics, and importantly, the implications for accurate clinical interpretations. ..
  42. pmc Copy number variation in the human Y chromosome in the UK population
    Wei Wei
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
    Hum Genet 134:789-800. 2015
    ....
  43. pmc Insights into the origin of rare haplogroup C3* Y chromosomes in South America from high-density autosomal SNP genotyping
    Massimo Mezzavilla
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK Medical Genetics, Department of Reproductive Sciences and Development, IRCCS Burlo Garofolo, University of Trieste, Trieste, Italy
    Forensic Sci Int Genet 15:115-20. 2015
    ..In summary, we can exclude recent migration and probably admixture 6 Kya as the source of the C3* Y chromosomes in Ecuador, and thus suggest that they represent a rare founding lineage lost by drift elsewhere...
  44. pmc Genome-wide meta-analysis of common variant differences between men and women
    Vesna Boraska
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Hum Mol Genet 21:4805-15. 2012
    ..The absence of sex-specific differences is useful in guiding genetic association study design, for example when using mixed controls for sex-biased traits...
  45. pmc Recent spread of a Y-chromosomal lineage in northern China and Mongolia
    Yali Xue
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
    Am J Hum Genet 77:1112-6. 2005
    ..4% of the minority population by the end of the dynasty...
  46. pmc Spread of an inactive form of caspase-12 in humans is due to recent positive selection
    Yali Xue
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, United Kingdom
    Am J Hum Genet 78:659-70. 2006
    ..We further propose that its selective advantage was sepsis resistance in populations that experienced more infectious diseases as population sizes and densities increased...
  47. pmc Sibling rivalry among paralogs promotes evolution of the human brain
    Chris Tyler-Smith
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Cell 149:737-9. 2012
    ..Two papers in this issue suggest that partial duplication of SRGAP2, producing an incomplete protein that antagonizes the original, contributed to human brain evolution...
  48. ncbi request reprint Response to the comment on "The hare and the tortoise: One small step for four SNPs, one giant leap for SNP-kind"
    Yali Xue
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, UK
    Forensic Sci Int Genet 5:361-2. 2011
    ..However, changes to ethical and legal structures may be needed before the new information could be used...