Publications

  1. Xing, J.*, T. Wuren*, T. S. Simonson*, W. S. Watkins, D. J. Witherspoon, W. Wu, G. Qin, C. D. Huff, L. B. Jorde, and R. L. Ge (2013) Genomic analysis of nature selection and phenotypic variation in high-altitude Mongolians. PLOS Genetics 9(7): e1003634 [news feature in ChinaDaily]
  2. Ge, R. L., Q. Cai, Y. Y. Shen, A. San, L. Ma, Y. Zhang, X. Yi, Y. Chen, L. Yang, Y. Huang, R. He, Y. Hui, M. Hao, Y. Li, B. Wang, X. Ou, J. Xu, Y. Zhang, K. Wu, C. Geng, W. Zhou, T. Zhou, D. M. Irwin, Y. Yang, L. Ying, H. Bao, J. Kim, D. M. Larkin, J. Ma, H. A. Lewin, J. Xing, R. N. Platt II, D. A. Ray, L. Auvil, B. Capitanu, X. Zhang, G. Zhang, R. W. Murphy, J. Wang, Y. P. Zhang, J. Wang (2013) Draft genome sequence of the Tibetan antelope. Nature Communications 4:1858 [news feature in ScienceDaily]
  3. Wu, W., E. A. Clark, G. J. Stoddard, W. S. Watkins, M. S. Esplin, T. A. Manuck, J. Xing, M. W. Varner, and L. B. Jorde (2013) Effect of interleukin-6 polymorphism on risk of preterm birth within population strata: a meta-analysis. BMC Genetics 14:30
  4. Witherspoon, D. J., Y. Zhang, J. Xing, W. S. Watkins, H. Ha, M. A. Batzer and L. B. Jorde (2013) Mobile Element Scanning (ME-Scan) identifies thousands of novel Alu insertions in diverse human populations. Genome Research 23:1170-1181[news feature in Nature Reviews Genetics]
  5. Xing, J., D. J. Witherspoon, and L. B. Jorde (2013) Mobile element biology – new possibilities with high-throughput sequencing. Trends in Genetics 29(5):280-9
  6. Kim, W. , D. Londono, L. Zhou, J. Xing, A. Nato, A. Musolf, T. C. Matise, S. J. Finch, and D. Gordon (2012) Single variant and multi-variant trend tests for genetic association with next generation sequencing that are robust to sequencing error. Human Heredity 74:172-183
  7. The 1000 Genomes Project Consortium (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491:56–65 [news feature in ScienceDaily]
  8. Watkins W. S., J. Xing, C. Huff, D. J. Witherspoon, Y. Zhang, U. A. Perego, S. R. Woodward and L. B. Jorde (2012) Genetic analysis of ancestry, admixture and selection in Bolivian and Totonac populations of the New World. BMC Genetics 2012, 13:39
  9. Ge, R. L., T. S. Simonson, R. C. Cooksey, U. Tanna, G. Qin, C. D. Huff, D. J. Witherspoon, J. Xing, B. Zhengzhong, J. T. Prchal, L. B. Jorde, and D. A. McClain (2012) Metabolic insight into mechanisms of high-altitude adaptation in Tibetans. Molecular Genetics and Metabolism 106(2):244-7
  10. Stringham, S. A., E. E. Mulroy, J. Xing, D. Record, M. W. Guernsey, J. T. Aldenhoven, E. J. Osborne, and M. D. Shapiro (2012) Divergence, Convergence, and the Ancestry of Feral Populations in the Domestic Rock Pigeon. Current Biology [news feature in ScienceDaily]
  11. Stewart, C.*, D. Kural*, M. P. Stromberg*, J. A. Walker, M. K. Konkel, A. M. Stutz, A. E. Urban, F. Grubert, H. Y. K. Lam, W. P. Lee, M. Busby, A. R. Indap, E. Garrison, C. Huff, J. Xing, M. P. Snyder, L. B. Jorde, M. A. Batzer, J. O. Korbe, G. T. Marth, and the 1000 Genomes Project (2011) A Comprehensive Map of Mobile Element Insertion Polymorphisms in Humans. Plos Genetics 7(8): e1002236
  12. Huff, C. D., D. Witherspoon, Y. Zhang, C. Gatenbee, L. A. Denson, S. Kugathasan, H. Hakonarson, A. Whiting, C. Davis, W. Wu, J. Xing, W. S. Watkins, M. Bamshad, J. P. Bradfield, K. Bulayeva, T. S. Simonson, L. B., Jorde, and S. L. Guthery (2011) Crohn's disease and genetic hitchhiking at IBD5. Mol Biol Evol. 2011 Aug 4.
  13. Lyon, G. J. , T. Jiang, R. Van Wijk, W. Wang, P. M. Bodily, J. Xing, L. Tian, R. J. Robison, M. Clement, Y. Lin, P. Zhang, Y. Liu, B. Moore, J. T. Glessner, J. Elia, F. Reimherr, W. W. van Solinge, M. Yandell, H. Hakonarson, J. Wang, W. E. Johnson, Z. Wei, and K. Wang (2011) Exome sequencing and unrelated findings in the context of complex disease research: ethical and clinical implications. Discovery Medicine 12(62):41-55.
  14. Rope, A. F., K. Wang, R. Evjenth, J. Xing, J. J. Johnston, J. J. Swensen, W. E. Johnson, B. Moore, C. D. Huff, L. M. Bird, J. C. Carey, J. M. Opitz, C. A. Stevens, T. Jiang, C. Schank, H. D. Fain, R. Robison, B. Dalley, S. Chin, S. T. South, T. J. Pysher, L. B. Jorde, H. Hakonarson, J. R. Lillehaug, L. G. Biesecker, M. Yandell, T. Arnesen, and G. J. Lyon (2011) Using VAAST to identify an X-Linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency. American Journal of Human Genetics 89(1):28-43 [news feature in Nature]
  15. Yandell, M., C. D. Huff, H. Hu, M. Singleton, B. Moore, J. Xing, L. B. Jorde, and M. G. Reese (2011) A probabilistic disease-gene finder for personal genomes. Genome Research [news feature in Nature]
  16. Roos, C., D. Zinner, L. S. Kubatko, C. Schwarz, M. Yang, D. Meyer, S. D. Nash, J. Xing, M. A. Batzer, M. Brameier, F. H. Leendertz, T. Ziegler, D. Perwitasari-Farajallah, T. Nadler, L. Walter and M. Osterholz (2011) Nuclear versus mitochondrial DNA: Evidence for hybridization in colobine monkeys. BMC Evolutionary Biology 11:77
  17. Huff, C. D.*, Witherspoon, D. J.*, Simonson, T. S., J. Xing, W. S. Watkins, Y. Zhang, T. M. Tuohy, D. W. Neklason, R. W. Burt, S. L. Guthery, S. R. Woodward, and L. B. Jorde (2011) Maximum-likelihood estimation of recent shared ancestry (ERSA) using shared genome segments. Genome Research
  18. Simonson, T. S., J. Xing, R. Barrett, E. Jerah, P. Loa, Y. Zhang, W. S. Watkins, D. J. Witherspoon, C. D. Huff, S. Woodward, B. Mowry, and L. B. Jorde (2011) Ancestry of the Iban is predominantly Southeast Asian: genetic evidence from autosomal, mitochondrial, and Y chromosomes. PLoS One 6(1): e16338
  19. Xing, J., W. S. Watkins, Y. Hu, C. D. Huff, A. Sabo, D. M. Muzny, M. J. Bamshad, R. A. Gibbs, L. B. Jorde, and F. Yu (2010) Inference of human expansion in Eurasia and genetic diversity in India. Genome Biology 11:R113 
  20. The 1000 Genomes Project Consortium (2010) A map of human genome variation from population scale sequencing. Nature 467:1061-1073 [cover article] [news feature in Nature]
  21. Xing, J., W. S. Watkins, A. Shlien, E. Walker, C. D. Huff, D. J. Witherspoon, Y. Zhang, T. S. Simonson, R. B. Weiss, J. D. Schiffman, D. Malkin, S. R. Woodward and L. B. Jorde (2010) Toward a more Uniform Sampling of Human Genetic Diversity: A Survey of Worldwide Populations by High-density Genotyping. Genomics 96:199-210
  22. Witherspoon, D. J., J. Xing, Y. Zhang, W. S. Watkins, M. A. Batzer and L. B. Jorde (2010) Mobile element scanning (ME-Scan) by targeted high-throughput sequencing. BMC Genomics 11(1):410
  23. Simonson, T. S., Y. Yang, C. D. Huff, H. Yun, G. Qin, D. J. Witherspoon, Z. Bai, F. R. Lorenzo, J. Xing, L. B. Jorde, J. T. Prchal, and R. Ge (2010) Genetic Evidence for High-Altitude Adaptation in Tibet. Science 329(5987):72-5 [comment in Science]
  24. Simonson, T. S., Y. Zhang, C. D. Huff, J. Xing, W. S. Watkins, D. J. Witherspoon, S. R. Woodward and L. B. Jorde (2010) Limited Distribution of a Cardiomyopathy-Associated Variant in India. Annals of Human Genetics 74(2):184-8
  25. Huff, C. D., J. Xing, A. R. Rogers, D. J. Witherspoon, and L. B. Jorde (2010) Mobile elements reveal small population size in the ancient ancestors of Homo sapiens. Proceedings of the National Academy of Sciences, USA 107:2147-2152
  26. Witherspoon, D. J., W. S. Watkins, Y. Zhang, J. Xing, W. L. Tolpinrud, D. J. Hedges, M. A. Batzer and L. B. Jorde (2009) Alu repeats increase local recombination rates. BMC Genomics 10:530
  27. Damert, A., J. Raiz, A. V. Horn, J. Löwer, H. Wang, J. Xing, M. A. Batzer, R. Löwer and G. G. Schumann (2009) 5'-transduced SVA retrotransposon groups spread efficiently throughout the human genome. Genome Research 19(11):1992-2008
  28. Li, J., K. Han, J. Xing, H.-S. Kim, J. Rogers, O. A. Ryder, T. Disotell, B. Yue and M. A. Batzer (2009) Phylogeny of the macaques (Cercopithecidae: Macaca) based on Alu elements. Gene 448(2):242-9.
  29. Xing, J., Y. Zhang, K. Han, A. H. Salem, S. K. Sen, C. D. Huff, Q. Zhou, E. F. Kirkness, S. Levy, M.A. Batzer, and L. B. Jorde (2009) Mobile elements create structural variation: analysis of a complete human genome.Genome Research 19(9):1516-26 Supplemental Data
  30. Marchani E. E., J. Xing, D. J. Witherspoon, L. B. Jorde, and A. R. Rogers (2009) Estimating the age of retrotransposon subfamilies using maximum likelihood. Genomics 94(1):78-82.
  31. Xing, J.,W. S. Watkins, D. J. Witherspoon, Y. Zhang, S. L. Guthery, R. Thara, B. J. Mowry, K. Bulayeva, R. B. Weiss, and L. B. Jorde (2009) Fine-Scaled Human Genetic Structure Revealed by SNP Microarrays. Genome Research 19(5):815-25. Supplemental Data
  32. Xing, J., W. S. Watkins, Y. Zhang, D. J. Witherspoon, and L. B. Jorde (2008) High Fidelity of Whole-Genome Amplified DNA on High-Density Single Nucleotide Polymorphism Arrays. Genomics 92(6):452-6 Supplemental Data
  33. Xing, J., D. J. Witherspoon, W. S. Watkins, Y. Zhang, W. Tolpinrud and L. B. Jorde (2008) HapMap tagSNP transferability in multiple populations:general guidelines. Genomics 92:41-51
  34. Xing, J., D. J. Witherspoon, D. A. Ray, M. A. Batzer and L. B. Jorde (2007) Mobile elements and primate evolution. Yearbook of Physical Anthropology 50:2-19
  35. Rhesus Macaque Genome Sequencing and Analysis Consortium (2007) Evolutionary and Biomedical Insights from the Rhesus Macaque Genome. Science 316: 222-234 [cover article]
  36. Han K.*, M. K. Konkel*, J. Xing*, H. Wang*, J. Lee, T. J. Meyer, C. T. Huang, E. Sandifer, K. Hebert, E. W. Barnes, R. Hubley, W. Miller, A. F. A. Smit, B. Ullmer and M. A. Batzer (2007) Old World monkey mobile DNA: a glimpse through the rhesus macaque genome.Science 316: 238-240 * These authors contributed equally to this work.
  37. Herke S. W., J. Xing, D. A. Ray, J. W. Zimmerman, R. Cordaux and M. A. Batzer (2007) A SINE-based dichotomous key for primate identification. Gene 390:39-51
  38. Xing, J., H. Wang, Y. Zhang, D. A. Ray, A. J. Tosi, T. R. Disotell and M. A. Batzer (2007) A mobile element based evolutionary history of guenons (Tribe Cercopithecini). BMC Biology 5:5
  39. Ray, D. A., J. Xing, A.-H. Salem and M. A. Batzer (2006) SINEs of a nearly perfect character.Systematic Biology 55(6): 928-935
  40. Xing, J.*, H. Wang*, V. P. Belancio, R. Cordaux, P. L. Deininger and M. A. Batzer (2006) Emergence of new primate genes by retrotransposon-mediated sequence transduction. Proceedings of the National Academy of Sciences, USA 103(47):17608-13.*These authors contributed equally to this work. [cover article]
  41. Wang, H.*, J. Xing*, D. Grover*, D. J. Hedges, K. Han, J. A. Walker and M. A. Batzer (2005) SVA elements: a hominid specific retroposon family.Journal of Molecular Biology 354:994-1007 *These authors contributed equally to this work. [cover article]
  42. Xing, J., H. Wang, K. Han, D. A. Ray, C. H. Huang, L. G. Chemnick, C.-B. Stewart, T. Disotell, O. A. Ryder and M. A. Batzer (2005) A mobile element based phylogeny of Old World monkeys.Molecular Phylogenetics and Evolution 37:872-880
  43. Hedges, D. J., R. Cordaux, J. Xing, D. J. Witherspoon, A. R. Rogers, L. B. Jorde and M. A. Batzer (2005) Modeling the amplification dynamics of human Alu retrotransposons. PLOS Computational Biology 1: e44
  44. Han, K.*, J. Xing*, H. Wang, D. J. Hedges, R. K. Garber, R. Cordaux and M. A. Batzer (2005) Under the Genomic Radar: The Stealth Model of Alu Amplification.Genome Research 15:655-664 *These authors contributed equally to this work. [cover article]
  45. Ray, D. A., J. Xing, D. J. Hedges, M. Hall, M. E. Laborde, B. A. Anders, B. R. White, J. D. Fowlkes, L. Chemnick, O. A. Ryder, and M. A. Batzer (2005) Alu insertion polymorphisms and Platyrrhine primate phylogenetic relationships.Molecular Phylogenetics and Evolution 35:117-126
  46. Xing J., D. J. Hedges, K.D. Han, H. Wang, R. Cordaux and M.A. Batzer (2004) Alu elements mutation spectra: Molecular clocks and the effect of DNA methylation.Journal of Molecular Biology 344:657-682
  47. Hedges, D. J., P. A. Callinan, R. Cordaux, J. Xing, E. Barnes and M. A. Batzer. (2004) Differential Alu mobilization and polymorphism among the human and chimpanzee lineages. Genome Research 14: 1068-1075
  48. Walker, J. A., R. K. Garber, D. J. Hedges, G. E. Kilroy, J. Xing and M. A. Batzer (2004) Resolution of mixed human DNA samples using mtDNA sequence variants. Analytical Biochemistry 325: 171-173
  49. Salem, A.-H., D. A. Ray, J. Xing, P. A. Callinan, J. S. Myers, D. J. Hedges, R. K. Garber, D. J. Witherspoon, L. B. Jorde and M. A. Batzer (2003) Alu elements and Hominid phylogenetics.Proceedings of the National Academy of Sciences, USA. 22: 12787-12791
  50. Xing, J., A.-H. Salem, D. J. Hedges, G. E. Kilroy, W. S. Watkins, J. E. Schienman, C.-B. Stewart, J. Jurka, L. B. Jorde and M. A. Batzer (2003) Comprehensive analysis of two Alu Yd subfamilies. Journal of Molecular Evolution 57: S76-S89
  51. Callinan, P. A., D. J. Hedges, A.-H. Salem, J. Xing, J. A. Walker, R. K. Garber, W. S. Watkins, M. J. Bamshad, L. B. Jorde and M. A. Batzer (2003) Comprehensive analysis of Alu associated diversity on the human sex chromosomes. Gene 317: 103-110
  52. Walker, J. A., G. E. Kilroy, J. Xing, J. Shewale, S. Sinha, and M. A. Batzer (2003) Human DNA quantitation using Alu element based PCR. Analytical Biochemistry 315: 122-128
  53. Gao Y, J. Xing, M Streuli, TL Leto and Y Zheng (2001) Trp(56) of Rac1 specifies interaction with a subset of guanine nucleotide exchange factors.Journal of Biological Chemistry 276: 47530-47541