Technical Journal Articles (Refereed):

  1. Xu, S. 1986. Studies on combined selections. Acta Genetica Sinica 13:221-226.
  2. Xu, S. 1986. Research on the selection simulations. Journal of Northeast Agricultural College 17:429-434.
  3. Xu, S. and W. M. Muir. 1990. The application of ridge regression to multiple trait selection indices. Journal of Animal Breeding and Genetics 107:81-88.
  4. Xu, S. and W. M. Muir. 1991. Multistage selection for genetic gain by orthogonal transformation. Genetics 129:963-974.
  5. Muir, W. M. and S. Xu. 1991. An approximate method for optimal independent culling level selection for N traits with explicit solutions. Theoretical and Applied Genetics 82:450-459.
  6. Xu, S. and W. M. Muir. 1992. Selection index updating. Theoretical and Applied Genetics 83: 451-458.
  7. Muir, W. M., W. E. Nyquist and S. Xu. 1992.Alternative partitioning of the genotype by environment interaction. Theoretical and Applied Genetics 84:193-200.
  8. Levy, M., F. J. Correa-Victoria, R. S. Zeigler, S. Xu and J. E. Hamer. 1993. Genetic diversity of the rice blast fungus in a disease nursery in Colombia. Phytopathology 83:1427-1433.
  9. Atchley, W. R., S. Xu and C. Vogl. 1994. Developmental quantitative genetic models of evolutionary change. Developmental Genetics 15:92-103.
  10. Xu, S. 1994. Weighted least squares estimation of DNA fragment lengths. The Journal of Heredity 85:151-152.
  11. Xu, S., C.J. Kobak and P.E. Smouse. 1994. Constrained least squares estimation of mixed population stock composition from mtDNA haplotype frequency data. Canadian Journal of Fisheries and Aquatic Sciences 51:417-425.
  12. Vogl, C., W. R. Atchley and S. Xu. 1994.The ontogeny of morphological differences in the mandible in two inbred strains of mice. Journal of Craniofacial Genetics and Developmental Biology 14:97-110.
  13. Xu, S., W. R. Atchley and W. M. Muir. 1994. Partial and conditional maximum likelihood for variance component estimation. Journal of Animal Breeding and Genetics 111:178-188.
  14. Xu, S., W. R. Atchley and W. Fitch. 1994. Phylogenetic inference under the pure drift model. Molecular Biology and Evolution 11:949-960.
  15. Xu, S., T. G. Martin and W.M. Muir. 1995. Multistage selection for maximum economic return with an application to beef cattle breeding. Journal of Animal Science 73:699-710.
  16. Xu, S. and W. R. Atchley. 1995. A random model approach to interval mapping of quantitative trait loci. Genetics 141:1189-1197.
  17. Xu, S. and W. R. Atchley. 1995. Heterozygosity of F2 from two segregating populations. The Journal of Heredity 86:477-480.
  18. Xu, S. 1995. A comment on the simple regression method for interval mapping. Genetics 141:1657-1659.
  19. Xu, S. and W. R. Atchley. 1996. Mapping quantitative trait loci for complex binary diseases using line crosses. Genetics 143:1417-1424.
  20. Xu, S. 1996. Mapping quantitative trait loci using four-way crosses. Genetical Research 68:175-181.
  21. Xu, S. and W. R. Atchley. 1996. A Monte Carlo algorithm for maximum likelihood estimation of variance components. Genetics, Selection and Evolution 28:329-343.
  22. Xu, S. 1996. Computation of the full likelihood function for estimating variance at a quantitative trait locus. Genetics 144:1951-1960.
  23. Gessler, D. D. G. and S. Xu. 1996. Using the expectation or the distribution of identical-by-descent for mapping quantitative trait loci under the random model. American Journal of Human Genetics 59:1382-1390.
  24. Xie, C. and S. Xu. 1996. Best linear unbiased prediction under selection. Journal of Genetics and Breeding 50:287-294.
  25. Atchley, W. R., S. Xu and D. E. Cowley. 1997. Altering developmental trajectories in mice by restricted index selection. Genetics 146:629-640.
  26. Xie, C. and S. Xu. 1997. Restricted multistage selection indices. Genetics, Selection and Evolution 29:193-203.
  27. Xie, C., S. Xu and J. A. Mosjidis. 1997. Multistage selection indices for maximum genetic gain and economic efficiency in red clover. Euphytica 98:75-82.
  28. Xu, S. 1998. Further investigation on the regression method of mapping quantitative trait loci. Heredity 80:364-373.
  29. Xie, C. and S. Xu. 1998. Efficiency of marker-assisted multistage selection in the improvement of multiple quantitative traits. Heredity 80:489-498.
  30. Xu, S. 1998. Mapping quantitative trait loci using multiple families of line crosses. Genetics 148:517-524.
  31. Xu, S. and D. D. G. Gessler. 1998. Multipoint genetic mapping of quantitative trait loci using a variable number of sibs per family. Genetical Research 71:73-83.
  32. Xie, C., D. D. G. Gessler and S. Xu. 1998. Combining different line crosses for mapping quantitative trait loci using the identica-by-descent based variance component method. Genetics 149:1139-1146.
  33. Gessler, D. D. G. and S. Xu. 1998. An embarrassment of riches: the stochastic generation of beneficial mutations. Genetica 102/103:145-155.
  34. Rao, S. Q. and S. Xu. 1998. Mapping quantitative trait loci for categorical traits in four-way crosses. Heredity 81:214-224.
  35. Xie, C, D. Gessler and S. Xu. 1998. Sib mating designs for mapping quantitative trait loci. Genetica 104:9-19.
  36. Xie, C. and S. Xu. 1998. Strategies of marker-aided recurrent selection. Crop Science 38:1526-1535.
  37. Xu, S. 1998. Iteratively reweighted least squares mapping of quantitative trait loci. Behavior Genetics 28:341-355.
  38. Xu, S., N. Yonash, R. L. Vallejo and H. H. Cheng. 1998. Mapping quantitative trait loci for binary traits using a heterogeneous residual variance model: An application to Marek's disease susceptibility in chickens. Genetica 104:171-178.
  39. Gessler, D. D. G. and S. Xu. 1999. On the evolution of recombination and meiosis. Genetical Research 73:119-131.
  40. Xie, C. and S. Xu. 1999. Mapping quantitative trait loci with dominant and missing markers in four-way crosses. Theoretical and Applied Genetics 98:1014-1021.
  41. Yi, N. and S. Xu. 1999. Mapping quantitative trait loci for complex binary traits in outbred populations. Heredity 82:668-676.
  42. Yi, N. and S. Xu. 1999. A random model approach to mapping quantitative trait loci for complex binary traits in outbred populations. Genetics 153:1029-1040.
  43. Gessler, D. D. G. and S. Xu. 2000. Multipoint genetic mapping of quantitative trait loci with dominant markers in outbred populations. Genetica 105:281-291.
  44. Xu, S. 2000. Phylogenetic analysis under reticulate evolution. Molecular Biology and Evolution 17:897-907.
  45. Xu, S. and C. Vogl. 2000. Maximum likelihood analysis of quantitative trait loci under selective genotyping. Heredity 84:525-537.
  46. Yi, N. and S. Xu. 2000. Bayesian mapping of quantitative trait loci for complex binary traits. Genetics 155:1391-1403.
  47. Vogl, C. and S. Xu. 2000. Multipoint mapping of segregation distorting loci using molecular markers. Genetics 155:1439-1447.
  48. Xie, C. and S. Xu. 2000. Mapping quantitative trait loci in tetroploid populations. Genetical Reseach 76:105-115.
  49. Yi, N. and S. Xu. 2000. Bayesian mapping of quantitative trait loci under the IBD-based variance component model. Genetics 156:411-422.
  50. Gessler, D. D. G. and S. Xu. 2000. Meiosis and recombination at low mutation rates. Genetics 156:449-456.
  51. Xu, S. and N. Yi. 2000. Mixed model analysis of quantitative trait loci. Proc. Natl. Acad. Sci. USA 97:14542-14547.
  52. Yi, N. and S. Xu. 2001. Bayesian mapping of quantitative trait loci under complicated mating designs. Genetics 157:1759-1771.
  53. Li, X., W. Gu, G. Masinde, M. Hamilton-Ulland, S. Xu, S. Mohan and D. J. Baylink. 2001. Genetic control of the rate of wound healing in mice. Heredity 86:668-674.
  54. Li, X., G. Masinde, W. Gu, J. Wergedal, M. Hamilton-Ulland, S. Xu, S. Mohan and D. J. Baylink. 2002. Chromosomal regions harboring genes for the work to femur failure in mice. Functional and Integrative Genomics 1:367-374.
  55. Yi, N. and S. Xu. 2002. Mapping quantitative trait loci with epistatic effects. Genetical Research 79:185-198.
  56. Yi, N. and S. Xu. 2002. Linkage analysis of quantitative trait loci in multiple line crosses. Genetica 114:217-230.
  57. Vogl, C. and S. Xu 2002. QTL analysis in arbitrary pedigrees with incomplete marker information. Heredity 89:339-345.
  58. Kopp, A., R. M. Graze, S. Xu, S. B. Carroll and S. V. Nuzhdin 2003. Quantitative trait loci responsible for variation in sexually dimorphic traits in Drosophila melanogaster. Genetics 163:771-787.
  59. Xu, S. 2003. Estimating polygenic effects using markers of the entire genome. Genetics 163:789-801.
  60. Xu, C., X. He and S. Xu 2003. Mapping quantitative trait loci underlying triploid endosperm traits. Heredity 90:228-235.
  61. Luo, L., Y. Mao and S. Xu 2003. Correcting the bias in estimation of genetic variances contributed by individual QTL. Genetica 119:107-113.
  62. Luo, L. and S. Xu 2003. Mapping viability loci using molecular markers. Heredity 90:459-467.
  63. Yi, N., S. Xu and D. B. Allison 2003. Bayesian Model choice and search strategies for mapping interacting quantitative trait loci. Genetics 165:867-883.
  64. Yi, N., S. Xu, V. George and D. B. Allison 2004. Mapping multiple quantitative trait loci for ordinal traits. Behavior Genetics 34:3-15.
  65. XU, S., N. YI, D. BURKE, A. GALECKI and R. A. MILLER 2003. An EM algorithm for mapping binary disease loci : application to fibrosarcoma in a four-way cross mouse family. Genetical Research 82:127-138.
  66. XU, S. 2003. Theoretical basis of the Beavis effect. Genetics 165:2259-2268.
  67. Qu, Y. and S. Xu 2004. Supervised cluster analysis for microarray data based on multivariate Gaussian mixture. Bioinformatics 20:1905-1913.
  68. Zhang, Y. and S. Xu 2004. Mapping quantitative trait loci in F2 incorporating phenotypes of F3 progeny. Genetics 166:1981-1993.
  69. Mao, Y. and S. Xu 2004. Mapping QTLs for traits measured as percentages. Genetical Research 83:159-168.
  70. Beasley, T. M., D. Yang, N. Yi, D. C. Bullard, E. L. Travis, C. I. Amos, S. Xu and D. B. Allison 2004. Joint tests for quantitative trait loci in experimental crosses. Genetics, Selection & Evolution 36:601-619.
  71. Xu, C., Y. Zhang and S. Xu 2005. An EM algorithm for mapping quantitative resistance loci. Heredity 94:119-128.
  72. Mao, Y. and S. Xu 2005. A Monte Carlo algorithm for computing the IBD matrices using incomplete marker information. Heredity 94:305-315.
  73. Luo, L., Y. Zhang and S. Xu 2005. A quantitative genetics model for viability selection. Heredity 94:347-355.
  74. Xu, C., Z. Li and S. Xu 2005. Joint mapping of quantitative trait loci for multiple binary characters. Genetics 169:1045-1059.
  75. Zhang,Y., Y. Mao, C. Xie, H. Smith, L. Luo and S. Xu 2005. Mapping quantitative trait loci using naturally occurring genetic variance among commercial inbred lines of maize (Zea mays L.). Genetics 169:2267-2275.
  76. Wang, H., Y. Zhang, X. Li, G. L. Masinde, S. Mohan, D. J. Baylink and S. Xu 2005. Bayesian shrinkage estimation of quantitative trait loci parameters. Genetics 170:465-480.
  77. Zhang, Y. and S. Xu 2005. A penalized maximum likelihood method for estimating epistatic effects of QTL. Heredity 95:96-104.
  78. Hansen, C., N. Yi, Y. Zhang, S. Xu, J. Gavora and H. H. Cheng 2005. Identification of QTL for production traits in chickens. Animal Biotechnology 16:67-79.
  79. Li, X., R. J. Quigg, J. Zhou, S. Xu, G. Masinde, S. Mohan and D. J. Baylink 2006. A critical evaluation of the effect of population size and phenotypic measurement on QTL detection and localization using a large F2 murine mapping population. Genetics and Molecular Biology 29: 166-173.
  80. Jia, Z. and S. Xu 2005. Clustering expressed genes on the basis of their association with a quantitative phenotype. Genetical Research 86:193-207.
  81. Yang, R., N. Yi and S. Xu 2006. Box-Cox transformation for QTL mapping. Genetica 128:133-143.
  82. Qu, Y. and S. Xu 2006. Quantitative trait associated microarray gene expression data analysis. Molecular Biology and Evolution 23:1558-1573.
  83. Yang, R., Q. Tian and S. Xu 2006. Mapping quantitative trait loci for longitudinal traits in line crosses. Genetics 173:2339-2356.
  84. Xu, S. and Z. Jia 2007. Genomewide analysis of epistatic effects for quantitative traits in barley. Genetics 175:1955-1963.
  85. Chen, H., V. E. T. M. Ashworth and M. T. Clegg. 2007. Quantitative genetic analysis of growth rate in avocado. Journal of American Society of Horticultual Science 132:691-696.
  86. Jia, Z., and S. Xu, 2007. Mapping quantitative trait loci for expression abundance. Genetics 176: 611-623.
  87. Xu, S. 2007. Derivation of the shrinkage estimate of quantitative trat locus effects. Genetics 177:1255-1259.
  88. Xu, S., 2007. An empirical Bayes method for estimating epistatic effects of quantitative trait loci. Biometrics 63: 513-521.
  89. Yu, H., D. J. Baylink, G. L. Masinde, R. Li, B. Nguyen, H. M. Davidson, S. Xu and S. Mohan, 2007. Mouse chromosome 9 quantitative trait loci for soft tissue regeneration: congenic analysis and fine mapping. Wound Repair Regen 15: 922-927.
  90. Yang, R., and S. Xu, 2007. Bayesian shrinkage analysis of quantitative trait Loci for dynamic traits. Genetics 176: 1169-1185.
  91. Han, L., and S. Xu, 2008. A Fisher scoring algorithm for the weighted regression method of QTL mapping. Heredity 101: 453-464.
  92. Hu, Z., and S. Xu, 2008. A simple method for calculating the statistical power for detecting a QTL located in a marker interval. Heredity 101: 48-52.
  93. Xu, C., X. Wang, Z. Li and S. Xu, 2008. Mapping QTL for multiple traits using Bayesian statistics. Genetics Research 90: 1-15.
  94. Xu, S., 2008. Quantitative trait locus mapping can benefit from segregation distortion. Genetics 180: 2201-2208.
  95. Yang, R., J. Li and S. Xu, 2008. Mapping quantitative trait loci for traits defined as ratios. Genetica 132: 323-329.
  96. Yi, N., and S. Xu, 2008. Bayesian LASSO for quantitative trait loci mapping. Genetics 179: 1045-1055.
  97. Jia, Z. and S. Xu. 2009. Bayesian mixture model analysis for detecting differentially expressed genes. International Journal of Plant Genomics doi:10.1155/2008/892927
  98. Muir, W. M., G.J.M. Rosa, B.R. Pittendrigh, S. Xu, S.D. Rider, M. Fountain and J. Ogas 2008. A mixture model approach for the analysis of small exploratory microarray experiments. Computational Statistics and Data Analysis doi:10.1016/j.csda.2008.06.011

Computer Programs (refereed):

  1. Xu, S 1993. INDUPDAT: A SAS/IML program for selection index updating. The Journal of Heredity 84:316.
  2. Xu, C. and S. Xu 2003. A SAS/IML program for mapping QTL in line crosses. Proceedings of the Twenty-Eighth Annual SAS Users Group International Conference (SUGI) March 30-April 2, 2003, Cary, NC, SAS Institute, Inc., Paper 235-28:1-6.

Reviews, Chapters and Symposia Proceedings:

  1. Levy, M., S. Xu and J. E. Hamer 1992. MGR-DNA fingerprinting for rice blast population analysis: SAS programs for inferring lineage phylogenies. Proc. Intl. Rice Res. Conf., 21-25 April, 1992, I.R.R.I., Los Banos, The Philippines.
  2. Muir, W. M. and S. Xu 1992. Estimation of response to selection and standard error with non-replicated selected populations. Proceedings of the 41th National Breeders Round Table. May 7-8, St. Louis, Missouri.
  3. Muir, W. M. and S. Xu 1992. Optimizing profits in breeding programs using selection index updating. Proceedings of the XIX World's Poultry Congress, September 23, Amsterdam, The Netherlands.
  4. Xu, S., W. R. Atchley and W. M. Muir 1994. Multistage selection incorporating information from relatives. Proceedings of The 5th World Congress on Genetics Applied to Livestock Production, August 7-12, Guelph, Canada.Vol. 18:463-466.
  5. Smouse, P.E., C. J. Kobak and S. Xu 1994. Some thoughts on information content in allozyme and DNA markers. In: NOAA Tech. Memo. NMFS-NWFSC-17. Application of DNA Technology to the Management of Pacific Salman, Proceedings of the Workshop, March 22-23, 1993, Seattle, Washington, Edited by L. K. Park, P. Moran and R. S. Waples, pp 121-126.
  6. Xu, S. 1995. Sequential regression and its Applications in Biology. In:Animal Genetics and Breeding, Edited by Y.C. Pan and Y.Q. Yang, Harbin Engineering University Press, pp 93-112.
  7. Xu, S. 1998. Mapping quantitative trait loci and marker assisted selection in small domesticated populations. p. 62-87, In Research Council Secretariat of MAFF (ed.), Proceedings of the 6th MAFF International Workshop on genetic Resources - Genetic Diversity and Conservation of Genetic Resources,National Institute of Agrobiological Resources, Tsukuba, Ibaraki, Japan, Nov. 4-5, 1998.
  8. Xu, S. 2002. Linkage Analysis of Quantitative Traits. In Tao, J., Xu, Y., and Zhang, M. Q. (eds), Current Topics in Computational Biology,Tsinghua University Press and Massachusetts Institute of Technology, pp 175-199.
  9. Xu, S. 2002. QTL analysis in plants. In Camp, N. and Cox, A (eds), Quantitative Trait Loci: Methods and Protocols,Humana Press, Totowa, NJ, pp 283-310.
  10. Yi, N. and S. Xu 2003. Designs and methods to detect QTLs for production traits based on random genetic models. In Muir, W. M. and Aggrey, S. E. (eds),Poultry Genetics, Breeding and Biotechnology,CABI Publishing Oxon, UK, pp 465-496.
  11. Xu, S. 2003. Advanced statistical methods for estimating genetic variances in plants. Plant Breeding Reviews 22:113-163.
  12. Xu, C. and S. Xu 2004. The extended sib-pair method for mapping QTL. In Saxton, R. (ed), Genetic Analysis of Complex Traits Using SAS.SAS Institute, Inc., Cary, North Carolina, Chapter 9: pp 201-223.
  13. Zhang, Y. and S. Xu 2005. Advanced statistical methods for detecting multiple quantitative trait loci. Recent Research Development in Genetics and Breeding 2:1-23.
  14. Xu, S. 2006. Separating nurture from nature in estimating heritability. Heredity 97, 256–257.