11/03/2008

11/03/2008

List of Refereed Publications for NCCC204


1. Abasht, B., J.C.M. Dekkers, and S.J. Lamont. 2006. Review of quantitative trait loci identified in the chicken. Poultry Sci. 85: 2079-2096


2. Andreescu, C., J.H. Ralph, A. Hassen, S.J. Lamont, and J.C.M. Dekkers. 2007. Correspondence of relationships between breeding lines based on marker allele frequencies and marker-marker linkage disequilibrium. Midwest Animal Science Meeting, Des Moines.


3. Bijma, P. and W. M. Muir 2006. Genetic analysis and improvement of traits affected by interaction among individuals WCGALP 17:974-980


4. Bijma, P., W.M. Muir, and J.A.M. Van Arendonk. 2006. Quantitative genetics of inheritance and response with multilevel selection. Genetics (In press)


5. Bijma, P., W.M. Muir, E. Ellen, J.B. Wolf and J.A.M. Van Arendonk. 2006. Estimating the genetic parameters determining response to multilevel selection of traits affected by interaction among individuals. Genetics (In press)


6. Bijma, P., William M. Muir, Rolf F. Hoekstra and Johan A. M. Van Arendonk. 2007. Quantitative genetics of kin selection. American Naturalist.


7. Bohmanova, J., I. Misztal and J. Cole. 2007. Comparison of seven temperature humidity indices as indicators of milk production losses due to heat stress in semi-arid and humid climates. J. Dairy Sci. 90:1947-1956.


8. Bueno, J. S. S., Gilmour, S. G. and Rosa, G. J. M. (2006) Design of microarray experiments for genetical genomics studies. Genetics 174(2): 945-957.


9. Bueno, J. S., Gilmour, S. G., Rosa, G. J. M. Design of microarray experiments for genetical genomics studies. Royal Statistical Society 2006, Queen's University Belfast, September 10-14, 2006.


10. Bueno, J. S., Gilmour, S. G., Rosa, G. J. M. Efficiency and robustness of some designs for two color microarray experiments. SCRA 2006-FIM XIII-Thirteenth International Conference of the Forum for Interdisciplinary Mathematics on Interdisciplinary Mathematical and Statistical Techniques, Lisbon-Tomar, Portugal, September 1-4, 2006.


11. Burton, J. L. and Rosa, G. J. M. (2006) Physiological genomics special issue on animal genomics. Physiological Genomics 28: 1-4.


12. Cardoso, F. F., Rosa, G. J. M. and Tempelman, R. J. Accounting for outliers and heteroskedasticity on multiple-breed genetic evatualtions. In: 8th World Congress on Genetics Applied to Livestock Production, Belo Horizonte, Brazil, Aug. 13-18, 2006 (CD Rom, paper 03-05; on line: http://www.wcgalp8.org.br/wcgalp8/articles/paper/3_201-271.pdf)


13. Cardoso, F. F., Rosa, G. J. M., Tempelman, R. J. (2007) Accounting for outliers and heteroskedasticity on multibreed genetic evaluations of post-weaning gain of Hereford-Nelore cattle. Journal of Animal Science (in press)


14. Chen, K., T. Baxter, W.M. Muir, M.A. Groenen, .L.B. Schook. 2006. Genome Evolution and Biodiversity in Pig (Sus scrofa). International Journal of Biological Sciences. In Press


15. Cheng, H., Yong Zhang and W.M. Muir. 2006. Evidence for widespread epistatic interactions influencing Marek s disease virus viremia levels in chicken. Cytogenetic and Genome Research (In press)


16. Dekkers, J.C.M., H.H. Zhao, and RL. Fernando. 2006. Linkage disequilibrium mapping in livestock. 8th World Congress on Genetics Applied to Livestock Production. Paper 21-05. Belo Horizonte, Brazil.


17. Devlin, RH Sundström, LF and WM Muir. 2006. Interface of biotechnology and ecology for environmental risk assessments of transgenic fish. Trends in Biotechnology 24:89-97.


18. Ellen, E.D., William M. Muir and Piter Bijma. 2007. Genetic improvement of traits affected by interactions among individuals. Genetical Research.


19. Farber C. & Medrano J.F. (2007) Subcongenic partitioning of multiple growth and obesity quantitative trait loci (QTL) closely linked in repulsion on mouse chromosome 2. Mammalian Genome 18:635-645.


20. Farber, C.R., J. Chitwood, S.N Lee, R. Verdugo, A. Islas-Trejo, G. Rincon, I. Lindberg and J.F. Medrano 2007. Overexpression of secretory granule neuroendocrine protein 1 (Sgne1) increases enzymatic activity of PCSK2 and is negatively correlated with body weight and obesity in congenic mouse models. BMC Genetics (Submitted)


21. Gianola, D., Fernando, R.L. and Stella, A. 2006. Genomic assisted prediction of genetic value with semi-parametric procedures. Genet. 173:1761-1776.


22. Grapes, L., M. Z. Firat, J.C.M. Dekkers, M.F. Rothschild, and R.L. Fernando. 2006. Optimal haplotype structure for linkage disequilibrium-based fine mapping of quantitative trait loci using identity-by-descent. Genetics 172: 1955-1965.


23. Hasenstein, J.R., J.C.M. Dekkers, and S.J. Lamont. 2006. Chromosomal Linkage Disequilibrium in Two Advanced Intercross Lines of Poultry Designed for Disease Resistance Genetic Studies. In: Proc Stadler Genetics Symposium, Columbia, MO. Oct. 2-4, 2006.


24. Hassen, A., s. Avendano, S.J. Lamont, W.G. Hill, and J.C.M. Dekkers. 2007. The effect of heritability estimates on high-density SNP analyses with related animals. Midwest Animal Science Meeting, Des Moines.


25. Jia, Z. and S. Xu. 2007. Mapping quantitative trait loci for expression abundance. Genetics (in press).


26. Johanson, J.M., Berger, P.J., Tsuruta, S. and Misztal, I. 2006. Genetic parameters for birth weight, dystocia, gestation length, and perinatal mortality in Holstein cattle. J. Dairy Sci. 89(Suppl. 1): M31, Abstract.


27. Khatib H, Rosa G J M, Weigel K, Schiavini F, Santus E and Bagnato A (2007) Confirmation of association between OLR1 and milk fat traits in cattle. Animal Genetics (in press).


28. Khatib, H., Schutzkus, V., Chang, Y. M. and Rosa, G. J. M. (2007) Pattern of expression of the uterine milk protein gene and its association with productive life in dairy cattle. Journal of Dairy Science (accepted for publication)


29. Khatib, H., Zaitoun, I., Wiebelhaus-Finger, J., Chang, Y. M. and Rosa, G. J. M. (2007) The bovine PPARGC1A and OPN genes are associated with milk composition in two independent Holstein cattle populations. Journal of Dairy Science (accepted for publication)


30. Kocabas, A. M., Crosby, J., Ross, J. P., Out, H. H., Beyhan, Z., Can, K., Tam, W. L., Rosa, G. J. M., Halgren, R. G., Lim, B., Fernandez, E., and Cibelli, J. B. (2006) The transcriptome of human oocytes. Proc. Natl. Acad. Sci. USA 103(38): 14027-14032.


31. Kocabas, A. M., Crosby, J., Rosa, G. J. M., Fernandez, E., Cibelli, J. B. Identification of pregnancy associated transcripts in human cumulus cells using Affymetrix GeneChip technology. American Society for Reproductive Medicine (ASRM) Annual Meeting, New Orleans, Louisiana, October 21-25, 2006.


32. Legarra, A., J. K. Bertrand, T. Strabel, R. L. Sapp, J. P. Sanchez, and I. Misztal. 2007. Multi-breed genetic evaluation in a Gelbvieh population. J. Anim. Breed. Genet. 124:286-295.


33. Li, Y., H.N. Kadarmideen, and J.C.M Dekkers. 2006. Selection on multiple QTL with controlled gene diversity and inbreeding for long-term benefit. 8th World Congress on Genetics Applied to Livestock Production. Paper 22-17. Belo Horizonte, Brazil.


34. Livant, E.J., S. Avendano, S. McLeod, X. Ye., S.J. Lamont, J.C.M. Dekkers, and S.J. Ewald. 2007. Mx gene exon 13 polymorphisms in broiler breeder chickens and associations with commercial traits. Animal Genetics (accepted) Madsen-Bouterse, S. A., Rosa, G. J. M. and Burton, J. L. (2006) Glucocorticoid modulation of Bcl-2 family members A1 and Bak during delayed spontaneous apoptosis of bovine blood neutrophils. Endocrinology 147(8): 3826-3834.


35. McElroy, J.P., J.-J. Kim, D.E. Harry, S.R. Brown, J.C.M. Dekkers, and S.J. Lamont. 2006 Identification of Trait Loci Affecting White Meat Percentage and Other Growth and Carcass Traits in Commercial Broiler Chickens. Poultry Sci. 85:593-605


36. McElroy, J.P., W. Zhang, K.J. Koehler, S.J. Lamont, and J.C.M. Dekkers. 2006. Comparison of methods for analysis of selective genotyping survival data. Genet. Sel. Evol. 38: 637-655.


37. Meade, K. G., Gormley, E., Fitzsimons, T., Rosa, G. J. M., Costello, E., Keane, J., Coussens, P. M. and MacHugh, D. E. (2006) Gene expression profiling of peripheral blood mononuclear cells (PBMC) from Mycobacterium bovis infected cattle after in vitro antigenic stimulation with purified protein derivative of tuberculin (PPD). Veterinary Immunology and Immunopathology 113: 73-89, 2006.


38. Minin, V.N., Dorman, K.S., Fang, F. and Suchard, M.A. 2006. Phylogenetic mapping of recombination hot-spots in HIV via spatially smoothed change-point processes. Genetics. Epub


39. Muir, W.M. and P. Bijma. 2006. Incorporation of competitive effects in breeding programs for improved performance and animal well-being. WCGALP 17:806-812


40. Muir, W.M., J. Romero-Severson, S.D. Rider Jr., A. Simons, and J. Ogas. 2006. Application of One Sided t-tests and a Generalized Experiment Wise Error Rate to High-Density Oligonucleotide Microarray Experiments: An Example Using Arabidopsis. J. Data Science 4, 323-341.


41. Muir, W.M., G.J.M. Rosa, B.R. Pittendrigh, S. Xu, S.D. Rider, M. Fountain and J. Ogas. 2007. A Quantitative Genetics Approach to Discovery of Biologically Significant Genes in Microarray Analysis. Genetics. (submitted)


42. Nettleton, D. (2006). A Discussion of statistical methods for design and analysis of microarray experiments for plant scientists. The Plant Cell. 18 2112-2121.


43. Nettleton, D., Hwang, J.T.G., Caldo, R.A., Wise, R.P. (2006). Estimating the number of true null hypotheses from a histogram of p-values. Journal of Agricultural, Biological, and Environmental Statistics. 11 337-356.


44. Nettleton, D., Wang, D. (2006). Selective transcriptional profiling for trait-based eQTL mapping. Animal Genetics. 37 13-17


45. Piyasatian, N., L.R. Totir, R.L. Fernando, and J.C.M. Dekkers. 2006. QTL detection and marker-assisted composite line development. Midwest Animal Science Meeting, Des Moines.


46. Piyasatian, N., R.L. Fernando, and J.C.M. Dekkers. 2006. Genomic selection for composite line development using low density marker maps. 8th World Congress on Genetics Applied to Livestock Production. Paper 22-65. Belo Horizonte, Brazil.


47. Pribyl, J., H. Krejcova, J. Pribylova, I. Misztal, J. Bohmanova, and M. Stipkova. 2007. Trajectory of body weight of performance tested dual-purpose bulls. Czech J. Anim.Sci. 52: 315-324.


48. Qu, L., D. Nettleton, and J. C. M. Dekkers. 2006. The effect of single nucleotide polymorphisms on one-step Tukey s biweight estimates from affymetrix microarray data. Midwest Animal Science Meeting, Des Moines.


49. Qu, L., D. Nettleton, and J.C.M. Dekkers. 2006. Evaluation of common Affymetrix GeneChip preprocessing methods based on performance in statistical tests and the validity of benchmarking datasets. Abstract presented at the 2nd International Symposium on Animal Functional Genomics, Michigan State University, May, 2006


50. Qu, L., D. Nettleton, and J.C.M. Dekkers. 2007. An A-optimal statistical design for post-hybridization washing procedures in Affymetrix microarray experiments. Midwest Animal Science Meeting, Des Moines.


51. Qu, Y. and S. Xu. 2006. Quantitative trait associated microarray gene expression data analysis. Molecular Biology and Evolution 23:1558-1573.


52. Rosa, G. J. M. and Steibel, J. P. Recovery of inter slide information in the analysis of microarray reference designs. In: 8th World Congress on Genetics Applied to Livestock Production, Belo Horizonte, Brazil, Aug. 13-18, 2006 (CD Rom, paper 23-23; on line: http://www.wcgalp8.org.br/wcgalp8/articles/paper/23_970-1896.pdf)


53. Rosa, G. J. M. Design and analysis of genetical genomics studies involving complex traits. In: 34th Annual Meeting of the Statistical Society of Canada, London, ON, 2006.


54. Rosa, G. J. M. Optimal designs for genetical genomics studies. In: Plant and Animal Genome XIV, San Diego, CA, Jan. 14 - 18, 2006.


55. Rosa, G. J. M., de Leon N. and Rosa, A. J. M. (2006) A review of microarray experimental design strategies for genetical genomics studies. Physiological Genomics 28: 15-23.


56. Rosa, G. J. M., de Leon, N., Rosa, A. J. M. On design of microarray experiments for genetical genomics studies. In: 2nd International Symposium on Animal Functional Genomics (2nd ISAFG), East Lansing, MI, May 16-19, 2006.


57. Rosa, G. J. M., Tempelman, R. J., Ernst, C. W. and Bates, R. O. Combining molecular marker information and gene expression profiling for studying complex traits. In: 8th World Congress on Genetics Applied to Livestock Production, Belo Horizonte, Brazil, Aug. 13-18, 2006 (CD Rom, paper 23-11; on line: http://www.wcgalp8.org.br/wcgalp8/articles/paper/23_795-1869.pdf)


58. Ruppert, D., Nettleton, D., Hwang, J.T.G. (2006). Exploring the information in p-values for the analysis and planning of multiple-test experiments. Biometrics. In press.


59. Siewerdt, F., 2006. On the estimation of realized genetic correlations from selection experiments. In: Proceedings of the 8th World Congress on Genetics Applied to Livestock Production, Belo Horizonte, Brazil. Paper 28-02 (4p).


60. Smith, C., McFarland, D. C., Oliveira, H. N., Rosa, G. J. M., Sanborn, A. M., Lindblom, S. J. and Rosa, A. J. M. Gene expression analysis of differentiating avian myogenic satellite cells. In: 8th World Congress on Genetics Applied to Livestock Production, Belo Horizonte, Brazil, Aug. 13-18, 2006 (CD Rom, paper 13-24; on line:
http://www.wcgalp8.org.br/wcgalp8/articles/paper/13_926-2066.pdf)


61. Smith, G. W. and Rosa, G. J. M. (2007) Interpretation of microarray data: Trudging out of the abyss towards elucidation of biological significance. Journal of Animal Science (in press).


62. Smith, G. W., Rosa, G. J. M., Coussens, P. M., Halgren, R., Evans, A. C. O., Mihm, M., Lonergan, P., and Ireland J. J. Interpretation of microarray data: Trudging out the abyss towards elucidation of biological significance. J. Dairy Sci. Vol 89, Suppl. 1, 2006.


63. Steibel, J. P. and Rosa, G. J. M. Linear mixed model analysis of relative quantification of reverse transcription polymerase chain reaction data. In: 8th World Congress on Genetics Applied to Livestock Production, Belo Horizonte, Brazil, Aug. 13-18, 2006 (CD Rom, paper 23-04; on line: http://www.wcgalp8.org.br/wcgalp8/articles/paper/23_528-1915.pdf)


64. Steibel, J. P., Tempelman, R. J., Rosa, G. J. M. Linear models for microarray experiments: a comprehensive review. 2nd International Symposium on Animal Functional Genomics (2nd ISAFG), East Lansing, MI, May 16-19, 2006.


65. Soller, M., S. Weigend, M.N. Romanov, J.C.M. Dekkers, and S.J. Lamont. 2006. Strategies to Assess Structural Variation in the Chicken Genome and its Associations with Biodiversity and Biological Performance. Poultry Sci. 85: 2061-2078.


66. Sun,W., V. M. Margam, L. Sun, G. Buczkowski, G. W. Bennett, B. Schemerhorn, W. M. Muir and B. R. Pittendrigh 2006. Genome-wide analysis of phenobarbital-inducible genes in Drosophila melanogaster Insect Molecular Biology. Insect Molecular Biology 15: 455 464


67. Tarver, M., W. Muir, L. Murocm, B. Pittendrigh, 2006. Pyramiding of insecticidal compounds for control of the cowpea bruchid (Callosobruchus maculatus F.) Pest Management Science (in press)


68. Tuggle, C., L. Qu, Y. Wang, O. Couture, D. Nettleton, J. Dekkers, S. Zhao, J. Uthe, and S. Bearson. 2006. Using a First-Generation Porcine Affymetrix Genechip® to Investigate the Functional Genomics of Immune Response and Reproductive Biology. Plant and Animal Genome XIV Abstract W242, page 61.


69. Urioste, J. I., I. Misztal and J.K. Bertrand. 2007.Fertility traits in spring-calving Aberdeen Angus cattle. 1. Model development and genetic parameters. J. Anim. Sci. 85:2854-2860.


70. Urioste, J. I., I. Misztal and J.K. Bertrand. 2007.Fertility traits in spring-calving Aberdeen Angus cattle. 2. Model comparison . J. Anim. Sci. 85: 2861-2865.


71. Van Mellis, M. H., Eler*, J. P., Oliveira, H. N, Silva, J. A. II V., Ferraz*, J. B. S., Rosa, G. J. M. and Pereira, E. (2007) Study of stayability in Nellore cows using a threshold model. Journal of Animal Science (accepted for publication)


72. Van Mellis, M. H., Eler, J. P., Oliveira, H. N., Rosa, G. J. M., Ferraz, J. B. S. and Pereira, E. Additive genetic relationship among stayability at five, six and seven years. In: 8th World Congress on Genetics Applied to Livestock Production, Belo Horizonte, Brazil, Aug. 13-18, 2006 (CD Rom, paper 03-88; on line: http://www.wcgalp8.org.br/wcgalp8/articles/paper/3_531-1750.pdf)


73. Wang X.*, Rosa, A. J. M., Oliverira, H. N., Rosa, G. J. M., Guo, X., Travnicek, M.# and Girshick, T. (2006) Transcriptome of local innate and adaptive immunity during early phase of infectious bronchitis virus infection. Viral Immunology 19(4): 768-774.


74. Weber, P. S., Madsen-Bouterse, S. A., Rosa, G. J. M., Sipkovsky, S., Ren, X., Almeida, P. E., Kruska, R., Halgren, R. G., Barrick, J. L. and Burton, J. L. (2006) Analysis of the bovine neutrophil transcriptome during glucocorticoid treatment. Physiological Genomics 28: 97-112.


75. Weber, P. S., Madsen-Bouterse, S. A., Rosa, G. J. M., Sipkovsky, S., Ren, X., Almeida, P. E., Kruska, R., Halgren, R. G., Barrick, J. L. and Burton, J. L. Analysis of the bovine neutrophil transcriptome during glucocorticoid treatment. In: 2nd International Symposium on Animal Functional Genomics (2nd ISAFG), East Lansing, MI, May 16-19, 2006.


76. Xu, S. and C. Xu. 2006. A multivariate model for ordinal trait analysis. Heredity 97:409-417.


77. Xu, S. 2007. An empirical Bayes method for estimating epistatic effects of quantitative trait loci. Biometrics (in press)


78. Xu, S. and Z. Jia. 2007. Genome-wide analysis of epistatic effects for quantitative traits in barley. Genetics (in press)


79. Yang, R., Q. Tian and S. Xu. 2006. Mapping QTL for longitudinal traits in line crosses. Genetics 173:2339-2356.


80. Yang, R., J. Li and S. Xu. 2007. Mapping quantitative trait loci for traits defined as ratios. Genetica (in press)


81. Yang, R. and S. Xu. 2007. Bayesian shrinkage analysis of quantitative trait loci for dynamic traits. Genetics (in press)


82. Ye, X. S.R. Brown, K. Nones, L.L. Coutinho, J.C.M. Dekkers, and S.J. Lamont. 2007. Associations of myostatin gene polymorphisms with performance and mortality traits in broiler chickens. Genet. Sel. Evol. 39: 73-89.


83. Ye, X., S. Avendano, D. J.C.M. Dekkers, and S. J. Lamont. 2006. Association of twelve immune-related genes with performance of three broiler lines in two different hygiene environments. Poultry Sci. 85: 1555-1569.


84. Ye, X., S. Avendano, J.C.M. Dekkers, and S.J. Lamont. 2006. Variation in immune genes associated with body weight and feed conversion in elite commercial broiler lines. Proc. Plant & Animal Genome XIV, San Diego, CA.


85. Ye, X., S. McLeod, D. Elfick, J.C. Dekkers, and S.J. Lamont. 2006. Rapid Identification of Single Nucleotide Polymorphisms and Estimation of Allele Frequencies Using Sequence Traces from DNA Pools. Poultry Sci. 85: 1165-1168.


86. Zhang, W., A. Carriquiry, D. Nettleton, and J.C.M. Dekkers. 2006. Estimation of correlations between phenotype and gene expression in microarray experiments with non-random pooling. Midwest Animal Science Meeting, Des Moines.


87. Zhao, H., R. Fernando, and J. Dekkers. 2006. Power and precision of linkage disequilibrium mapping of QTL in outbred populations. Midwest Animal Science Meeting, Des Moines.


88. Zhao, H.H., D. Nettleton, and J.C.M. Dekkers. 2007. Evaluation of linkage disequilibrium measures between multi-allelic markers as predictors of linkage disequilibrium between single nucleotide polymorphisms. Genetical Research (accepted)


89. Zhao, H.H., J.C.M. Dekkers, and R.L. Fernando. 2006. Power and precision of regression-based linkage disequilibrium mapping of QTL. 8th World Congress on Genetics Applied to Livestock Production. Paper 21-20. Belo Horizonte, Brazil.


90. Zhao, H.H., R.L. Fernando, and J.C.M. Dekkers. 2007. Effects of population structure on power and precision of regression-based linkage disequilibrium mapping of QTL. Midwest Animal Science Meeting, Des Moines.


91. Zhao, H.H., R.L. Fernando, and J.C.M. Dekkers. 2007. Power and precision of alternate methods for linkage disequilibrium mapping of QTL. Genetics: ahead of print pub. 10.1534/genetics.106.066480


92. Zumbach, B., I. Misztal, S. Tsuruta, J. Holl, W. Herring and T. Long. 2007. Genetic correlations between two strains of Durocs and crossbreds from differing production environments for slaughter traits. J. Anim. Sci. 85:901-908.

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