05/05/2003

Georgia



Tsuruta. S., I. Misztal, T. J. Lawlor, and B. Klei. 2002. Application of a Random Regression Model at Different Ages for Final Scores in Holsteins. J. Dairy Sci. 85:1324:1330.



Stranden, I., S. Tsuruta, and I. Misztal. 2002. Simple preconditioners for the conjugate gradient method: experience with the test day model. J. Anim. Breeding Genet. 119 (3):166_174.



Misztal, I., S. Tsuruta,T. Strabel, B. Auvray, T. Druet, and D. H. Lee. 2002. BLUPF90 and related programs (BGF90). Proc. 7th World Congress Gen. Appl. Livest. Prod., Monteplier, France. CD_ROM communication 28:07.



Lawlor, T. J., S. Tsuruta, L. Klei and I. Misztal. 2002. Use of a random regression model to investigate changes in genetic parameters over time. Proc. 7th World Congress Gen. Appl. Livest. Prod., Monteplier, France. CD_ROM communication 17:06.



Tsuruta S., I. Misztal, T. J. Lawlor, and L. Klei. 2002. Estimation of genetic parameters over time for final score in holsteins using a random regression model. Proc. 7th World Congress Gen. Appl. Livest. Prod., Monteplier, France. CD_ROM communication 17:20.

Misztal I., S. Tsuruta, T. J. Lawlor, and L. Klei. 2002. Use of a random regression model to investigate changes in genetic parameters over time. 18th Panamerican Congress of Veterinary Sciences, Havana, Cuba. CDROM communication.



Tsuruta, S., I. Misztal, T. J. Lawlor, and L. Klei. 2002. Changes of genetic correlation between milk production and body size over time in Holsteins using random regression models. J. Dairy Sci (Suppl. 1) 85: 197.



Michigan State



Rosa, G. J. M., Yandell, B. S., Gianola, D. A Bayesian approach for constructing genetic maps when markers are miscoded. Genetic, Selection, Evolution, 34(3): 353-369. 2002.



Coussens, P. M., Colvin, C. J., Rosa, G. J. M., Laspiur, J. P., Elftman, M. D. Novel gene expression differences in peripheral blood mononuclear cells from M. paratuberculosis infected and control cattle. Infection and Immunity (submitted)



Madsen, S. A., Rosa, G. J. M., Mccandless, E., Coussens, P. M., Burton, J. L. Microarray analysis of mRNA profiles in neutrophils from periparturient cows reveals a novel phenotype. Veterinary Immunology and Immunopathology (submitted)



Rosa, G. J. M., Gianola, D., Padovani, C. R. Robust linear mixed models with normal/independent distributions and Bayesian MCMC implementation. Biometrical Journal. (accepted)









Tennessee



Stalder, K. J., A. M. Saxton, R. K. Miller, and R. N. Goodwin. 2003. A comparison of hydrogen ion concentration and pH genetic predictions and fixed effect estimations when assessing pork quality. J. Anim. Sci. 81(3): 611-616.



Smiley, R.D., L.G. Stinnett, A.M. Saxton, and E.E. Howell. 2002. Breaking Symmetry: Mutations Engineered into R67 Dihydrofolate Reductase, A D2 Symmetric Homotetramer Possessing a Single Active Site Pore. Biochemistry 41(52): 15664-15675.



Pighetti, G. M., J. L. Edwards, F. N. Schrick, A. M. Saxton, C. J. Davies, and S. P. Oliver. 2003. Cloning adult dairy cows: A viable new tool in the fight against mastitis. National Mastitis Council Annual Meeting.



Youngerman, S. M., S. P. Oliver, A. M. Saxton, J. L. Edwards, F. N. Schrick, C. J. Davies, and G. M. Pighetti. 2003. Interleukin-8 receptor: A candidate gene for mastitis resistance. National Mastitis Council Annual Meeting.





Purdue



Muir, W.M. and R.D. Howard. 2002. Methods to Assess Ecological Risks of Transgenic Fish Releases. In Genetically Engineered Organisms: Assessing Environmental and Human Health Effects Eds. D.K. Letourneau and B. E. Burrows. CRC Press p355-383.



Muir, WM and R.D. Howard 2002. Environmental Risk Assessment of Transgenic Fish With Implications for Other Diploid Organisms. Transgenic Research 11:101-114.



Muir, W.M. 2002. Potential Environmental Risks And Hazards Of Biotechnology. Potential Environmental Risks And Hazards Of Biotechnology Part I: Risks and Hazards. http://www.isb.vt.edu/news/2001/news01.nov.html#nov0105. Information Systems For Biotechnology (online version)



Muir, W.M. 2002. Potential Environmental Risks And Hazards Of Biotechnology.Part II: Methods to Estimate Risks and Hazards http://www.isb.vt.edu/news/2002/news02.feb.html#feb0201. Information Systems For Biotechnology (online version)



Muir, W.M. and A. Schinckel. 2002. Incorporation of competitive effects in breeding programs to improve productivity and animal well being. Proc. 7th World Congress of Genetics Applied to Livestock Breeding. 32:35-36



Muir, W.M. 2002. Use of molecular genetics in poultry breeding. Proc. 7th World Congress of Genetics Applied to Livestock Breeding. 30:193-200



NRC (National Research Council). 2002. Animal Biotechnology: Science Based Concerns. Washington, DC: National Academy Press.



Muir, W.M.. 2002. Indirect Selection for Improvement of Animal Well-Being. In Poultry Breeding and Biotechnology Eds. WM Muir and S Aggrey. CABI Press (in press).



Muir, W.M.. 2002. Incorporating Molecular Information in Breeding Programs, Applications and Limitations. In Poultry Breeding and Biotechnology Eds. WM Muir and S Aggrey. CABI Press (in press).



Muir, W.M., D. Miles, and A.E. Bell, 2002. Long Term Selection Studies In Tribolium Castaneum, Alternative Selection Strategies, And Associated Nature Of Quantitative Genetic Variation. Plant Breeding Reviews (In Press)



Rider, Sj Jr, TE Henderson, RE Jerome. HJ Edenberg, J Romero-Severson, J Ogas. 2003 Coordinate Repression of Regulators of Embryonic Identity by PICKLE During Germination in Arabidopsis. The Plant Journal. In press.





Iowa



Chaiwong, N., J.C.M. Dekkers, R.L. Fernando, and M.F. Rothschild. 2002. Introgressing multiple QTL in backcross breeding programs of limited size. 7th World Congress on Genetics Applied to Livestock Production, Montpellier, France, 22:08.



Chakraborty, R., L. Moreau, and J. C. M. Dekkers. 2002. A method to optimize selection on multiple identified quantitative trait loci. Genet. Sel. Evol. 34: 145-170.



Cruickshank, J., M. R. Dentine, P. J. Berger, and B. W. Kirkpatrick. 2002. Mapping quantitative trait loci for twinning in Holstein dairy cattle. Proc. 28th Intl. Conf. Anim. Genet. p. 164. Goettingen, Germany.



Dekkers, J. C. M. and P. Settar. 2002. Long-term Selection with Known Quantitative Trait Loci. Plant Breeding Reviews. Wiley. (Accepted).



Dekkers, J. C. M., R. Chakraborty, and L. Moreau. 2002. Optimal selection on two quantitative trait loci with linkage. Genet. Sel. Evol. 34 171-192.



Dekkers, J.C.M., and R. Chakraborty. 2002. Purebred selection for crossbred performance using QTL. 7th World Congress on Genetics Applied to Livestock Production, Montpellier, France, 22:15.



Fernandez, S. A., and R. L. Fernando. 2002. Determining Peeling Order Using Sparse Matrix Algorithms. J. Dairy Sci. 85:1623-1629.



Fernandez, S. A., R. L. Fernando, B. Gulbrandtsen, C. Stricker, M. Schelling, and A. L. Carriquiry. 2002. Irreducibility and efficiency of ESIP to sample marker genotypes in large pedigrees with loops. Genet. Sel Evol. 34:537-555.



Fernando, R. L. and L. R. Totir. 2002. Advances in genetic and statistical models to predict breeding values. 7th World Congress Genet. Appl. Livest.\Prod. 20-01.



Fernando, R. L., J. C. M. Dekkers and M. Soller. 2002. Controlling the proportion of false positives (PFP) in a multiple test genome scan for marker-QTL linkage. 7th World Congress Genet. Appl. Livest. Prod. 20-01.



Fernando, R.L., J.C.M. Dekkers, and M. Soller. 2002. Controlling the proportion of false positive (PFP) in a multiple test genome scan for marker-QTL linkage. 7th World Congress on Genetics Applied to Livestock Production, Montpellier, France, 21:37.



Grapes, L., R. L. Fernando and M. F. Rothschild. 2002. Analysis of methods for fine mapping quantitative trait loci using linkage disequilibrium. 7th Wld Congress Genet. Appl. Livest. Prod. 21-19.



Heifetz, E., R. L. Fernando and M. Soller. 2002. Targeted recombinant progeny: a design for ultra high-resolution mapping of QTL using a saturated marker map. 7th World Congress Genet. Appl. Livest. Prod. 21-25.



Hwang, J. T. G. and Nettleton, D. (2003). Principal components regression with data-chosen components and related methods. Accepted for publication in Technometrics.



Jannink, J.-L. 2003. Selection dynamics and limits under additive-by-additive epistatic gene action. Crop Sci. 43: In Press.



Jannink, J.-L., and X.-L. Wu. 2003. Estimating allelic number and identity in state of QTL in interconnected families. Genet. Res. 81: In Press.



Jansen, R.C., J.-L. Jannink, and W.D. Beavis. 2003. Mapping quantitative trait loci in plant breeding populations: use of parental haplotype sharing. Crop Sci. 43:In Press.



Kachman, S. D. and R. L. Fernando. 2002. Analysis of generalized linear models with MATVEC. 7th World Congress Genet. Appl. Livest. Prod. 28-04.



Lee, H.K., J.C.M. Dekkers, M. Soller, M. Malek, R.L. Fernando, and M.F. Rothschild, 2002. Application of the false discovery rate to QTL interval mapping with multiple traits. Genetics 161: 905-914.



McElroy, J.P., D.E. Harry, J.C.M. Dekkers, and S.J. Lamont. 2002. Molecular markers associated with growth and carcass traits in meat-type chickens. 7th World Congress on Genetics Applied to Livestock Production, Montpellier, France, 04:04.



Settar, P., J.C.M. Dekkers, and H.A.M. van der Steen. 2002. Control of QTL frequency in breeding populations. 7th World Congress on Genetics Applied to Livestock Production, Montpellier, France, 23:04.



Stricker, C., M. Schelling, F. Du, I. Hoeschelle, S. A. Fernandez and R. L. Fernando. 2002. A comparison of efficient genotype samplers for complex pedigrees and multiple linked loci. 7th World Congress Genet. Appl. Livest. Prod. 21-12.



Thomsen, H., J.C.M. Dekkers, H.K. Lee, and M.F. Rothschild. 2002. Characterisation of quantitative loci for growth and meat quality in a breed cross in swine. 7th World Congress on Genetics Applied to Livestock Production, Montpellier, France, 15:05.



Totir, L.R., R.L. Fernando, J.C.M. Dekkers, and S.A. Fernandez. 2002. A strategy to improve the computational efficiency of marker assisted genetic evaluation under finite locus models. 7th World Congress on Genetics Applied to Livestock Production, Montpellier, France, 16:02.



Villanueva, B., J.C.M. Dekkers, J.A. Woolliams, and P. Settar. 2002. Maximising genetic gain with QTL information and control of inbreeding. 7th World Congress on Genetics Applied to Livestock Production, Montpellier, France, 22:18.



Wang, J., M. Soller, and J.C.M. Dekkers. 2002. Mapping QTL with selective DNA pooling by least squares interval mapping. 2002. 7th World Congress on Genetics Applied to Livestock Production, Montpellier, France, 21:08.

Minnesota



SOFTWARE RELEVANT TO NCR-204



GMO Risk Assessment Using Net Fitness Components Approach

Available at http://web.ics.purdue.edu/~bmuir/

Author: William Muir





COURSES GIVEN ON STATISTICAL GENETICS



ANS 824: Methods of Quantitative and Molecular Genetics for Livestock. Spring 2003. Credits 1-0, Michigan State University. Guillerme Rosa.



ANS 890/901: Design and analysis of microarray gene expression experiments. Fall 2002. Credits 1-0, Michigan State University. Guillerme Rosa.

08/05/2004

Georgia



Wiggans, G.R., I. Misztal, and C.P. Van Tassell. Calving ease (co)variance components for a sire-maternal grandsire threshold model. J. Dairy Sci. 86:1845?1848. 2003.



Van Tassell, C.P., G.R. Wiggans, and I. Misztal. Implementation of a sire-maternal grandsire model for evaluation of calving ease in the United States. J. Dairy Sci. 86:3366?3373. 2003.



Oseni, S., I. Misztal, S. Tsuruta, and R. Rekaya. Seasonality of days open in US Holsteins. J. Dairy Sci. 86: 3718?3725. 2003.



Nobre, P.R.C., I. Misztal, S. Tsuruta, J.K. Bertrand, L.O.C. Silva, and P.S. Lopes. Analyses of growth curves of Nellore cattle by multiple-trait and random regression models. J. Anim. Sci. 81:918?926. 2003.



Nobre, P.R.C., I. Misztal, S. Tsuruta, J.K. Bertrand, L.O.C. Silva, and P.S. Lopes. Genetic evaluation of growth in Nellore cattle by multiple-trait and random regression models. J. Anim. Sci. 81:927?932. 2003.



Pribyl, J., I. Misztal, J. Pribylová, and K. ?eba. Multiple-breed, multiple-traits evaluation of beef cattle in the Czech Republic. Czech J. Anim. Sci. 48:519?532. 2003.



Tsuruta, S., I. Misztal, T.J. Lawlor, and L. Klei. Estimation of genetic correlations among production, body size, udder, and productive life traits over time in Holsteins (abstract). J. Dairy Sci. 86(Suppl. 1)/J. Anim. Sci. 81(Suppl. 1):38. 2003.



Misztal, I., S. Oseni, and S. Tsuruta. Analyses of heat tolerance for milk in Holsteins using different sources of heat-stress information (abstract). J. Dairy Sci. 86(Suppl. 1)/J. Anim. Sci. 81(Suppl. 1):39. 2003.



Sapp, R.L., R. Rekaya, J.K. Bertrand, I. Misztal, and K.A. Donoghue. Genetic parameter estimates of udder scores in Gelbvieh cattle (abstract). J. Dairy Sci. 86(Suppl. 1)/J. Anim. Sci. 81(Suppl. 1):88. 2003.



Tsuruta, S., I. Misztal, and T. Druet. Comparison of estimation methods for heterogeneous residual variances with random regression models (abstract). J. Dairy Sci. 86(Suppl. 1)/J. Anim. Sci. 81(Suppl. 1):113. 2003.



Legarra, A., I. Misztal, and J. Jamrozik. Plotting covariance functions from random regression models (abstract). J. Dairy Sci. 86(Suppl. 1)/J. Anim. Sci. 81(Suppl. 1):114. 2003.



Oseni, S., and I. Misztal. Seasonality of days open in US Holsteins (abstract). J. Dairy Sci. 86(Suppl. 1)/J. Anim. Sci. 81(Suppl. 1):131. 2003.



Legarra, A., T. Strabel, J.K. Bertrand, and I. Misztal. Setting up the Gelbvieh multiple breed evaluation. J. Dairy Sci. 86(Suppl. 1)/J. Anim. Sci. 81(Suppl.):198. 2003.



Bohmanova, J., I. Misztal, and J. Pribyl. Differences in growth trajectories in seven beef breeds (abstract). J. Dairy Sci. 86(Suppl. 1)/J. Anim. Sci. 81(Suppl. 1):198. 2003.



Michigan State



Rosa, G. J. M. Accounting for genotyping errors in QTL analyses. J. Anim. Sci. 81 (Suppl. 1): 159-160, 2003.



De Leon, N., Coors, J. G., Kaeppler, S. M., Rosa, G. J. M. Genetic control of the number of ears per plant and related morphological traits in the Golden Glow maize population. Maize Genetics Conference Abstracts 45: P181, 2003.



Dreher, B. P., Rosa, G. J. M., Scribner, K. T., Winterstein, S. R., Lopez, V. A., Libants, S. V., Etter, D. R. How many bears, plus or minus: effects of errors associated with non-invasive population size estimation. Abstracts of the Wildlife Society National Meeting. Burlington, Vermont. September, 2003.



Coussens, P. M., Colvin, C. J., Rosa, G. J. M., Laspiur, J. P., Elftman, M. D. Evidence for a novel gene expression program in peripheral blood mononuclear cells from M. paratuberculosis-infected cattle. Infection and Immunity, 71(11): 6487-6498, 2003.



Madsen, S. A., Rosa, G. J. M., Mccandless, E., Coussens, P. M., Burton, J. L. Microarray analysis of gene expression in blood neutrophils of parturient cows. Physiological Genomics, 2003. (on line http://physiolgenomics.physiology.org/papbyrecent.shtml).



Rosa, G. J. M., Tempelman, R. J., Suchyta, S., Madsen, S. A., Burton, J. L., Coussens, P. M. Normalization, replication, and significance tests in cDNA microarray experiments. J. Dairy. Sci. 86 (Suppl. 1): 159, 2003.



Etchebarne, B. E. Silva, L. F. P., Rosa, G. J. M., Coussens, P. M., Weber Nielsen, M. S., Vandehaar, M. J. IGF-I infusion alters gene expression profile of prepuberal bovine mammary parenchyma. J. Dairy. Sci. 86 (Suppl. 1): 165, 2003.



Etchebarne, B. E. Silva, L. F. P., Rosa, G. J. M., Coussens, P. M., Weber Nielsen, M. S., Vandehaar, M. J. Leptin intramammary infusion alters gene expression profile of prepuberal bovine mammary parenchyma. J. Dairy. Sci. 86 (Suppl. 1): 166, 2003.



Chan, P. S., Schlueter, A. E., Coussens, P. M., Rosa, G. J. M., Haut, R. C., Orth, M. W. (2003) Gene Expression Profile of Mechanically Impacted Bovine Articular Cartilage Explants. Proc. International Symposium on Animal Functional Genomics, East Lansing, MI. May 9-11, 2003.



Madsen, S. A., Chang, L.-C., Hickey, M.-C., Coussens, P. M., Rosa, G. J. M., Burton, J. L. (2003) Gene expression profiling and apoptosis phenotyping indicate that parturient steroids promote survival in bovine blood neutrophils. Proc. International Symposium on Animal Functional Genomics, East Lansing, MI. May 9-11, 2003.



Steibel, J. P., Tempelman, R. J., Rosa, G. J. M. Thick-tailed and heteroskedastic linear models for the analysis of cDNA microarray data. Proc. International Symposium on Animal Functional Genomics, East Lansing, MI. May 9-11, 2003.



Hill, E. W., O?gorman, G. M., Gormley, E., Fitzpatrick, T., Rosa, G. J. M., Coussens, P. M., Machugh, D. E. Functional Genomics Analysis of the Bovine Immune Response of In Vitro Co-Culture with Trypanosomes (Trypanosoma brucei). Proc. International Symposium on Animal Functional Genomics, East Lansing, MI. May 9-11, 2003.



Meade, K., Gormley, E., Fitzpatrick, T., Rosa, G. J. M., Coussens, P. M., Machugh, D. E. Analysis of Host Gene Expression in Tuberculosis-Infected Cattle Using In Vitro Stimulation of Peripheral Blood Mononuclear Cells (PBMC) and cDNA Microarrays. Proc. International Symposium on Animal Functional Genomics, East Lansing, MI. May 9-11, 2003.



Etchebarne, B. E., Silva, L. F. P., Rosa, G. J. M., Coussens, P. M., Weber Nielsen, M., Vandehaar, M. J. How do the hormones leptin and IGF-I affect the nutritional regulation of mammary development? Proc. International Symposium on Animal Functional Genomics, East Lansing, MI. May 9-11, 2003.



Rosa, G. J. M., Gianola, D., Padovani, C. R. Robust linear mixed models with normal/independent distributions and Bayesian MCMC implementation. Biometrical Journal, 45(5): 573-590, 2003.



Rosa, G. J. M., Gianola, D., Padovani, C. R. Bayesian longitudinal data analysis with mixed models and thick-tailed distributions using MCMC. Journal of Applied Statistics. (accepted)



Purdue



Cheng, H.W., P. Singleton and W.M. Muir. 2003. Social stress differentially regulates neuroendocrine responses in laying hens: I. Genetic basis of dopamine responses under three different social conditions. Psychoneuroendocrinology 28:597-611.



Cheng, H.W., P. Singleton and W.M. Muir. 2003. Social stress in laying hens: Differential effect of stress on plasma dopamine concentrations and adrenal function in genetically selected chickens. Poult. Sci. 82:192-198.



Muir, W.M.. 2003. Incorporating Molecular Information in Breeding Programs, Applications and Limitations. Chapter 28 p549-562. In Poultry Breeding and Biotechnology Eds. WM Muir and S Aggrey. CABI Press Cambridge MA.



Muir, W.M.. 2003. Indirect Selection for Improvement of Animal Well-Being. Chapter 14, p247-256. In Poultry Breeding and Biotechnology Eds. WM Muir and S Aggrey. CABI Press Cambridge MA.



Muir, W.M., D. Miles, and A.E. Bell, 2003. Long Term Selection Studies In Tribolium Castaneum, Alternative Selection Strategies, And Associated Nature Of Quantitative Genetic Variation. Plant Breeding Reviews (In Press)



Hostetler, HA., SL Peck, and W.M. Muir. 2003 High efficiency production of germ-line transgenic Japanese medaka (Oryzias latipes) by electroporation with direct current-shifted radio frequency pulses. Transgene Research (in press)



Notre Dame



Rider S.D., J.T. Henderson, R.E. Jerome, H.J. Edenberg, J. Romero-Severson, J.P.Ogas. 2003 Coordinate repression of regulators of embryonic identity by pickle during germination in Arabidopsis. The Plant Journal 35 (1): 33-43



Lobo N.F, L.Q. Ton, C.A. Hill, C.Emore, J. Romero-Severson, G.J. Hunt, F.H. Collins. 2003. Genomic Analysis in the sting-2 Quantitative Trait Locus for Defensive Behavior in the Honey Bee, Apis mellifera. Genome Res. 13:2588-2593



Lu H., J. Romero-Severson , R. Bernardo 2003 Genetic basis of heterosis explored by simple sequence repeat markers in a random-mated maize population. Theor Appl Genet 107 (3): 494-502



Feder J.L. J. Roethele, K. Fichak, J. Niebdalski, J. Romero-Severson. 2003 Evidence for inversion polymorphism related to sympatric host race formation in the apple maggot fly, Rhagoletis pomonella. Genetics 163: 939-953



Aldrich P.R., G. R. Parker, C. H. Michler, J. Romero-Severson. 2003 Whole-tree silvic identifications and the microsatellite genetic structure of a red oak species complex in an Indiana old-growth forest. Can J Forest Res 33:2228-2237



Iowa



Chen, P., T.J. Baas, J.C.M. Dekkers, K.J. Koehler and J.W. Mabry J. 2003. Evaluation of strategies for selection for lean growth rate in pigs. J. Anim. Sci. 81:1150-1157



Chen, P., T.J. Baas, J.W. Mabry, K.J. Koehler, and J.C.M. Dekkers. 2003. Genetic parameters and trends for litter traits in U.S. Yorkshire, Duroc, Hampshire, and Landrace pigs. J. Animal Sci. 81:46-53



Ciobanu, D.C., J.W.M. Bastiaansen, S.M. Lonergan, H. Thomsen, J.C.M. Dekkers, G.S. Plastow, and M.F. Rothschild. 2004. New alleles in calpastatin gene are associated with meat quality traits in pigs. J. Animal Sci. (Accepted).



Dekkers, J.C.M. 2004. Commercial application of marker- and gene-assisted selection in livestock: strategies and lessons. J. Anim. Sci. (Accepted subject to minor revision)



Dekkers, J.C.M., and P. Settar. 2003. Long-term Selection with Known Quantitative Trait Loci. Plant Breeding Reviews. Wiley. Plant Breeding Reviews, Volume 24, Part 1, Long Term Selection: Maize. edited by Jules Janick. John Wiley&Sons, Inc. Pp: 311-336 (invited presentation).



Dekkers, J.C.M., and R. Chakraborty. 2004. Optimizing purebred selection for crossbred performance using QTL. Genet. Sel. Evol. (Accepted)



Dorman, K. S., Sinsheimer, J. S. and K. Lange (2004) In the Garden of Branching Processes. SIAM Review. Accepted for publication.



Fernando, R.L. and L.R. Totir. 2003. Incorporating Molecular Informationin Breeding Programs: Methodology. In ?Poultry Breeding andBiotechnology?. CABI Publishing, Cambridge.



Fernando, R.L., D. Nettleton, B.R. Southey, J.C.M. Dekkers, M.F. Rothschild, and M. Soller. 2004. Controlling the proportion of false positives (PFP) in multiple dependent tests. Genetics (In press)



Grapes, L., J.C.M. Dekkers, M.F. Rothschild, and R.L. Fernando. 2004. Comparing linkage disequilibrium-based methods for fine mapping quantitative trait loci. Genetics (Accepted).



Jannink, J.-L., and R.L. Fernando. 2003. On the Metropolis-Hastings acceptance probability to add or drop a QTL in MCMC-based Bayesian analyses. Genetics 165:In Press.



Jannink, J.-L., and X.-L. Wu. 2003. Estimating allelic number and identity in state of QTL in interconnected families. Genet Res 81:133-144.



Kulak, K., J. Wilton, G. Fox and J. Dekkers. 2003. Comparisons of economic values with and without risk for livestock trait improvement Livestock Production Science, 79: 183-191.



Lall, S., Nettleton, D., DeCook, R., Che, P., Howell, S. H. (2004). QTLs affecting adventitious shoot formation in tissue culture and the program of shoot development in Arabidopsis. Acceptance pending revisions from Genetics.



Thomsen, H., J.C.M. Dekkers, H. K. Lee, and M. F. Rothschild 2004. Characterization of quantitative trait loci for growth and meat quality in a cross between commercial breeds of swine J. Anim. Sci. (Accepted subject to minor revision)



Totir, L. R., R.L. Fernando, J.C.M. Dekkers, S.A. Fernandez, and B.Guldbrandtsen. 2003. A comparison of alternative methods to computeconditional genotype probabilities for genetic evaluation with finite locusmodels. Genet. Sol. Evol 35: 1-20.



Totir, L.R., R.L. Fernando, and J.C.M. Dekkers. 2003. Response to selectionby marker assisted BLUP with use of approximate gametic variancecovariance matrices. J. Anim. Sci. 81 (Suppl. 1)



Totir, L.R., R.L. Fernando, J.C.M. Dekkers, S.A. Fernandez, and B. Guldbrandtsen. 2004. Effect of using approximate gametic variance covariance matrices on marker assisted selection by BLUP. Genet. Sel. Evol. 36:29-48.



Totir, L.R., R.L. Fernando, J.C.M. Dekkers, S.A. Fernandez, and B Guldbrandtsen. 2003. A comparison of alternative methods to compute conditional genotype probabilities for genetic evaluation with finite locus models. Genet. Sel. Evol. 35:1-20



Villanueva, B., J.C.M. Dekkers, J.A. Woolliams and P. Settar. 2004. Maximising genetic gain over multiple generations with QTL information and control of inbreeding. Genet. Sel. Evol. (Accepted).



Wagter, L.C., B.A. Mallard, B.N. Wilkie, K.E. Leslie, P.J. Boettcher, and J.C.M. Dekkers. 2003. The Relationship Between Milk Production and Antibody Response to Ovalbumin During the Peripartum Period. J. Dairy Sci. 86: 169-173.



Wu, X.-L., and J.-L. Jannink. 2003. Optimal sampling of a population to determine QTL location, variance, and allelic number. Theor Appl Genet:Accepted.



Zhao, H., M. F. Rothschild, R.L. Fernando, and J.C.M. Dekkers. 2003. Tests of candidate genes in breed cross population for QTL mappping in livestock. Mammalian Genome 14: 472-482



UC Riverside



Yi, N., S. Xu and D. B. Allison. 2003. Bayeisan model choice and search strategies for mapping interacting quantitative trait loci. Genetics 165:867-883.



Yi, N., S. Xu, V. George and D. B. Allison. 2004. Mapping multiple quantitative trait loci for ordinal traits. Behavior Genetics 34:3-14.



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.



Xu, S. 2003. Theoretical basis of the Beavis effect. Genetics 165:2259-2268.



Qu, Y. and S. Xu. 2004. Supervised cluster analysis for microarray data based on multivariate Gaussian mixture. Bioinformatics (in press)



Zhang, Y.?M. and S. Xu. 2004. Mapping quantitative trait loci in F2 incorporating phenotypes of F3 progeny. Genetics (in press)



Mao, Y. and S. Xu. 2004. Mapping QTL for traits measured as percentage. Genetical Research (in press)



Xu, S., C. Xu and Z. Li. 2004. Joint mapping of quantitative trait loci for multiple binary characters. Genetics (accepted, pending revision)



Wang, H., X. Li, G. L. Masinde, S. Mohan, D. J. Baylink, and S. Xu. 2004. Bayesian shrinkage estimation of QTL parameters. Genetics (submitted).



Mao, Y. and S. Xu. 2004. A Monte Carlo algorithm for computing the IBD matrices using incomplete marker information. Heredity (submitted)



Zhang, Y.-M., Y. Mao, C. Xie, H. Smith, L. Luo, and S. Xu. 2004. Mapping QTL using naturally occurring genetic variance among commercial inbred lines. Genetics (submitted).



Illinois



Bohn, M., T. Magg, D. Klein, and A.E. Melchinger. 2003. Breeding early maturing European Dent maize (Zea mays L.) for improved agronomic performance and resistance against the European corn borer (Ostrinia nubilalis Hb.). Maydica 48:239-247.



Magg, T., M. Bohn, D. Klein, and A.E. Melchinger. 2003. Concentration of moniliformin produced by Fusarium species in grains of transgenic Bt maize hybrids compared to their isogenic counterparts and commercial varieties under European corn borer (Ostrinia nubilalis Hb.) pressure. Plant Breeding 122:322-327.



Heckenberger, M., M. Bohn, J.R. van der Voort, J. Peleman, and A.E. Melchinger. 2003. Variation of DNA fingerprints among accessions within maize inbred lines and implications for identification of essentially derived varieties: II. Genetic and technical sources of variation in AFLP data and comparison with SSR data. Molecular Breeding. 12:97-106.



Reif, J.C., A.E. Melchinger, X.C. Xia, M. Warburton, D.A. Hoisington, S.K. Vasal, D. Beck, M. Bohn, and M. Frisch. 2003. Use of SSRs for establishing heterotic groups in subtropical maize. Theor. Appl. Genet. 107:947-957.



Reif, J. C., A. E. Melchinger, X. C. Xia, M. L. Warburton, D. A. Hoisington, S. K. Vasal, G. Srinivasan, M. Bohn, and M. Frisch. 2003. Genetic distance based on simple sequence repeats and heterosis in tropical maize. Crop Sci. 43: 1275-1282.



SOFTWARE RELEVANT TO NCR-204



QXPAK to jointly analyze QTL and polygenic traits in single-and multiple-trait models.

http://nce.ads.uga.edu/~ignacy/newprograms.html

Developed by Ignacy Misztal at U. Georgia

07/07/2005

07/03/2006

Bijma, P. and W. M. Muir 2006. Genetic Analysis And Improvement Of Traits Affected By Interaction Among Individuals. Proc. 8th World Congress of Genetics Applied to Livestock Breeding (In press).

Burton, J. L., Madsen, S. A., Chang, L.-C., Weber, P. S. D., Coussens, P. M., Rosa, G. J. M., Matukumalli, L. K, Sonstegard, T., Smith, T. P. Immunogenomics and the transition dairy cow: physiological insights and future possibilities for improving animal health. ASAS-ADSA-CSAS Joint Annual Meeting, July 24-28, 2005.

Burton, J. L., Madsen, S. A., Chang, L.-C., Weber, P. S. D., Rosa, G. J. M., Matukumalli, L. K, Sonstegard, T. Expression profiles and SNP analysis of genes that regulate neutrophil apoptosis, endothelial adhesion, and extracellular matrix remodeling at parturition in dairy cows. Plant and Animal Genome XIII, p.243, 2005.

Cardoso, F. F., Rosa, G. J. M., Tempelman, R. J. Modelos estruturais de variancia heteroscedastica para inferencia robusta no merito genetico de bovines cruzados. 50th Meeting of the Brazilian Region (International Biometry Society), Londrina  Brazil, July 4-8, 2005.

Cardoso, F. F., Rosa, G. J. M., Tempelman, R. J. Multiple breed genetic inference using heavy-tailed structural models for heterogeneous residual variances. Journal of Animal Science, 83: 1766-1779, 2005.

Chan, P. S., Caron, J. P., Rosa, G. J. M., Orth, M. W. Glucosamine and chondroitin sulfate regulate gene expression and synthesis of nitric oxide and prostaglandin E2 in articular cartilage explants. Osteoarthritis and Cartilage, 13(5): 387-394, 2005.

Chan, P.S., Schlueter, A.E., Coussens, P.M., Rosa, G. J. M., Haut, R.C., Orth, M.W. Gene expression profile of mechanically impacted bovine articular cartilage explants. Journal of Orthopedic Research 23(5): 1146-1151, 2005.

Cheng, H., and W. M. Muir, 2005 The effects of genetic selection for survivability and productivity on chicken physiological homeostasis. Worlds Poultry Science Journal 61: 383-397

DeCook, R., Nettleton, D., Foster, C.M., Wurtele, E. (2006). Identifying differentially expressed genes in unreplicated multiple-treatment microarray timecourse experiments. Computational Statistics and Data Analysis. 50 518-532.

De Leon, N. and Rosa, G. J. M. Optimization of selective phenotyping for QTL mapping. Plant and Animal Genome XIII, P860, p.283, 2005.

De Leon, N., Coors, J. G., Kaeppler, S.M., Rosa, G. J. M. Genetic control of prolificacy and related traits in the Golden Glow Maize Population: I. Phenotypic evaluation. Crop Science, 45: 1361-1369, 2005.

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.

Festucci-Buselli, R. A., A. S. Carvalho-Dias, M. de Oliveira-Andrade, C. Caixeta-Nunes, H. M. LI et al., 2005 Expression of Cyp6g1 and Cyp12d1 in DDT resistant and susceptible strains of Drosophila melanogaster. Insect Molecular Biology 14: 69-77

L. Galina-Pantoja, G. Solano-Aguilar, M. A. Mellencamp, J. Bastiaansen, R. Cabrera, J. K. Lunney. 2006. Relationship between Immune Cell Phenotypes and Pig Growth in a Commercial Farm. Animal Biotechnology (In press).

Gilmour, S. G., Bueno Filho, J. S. S. and Rosa, G. J. M. Design of genetical genomics studies which use two-color microarrays. Workshop on Statistics in Genomics and Proteomics, Monte Estoril, Portugal, October 5-8, 2005, on line: http://wsgp.deio.fc.ul.pt/Abstracts%20Partic/Steven_Gilmour.html

Gomez-Raya L. 2006. Inferring unknown sires genotype at co-dominant DNA markers in half-sib families. (In preparation).

Gomez-Raya L. 2004. Strategies for Marker Assisted Selection in Cattle. Satellite symposium at the ISAG meeting in Tokyo (Japan).

Gomez-Raya L., W. M. Rauw, C. Beattie, Y. Da, D. Smith, O. Ash, and M.S. Amoss. 2006. A Selection Experiment in Sinclair Swine Supports that a Tumor Initiator Locus is involved in Melanoma Susceptibility (manuscript to be submitted).

Heifetz, E. M., J. E. Fulton, N. O'Sullivan, H. Zhao, J. C. M. Dekkers, and M. Soller. 2005. Extent and consistency across generations of linkage disequilibrium in commercial layer chicken breeding populations. Genetics 171: 1173-1181

Heifetz, E. M., J. E. Fulton, N. OSullivan, H. Zhao, J. C. M. Dekkers, and M. Soller. 2005. Marker to marker linkage disequilibrium in commercial chicken breeding populations. Abstract presented at the 2005 Midwest Animal Science meeting, J. Anim. Sci. 83 (Suppl. 1).

Heifetz, E. M., J. E. Fulton, N. OSullivan, M. Soller, and J. C. M. Dekkers. 2005. Interval mapping of QTL for Mareks disease resistance with selective DNA pooling in crosses of commercial layer chicken lines. Abstract presented at the 2005 Midwest Animal Science meeting, J. Anim. Sci. 83 (Suppl. 1).

HA Hostetler, P. Collodi, RH Devlin, and WM Muir. 2005. Improved Phytate Phosphorus Utilization by Japanese Medaka Transgenic for the Aspergillus niger Phytase Gene. Zebrafish 2:19-31

Jia, Z. and S. Xu. 2005. Clustering expressed genes based on their association with a quantitative phenotype. Genetical Research (in press).

J.-J. Kim, J.-J., M.F. Rothschild, J. Beever, S. Rodriguez-Zas, and J.C.M. Dekkers. 2005. Joint analysis of two breed cross populations in pigs to improve detection and characterization of quantitative trait loci. J. Anim Sci. 83: 1229-1240.

Kim, J.J., H.H. Zhao, H. Thomsen, M.F. Rothschild, and J.C.M. Dekkers. 2005. Combined line-cross and half-sib QTL analysis of crosses between outbred lines. Genet. Res. Camb. 85: 235-248.

Kim, J.-J., K.S. Kim, M. Rothschild, J. Beever, S. Rodriguez-Zas, and J.C.M. Dekkers. 2005. Joint analysis of two breed-cross populations in pigs to detect polar overdominance QTL. Proc. Integration of Structural and Functional Genomics conference, Sept. 22-25, Iowa State University.

B.P. Kinghorn, J.W.M. Bastiaansen, H.A.M. van der Steen, N. Deeb, N. Yu, and A.J. Mileham, 2006. Visually-aided interpretation of results from a genome scan. Proc. 8th World Congress of Genetics Applied to Livestock Breeding (In press).

Li, X., R. J. Quigg, J. Zhou, S. Xu, G. Masinde, S. Mohan and D. J. Baylink. 2005. 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 (in press).

McElroy, J.P., J.C.M. Dekkers, J.E. Fulton, N.P. O'Sullivan, M. Soller, E. Lipkin, W. Zhang, K.J. Koehler, S.J. Lamont, and H.H. Cheng. 2005. Microsatellite markers associated with resistance to Mareks disease in commercial layer chickens. Poultry Sci. (Accepted).

Muir, W. M., 2005 Incorporation of competitive effects in forest tree or animal breeding programs. Genetics 170: 1247-1259

Muir, W.M. and P. Bijma. 2006. Incorporation Of Competitive Effects In Breeding Programs For Improved Performance And Animal Well-Being. Proc. 8th World Congress of Genetics Applied to Livestock Breeding (In press)

W.M. Muir, 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, (In Press)

Pedra, J. H. F., R. A. Festucci-Buselli, W. L. Sun, W. M. Muir, M. E. Scharf et al., 2005 Profiling of abundant proteins associated with dichlorodiphenyltrichloroethane resistance in Drosophila melanogaster. Proteomics 5: 258-269

Piyasatian, N., L. R. Totir, R. L. Fernando, and J. C. M. Dekkers. 2005. Marker-assisted selection on multiple QTL in a crossbred population. Abstract presented at the 2005 Midwest Animal Science meeting, J. Anim. Sci. 83 (Suppl. 1).

Ragavendran, A., Muir, W. M., Howard, R. and Rosa, G. J. M. A Monte Carlo approach for risk assessment of transgene invasion. Symposium on Invasive Species: Challenges and Opportunities, MSU Invasive Species Initiative - Michigan State University, May 13, 2005.

Ragavendran, A., Muir, W. M., Howard, R. and Rosa, G. J. M. Probabilistic risk assessment of transgene invasion. V Transgenic Animal Research Conference, Davis, CA, August 14-18, 2005

Rosa, A. J. M., McFarland, D., Vanier, C., Henderson, D., Rosa, G. J. M., Sanborn, A., Dreis, S., Pesall, J. Analysis of gene expression of myogenetic cells having different proliferation rates. Plant and Animal Genome XIII, p.246, 2005

Rosa, G. J. M., Invited talk, Reassessing Design and Analysis of Microarray Experiments Using Mixed Effects Models. Plant and Animal Genome XIII, San Diego, CA, January 15-19, 2005.

Rosa, G. J. M, Invited talk, Microarray: Design & Processing. Short Course Fifth Annual Short Course on Statistical Genetics for Obesity & Nutrition Researchers, Birmingham  AL, May 16-19, 2005.

Rosa, G. J. M, Seminar, Reassessing Design and Analysis of Two-Colour Microarray Experiments Using Mixed Effects Models. Department of Biostatistics and Medical Informatics, UW-Madison, March 11, 2005.

Rosa, G. J. M, Seminar, Animal Functional Genomics Project at MSU. Bovine Genome Round Table, University of Guelph, Toronto, Canada, April 13, 2005.

Rosa, G. J. M, Seminar, Optimal Designs for Genetical Genomics Studies Using Two-Colour Microarrays. Brian W. Kennedy Memorial Colloquium, East Lansing, MI, May 8-10, 2005.

Rosa, G. J. M, Seminar, Optimal Designs for Genetical Genomics Studies Using Two-Colour Microarrays. Department of Animal Sciences, UW-Madison, May 23, 2005.

Rosa, G. J. M, Seminar, Bayesian Inference and Monte Carlo Methods in Fisheries and Wildlife Research. University of Notre Dame, Notre Dame, IN, Nov. 11, 2005.

Rosa, G. J. M, Course, ANS 824: Methods of Quantitative and Molecular Genetics for Livestock, Michigan State University, Spring 2005.

Rosa, G. J. M. Reassessing Design and Analysis of Microarray Experiments Using Mixed Effects Models. Plant and Animal Genome XIII, p.77, 2005.

Rosa, G. J. M., Steibel, J. P., Tempelman, R. J. Linear mixed effects models for dual color microarray intensity ratios. ENAR Spring Meeting, March 20-23, 2005.

Rosa, G. J. M., Steibel, J. P., Tempelman, R. J. Reassessing design and analysis of two-color microarray experiments using mixed effects models. Comparative and Functional Genomics 6: 123-131, 2005.

Scribner, K., Jones, M., Rosa, G. J. M., Gilmore, S. Parentage analysis and estimation of environmental and genetic sources of variation in juvenile sea lamprey body size. Proceedings of the American Fisheries Society Meeting, 2005, on line: http://209.66.94.27/2005Abs/afssearch.cfm.

Steibel, J. P. and Rosa, G. J. M. On reference designs for microarray experiments. Plant and Animal Genome XIII, p.248, 2005.

Steibel, J. P., Poletto, R., Rosa, G. J. M. Statistical analysis of relative quantification of gene expression using real time RT-PCR data. ASAS-ADSA-CSAS Joint Annual Meeting, July 24-28, 2005.

Steibel, J. P. and Rosa, G. J. M. On reference designs for microarray experiments. Statistical Applications in Genetics and Molecular Biology Vol. 4, No. 1, Article 36, 2005. (http://www.bepress.com/sagmb/vol4/iss1/art36)

Steibel, J. P., Suchyta, S., Rosa, G. J. M. Tackling high variability in gene expression studies. Genomics & Proteomics 5(1): 30-32, 2005.

Varona L., L. Gomez-Raya, W.M. Rauw and J.L. Noguera, 2005. A simulation study on the detection of causal mutations from F2 experiments. Journal of Animal Breeding and Genetics 122:30-36.

Varona L., L. Gomez-Raya, W.M. Rauw, C. Ovilo, A. Clop and J.L. Noguera, 2005. The value of prior information for detection of QTL affecting longitudinal traits: an example using Von Bertallanffy growth function. Journal of Animal Breeding and Genetics 122:37-48

Verhoeven, K.J.F., J.-L. Jannink, and L.M. McIntyre. 2006. Using mating designs to uncover QTL and the genetic architecture of complex traits. Heredity 96:139-149.

Wang, D., Nettleton, D. (2006). Identifying genes associated with a quantitative trait or quantitative trait locus via selective transcriptional profiling. Biometrics. In press.

Yang, R., N. Yi and S. Xu. 2006. Box-Cox Transformation for QTL Mapping, Genetica (in press).

Zhang, W., A. Carriquiry, D. Nettleton, and J. Dekkers. 2005. The effect of pooling mRNA in microarray experiments on power. Proc. Integration of Structural and Functional Genomics conference, Sept. 22-25, Iowa State University.

Zhang, Y. M. and S. Xu. 2005a. A penalized maximum likelihood method for estimating epistatic effects of QTL. Heredity 95:96-104.

Zhang, Y. M. and S. Xu. 2005b. Advanced statistical methods for detecting multiple quantitative trait loci. Recent Research Development in Genetics and Breeding 2:1-23.

Zhao, H., H. Gilbert, and J. C. M. Dekkers. 2005 Discriminant analysis for multitrait quantitative trait loci detection in a Berkshire x Yorkshire F2 population. Abstract presented at the 2005 Midwest Animal Science meeting, J. Anim. Sci. 83 (Suppl. 1).

Zhao, H., Nettleton, D., Soller, M., Dekkers, J.C.M. (2005). Evaluation of linkage disequilibrium measures between multi-allelic markers as predictors of linkage disequilibrium between markers and QTL. Genetical Research. 86 77-87.

Zhao, H.H., R.L. Fernando, and J.C.M. Dekkers. 2005. Power and precision of linkage disequilibrium mapping of quantitative trait loci in outbred populations. Proc. Integration of Structural and Functional Genomics conference, Sept. 22-25, Iowa State University.

01/08/2008

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 Mareks 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 Tukeys 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: 455464

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.