Allison, D. B., Visscher, P. M., Rosa, G. J. M., Amos, C. I.

Statistical genetics & statistical genomics: Where biology, epistemology, statistics, and computation collide. Computational Statistics and Data Analysis 53: 1531-1534, 2009.

Cardoso, F. F., Rosa, G. J. M., Tempelman, R. J. and Torres Jr., R. A. A. (2009)

Hierarchical Bayesian models for robust estimation and censored data analysis in animal breeding. Braz. J. Anim. Sci. 38: 72-80.

David, I., L. Bodin, D. Gianola, A. Legarra, E. Manfredi and C. Robert-Granie. 2009.

Product versus additive threshold models for analysis of reproduction outcomes in animal genetics. Journal of Animal Science 87, 2510-2518.

de los Campos, G., D. Gianola and G. J. M. Rosa. 2009.

Reproducing kernel Hilbert spaces regression: a general framework for genetic evaluation. Journal of Animal Science 87, 1883-1887.

de los Campos, G., H. Naya, D. Gianola, J. Crossa, A. Legarra, E. Manfredi, K. Weigel, and J. M. Cotes. 2009.

Predicting quantitative traits with regression models for dense molecular markers and pedigrees. Genetics 182:375-385.

Dreher, B. P., Rosa, G. J. M., Lukacs, P. M., Scribner, K. T., Winterstein, S. R.

Subsampling non-invasively collected hair samples affects accuracy and precision of DNA-based population estimates. Journal of Wildlife Management 73(7): 1184-1188, 2009.

Driver AForni, S., D. Gianola, G. J. M. Rosa and G. de los Campos. 2009.

A dynamic linear model for genetic analysis of longitudinal traits. Journal of Animal Science 87, 3845-3853.M, Huang W, Gajic S, Monson RL, Rosa GJM, Khatib H (2009)

Effects of the Progesterone Receptor Variants on Fertility Traits in Cattle. J Dairy Sci. 92(8):4082-4085.

Forni, S., Gianola, D. and Rosa, G. J. M.

Predictive ability and covariance parameters of dynamic linear models for analysis of longitudinal traits. J. Anim. Sci. 87: 3854-3864, 2009.

Gianola, D., G. de los Campos, W. G. Hill, E. Manfredi and R. L. Fernando. 2009.

Additive genetic variability and the Bayesian alphabet. Genetics 187, 347-363.

Gonzalez-Recio, O., D. Gianola, G J. M. Rosa, K. A. Weigel and A. Kranis. 2009.

Genome-assisted prediction of a quantitative trait measured in parents and progeny: application to food conversion rate in chickens. Genetics, Selection, Evolution 41, 3-13.

Heringstad, B., Xiao-Lin Wu and D. Gianola. 2009.

Inferring Relationships between Health and Fertility in Norwegian Red Cows using Recursive Models. Journal of Dairy Scienc 92, 1778-1784.

Huang W, Mikheil D, Bindrin A, Khatib H (2009)

A SNP in bovine placental lactogen and its interactions with hormone receptors are associated with fertility traits in cattle. Animal 3: 1743-1745.

Khatib and collaborators. The Bovine Genome Sequencing and Analysis Consortium (2009)

The Genome sequence of taurine cattle: A window to ruminant biology and evolution. Science 324(5926):522-528.

Khatib H, Huang W, Mikheil D, Schutzkus V, and Monson RL (2009)

Effects of signal transducer and activator of transcription (STAT) genes STAT1 and STAT3 genotypic combinations on fertilization and embryonic survival rates in Holstein cattle. J. Dairy Sci. 92:6186-6191.

Khatib H, Huang W, Wang X, Tran AH, Bindrim AB, Schutzkus V, Monson RL, Yandell BS (2009).

Single Gene and Gene Interaction Effects on Fertilization and Embryonic Survival Rates in Cattle. J Dairy Sci. 92, 2238-2247.

Khatib H, Maltecca C, Monson RL, Schutzkus V, and Rutledge JJ (2009)

Monoallelic maternal expression of STAT5A affects embryonic survival in cattle. BMC Genetics 10:13.

Kim, E. S., X. Shi, O. Cobanoglu, K. Weigel, P. J. Berger, and B. W. Kirkpatrick. 2009.

Refined mapping of twinning rate QTL on bovine chromosome 5 and analysis of IGF1 as a positional candidate gene. Journal of Animal Science 87:835-843.

Long, N., D. Gianola, G. J. M. Rosa, K. A. Weigel, and S. Avendaño. 2009.

Comparison of classification methods for detecting associations between SNPs and chick mortality. Genetics, Selection, and Evolution 41:18.

López de Maturana, E., D. Gianola, G. J.M. Rosa and Kent A. Weigel. 2009.

Predictive Ability of Models for Calving Difficulty in US Holsteins. Journal of Animal Breeding and Genetics 126, 179-188.

López de Maturana, E., X. L. Wu, D. Gianola, K. A. Weigel, and G. J. M. Rosa. 2009.

Exploring biological relationships between calving traits in primiparous cattle with a Bayesian recursive model. Genetics 181:277-287.

Maltecca, C., K. A. Weigel, H. Khatib, M. Cowan, and A. Bagnato. 2009.

Whole genome scan for quantitative trait loci for birth weight, gestation length, and passive immune transfer in a Holstein x Jersey crossbred population. Animal Genetics (DOI: 10.1111/j.1365-2052.2008.01793).

Maturana, E. L., Gianola, D., Rosa, G. J. M. and Weigel, K. A.

Predictive ability of models for calving difficulty in US Holsteins. Journal of Animal Breeding and Genetics 126(3): 179-188, 2009.

Maturana, E. L., Wu, X.-L., Gianola, D., Weigel, K. A. and Rosa, G. J. M.

Exploring biological relationships between calving traits in primiparous cattle with a Bayesian recursive model. Genetics 181: 277-287, 2009.

Muir, W. M., Rosa, G. J. M., Pittendrigh, B. R., Xu, S., Rider, S. D., Fountain, M. and Ogas, J.

A mixture model approach for the analysis of small exploratory microarray experiments. Computational Statistics and Data Analysis 53: 1566-1576,

Norman, H. D., J. R. Wright, and K. A. Weigel. 2009.

Our Industry Today: Alternatives for examining daughter performance of progeny test bulls between official evaluations. Journal of Dairy Science 92:2348-2355.

Pérez-Cabal, M. A., de los Campos, G., Vazquez, A. I., Gianola, D., Rosa, G. J. M., Weigel, K. A. and Alenda, R.

Genetic evaluation of susceptibility to clinical mastitis in Spanish Holstein cows. J. Dairy Sci. 92: 3472-3480, 2009.

Quintans, G., A. Vazquez, and K. A. Weigel. 2009.

Effect of suckling restriction with nose plates and premature weaning on postpartum anoestrous interval in primiparous cows under range conditions. Animal Reproduction Science 116:10-18.

Steibel, J. P., Rosa, G. J. M. and Tempelman, R. J.

Optimizing design of two-stage experiments for transcriptional profiling. Computational Statistics and Data Analysis 53: 1639-1649, 2009.

Vazquez, A. I., D. Gianola, D. Bates, K. A. Weigel and B. Heringstad. 2009.

Assessment of Poisson, logit and linear models for genetic analysis of clinical mastitis in Norwegian Red cows. Journal of Dairy Science 92, 739-748.

Vazquez, A., D. Bates, D. Gianola, K. A. Weigel, and G. J. M. Rosa. 2009.

Technical note: An R package for fitting generalized mixed linear models in animal breeding. Journal of Animal Science doi:10.2527/jas.2009-1952.

Vazquez, A.I., K. A. Weigel, D. Gianola, D. Bates, M. A. Perez-Cabal, G. J. M. Rosa and Y. M. Chang. 2009.

Poisson versus Threshold Models for Genetic Analysis of Clinical Mastitis in US Holsteins. Journal of Dairy Science 92, 5239-5247.

Wang X, Schutzkus V, Huang W, Rosa GJM, and Khatib H (2009)

Analysis of segregation distortion and association of the bovine FGF2 with fertilization rate and early embryonic survival. Animal Genetics 40: 722-728.

Weigel K A, Khatib H, Cowan M and Bagnato A (2009)

Whole-genome scan for quantitative trait loci associated with birth weight, gestation length and passive immune transfer in a Holstein Jersey crossbred population. Animal Genetics 40(1):27-34.

Weigel, K. A., de los Campos, G., González-Recio, O., Naya, H., Wu, X. L., Long, N., Rosa, G. J. M. and Gianola, D.

Predictive ability of direct genomic values for lifetime net merit of Holstein sires using selected subsets of single nucleotide polymorphism markers. J. Dairy Sci. 92 :5248-5257, 2009.

Weigel, K. A., G. de los Campos, O. González-Recio, H. Naya, X. L. Wu, N. Long, G. J. M. Rosa, and D. Gianola. 2009.

Predictive ability of direct genomic values for lifetime net merit of Holstein sires using selected subsets of single nucleotide polymorphism markers. Journal of Dairy Science 92:5248-5257.

Wu, X. L., D. Gianola and K. Weigel. 2009.

Bayesian joint mapping of quantitative trait loci for Gaussian and categorical characters in line crosses. Genetica 135, 367-377.

Cardoso, F. F., Rosa, G. J. M., Steibel, J. P., Ernst, C. W., Bates, R. O. and Tempelman, R. J. (2008)

Selective transcriptional profiling and data analysis strategies for eQTL mapping in outbred F2 populations. Genetics 180(3): 1679-1690.

Edwards, D. B., Ernst, C. W., Tempelman, R. J., Rosa, G. J. M., Raney, N. E., Hoge, M. D., Bates, R. O. (2008)

QTL mapping in an F2 Duroc x Pietrain resource population: I. Growth traits. Journal of Animal Science, 86: 241-253.

Gianola, D., and G. de los Campos. 2008.

Inferring genetic values for quantitative traits non-parametrically. Genetics Research 90, 525-540.

Gianola, D., and J. B. C. H. M. van Kaam. 2008.

Reproducing Kernel Hilbert Spaces Regression Methods for Genomic Assisted Prediction of Quantitative traits. Genetics 178, 2289-2303.

Gonzalez-Recio, O., D. Gianola, N. Long, K. A. Weigel, G. J. M. Rosa, and S. Avendaño. 2008.

Non-parametric methods for incorporating genomic information into genetic evaluations: An application to mortality in broilers. Genetics 178:2305-2313.

Heringstad, B., Y. M. Chang, D. Gianola and O. Osteras. 2008.

Genetic analysis of respiratory disease in Norwegian Red calves. Journal of Dairy Science 91, 367-370.

Huang W, Maltecca C, Khatib H (2008)

A proline-to-histidine mutation in POU1F1 is associated with production traits in dairy cattle. Animal Genetics, 39, 554-557.

Khatib H and Kim E (2008)

The distribution and conservation of retrotransposable elements in cattle. Epigenetics 3(2).

Khatib H, Maltecca C, Monson RL, Schutzkus V, Wang X, Rutledge JJ (2008)

The fibroblast growth factor 2 gene is associated with embryonic mortality in cattle. J Anim Sci. 86(9):2063-7.

Khatib H, Monson RL, Schutzkus V, Kohl DM, Rosa GJ, Rutledge JJ (2008)

Mutations in the STAT5A gene are associated with embryonic survival and milk composition in cattle. J Dairy Sci. 91(2):784-93.

Khatib, H., Monson, R. L., Schutzkus, V., Kohl, D. M., Rosa, G. J. M. and Rutledge, J. J. (2008)

Mutations in the STAT5A gene are associated with embryo survival and milk composition in cattle. Journal of Dairy Science, 91: 784-793.

König, S., X. L. Wu, D. Gianola. B. Heringstad and H. Simianer. 2008.

Exploration of relationships between claw disorders and milk yield in Holstein cows via recursive linear and threshold models. Journal of Dairy Science 91, 395-406.

König, S., Y. M. Chang, U. U. v. Borstel, D. Gianola, and H. Simianer. 2008.

Genetic and Phenotypic Relationships Among Milk Urea Nitrogen, Fertility, and Milk Yield in Holstein Cows. Journal of Dairy Science 91, 4372-4382.

Long, N., D. Gianola, G. J. M. Rosa, K. A. Weigel, and S. Avendaño. 2008.

Marker-assisted assessment of genotype by environment interaction: A case study of single nucleotide polymorphism-mortality association in broilers in two hygiene environments. Journal of Animal Science 86:3358-3366.

López de Maturana, E., Xiao-Lin Wu, D. Gianola, K. A. Weigel and G. J.M. Rosa. 2009.

Exploring biological relationships between calving traits in primiparous cattle with a Bayesian recursive model. Genetics 18, 277-287.

Naya, H., J. I. Urioste, Y-Mei Chang, M. Rodrigues-Motta, R. Kremer and D. Gianola. 2008.

A comparison between Poisson and zero-inflated Poisson regression models with an application to number of black spots in Corriedale sheep. Genetics, Selection, Evolution 40, 379-394.

Santellano-Estrada, E., C. M. Becerril-Pérez, J. de Alba, Y. M. Chang, D. Gianola, G. Torres-Hernández, and R. Ramírez-Valverde. 2008.

Inferring Genetic Parameters of Lactation in Tropical Milking Criollo Cattle with Random Regression Test-Day Models. Journal of Dairy Science 91, 4393-4400.

Wang X, Maltecca C, Tal-Stein R, Lipkin E, Khatib H (2008)

Association of bovine fibroblast growth factor 2 (FGF2) gene with milk fat and productive life: an example of the ability of the candidate pathway strategy to identify quantitative trait genes. J Dairy Sci. 91(6):2475-80.

Wu, X. L., D. Gianola, and K. A. Weigel. 2008.

Bayesian joint mapping of quantitative trait loci for Gaussian and categorical characters in line crosses. Genetica (DOI 10.1007/s10709-008-9283-5).

X-Lin Wu, B. Heringstad and D. Gianola.

Exploration of lagged relationships between mastitis and milk yield in dairy cows using a Bayesian structural equation Gaussian-threshold model. 2008. Genetics, Selection, Evolution 40, 333- 357.

X-Lin Wu, D. Gianola and K. A. Weigel. 2008.

Bayesian joint mapping of quantitative trait loci for Gaussian and categorical characters in line crosses. Genetica (on line http://www.springerlink.com/content/0v12485r502228t7/).

Yooko, M. J. I., Ortelan, A. A., Sarmento, J. L. R., Albuquerque, L. G., Resende, K. T., Reis, R. A., Teixeira, I. A. M. A. and Rosa, G. J. M. (2008)

Estudo de caracteristicas de crescimento e de carcaca medidas por ultra-sonografia em novilhas de dois gruppos geneticos. Ciencia Animal Brasileira, 9(4): 948-957.

Zaitoun I, Khatib H (2008)

Comparative genomic imprinting and expression analysis of six cattle genes. J Anim Sci. 86(1):25-32.

Beyhan, Z., Ross, P. J., Iager, A. E., Kocabas, A. M., Cunniff, K., Rosa, G. J. M., Cibelli, J. B.

Transcriptional reprogramming of somatic cell nuclei during preimplantation development of cloned bovine embryos. Developmental Biology 305: 637-649, 2007.

Boettcher, P. J., D. Caraviello and D. Gianola. 2007.

Genetic analysis of somatic cell Scores of Holstein cows with a Bayesian mixture model. Journal of Dairy Science 90, 435-443.

Cardoso, F. F., Rosa, G. J. M., Tempelman, R. J.

Accounting for outliers and heteroskedasticity on multibreed genetic evaluations of post-weaning gain of Hereford-Nelore Cattle. Journal of Animal Science 85: 909-918, 2007.

Cezar, G. G., Quam, J. A., Smith, A. M., Rosa, G. J. M., Piekarczyk, M. S., Barron, T. L., Brown, J. F., Harms, A. C., Berggren, T. W., Gage, F. Muotri, A.

Identification of small molecules from human embryonic stem cells using metabolomics. Stem Cells and Development 16(6), 1:14, 2007.

Chang, D. Gianola, Y. M., B. Heringstad and G. Klemetsdal. 2006.

A periodic analysis of longitudinal binary responses: a case study of clinical mastitis in Norwegian Red cows. Genetics, Selection, Evolution 39, 249-265.

Chang, Y. M., O. Gonzalez-Recio, K. A. Weigel, and P. M. Fricke. 2007.

Genetic analysis of 21-day pregnancy rate in US Holsteins using an ordinal censored threshold model with unknown voluntary waiting period. Journal of Dairy Science 90:1987-1997.

De los Campos, G., and D. Gianola. 2007.

Factor analysis models for structuring covariance matrices of additive genetic effects: a Bayesian implementation. Genetics, Selection, Evolution 39, 481-494.

Dreher, B. P, Winterstein, S. R., Scribner, K. T., Lukacs, P. M., Etter, D. R., Rosa, G. J. M., Lopez, V. A., Libants, S. and Filcek, K. R.

Non-invasive estimation of black bear abundance in Michigan incorporating genotyping errors and harvest bear. Journal of Wildlife Management, 71(8): 2684-2693, 2007.

Gianola, D., and D. Sorensen. 2007.

Inferring fixed effects in a mixed linear model from an integrated likelihood. Acta Agriculturae Scandinavica Section A 57, 183-191.

Gianola, D., P. J. Boettcher, J. Ødegård and B. Heringstad. 2007.

Mixture models in quantitative genetics and applications to animal breeding. Revista Brasileira de Zootecnia 36, 171-183.

Gulisija, D., D. Gianola, and K. A. Weigel. 2007.

Nonparametric analysis of the impact of inbreeding depression on production in Jersey cows. Journal of Dairy Science 90:493-500.

Heringstad, B., Y. M. Chang, M. Svendsen and D. Gianola. 2007.

Genetic Analysis of calving difficulty and stillbirth in Norwegian Red Cows. Journal of Dairy Science Dairy Sci. 90, 3500-3507.

Khatib H (2007) Is it genomic imprinting or preferential expression? BioEssays 29, 1022-1028.

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. Anim Genet. 38, 308-310.

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. J Dairy Sci 90, 2427-2433.

Khatib H, Zaitoun I and Kim E (2007)

Comparative analysis of sequence characteristics of imprinted genes in human, mouse, and cattle. Mamm Genome 18, 538-547.

Khatib H, Zaitoun I, Chang YM, Maltecca C, and Boettcher P (2007)

Evaluation of Association Between Thyroglobulin Gene Variants and Milk Production Traits in Dairy Cattle. J. Anim. Breed. Genet. 124, 26-28

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 Holstein Dairy Cattle. J Dairy Sci 90, 2966-2970.

Khatib, H., G. Rosa, K. Weigel, F. Schiavini, E. Santus, and A. Bagnato. 2007.

Additional support for an association between OLR1 and milk fat traits in cattle. Animal Genetics 38:308-310.

Khatib, H., Schutzkus, V., Chang, Y. M. and Rosa, G. J. M.

Pattern of expression of the uterine milk protein gene and its association with productive life in dairy cattle. Journal of Dairy Science 90: 2427-2433, 2007.

Khatib, H., Zaitoun, I., Wiebelhaus-Finger, J., Chang, Y. M. and Rosa, G. J. M.

The association of bovine PPARGC1A and OPN genes with milk composition in two independent Holstein cattle populations. Journal of Dairy Science 90: 2966-2970, 2007.

Long, N., D. Gianola, G. J. M. Rosa, K. A. Weigel and S. Avendaño. 2007.

Machine learning procedure for selecting SNPs in genomic selection: application to early mortality in broilers. Journal of Animal Breeding and Genetics 124, 377-389.

Maltecca, C., A. Rossoni, C. Nicoletti, E. Santus, K. A. Weigel, and A. Bagnato. 2007.

Estimation of genetic parameters for perinatal suckling behavior of Italian Brown Swiss calves. Journal of Dairy Science 90:4814-4820.

Ogden, E. R., and K. A. Weigel. 2007.

Can you shrink wrap a cow? Protections available for the intellectual property of the animal breeding industry. Animal Genetics 38:647-654.

Pereira, I. G., Oliveira, H. N. and Rosa, G. J. M.

Simulation study of linear mixed models with contaminated normal distribution in animal breeding. Brazilian Journal of Animal Science 36(5): 1304-1315, 2007.

Rodrigues-Motta, M., D. Gianola, B. Heringstad, G. Rosa and Y. M. Chang. 2007.

A zero-inflated Poisson model for genetic analysis of number of mastitis cases in Norwegian Red cows. Journal of Dairy Science 90, 5306-5315.

Rosa, G. J. M.

Experimental design in genetical genomics. Brazilian Journal of Animal Science 36(SE): 211-218, 2007.

Rosa, G. J. M., Rocha, L. B and Furlan L. R.

Microarray gene expression studies: experimental design, statistical data analysis, and applications in livestock research. Brazilian Journal of Animal Science 36(SE): 185-210, 2007.

Smith, G. W. and Rosa, G. J. M.

Interpretation of microarray data: Trudging out of the abyss towards elucidation of biological significance. Journal of Animal Science 85(E. Suppl): E20-E23, 2007.

Urioste, J.I, Y. M. Chang, H. Naya and D. Gianola. 2007.

Genetic variability of calving success in Aberdeen Angus cows under extensive recording. Animal Science 1, 1081-1088.

Van Melis, M. H., Eler, J. P., Oliveira, H. N., Rosa, G. J. M., Silva, J. A. II V., Ferraz, J. B. S. and Pereira, E.

Study of stayability in Nellore cows using a threshold model. Journal of Animal Science 85: 1780-1786, 2007.

Wu X. L. , B. Heringstad, Y. M. Chang, G. de los Campos and D. Gianola. 2007.

Inferring relationships between somatic cell score and milk yield using simultaneous and recursive models. Journal of Dairy Science 90, 3508-3521.

Bagnato A, Khatib H, Ajmone-Marsan P, Schiavini F, Lipkin E (2007)

Achievements of research in the field of molecular genetics - Recent advance and perspectives in cattle genome discovery and in application of genomic selection to breeding plans. In WAAP book of the year 2006, Animal production and Animal Science Worldwide. Wageningen Academic Publishers, The-Netherlands

D. Gianola. 2007.

Inferences from mixed models in quantitative genetics. Pp. 678-717 In: "Handbook of Statistical Genetics". Third Edition. D. J. Balding, M. Bishop and C. Cannings, Eds. John Wiley & Sons. (invited)