• Albrecht, T., Wimmer, V., Auinger, H.J., Erbe, M., Knaak, C., Ouzunova, M., Simianer, H. and Schön, C.C.(2011): Genome-based prediction of testcross values in maize. Theoretical and Apllied Genetics, 123, 2, 339-350.
• Cuc, N.T.K., Weigend, S, Tieu, H V and Simianer, H (2011):Conservation priorities and optimum allocation of conservation funds for Vietnamese local chicken breeds. J. Anim. Breed. Genet., 1–11.
• Di, R, Vahidi, F, Ma, Y, He, X, Zhao, Q, Han, Q, Guan, W, Chu, M, Sun, W and Pu, Y (2010): Microsatellite analysis revealed genetic diversity and population structure among Chinese cashmere goats. Animal Genetics, doi:10.1111/j.1365-2052.2010.02072.x
• Erbe, M, Ytournel,F, Pimentel, E, Sharifi,A R and Simianer, H (2011): Power and robustness of three whole genome association mapping approaches in selected populations. J. Anim. Breed. Genet., 1–12.
• Edwards, C J, Ginja, C, Kantanen, J, Pérez-Pardal, L, Tresset, A, Stock, F, European Cattle Genetic Diversity Consortium, Gama, L T, Penedo, M C T, Bradley, D G, Lenstra and J A, Nijman, I J (2011): Dual Origins of Dairy Cattle Farming – Evidence from a Comprehensive Survey of European Y-Chromosomal Variation. PLoS ONE 6, 1, e15922.
• Gärke, C.,Ytournel, F., Bed’hom, B., Gut, I., Lathrop, M., Weigend, S. and Simianer, H. (2011): Comparison of SNPs and microsatellites for assessing the genetic structure of chicken populations. Anim. Genet. doi:10.1111/j.1365-2052.2011.02284.x
• Hasler, H, Flury, C, Menet, S, Haase, B, Leeb, T, Simianer, H, Poncet, P A, Rieder, S (2011): Genetic diversity in an indigenous horse breed – implications for mating strategies and the control of future inbreeding. J. Anim. Breed. Genet., 128, 394–406.
• Ober, U., Erbe, M., Long, N., Porcu, E., Schlather, M. and Simianer, H. (2011): Predicting Genetic Values: a Kernel-Based Best Linear Unbiased Prediction with Genomic Data. Genetics, 188, 695-708.
• Pimentel, E, Bauersachs, S, Tietze, M, Simianer, H, Tetens, J, Thaller, G, Reinhardt, F, Wolf, E and König, S (2010): Exploration of relationships between production and fertility traits in dairy cattle via association studies of SNPs within candidate genes derived by expression profiling. Animal Genetics, doi:10.1111/j.1365-2052.2010.02148.x.
• Pimentel, E, Erbe, M, Koenig, S and Simianer, H (2011): Genome partitioning of genetic variation for milk production and composition traits in Holstein cattle. Front. Gene. 2,19, doi: 10.3389/fgene.2011.00019.
• Qanbari, S., Gianola, D., Hayes, B., Schenkel, F., Miller, S., Moore, S., Thaller, G. and Simianer, H. (2011): Application of Site and Haplotype-Frequency Based Approaches for Detecting Selection Signatures in Cattle. BMC Genomics, 12, 318.
• Schierenbeck, S., Reinhardt, F., Reents, R., Simianer, H. and König, S. (2011): Identification of informative cooperator herds for progeny testing based on yield deviations. J. Dairy Sci., 94, 4, 2071-2082
• Schierenbeck, S., Pimentel, E.C.G., Tietze, M., Körte, J., Reinhardt, F., Reents, R., Simianer, H. and König, S. (2011): Controlling inbreeding and maximizing genetic gain using semi-definite programming with pedigree-based and enomic relationships. J. Dairy Sci., 94, 12, 6143-6152.
• Wensch-Dorendorf, M., Yin, T., Swalve, H.H. and König, S. (2011): Optimal strategies for the use of genomic selection in dairy cattle breeding programs. J Dairy Sci, 94, 8, 4140-4151.
• Willam, A and Simianer, H (2011): Tierzucht. Grundwissen Bachelor, Verlag Eugen Ulmer, Stuttgart
  
• Zhang, G., Vahidi, S.M.F.,Ma, Y.H. and Han, J.L. (2011): Limited polymorphisms of two Y-chromosomal SNPs in Chinese and Iranian sheep. Animal Genetics, doi:10.1111/j.1365-2052.2011.02269.x.