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*: General methodology paper.

28. Wu, X., S. Scott, J.L. Propheter, W.L. Rooney, J. Yu, and D. Wang. 2009. Features and fermentation performance of sweet sorghum juice after harvest. Industrial Crops and Products (in press).

27. Wang, M.L., C. Zhu, N.A. Barkley, Z. Chen, J.E. Erpelding, S.C. Murray, M.R. Tuinstra, T. Tesso, G.A. Pederson, J. Yu. 2009. Genetic diversity and population structure analysis of accessions in the US historic sweet sorghum collection. Theoretical and Applied Genetics 102:13-23.

26. Buckler, E.S., J.B. Holland, P. Bradbury, C. Acharya, P.Brown, C. Browne, M. Eller, E. Ersoz, S. Flint-Garcia, A. Garcia, J. Glaubitz, M.M. Goodman, C. Harjes, K. Guill, D.E. Kroon, S. Larsson, N. Lepak, H. Li, S.E. Mitchell, G. Pressoir, J.A. Peiffer, M.O. Rosas, T.R. Rocheford, M.C. Romay, S. Romero, S. Salvo, H.S. da Villeda, Q. Sun, F. Tian, N. Upadyayula, D. Ware, H. Yates, J. Yu, Z. Zhang, S. Kresovich, and M.M. Mullen 2009. The genetic architecture of maize flowering time. Science 325:714-718.

25*. Zhu, C., and J. Yu. 2009. Nonmetric multidimensional scaling corrects for population structure in whole genome association studies. Genetics 182:875-888.

24. Yu, J. 2009. Realizing the potential of ultrahigh throughput genomic technologies in plant breeding. The Plant Genome 2:2.

23*. Yu, J., Z. Zhang, C. Zhu, D. Tabanao, G. Pressoir, M.R. Tuinstra, S. Kresovich, R.J. Todhunter, and E.S. Buckler. 2009. Simulation appraisal of the adequacy of number of background markers for relationship estimation in association mapping. The Plant Genome 2:63-77.

22. Ochanda, N., J. Yu, P.J. Bramel, A. Menkir, M.R. Tuinstra, and M.D. Witt. 2009. Selection before backcross during exotic germplasm introgression. Field Crops Research 112:37–42.

21. Sorrells, M.E., and J. Yu. 2009. Linkage disequilibrium and association mapping in the Triticeae. In C. Feuillet and G.J. Muehlbauer (ed.) Genetics and Genomics of the Triticeae, Plant Genetics/Genomics, Vol 6, 655-684. Springer Verlag.

20. Ersoz, E., J. Yu, and E.S. Buckler. 2009. Applications of linkage disequilibrium and association mapping in maize. In A.L. Kriz and B.A. Larkins (ed.) Molecular Genetic Approaches to Maize Improvement, Biotechnology in Agriculture and Forestry, Vol 63, 173-195. Springer Verlag.

19. Zhu, C., M. Gore, E.S. Buckler, and J. Yu. 2008. Status and prospects of association mapping in plants. The Plant Genome 1:5-20.

18*. Yu, J., J.B. Holland, M.D. McMullen, and E.S. Buckler. 2008. Genetic design and statistical power of nested association mapping in maize. Genetics 138:539-551.

17. Ersoz, E., J. Yu, and E.S. Buckler. 2008. Applications of linkage disequilibrium and association mapping in crop plants. In R. Varshney and R. Tuberosa (ed.) Genomics-Assisted Crop Improvement: Vol 1: Genomics Approaches and Platforms, 97-120. Springer Verlag.

16. Weber, A., R.M. Clark, L. Vaughn, J.D.J. Sánchez-Gonzalez, J. Yu, B.S. Yandell, P. Bradbury, and J.F. Doebley. 2007. Major regulatory genes in maize contribute to standing variation in Teosinte (Zea mays ssp. parviglumis). Genetics 177:2349–2359.

15*. Tabanao, D.A., J. Yu, and R. Bernardo. 2007. Multilocus epistasis, linkage, and genetic variance in breeding populations with few parents. Theoretical and Applied Genetics 115:335-342.

14*. Bernardo, R, and J. Yu. 2007. Prospects for genomewide selection for quantitative traits in maize. Crop Science 47:1082-1090.

13. Yang, X.H., J.B. Yan, Y.P. Zheng, J. Yu, and J.S. Li. 2007. Reviews of association analysis of quantitative traits in plants. Acta Agronomica Sinica 33:523-530.

12*. Stich, B., J. Yu, A.E. Melchinger, H.-P. Piepho, F. Utz, H.P. Maurer, and E.S. Buckler. 2007. Power to detect high-order epistatic interactions in a metabolic pathway using a new mapping strategy. Genetics 176:563-570.

11*. Yu, J., G. Pressoir, W.H. Briggs, I. Vroh Bi, M. Yamasaki, J.F. Doebley, M.D. McMullen, B.S. Gaut, D. Nielsen, J.B. Holland, S. Kresovich, and E.S. Buckler. 2006. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nature Genetics 38:203-208.

10*. Arbelbide, M., J. Yu, and R. Bernardo. 2006. Power of mixed-model QTL mapping from phenotypic, pedigree, and marker data in self-pollinated crops. Theoretical and Applied Genetics 112:876-884.

9. Yu, J., and E.S. Buckler. 2006. Genetic association mapping and genome organization of maize. Current Opinion in Biotechnology 17:155-160.

8. S.A. Flint-Garcia, A. Thuillet, J. Yu, G. Pressoir, S.M. Romero, S.E. Mitchell, J.F. Doebley, S. Kresovich, M.M. Goodman, and E.S. Buckler. 2005. Maize association population: a high resolution platform for QTL dissection. Plant Journal 44:1054-1064.

7. Bernardo, R., M. Arbelbide, B. Parisseaux, and J. Yu. 2005. In silico QTL mapping with phenotypic, pedigree, and genomic data in plant breeding programs. Proceedings of the 10th International Congress of "The Society for the Advancement of Breeding Researches in Asia and Oceania".

6*. Yu, J., M. Arbelbide, and R. Bernardo. 2005. Power of in silico QTL mapping from phenotypic, pedigree, and marker data in a hybrid breeding program. Theoretical and Applied Genetics 110:1061-1067.

5*. Yu, J., and R. Bernardo. 2004. Metabolic control analysis as a mechanism for maintaining genetic variance during advanced cycle breeding. Theoretical and Applied Genetics 108:1614-1619.

4. Yu, J., and R. Bernardo. 2004. Changes in genetic variance during advanced cycle breeding in maize. Crop Science 44:405-410.

3. Yu, J., M.R. Tuinstra, M.M. Claassen, W.B. Gordon, and M.D. Witt. 2004. Analysis of cold tolerance in sorghum under controlled environment conditions. Field Crops Research 85:21-30.

2. Yu, J., H. Lu, and R. Bernardo. 2001. Inconsistency between SSR groupings and genetic backgrounds of white corn inbreds. Maydica 46:133-139.

1. Yu, J., and M.R. Tuinstra. 2001. Genetic analysis of seedling growth under cold temperatures.Crop Science 41:1438-1443.