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L. E. Flagel, Chen, L., Chaudhary, B., and Wendel, J. F., Coordinated and fine-scale control of homoeologous gene expression in allotetraploid cotton, Journal of heredity, p. esp003, 2009.
J. F. Wendel, Brubaker, C., Álvarez, I., Cronn, R., and Stewart, J. McD., Evolution and natural history of the cotton genus, in Genetics and genomics of cotton, Springer US, 2009, pp. 3-22.
L. E. Flagel and Wendel, J. F., Gene duplication and evolutionary novelty in plants, New Phytologist, vol. 183, no. 3, pp. 557-564, 2009.
L. Schmidt, Hu, G., and Wendel, J. F., Genetic Analysis of Seed Storage Proteins in Gossypium, 2009.
R. A. Rapp, Udall, J. A., and Wendel, J. F., Genomic expression dominance in allopolyploids, Bmc Biology, vol. 7, no. 1, p. 18, 2009.
K. M. Butterworth, Adams, D. C., Horner, H. T., and Wendel, J. F., Initiation and early development of fiber in wild and cultivated cotton, International Journal of Plant Sciences, vol. 170, no. 5, pp. 561-574, 2009.
B. Chaudhary, Hovav, R., Flagel, L., Mittler, R., and Wendel, J. F., Parallel expression evolution of oxidative stress-related genes in fiber from wild and domesticated diploid and polyploid cotton (Gossypium), Bmc Genomics, vol. 10, no. 1, p. 378, 2009.
J. S. Hawkins, Proulx, S. R., Rapp, R. A., and Wendel, J. F., Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants, Proceedings of the National Academy of Sciences, vol. 106, no. 42, pp. 17811-17816, 2009.
B. Chaudhary, Flagel, L., Stupar, R. M., Udall, J. A., Verma, N., Springer, N. M., and Wendel, J. F., Reciprocal silencing, transcriptional bias and functional divergence of homeologs in polyploid cotton (Gossypium), Genetics, vol. 182, no. 2, pp. 503-517, 2009.
K. L. Adams, Flagel, L., and Wendel, J. F., Responses of the cotton genome to polyploidy, in Genetics and Genomics of Cotton, Springer US, 2009, pp. 419-429.
L. E. Flagel and Wendel, J. F., Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation, New Phytologist, vol. 186, no. 1, pp. 184-193, 2010.
R. A. Rapp, Haigler, C. H., Flagel, L., Hovav, R. H., Udall, J. A., and Wendel, J. F., Gene expression in developing fibres of Upland cotton (Gossypium hirsutum L.) was massively altered by domestication, BMC biology, vol. 8, no. 1, p. 139, 2010.
T. Bureau, Hu, G., Hawkins, J. S., Grover, C. E., and Wendel, J. F., The history and disposition of transposable elements in polyploid Gossypium, Genome, vol. 53, no. 8, pp. 599-607, 2010.
A. Salmon, Flagel, L., Ying, B., Udall, J. A., and Wendel, J. F., Homoeologous nonreciprocal recombination in polyploid cotton, New Phytologist, vol. 186, no. 1, pp. 123-134, 2010.
Y. Bao, Wendel, J. F., and Ge, S., Multiple patterns of rDNA evolution following polyploidy in Oryza, Molecular phylogenetics and evolution, vol. 55, no. 1, pp. 136-142, 2010.
J. F. Wendel, Brubaker, C. L., and Seelanan, T., The origin and evolution of Gossypium, in Physiology of cotton, Springer Netherlands, 2010, pp. 1-18.
L. Betancur, Singh, B., Rapp, R. A., Wendel, J. F., M Marks, D., Roberts, A. W., and Haigler, C. H., Phylogenetically distinct cellulose synthase genes support secondary wall thickening in arabidopsis shoot trichomes and cotton fiber, Journal of integrative plant biology, vol. 52, no. 2, pp. 205-220, 2010.
C. E. Grover and Wendel, J. F., Recent insights into mechanisms of genome size change in plants, Journal of Botany, vol. 2010, 2010.
J. M. Pleasants and Wendel, J. F., Reproductive and Pollination Biology of the Endemic Hawaiian Cotton, Gossypium tomentosum (Malvaceae) 1, Pacific Science, vol. 64, no. 1, pp. 45-55, 2010.
C. E. Grover, Grupp, K. K., Wanzek, R. J., and Wendel, J. F., Assessing the monophyly of polyploid Gossypium species, Plant systematics and evolution, vol. 298, no. 6, pp. 1177-1183, 2012.
L. Gong, Salmon, A., Yoo, M. - J., Grupp, K. K., Wang, Z., Paterson, A. H., and Wendel, J. F., The cytonuclear dimension of allopolyploid evolution: an example from cotton using rubisco, Molecular biology and evolution, vol. 29, no. 10, pp. 3023-3036, 2012.
L. E. Flagel, Wendel, J. F., and Udall, J. A., Duplicate gene evolution, homoeologous recombination, and transcriptome characterization in allopolyploid cotton, BMC genomics, vol. 13, no. 1, p. 302, 2012.
C. E. Grover, Gallagher, J. P., Szadkowski, E. P., Yoo, M. J., Flagel, L. E., and Wendel, J. F., Homoeolog expression bias and expression level dominance in allopolyploids, New Phytologist, vol. 196, no. 4, pp. 966-971, 2012.
J. F. Wendel, Flagel, L. E., and Adams, K. L., Jeans, genes, and genomes: cotton as a model for studying polyploidy, in Polyploidy and genome evolution, Springer Berlin Heidelberg, 2012, pp. 181-207.
J. Greilhuber, Dolezel, J., Leitch, I. J., and Wendel, J. F., Plant Genome Diversity: Vol. 1: Plant Genomes, Their Residents, and Their Evolutionary Dynamics. Springer, 2012.
I. J. Leitch, Greilhuber, J., Dolezel, J., and Wendel, J. F., Plant Genome Diversity Volume 2: Physical Structure, Behaviour and Evolution of Plant Genomes, vol. 2. Springer Science & Business Media, 2012.
A. H. Paterson, Wendel, J. F., Gundlach, H., Guo, H., Jenkins, J., Jin, D., Llewellyn, D., Showmaker, K. C., Shu, S., and Udall, J., Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres, Nature, vol. 492, no. 7429, pp. 423-427, 2012.
A. Salmon, Udall, J. A., Jeddeloh, J. A., and Wendel, J. F., Targeted capture of homoeologous coding and noncoding sequence in polyploid cotton, G3: Genes| Genomes| Genetics, vol. 2, no. 8, pp. 921-930, 2012.
C. E. Grover, Salmon, A., and Wendel, J. F., Targeted sequence capture as a powerful tool for evolutionary analysis1, American journal of botany, vol. 99, no. 2, pp. 312-319, 2012.
K. M. Olsen and Wendel, J. F., A bountiful harvest: genomic insights into crop domestication phenotypes, Annual Review of Plant Biology, vol. 64, pp. 47-70, 2013.
L. Gong, Kakrana, A., Arikit, S., Meyers, B. C., and Wendel, J. F., Composition and expression of conserved microRNA genes in diploid cotton (Gossypium) species, Genome biology and evolution, vol. 5, no. 12, pp. 2449-2459, 2013.
K. M. Olsen and Wendel, J. F., Crop plants as models for understanding plant adaptation and diversification, Frontiers in plant science, vol. 4, 2013.
K. L. Adams and Wendel, J. F., Dynamics of duplicated gene expression in Polyploid Cotton, Polyploid and hybrid genomics, pp. 187-194, 2013.
A. Madlung and Wendel, J. F., Genetic and epigenetic aspects of polyploid evolution in plants, Cytogenetic and genome research, vol. 140, no. 2-4, pp. 270-285, 2013.
M. J. Yoo, Szadkowski, E., and Wendel, J. F., Homoeolog expression bias and expression level dominance in allopolyploid cotton, Heredity, vol. 110, no. 2, pp. 171-180, 2013.
J. T. Page, Huynh, M. D., Liechty, Z. S., Grupp, K., Stelly, D., Hulse, A. M., Ashrafi, H., Van Deynze, A., Wendel, J. F., and Udall, J. A., Insights into the evolution of cotton diploids and polyploids from whole-genome re-sequencing, G3: Genes| Genomes| Genetics, vol. 3, no. 10, pp. 1809-1818, 2013.
J. F. Wendel, Jeans, Genes, and The Independent Domestications Of Cotton, Plant and Animal Genome XXI Conference. Plant and Animal Genome, 2013.
G. Hu, Koh, J., Yoo, M. ‐J., Grupp, K., Chen, S., and Wendel, J. F., Proteomic profiling of developing cotton fibers from wild and domesticated Gossypium barbadense, New Phytologist, vol. 200, no. 2, pp. 570-582, 2013.