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J. A. Udall, Flagel, L. E., Cheung, F., Woodward, A. W., Hovav, R., Rapp, R. A., Swanson, J. M., Lee, J. J., Gingle, A. R., and Nettleton, D., “Spotted cotton oligonucleotide microarrays for gene expression analysis”, Bmc Genomics, vol. 8, no. 1, p. 81, 2007.
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S. E. McGaugh, Bronikowski, A. M., Kuo, C. - H., Reding, D. M., Addis, E. A., Flagel, L. E., Janzen, F. J., and Schwartz, T. S., “Rapid molecular evolution across amniotes of the IIS/TOR network”, Proceedings of the National Academy of Sciences, p. 201419659, 2015.
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L. E. Flagel, Rapp, R. A., Grover, C. E., Widrlechner, M. P., Hawkins, J., Grafenberg, J. L., Álvarez, I., Chung, G. Young, and Wendel, J. F., “Phylogenetic, morphological, and chemotaxonomic incongruence in the North American endemic genus Echinacea”, American journal of botany, vol. 95, no. 6, pp. 756-765, 2008.
D. S. Senchina, Flagel, L. E., Wendel, J. F., and Kohut, M. L., “Phenetic comparison of sevenEchinacea species based on immunomodulatory characteristics”, Economic botany, vol. 60, no. 3, pp. 205-211, 2006.
Y. Bao, Hu, G., Flagel, L. E., Salmon, A., Bezanilla, M., Paterson, A. H., Wang, Z., and Wendel, J. F., “Parallel up-regulation of the profilin gene family following independent domestication of diploid and allopolyploid cotton (Gossypium)”, Proceedings of the National Academy of Sciences, vol. 108, no. 52, pp. 21152-21157, 2011.
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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.
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L. E. Flagel and Wendel, J. F., “Gene duplication and evolutionary novelty in plants”, New Phytologist, vol. 183, no. 3, pp. 557-564, 2009.
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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.
J. J. Doyle, Flagel, L. E., Paterson, A. H., Rapp, R. A., Soltis, D. E., Soltis, P. S., and Wendel, J. F., “Evolutionary genetics of genome merger and doubling in plants”, Annual review of genetics, vol. 42, pp. 443-461, 2008.
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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.
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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.