Publications

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Journal Article
S. Renny-Byfield, Gallagher, J. P., Grover, C. E., Szadkowski, E., Page, J. T., Udall, J. A., Wang, X., Paterson, A. H., and Wendel, J. F., Ancient gene duplicates in Gossypium (Cotton) exhibit near-complete expression divergence, Genome biology and evolution, vol. 6, no. 3, pp. 559-571, 2014.
A. E. Bennett, Preedy, K., Golubski, A., Umbanhowar, J., Borrett, S. R., Byrne, L., Apostol, K., Bever, J. D., Biederman, L., and Classen, A. T., Beyond the black box: promoting mathematical collaborations for elucidating interactions in soil ecology, Ecosphere, vol. 10, no. 7, p. e02799, 2019.
K. Schiffers, Schurr, F. M., Tielbörger, K., Urbach, C., Moloney, K., and Jeltsch, F., Dealing with virtual aggregation–a new index for analysing heterogeneous point patterns, Ecography, vol. 31, no. 5, pp. 545-555, 2008.
L. L. Hinze, Hulse-Kemp, A. M., Wilson, I. W., Zhu, Q. - H., Llewellyn, D. J., Taylor, J. M., Spriggs, A., Fang, D. D., Ulloa, M., and Burke, J. J., Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array, BMC Plant Biology, vol. 17, no. 1, p. 37, 2017.
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.
L. Flagel, Udall, J., Nettleton, D., and Wendel, J. F., Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution, BMC biology, vol. 6, no. 1, p. 16, 2008.
R. Hovav, Udall, J. A., Chaudhary, B., Hovav, E., Flagel, L., Hu, G., and Wendel, J. F., The evolution of spinnable cotton fiber entailed prolonged development and a novel metabolism, PLoS Genet, vol. 4, no. 2, p. e25, 2008.
G. Hu, Hovav, R., Grover, C. E., Faigenboim-Doron, A., Kadmon, N., Page, J. T., Udall, J. A., and Wendel, J. F., Evolutionary Conservation and Divergence of Gene Coexpression Networks in Gossypium (Cotton) Seeds, Genome Biology and Evolution, p. evw280, 2017.
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.
R. A. Rapp, Udall, J. A., and Wendel, J. F., Genomic expression dominance in allopolyploids, Bmc Biology, vol. 7, no. 1, p. 18, 2009.
B. Chaudhary, Hovav, R., Rapp, R., Verma, N., Udall, J. A., and Wendel, J. F., Global analysis of gene expression in cotton fibers from wild and domesticated Gossypium barbadense, Evolution & development, vol. 10, no. 5, pp. 567-582, 2008.
J. A. Udall, Swanson, J. M., Haller, K., Rapp, R. A., Sparks, M. E., Hatfield, J., Yu, Y., Wu, Y., Dowd, C., and Arpat, A. B., A global assembly of cotton ESTs, Genome research, vol. 16, no. 3, pp. 441-450, 2006.
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.
S. Renny-Byfield, Page, J. T., Udall, J. A., Sanders, W. S., Peterson, D. G., Arick, M. A., Grover, C. E., and Wendel, J. F., Independent domestication of two old world cotton species, Genome biology and evolution, vol. 8, no. 6, pp. 1940-1947, 2016.
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.
R. Hovav, Udall, J. A., Hovav, E., Rapp, R., Flagel, L., and Wendel, J. F., A majority of cotton genes are expressed in single-celled fiber, Planta, vol. 227, no. 2, pp. 319-329, 2008.
I. Ibáñez, Gornish, E. S., Buckley, L., Debinski, D. M., Hellmann, J., Helmuth, B., HilleRisLambers, J., Latimer, A. M., Miller‐Rushing, A. J., and Uriarte, M., Moving forward in global‐change ecology: capitalizing on natural variability, Ecology and evolution, vol. 3, no. 1, pp. 170-181, 2013.
J. A. Udall, Swanson, J. M., Nettleton, D., Percifield, R. J., and Wendel, J. F., A novel approach for characterizing expression levels of genes duplicated by polyploidy, Genetics, vol. 173, no. 3, pp. 1823-1827, 2006.
R. Hovav, Chaudhary, B., Udall, J. A., Flagel, L., and Wendel, J. F., Parallel domestication, convergent evolution and duplicated gene recruitment in allopolyploid cotton, Genetics, vol. 179, no. 3, pp. 1725-1733, 2008.
R. Hovav, Udall, J. A., Chaudhary, B., Rapp, R., Flagel, L., and Wendel, J. F., Partitioned expression of duplicated genes during development and evolution of a single cell in a polyploid plant, Proceedings of the National Academy of Sciences, vol. 105, no. 16, pp. 6191-6195, 2008.
C. A. Phillips, Uzzell, T., Spolsky, C. M., Serb, J. M., Szafoni, R. E., and Pollowy, T. R., Persistent high levels of tetraploidy in salamanders of the Ambystoma jeffersonianum complex, Journal of Herpetology, pp. 530-535, 1997.
J. A. Udall and Wendel, J. F., Polyploidy and crop improvement, Crop Science, vol. 46, no. Supplement_1, p. S-3-S-14, 2006.
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.
C. E. Grover, Gallagher, J. P., Jareczek, J. J., Page, J. T., Udall, J. A., Gore, M. A., and Wendel, J. F., Re-evaluating the phylogeny of allopolyploid Gossypium L., Molecular phylogenetics and evolution, vol. 92, pp. 45-52, 2015.
C. E. Grover, Gallagher, J. P., Jareczek, J. J., Page, J. T., Udall, J. A., Gore, M. A., and Wendel, J. F., Re-evaluating the phylogeny of allopolyploid Gossypium L, Molecular Phylogenetics and Evolution, 2015.
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.
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.
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.