Publications

Goicoechea, J. L., Ammiraju, J. S. S., Marri, P. R., Chen, M., Jackson, S., Yu, Y., Rounsley, S., & Wing, R. A. (2010). The Future of Rice Genomics: Sequencing the Collective Oryza Genome. Rice, 3(2–3), 89–97. https://doi.org/10.1007/s12284-010-9052-9

Zuccolo, A., Sebastian, A., Yu, Y., Jackson, S., Rounsley, S., Billheimer, D., & Wing, R. A. (2010). Assessing the Extent of Substitution Rate Variation of Retrotransposon Long Terminal Repeat Sequences in Oryza sativa and Oryza glaberrima. Rice, 3(4), 242–250. https://doi.org/10.1007/s12284-010-9046-7

Lin, L., Pierce, G. J., Bowers, J. E., Estill, J. C., Compton, R. O., Rainville, L. K., Kim, C., Lemke, C., Rong, J., Tang, H., Wang, X., Braidotti, M., Chen, A. H., Chicola, K., Collura, K., Epps, E., Golser, W., Grover, C., Ingles, J., … Paterson, A. H. (2010). A draft physical map of a D-genome cotton species (Gossypium raimondii). BMC Genomics, 11(1). https://doi.org/10.1186/1471-2164-11-395

Geraldes, A., Rambo, T., Wing, R. A., Ferrand, N., & Nachman, M. W. (2010). Extensive Gene Conversion Drives the Concerted Evolution of Paralogous Copies of the SRY Gene in European Rabbits. Molecular Biology and Evolution, 27(11), 2437–2440. https://doi.org/10.1093/molbev/msq139

Sanyal, A., Ammiraju, J. S. S., Lu, F., Yu, Y., Rambo, T., Currie, J., Kollura, K., Kim, H.-R., Chen, J., Ma, J., San Miguel, P., Mingsheng, C., Wing, R. A., & Jackson, S. A. (2010). Orthologous Comparisons of the Hd1 Region across Genera Reveal Hd1 Gene Lability within Diploid Oryza Species and Disruptions to Microsynteny in Sorghum. Molecular Biology and Evolution, 27(11), 2487–2506. https://doi.org/10.1093/molbev/msq133

Ammiraju, J. S. S., Fan, C., Yu, Y., Song, X., Cranston, K. A., Pontaroli, A. C., Lu, F., Sanyal, A., Jiang, N., Rambo, T., Currie, J., Collura, K., Talag, J., Bennetzen, J. L., Chen, M., Jackson, S., & Wing, R. A. (2010). Spatio-temporal patterns of genome evolution in allotetraploid species of the genus Oryza: Genome evolution in polyploid Oryza. The Plant Journal, 63(3), 430–442. https://doi.org/10.1111/j.1365-313x.2010.04251.x

Dai, L., Wu, J., Li, X., Wang, X., Liu, X., Jantasuriyarat, C., Kudrna, D., Yu, Y., Wing, R. A., Han, B., Zhou, B., & Wang, G.-L. (2010). Genomic structure and evolution of the Pi2/9 locus in wild rice species. Theoretical and Applied Genetics, 121(2), 295–309. https://doi.org/10.1007/s00122-010-1310-0

Schmutz, J., Cannon, S. B., Schlueter, J., Ma, J., Mitros, T., Nelson, W., Hyten, D. L., Song, Q., Thelen, J. J., Cheng, J., Xu, D., Hellsten, U., May, G. D., Yu, Y., Sakurai, T., Umezawa, T., Bhattacharyya, M. K., Sandhu, D., Valliyodan, B., … Jackson, S. A. (2010). Genome sequence of the palaeopolyploid soybean. In Nature (Vols. 463, Issues 7278, pp. 178–183). Springer Science and Business Media LLC. https://doi.org/10.1038/nature08670

Ammiraju, J. S., Song, X., Luo, M., Sisneros, N., Angelova, A., Kudrna, D., Kim, H., Yu, Y., Goicoechea, J. L., Lorieux, M., Kurata, N., Brar, D., Ware, D., Jackson, S., & Wing, R. A. (2010). The Oryza BAC resource: a genus-wide and genome scale tool for exploring rice genome evolution and leveraging useful genetic diversity from wild relatives. Breeding Science, 60(5), 536–543. https://doi.org/10.1270/jsbbs.60.536

Gao, D., Gill, N., Kim, H., Walling, J. G., Zhang, W., Fan, C., Yu, Y., Ma, J., SanMiguel, P., Jiang, N., Cheng, Z., Wing, R. A., Jiang, J., & Jackson, S. A. (2009). A lineage‐specific centromere retrotransposon in Oryza brachyantha. The Plant Journal, 60(5), 820–831. https://doi.org/10.1111/j.1365-313x.2009.04005.x

Zhou, S., Wei, F., Nguyen, J., Bechner, M., Potamousis, K., Goldstein, S., Pape, L., Mehan, M. R., Churas, C., Pasternak, S., Forrest, D. K., Wise, R., Ware, D., Wing, R. A., Waterman, M. S., Livny, M., & Schwartz, D. C. (2009). A Single Molecule Scaffold for the Maize Genome. PLoS Genetics, 5(11), e1000711. https://doi.org/10.1371/journal.pgen.1000711

Wei, F., Stein, J. C., Liang, C., Zhang, J., Fulton, R. S., Baucom, R. S., De Paoli, E., Zhou, S., Yang, L., Han, Y., Pasternak, S., Narechania, A., Zhang, L., Yeh, C.-T., Ying, K., Nagel, D. H., Collura, K., Kudrna, D., Currie, J., … Wing, R. A. (2009). Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome. PLoS Genetics, 5(11), e1000728. https://doi.org/10.1371/journal.pgen.1000728

Soderlund, C., Descour, A., Kudrna, D., Bomhoff, M., Boyd, L., Currie, J., Angelova, A., Collura, K., Wissotski, M., Ashley, E., Morrow, D., Fernandes, J., Walbot, V., & Yu, Y. (2009). Sequencing, Mapping, and Analysis of 27,455 Maize Full-Length cDNAs. PLoS Genetics, 5(11), e1000740. https://doi.org/10.1371/journal.pgen.1000740

Schnable, P. S., Ware, D., Fulton, R. S., Stein, J. C., Wei, F., Pasternak, S., Liang, C., Zhang, J., Fulton, L., Graves, T. A., Minx, P., Reily, A. D., Courtney, L., Kruchowski, S. S., Tomlinson, C., Strong, C., Delehaunty, K., Fronick, C., Courtney, B., … Wilson, R. K. (2009). The B73 Maize Genome: Complexity, Diversity, and Dynamics. Science, 326(5956), 1112–1115. https://doi.org/10.1126/science.1178534

Wei, F., Zhang, J., Zhou, S., He, R., Schaeffer, M., Collura, K., Kudrna, D., Faga, B. P., Wissotski, M., Golser, W., Rock, S. M., Graves, T. A., Fulton, R. S., Coe, E., Schnable, P. S., Schwartz, D. C., Ware, D., Clifton, S. W., Wilson, R. K., & Wing, R. A. (2009). The Physical and Genetic Framework of the Maize B73 Genome. PLoS Genetics, 5(11), e1000715. https://doi.org/10.1371/journal.pgen.1000715

Cranston, K. A., Hurwitz, B., Ware, D., Stein, L., & Wing, R. A. (2009). Species Trees from Highly Incongruent Gene Trees in Rice. Systematic Biology, 58(5), 489–500. https://doi.org/10.1093/sysbio/syp054

Degnan, P. H., Yu, Y., Sisneros, N., Wing, R. A., & Moran, N. A. (2009). Hamiltonella defensa , genome evolution of protective bacterial endosymbiont from pathogenic ancestors. Proceedings of the National Academy of Sciences, 106(22), 9063–9068. https://doi.org/10.1073/pnas.0900194106

Rounsley, S., Marri, P. R., Yu, Y., He, R., Sisneros, N., Goicoechea, J. L., Lee, S. J., Angelova, A., Kudrna, D., Luo, M., Affourtit, J., Desany, B., Knight, J., Niazi, F., Egholm, M., & Wing, R. A. (2009). De Novo Next Generation Sequencing of Plant Genomes. Rice, 2(1), 35–43. https://doi.org/10.1007/s12284-009-9025-z

Lu, F., Ammiraju, J. S. S., Sanyal, A., Zhang, S., Song, R., Chen, J., Li, G., Sui, Y., Song, X., Cheng, Z., Costa de Oliveira, A., Bennetzen, J. L., Jackson, S. A., Wing, R. A., & Chen, M. (2009). Comparative sequence analysis of MONOCULM1 -orthologous regions in 14 Oryza genomes. Proceedings of the National Academy of Sciences, 106(6), 2071–2076. https://doi.org/10.1073/pnas.0812798106

Zhang, H., DiBaise, J. K., Zuccolo, A., Kudrna, D., Braidotti, M., Yu, Y., Parameswaran, P., Crowell, M. D., Wing, R., Rittmann, B. E., & Krajmalnik-Brown, R. (2009). Human gut microbiota in obesity and after gastric bypass. Proceedings of the National Academy of Sciences, 106(7), 2365–2370. https://doi.org/10.1073/pnas.0812600106

Ammiraju, J. S., Lu, F., Sanyal, A., Yu, Y., Song, X., Jiang, N., Pontaroli, A. C., Rambo, T., Currie, J., Collura, K., Talag, J., Fan, C., Goicoechea, J. L., Zuccolo, A., Chen, J., Bennetzen, J. L., Chen, M., Jackson, S., & Wing, R. A. (2008). Dynamic Evolution ofOryzaGenomes Is Revealed by Comparative Genomic Analysis of a Genus-Wide Vertical Data Set. The Plant Cell, 20(12), 3191–3209. https://doi.org/10.1105/tpc.108.063727

Fan, C., Zhang, Y., Yu, Y., Rounsley, S., Long, M., & Wing, R. A. (2008). The Subtelomere of Oryza sativa Chromosome 3 Short Arm as a Hot Bed of New Gene Origination in Rice. Molecular Plant, 1(5), 839–850. https://doi.org/10.1093/mp/ssn050

Zuccolo, A., Ammiraju, J. S. S., Kim, H., Sanyal, A., Jackson, S., & Wing, R. A. (2008). Rapid and Differential Proliferation of the Ty3-Gypsy LTR Retrotransposon Atlantys in the Genus Oryza. Rice, 1(1), 85–99. https://doi.org/10.1007/s12284-008-9002-y

Maughan, P. J., Sisneros, N., Luo, M., Kudrna, D., Ammiraju, J. S. S., & Wing, R. A. (2008). Construction of an Amaranthus hypochondriacus Bacterial Artificial Chromosome Library and Genomic Sequencing of Herbicide Target Genes. Crop Science, 48(S1). https://doi.org/10.2135/cropsci2007.08.0434tpg

Wei, F., & Wing, R. A. (2008). A fruitful outcome to the papaya genome project. Genome Biology, 9(6), 227. https://doi.org/10.1186/gb-2008-9-6-227