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Souza, G. M., Van Sluys, M. A., Lembke, C. G., Lee, H., Margarido, G. R. A., Hotta, C. T., Gaiarsa, J. W., Diniz, A. L., Oliveira, M. M., Ferreira, S. S., Nishiyama, M. Y., Ten-Caten, F., Ragagnin, G. T., Andrade, P. M., de Souza, R. F., Nicastro, G. G., Pandya, R., Kim, C., Guo, H., Durham, A. M., Carneiro, M. S., Zhang, J., Zhang, X., Zhang, Q., Ming, R., Schatz, M. C., Davidson, B., Paterson, A. H., Heckerman, D. (December 2019) Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop. Gigascience, 8 (12). giz129. ISSN 2047-217x (Public Dataset)

Ming, R., VanBuren, R., Wai, C. M., Tang, H., Schatz, M. C., Bowers, J. E., Lyons, E., Wang, M. L., Chen, J., Biggers, E., Zhang, J., Huang, L., Zhang, L., Miao, W., Zhang, J., Ye, Z., Miao, C., Lin, Z., Wang, H., Zhou, H., Yim, W. C., Priest, H. D., Zheng, C., Woodhouse, M., Edger, P. P., Guyot, R., Guo, H. B., Guo, H., Zheng, G., Singh, R., Sharma, A., Min, X., Zheng, Y., Lee, H., Gurtowski, J., Sedlazeck, F. J., Harkess, A., McKain, M. R., Liao, Z., Fang, J., Liu, J., Zhang, X., Zhang, Q., Hu, W., Qin, Y., Wang, K., Chen, L. Y., Shirley, N., Lin, Y. R., Liu, L. Y., Hernandez, A. G., Wright, C. L., Bulone, V., Tuskan, G. A., Heath, K., Zee, F., Moore, P. H., Sunkar, R., Leebens-Mack, J. H., Mockler, T., Bennetzen, J. L., Freeling, M., Sankoff, D., Paterson, A. H., Zhu, X., Yang, X., Smith, J. A., Cushman, J. C., Paull, R. E., Yu, Q. (November 2015) The pineapple genome and the evolution of CAM photosynthesis. Nat Genet, 47. pp. 1435-1442. ISSN 1546-1718 (Electronic)1061-4036 (Linking)

Schatz, M. C., Maron, L. G., Stein, J. C., Hernandez Wences, A., Gurtowski, J., Biggers, E., Lee, H., Kramer, M., Antoniou, E., Ghiban, E., Wright, M. H., Chia, J. M., Ware, D., McCouch, S. R., McCombie, W. R. (December 2014) Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biol, 15 (11). p. 506. ISSN 1465-6906

Marcus, S., Lee, H., Schatz, M. C. (November 2014) SplitMEM: A graphical algorithm for pan-genome analysis with suffix skips. Bioinformatics, 30 (24). pp. 3476-3483. ISSN 1367-4803