College of Agricultural Sciences

M. Karey Tello-Ruiz, Stein, J., Wei, S., Youens-Clark, K., Jaiswal, P., and Ware, D., “Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways.”, in Methods in molecular biology (Clifton, N.J.), vol. 1374, 2016, pp. 141-63.

R. Bruskiewich, Senger, M., Davenport, G., Ruiz, M., Rouard, M., Hazekamp, T., Takeya, M., Doi, K., Satoh, K., Costa, M., Simon, R., Balaji, J., Akintunde, A., Mauleon, R., Wanchana, S., Shah, T., Anacleto, M., Portugal, A., Ulat, V. Jun, Thongjuea, S., Braak, K., Ritter, S., Dereeper, A., Skofic, M., Rojas, E., Martins, N., Pappas, G., Alamban, R., Almodiel, R., Barboza, L. Hendrix, Detras, J., Manansala, K., Mendoza, M. Jonathan, Morales, J., Peralta, B., Valerio, R., Zhang, Y., Gregorio, S., Hermocilla, J., Echavez, M., Yap, J. Michael, Farmer, A., Schiltz, G., Lee, J., Casstevens, T., Jaiswal, P., Meintjes, A., Wilkinson, M., Good, B., Wagner, J., Morris, J., Marshall, D., Collins, A., Kikuchi, S., Metz, T., McLaren, G., and van Hintum, T., “The generation challenge programme platform: semantic standards and workbench for crop science.”, International journal of plant genomics, vol. 2008, p. 369601, 2008.

A. A. Myburg, Grattapaglia, D., Tuskan, G. A., Hellsten, U., Hayes, R. D., Grimwood, J., Jenkins, J., Lindquist, E., Tice, H., Bauer, D., Goodstein, D. M., Dubchak, I., Poliakov, A., Mizrachi, E., Kullan, A. R. K., Hussey, S. G., Pinard, D., van der Merwe, K., Singh, P., van Jaarsveld, I., Silva-Junior, O. B., Togawa, R. C., Pappas, M. R., Faria, D. A., Sansaloni, C. P., Petroli, C. D., Yang, X., Ranjan, P., Tschaplinski, T. J., Ye, C. - Y., Li, T., Sterck, L., Vanneste, K., Murat, F., Soler, M., San Clemente, H., Saidi, N., Cassan-Wang, H., Dunand, C., Hefer, C. A., Bornberg-Bauer, E., Kersting, A. R., Vining, K., Amarasinghe, V., Ranik, M., Naithani, S., Elser, J., Boyd, A. E., Liston, A., Spatafora, J. W., Dharmwardhana, P., Raja, R., Sullivan, C., Romanel, E., Alves-Ferreira, M., Külheim, C., Foley, W., Carocha, V., Paiva, J., Kudrna, D., Brommonschenkel, S. H., Pasquali, G., Byrne, M., Rigault, P., Tibbits, J., Spokevicius, A., Jones, R. C., Steane, D. A., Vaillancourt, R. E., Potts, B. M., Joubert, F., Barry, K., Pappas, G. J., Strauss, S. H., Jaiswal, P., Grima-Pettenati, J., Salse, J., Van de Peer, Y., Rokhsar, D. S., and Schmutz, J., “The genome of Eucalyptus grandis.”, Nature, vol. 510, pp. 356-62, 2014.

A. A. Myburg, Grattapaglia, D., Tuskan, G. A., Hellsten, U., Hayes, R. D., Grimwood, J., Jenkins, J., Lindquist, E., Tice, H., Bauer, D., Goodstein, D. M., Dubchak, I., Poliakov, A., Mizrachi, E., Kullan, A. R. K., Hussey, S. G., Pinard, D., van der Merwe, K., Singh, P., van Jaarsveld, I., Silva-Junior, O. B., Togawa, R. C., Pappas, M. R., Faria, D. A., Sansaloni, C. P., Petroli, C. D., Yang, X., Ranjan, P., Tschaplinski, T. J., Ye, C. - Y., Li, T., Sterck, L., Vanneste, K., Murat, F., Soler, çal, San Clemente, élène, Saidi, N., Cassan-Wang, H., Dunand, C., Hefer, C. A., Bornberg-Bauer, E., Kersting, A. R., Vining, K. J., Amarasinghe, V., Ranik, M., Naithani, S., Elser, J., Boyd, A. E., Liston, A., Spatafora, J. W., Dharmwardhana, P., Raja, R., Sullivan, C., Romanel, E., Alves-Ferreira, M., ülheim, C., Foley, W., Carocha, V., Paiva, J., Kudrna, D., Brommonschenkel, S. H., Pasquali, G., Byrne, M., Rigault, P., Tibbits, J., Spokevicius, A., Jones, R. C., Steane, D. A., Vaillancourt, éE., Potts, B. M., Joubert, F., Barry, K., Pappas, G. J., Strauss, S. H., Jaiswal, P., Grima-Pettenati, J., Salse, érôme, Van de Peer, Y., Rokhsar, D. S., and Schmutz, J., “The genome of Eucalyptus grandis”, Nature, vol. 51, no. 75, pp. 356 - 362, 2014.

K. E. Bushley, Raja, R., Jaiswal, P., Cumbie, J. S., Nonogaki, M., Boyd, A. E., C Owensby, A., Knaus, B. J., Elser, J., Miller, D., Di, Y., McPhail, K. L., and Spatafora, J. W., “The Genome of Tolypocladium inflatum: Evolution, Organization, and Expression of the Cyclosporin Biosynthetic Gene Cluster”, PLOS Genetics, vol. 9, 2013.

V. Shulaev, Sargent, D. J., Crowhurst, R. N., Mockler, T. C., Folkerts, O., Delcher, A. L., Jaiswal, P., Mockaitis, K., Liston, A., Mane, S. P., Burns, P., Davis, T. M., Slovin, J. P., Bassil, N., Hellens, R. P., Evans, C., Harkins, T., Kodira, C., Desany, B., Crasta, O. R., Jensen, R. V., Allan, A. C., Michael, T. P., Setubal, J. Carlos, Celton, J. - M., D Rees, J. G., Williams, K. P., Holt, S. H., Rojas, J. Jairo Ruiz, Chatterjee, M., Liu, B., Silva, H., Meisel, L., Adato, A., Filichkin, S. A., Troggio, M., Viola, R., Ashman, T. - L., Wang, H., Dharmawardhana, P., Elser, J., Raja, R., Priest, H. D., Bryant, D. W., Fox, S. E., Givan, S. A., Wilhelm, L. J., Naithani, S., Christoffels, A., Salama, D. Y., Carter, J., Girona, E. Lopez, Zdepski, A., Wang, W., Kerstetter, R. A., Schwab, W., Korban, S. S., Davik, J., Monfort, A., Denoyes-Rothan, B., Arus, P., Mittler, R., Flinn, B., Aharoni, A., Bennetzen, J. L., Salzberg, S. L., Dickerman, A. W., Velasco, R., Borodovsky, M., Veilleux, R. E., and Folta, K. M., “The genome of woodland strawberry(Fragaria vesca).”, Nature genetics, vol. 43, pp. 109-16, 2011.

P. Dharmawardhana, Ren, L., Amarasinghe, V., Monaco, M., Thomason, J., Ravenscroft, D., McCouch, S., Ware, D., and Jaiswal, P., “A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress”, Rice, vol. 6, 2013.

M. K. Monaco, Stein, J., Naithani, S., Wei, S., Dharmawardhana, P., Kumari, S., Amarasinghe, V., Youens-Clark, K., Thomason, J., Preece, J., Pasternak, S., Olson, A., Jiao, Y., Lu, Z., Bolser, D., Kerhornou, A., Staines, D., Walts, B., Wu, G., D’Eustachio, P., Haw, R., Croft, D., Kersey, P. J., Stein, L., Jaiswal, P., and Ware, D., “Gramene 2013: comparative plant genomics resources.”, Nucleic acids research, vol. 42, pp. D1193-9, 2014.

M. K. Tello-Ruiz, Stein, J., Wei, S., Preece, J., Olson, A., Naithani, S., Amarasinghe, V., Dharmawardhana, P., Jiao, Y., Mulvaney, J., Kumari, S., Chougule, K., Elser, J., Wang, B., Thomason, J., Bolser, D. M., Kerhornou, A., Walts, B., Fonseca, N. A., Huerta, L., Keays, M., Y Tang, A., Parkinson, H., Fabregat, A., McKay, S., Weiser, J., D’Eustachio, P., Stein, L., Petryszak, R., Kersey, P. J., Jaiswal, P., and Ware, D., “Gramene 2016: comparative plant genomics and pathway resources.”, Nucleic acids research, vol. 44, pp. D1133-40, 2016.

M. K. Tello-Ruiz, Naithani, S., Stein, J. C., Gupta, P., Campbell, M., Olson, A., Wei, S., Preece, J., Geniza, M. J., Jiao, Y., Lee, Y. Koung, Wang, B., Mulvaney, J., Chougule, K., Elser, J., Al-Bader, N., Kumari, S., Thomason, J., Kumar, V., Bolser, D. M., Naamati, G., Tapanari, E., Fonseca, N., Huerta, L., Iqbal, H., Keays, M., Fuentes, A. Munoz- Pome, Tang, A., Fabregat, A., D’Eustachio, P., Weiser, J., Stein, L. D., Petryszak, R., Papatheodorou, I., Kersey, P. J., Lockhart, P., Taylor, C., Jaiswal, P., and Ware, D., “Gramene 2018: unifying comparative genomics and pathway resources for plant research.”, Nucleic acids research, vol. 46, pp. D1181-D1189, 2018.

P. Jaiswal, Ni, J., Yap, I., Ware, D., Spooner, W., Youens-Clark, K., Ren, L., Liang, C., Zhao, W., Ratnapu, K., Faga, B., Canaran, P., Fogleman, M., Hebbard, C., Avraham, S., Schmidt, S., Casstevens, T. M., Buckler, E. S., Stein, L., and McCouch, S., “Gramene: a bird’s eye view of cereal genomes.”, Nucleic acids research, vol. 34, pp. D717-23, 2006.

C. Liang, Jaiswal, P., Hebbard, C., Avraham, S., Buckler, E. S., Casstevens, T., Hurwitz, B., McCouch, S., Ni, J., Pujar, A., Ravenscroft, D., Ren, L., Spooner, W., Tecle, I., Thomason, J., Tung, C. - W., Wei, X., Yap, I., Youens-Clark, K., Ware, D., and Stein, L., “Gramene: a growing plant comparative genomics resource.”, Nucleic acids research, vol. 36, pp. D947-53, 2008.

D. Ware, Jaiswal, P., Ni, J., Pan, X., Chang, K., Clark, K., Teytelman, L., Schmidt, S., Zhao, W., Cartinhour, S., McCouch, S., and Stein, L., “Gramene: a resource for comparative grass genomics.”, Nucleic acids research, vol. 30, pp. 103-5, 2002.

D. H. Ware, Jaiswal, P., Ni, J., Yap, I. V., Pan, X., Clark, K. Y., Teytelman, L., Schmidt, S. C., Zhao, W., Chang, K., Cartinhour, S., Stein, L. D., and McCouch, S. R., “Gramene, a tool for grass genomics.”, Plant physiology, vol. 130, pp. 1606-13, 2002.

P. Jaiswal, “Gramene database: a hub for comparative plant genomics.”, Methods in molecular biology (Clifton, N.J.), vol. 678, pp. 247-75, 2011.

K. Youens-Clark, Buckler, E., Casstevens, T., Chen, C., Declerck, G., Derwent, P., Dharmawardhana, P., Jaiswal, P., Kersey, P., Karthikeyan, A. S., Lu, J., McCouch, S. R., Ren, L., Spooner, W., Stein, J. C., Thomason, J., Wei, S., and Ware, D., “Gramene database in 2010: updates and extensions.”, Nucleic acids research, vol. 39, pp. D1085-94, 2011.

P. Gupta, Naithani, S., Tello-Ruiz, M. Karey, Chougule, K., D’Eustachio, P., Fabregat, A., Jiao, Y., Keays, M., Lee, Y. Koung, Kumari, S., Mulvaney, J., Olson, A., Preece, J., Stein, J., Wei, S., Weiser, J., Huerta, L., Petryszak, R., Kersey, P., Stein, L. D., Ware, D., and Jaiswal, P., “Gramene Database: Navigating Plant Comparative Genomics Resources.”, Current plant biology, vol. 7-8, pp. 10-15, 2016.

P. Jaiswal, Ware, D., Ni, J., Chang, K., Zhao, W., Schmidt, S., Pan, X., Clark, K., Teytelman, L., Cartinhour, S., Stein, L., and McCouch, S., “Gramene: development and integration of trait and gene ontologies for rice.”, Comparative and functional genomics, vol. 3, pp. 132-6, 2002.

J. Ni, Pujar, A., Youens-Clark, K., Yap, I., Jaiswal, P., Tecle, I., Tung, C. - W., Ren, L., Spooner, W., Wei, X., Avraham, S., Ware, D., Stein, L., and McCouch, S., “Gramene QTL database: development, content and applications.”, Database : the journal of biological databases and curation, vol. 2009, p. bap005, 2009.