Biblio

Found 79 results
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Journal Article
M. K. Monaco, Sen, T. Z., Dharmawardhana, P. D., Ren, L., Schaeffer, M., Naithani, S., Amarasinghe, V., Thomason, J., Harper, L., Gardiner, J., Cannon, E. K. S., Lawrence, C. J., Ware, D., and Jaiswal, P., Maize Metabolic Network Construction and Transcriptome Analysis, The Plant Genome, vol. 6, pp. 1-12, 2013.
S. Naithani, Gupta, P., Preece, J., Garg, P., Fraser, V., Padgitt-Cobb, L. K., Martin, M., Vining, K., and Jaiswal, P., Involving community in genes and pathway curation., Database : the journal of biological databases and curation, vol. 2019, 2019.
J. Azevedo, Courtois, F., Hakimi, M. - A., Demarsy, E., Lagrange, T., Alcaraz, J. - P., Jaiswal, P., Maréchal-Drouard, L., and Lerbs-Mache, S., Intraplastidial trafficking of a phage-type RNA polymerase is mediated by a thylakoid RING-H2 protein., Proceedings of the National Academy of Sciences of the United States of America, vol. 105, pp. 9123-8, 2008.
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.
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.
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.
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. Jaiswal, Gramene database: a hub for comparative plant genomics., Methods in molecular biology (Clifton, N.J.), vol. 678, pp. 247-75, 2011.
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.
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.
M. Karey Tello-Ruiz, Jaiswal, P., and Ware, D., Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways., Methods Mol Biol, vol. 2443, pp. 101-131, 2022.
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.
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.
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.
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. 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.
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.
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.
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.
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.
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.
S. Naithani, Partipilo, C. M., Raja, R., Elser, J. L., and Jaiswal, P., FragariaCyc: A Metabolic Pathway Database for Woodland Strawberry Fragaria vesca., Frontiers in plant science, vol. 7, p. 242, 2016.
K. J. Vining, Romanel, E., Jones, R. C., Klocko, A., Alves-Ferreira, M., Hefer, C. A., Amarasinghe, V., Dharmawardhana, P., Naithani, S., Ranik, M., Wesley-Smith, J., Solomon, L., Jaiswal, P., Myburg, A. A., and Strauss, S. H., The floral transcriptome of Eucalyptus grandis, New Phytologist, vol. 20, no. 4, pp. 1406 - 1422, 2015.
K. J. Vining, Romanel, E., Jones, R. C., Klocko, A., Alves-Ferreira, M., Hefer, C. A., Amarasinghe, V., Dharmawardhana, P., Naithani, S., Ranik, M., Wesley-Smith, J., Solomon, L., Jaiswal, P., Myburg, A. A., and Strauss, S. H., The floral transcriptome of Eucalyptus grandis., The New phytologist, 2014.