Items where Subject is "rice"

B

Bajaj, S., Mohanty, A. (May 2005) Recent advances in rice biotechnology-towards genetically superior transgenic rice. Plant Biotechnology Journal, 3 (3). pp. 275-307. ISSN 1467-7644

Buell, C. R., McCombie, W. R., Wing, R. A., Yuan, Q., Ouyang, S., Liu, J., Zhu, W., Wang, A., Maiti, R., Haas, B., Wortman, J., Pertea, M., Jones, K. M., Kim, M., Overton, L., Tsitrin, T., Fadrosh, D., Bera, J., Weaver, J., Jin, S., Johri, S., Reardon, M., Webb, K., Hill, J., Moffat, K., Tallon, L., Van Aken, S., Lewis, M., Utterback, T., Feldblyum, T., Zismann, V., Iobst, S., Hsiao, J., De Vazeille, A. R., Salzberg, S. L., White, O., Fraser, C., Yu, Y., Kim, H., Rambo, T., Currie, J., Collura, K., Kernodle-Thompson, S., Wei, F., Kudrna, D., Ammiraju, J. S. S., Luo, M., Goicoechea, J. L., Henry, D., Oates, R., Palmer, M., Pries, G., Saski, C., Simmons, J., Soderlund, C., Nelson, W., De La Bastide, M., Spiegel, L., Nascimento, L., Huang, E., Preston, R., Zutavern, T., Palmer, L., O'Haughnessy, A., Dike, S., Minx, P., Cordum, H., Wilson, R., Jin, W., Lee, H. R., Jiang, J., Jackson, S. (2005) Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. The Rice Chromosome 3 Sequencing Consortium. Genome Research, 15 (9). pp. 1284-1291. ISSN 10889051 (ISSN)

C

Chia, J. M., Ware, D. H. (February 2011) Sequencing for the cream of the crop. Nature Biotechnology, 29 (2). pp. 138-9. ISSN 1546-1696 (Electronic) 1087-0156 (Linking)

Chitwood, D. H., Timmermans, M. C. P. (August 2007) Target mimics modulate miRNAs. Nat Genet, 39 (8). pp. 935-6. ISSN 1061-4036 (Print)

Choisne, N., Demange, N., Orjeda, G., Samain, S., D'Hont, A., Cattolico, L., Pelletier, E., Couloux, A., Segurens, B., Wincker, P., Scarpelli, C., Weissenbach, J., Salanoubat, M., Quetier, F., Singh, N. K., Mohapatra, T., Sharma, T. R., Gaikwad, K., Singh, A., Dalal, V., Srivastava, S. K., Dixit, A., Pal, A. K., Ghazi, I. A., Yadav, M., Pandit, A., Bhargava, A., Sureshbabu, K., Dixit, R., Singh, H., Swain, S. C., Pal, S., Ragiba, M., Singh, P. K., Singhal, V., Mendiratta, S. D., Batra, K., Raghuvanshi, S., Mohanty, A., Bharti, A. K., Gaur, A., Gupta, V., Kumar, D., Vydianathan, R., Vij, S., Kapur, A., Khurana, P., Sharma, S., Khurana, J. P., Tyagi, A. K., Yuan, Q. P., Ouyang, S., Liu, J., Zhu, W., Wang, A. H., Lin, H. N., Hamilton, J., Haas, B., Wortman, J., Jones, K. M., Kim, M., Overton, L., Tsitrin, T., Fadrosh, D., Bera, J., Weaver, B., Jin, S. H., Johri, S., Reardon, M., Vuong, H., Tallon, L., Van Aken, S., Lewis, M., Utterback, T., Feldblyum, T., Zismann, V., Iobst, S., Hsiao, J., de Vazeille, A. R., Salzberg, S. L., White, O., Fraser, C., Buell, C. R., Yu, Y., Rambo, T., Currie, J., Collura, K., Kim, H. R., Stum, D., Wang, W. M., Kudrna, D., Mueller, C., Wing, R. A., Kramer, M., Spiegel, L., Nascimento, L., Preston, R., Zutavern, T., Palmer, L., O'Shaughnessy, A., McCombie, W. R. (September 2005) The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications. BMC Biology, 3. ISSN 1741-7007

Cranston, K. A., Hurwitz, B. L., Ware, D. H., Stein, L. D., Wing, R. A. (October 2009) Species Trees from Highly Incongruent Gene Trees in Rice. Systematic Biology, 58 (5). pp. 489-500. ISSN 1063-5157

D

Dharmawardhana, P., Ren, L. Y., Amarasinghe, V., Monaco, M., Thomason, J., Ravenscroft, D., McCouch, S., Ware, D., Jaiswal, P. (May 2013) A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress. Rice, 6 (1). pp. 1-15. ISSN 1939-8425

H

Hass-Jacobus, B. L., Futrell-Griggs, M., Abernathy, B., Westerman, R., Goicoechea, J. L., Stein, J., Klein, P., Hurwitz, B., Zhou, B., Rakhshan, F., Sanyal, A., Gill, N., Lin, J. Y., Walling, J. G., Luo, M. Z., Ammiraju, J. S. S., Kudrna, D., Kim, H. R., Ware, D., Wing, Rod A., San Miguel, P., Jackson, S. A. (2006) Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum. BMC Genomics, 7. p. 199. ISSN 14712164

Hu, Y., Wu, Q., Peng, Z., Sprague, S. A., Wang, W., Park, J., Akhunov, E., Jagadish, K. S. V., Nakata, P. A., Cheng, N., Hirschi, K. D., White, F. F., Park, S. (November 2017) Silencing of OsGRXS17 in rice improves drought stress tolerance by modulating ROS accumulation and stomatal closure. Sci Rep, 7 (1). p. 15950. ISSN 2045-2322

Hurwitz, B. L., Kudrna, D., Yu, Y., Sebastian, A., Zuccolo, A., Jackson, S. A., Ware, D. H., Wing, R. A., Stein, L. D. (2010) Rice structural variation: A comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza. Plant Journal, 63 (6). pp. 990-1003.

I

International Rice Genome Sequencing Project, (August 2005) The map-based sequence of the rice genome. Nature, 436 (7052). pp. 793-800. ISSN 0028-0836

Itoh, T., Tanaka, T., Barrero, R. A., Yamasaki, C., Fujii, Y., Hilton, P. B., Antonio, B. A., Aono, H., Apweiler, R., Bruskiewich, R., Bureau, T., Burr, F., De Oliveira, A. C., Fuks, G., Habara, T., Haberer, G., Han, B., Harada, E., Hiraki, A. T., Hirochika, H., Hoen, D., Hokari, H., Hosokawa, S., Hsing, Y. I., Ikawa, H., Ikeo, K., Imanishi, T., Ito, Y., Jaiswal, P., Kanno, M., Kawahara, Y., Kawamura, T., Kawashima, H., Khurana, J. P., Kikuchi, S., Komatsu, S., Koyanagi, K. O., Kubooka, H., Lieberherr, D., Lin, Y. C., Lonsdale, D., Matsumoto, T., Matsuya, A., McCombie, W. R., Messing, J., Miyao, A., Mulder, N., Nagamura, Y., Nam, J., Namiki, N., Numa, H., Nurimoto, S., O'Donovan, C., Ohyanagi, H., Okido, T., Oota, S., Osato, N., Palmer, L. E., Quetier, F., Raghuvanshi, S., Saichi, N., Sakai, H., Sakai, Y., Sakata, K., Sakurai, T., Sato, F., Sato, Y., Schoof, H., Seki, M., Shibata, M., Shimizu, Y., Shinozaki, K., Shinso, Y., Singh, N. K., Smith-White, B., Takeda, J. I., Tanino, M., Tatusova, T., Thongjuea, S., Todokoro, F., Tsugane, M., Tyagi, A. K., Vanavichit, A., Wang, A., Wing, R. A., Yamaguchi, K., Yamamoto, M., Yamamoto, N., Yu, Y., Zhang, H., Zhao, Q., Higo, K., Burr, B., Gojobori, T., Sasaki, T. (2007) Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana: The Rice Annotation Project. Genome Research, 17 (2). pp. 175-183. ISSN 10889051 (ISSN)

J

Jaiswal, P., Ware, D., Ni, J. J., Chang, K., Zhao, W., Schmidt, S., Pan, X. K., Clark, K., Teytelman, L., Cartinhour, S., Stein, L., McCouch, S. (April 2002) Gramene: development and integration of trait and gene ontologies for rice. Comparative and Functional Genomics, 3 (2). pp. 132-136. ISSN 1531-6912

Joly-Lopez, Z., Platts, A. E., Gulko, B., Choi, J. Y., Groen, S. C., Zhong, X., Siepel, A., Purugganan, M. D. (February 2020) An inferred fitness consequence map of the rice genome. Nat Plants, 6 (2). pp. 119-130. ISSN 2055-0278 (Public Dataset)

K

Kawahara, Y., de la Bastide, M., Hamilton, J. P., Kanamori, H., McCombie, W. R., Ouyang, S., Schwartz, D. C., Tanaka, T., Wu, J., Zhou, S., Childs, K. L., Davidson, R. M., Lin, H., Quesada-Ocampo, L., Vaillancourt, B., Sakai, H., Lee, S. S., Kim, J., Numa, H., Itoh, T., Buell, C. R., Matsumoto, T. (2013) Improvement of the oryza sativa nipponbare reference genome using next generation sequence and optical map data. Rice, 6 (1). pp. 3-10. ISSN 19398425 (ISSN)

Kim, S. H., Kwon, C. T., Song, G., Koh, H. J., An, G., Paek, N. C. (January 2018) The rice zebra3 (z3) mutation disrupts citrate distribution and produces transverse dark-green/green variegation in mature leaves. Rice (N Y), 11 (1). p. 1. ISSN 1939-8425 (Print)1939-8425

Kwon, C. T., Song, G., Kim, S. H., Han, J., Yoo, S. C., An, G., Kang, K., Paek, N. C. (April 2018) Functional deficiency of phytochrome B improves salt tolerance in rice. Environmental and Experimental Botany, 148. pp. 100-108. ISSN 0098-8472

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Lanctot, Amy (February 2022) Branching out underground: brassinosteroid signaling promotes lateral root development in rice. Plant Physiology. ISSN 1532-2548

Liu, H., Sachidanandam, R., Stein, L. (December 2001) Comparative genomics between rice and Arabidopsis shows scant collinearity in gene order. Genome Research, 11 (12). pp. 2020-2026. ISSN 1088-9051

N

Naithani, S., Gupta, P., Preece, J., D'Eustachio, P., Elser, J. L., Garg, P., Dikeman, D. A., Kiff, J., Cook, J., Olson, A., Wei, S., Tello-Ruiz, M. K., Mundo, A. F., Munoz-Pomer, A., Mohammed, S., Cheng, T., Bolton, E., Papatheodorou, I., Stein, L., Ware, D., Jaiswal, P. (November 2019) Plant Reactome: a knowledgebase and resource for comparative pathway analysis. Nucleic Acids Res, 48. pp. 1093-1103. ISSN 0305-1048 (Public Dataset)

Ntakirutimana, Fabrice, Tranchant-Dubreuil, Christine, Cubry, Philippe, Chougule, Kapeel, Zhang, Jianwei, Wing, Rod A, Adam, Hélène, Lorieux, Mathias, Jouannic, Stefan (August 2023) Genome-wide association analysis identifies natural allelic variants associated with panicle architecture variation in African rice, Oryza glaberrima Steud. G3: Genes, Genomes, Genetics. jkad174. ISSN 2160-1836 (Public Dataset)

P

Pautler, M., Tanaka, W., Hirano, H. Y., Jackson, D. (March 2013) Grass meristems I: Shoot apical meristem maintenance, axillary meristem determinacy and the floral transition. Plant and Cell Physiology, 54 (3). pp. 302-312. ISSN 00320781 (ISSN)

S

Salzberg, S. L., Sommer, D. D., Schatz, M. C., Phillippy, A. M., Rabinowicz, P. D., Tsuge, S., Furutani, A., Ochiai, H., Delcher, A. L., Kelley, D., Madupu, R., Puiu, D., Radune, D., Shumway, M., Trapnell, C., Aparna, G., Jha, G., Pandey, A., Patil, P. B., Ishihara, H., Meyer, D. F., Szurek, B., Verdier, V., Koebnik, R., Maxwell, J. M., Ryan, R. P., Hirata, H., Tsuyumu, S., Won Lee, S., Ronald, P. C., Sonti, R. V., Van Sluys, M. A., Leach, J. E., White, F. F., Bogdanove, A. J. (2008) Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A. BMC Genomics, 9. ISSN 1471-2164

Singh, N. K., Raghuvanshi, S., Srivastava, S. K., Gaur, A., Pal, A. K., Dalal, V., Singh, A., Ghazi, I. A., Bhargav, A., Yadav, M., Dixit, A., Batra, K., Gaikwad, K., Sharma, T. R., Mohanty, A., Bharti, A. K., Kapur, A., Gupta, V., Kumar, D., Vij, S., Vydianathan, R., Khurana, P., Sharma, S., McCombie, W. R., Messing, J., Wing, R., Sasaki, T., Mohapatra, T., Khurana, J. P., Tyagi, A. K. (2004) Sequence analysis of the long arm of rice chromosome 11 for rice-wheat synteny. Functional and Integrative Genomics, 4 (2). pp. 102-117. ISSN 1438793X (ISSN)

Sobral, Bruno W. S., Mangalam, Harry, Siepel, Adam, Mendes, Pedro, Pecherer, Rob, McLaren, Graham (2007) Bioinformatics for Rice Resources. In: Novartis Foundation Symposium 236 - Rice Biotechnology: Improving Yield, Stress Tolerance and Grain Quality. John Wiley & Sons, Ltd., pp. 59-84. ISBN 9780470515778

Somssich, M., Je, B. I., Simon, R., Jackson, D. (September 2016) CLAVATA-WUSCHEL signaling in the shoot meristem. Development, 143 (18). pp. 3238-48. ISSN 1477-9129 (Electronic)0950-1991 (Linking)

Stein, J. C., Yu, Y., Copetti, D., Zwickl, D. J., Zhang, L., Zhang, C., Chougule, K., Gao, D., Iwata, A., Goicoechea, J. L., Wei, S., Wang, J., Liao, Y., Wang, M., Jacquemin, J., Becker, C., Kudrna, D., Zhang, J., Londono, C. E. M., Song, X., Lee, S., Sanchez, P., Zuccolo, A., Ammiraju, J. S. S., Talag, J., Danowitz, A., Rivera, L. F., Gschwend, A. R., Noutsos, C., Wu, C. C., Kao, S. M., Zeng, J. W., Wei, F. J., Zhao, Q., Feng, Q., El Baidouri, M., Carpentier, M. C., Lasserre, E., Cooke, R., Rosa Farias, D. D., da Maia, L. C., Dos Santos, R. S., Nyberg, K. G., McNally, K. L., Mauleon, R., Alexandrov, N., Schmutz, J., Flowers, D., Fan, C., Weigel, D., Jena, K. K., Wicker, T., Chen, M., Han, B., Henry, R., Hsing, Y. C., Kurata, N., de Oliveira, A. C., Panaud, O., Jackson, S. A., Machado, C. A., Sanderson, M. J., Long, M., Ware, D., Wing, R. A. (January 2018) Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nat Genet, 50 (2). pp. 285-296. ISSN 1061-4036

T

Tanaka, T., Antonio, B. A., Kikuchi, S., Matsumoto, T., Nagamura, Y., Numa, H., Sakai, H., Wu, J., Itoh, T., Sasaki, T., Aono, R., Fujii, Y., Habara, T., Harada, E., Kanno, M., Kawahara, Y., Kawashima, H., Kubooka, H., Matsuya, A., Nakaoka, H., Saichi, N., Sanbonmatsu, R., Sato, Y., Shinso, Y., Suzuki, M., Takeda, J. I., Tanino, M., Todokoro, F., Yamaguchi, K., Yamamoto, N., Yamasaki, C., Imanishi, T., Okido, T., Tada, M., Ikeo, K., Tateno, Y., Gojobori, T., Lin, Y. C., Wei, F. J., Hsing, Y. I., Zhao, Q., Han, B., Kramer, M. R., McCombie, R. W., Lonsdale, D., O'Donovan, C. C., Whitfield, E. J., Apweiler, R., Koyanagi, K. O., Khurana, J. P., Raghuvanshi, S., Singh, N. K., Tyagi, A. K., Haberer, G., Fujisawa, M., Hosokawa, S., Ito, Y., Ikawa, H., Shibata, M., Yamamoto, M., Bruskiewich, R. M., Hoen, D. R., Bureau, T. E., Namiki, N., Ohyanagi, H., Sakai, Y., Nobushima, S., Sakata, K., Barrero, R. A., Sato, Y., Souvorov, A., Smith-White, B., Tatusova, T., An, S., An, G., Oota, S., Fuks, G., Messing, J., Christie, K. R., Lieberherr, D., Kim, H., Zuccolo, A., Wing, R. A., Nobuta, K., Green, P. J., Lu, C., Meyers, B. C., Chaparro, C., Piegu, B., Panaud, O., Echeverria, M. (January 2008) The rice annotation project database (RAP-DB): 2008 update. Nucleic Acids Research, 36 (Databa). D1028-D1033. ISSN 0305-1048

V

Vaughn, Justin N, Korani, Walid, Stein, Joshua C, Edwards, Jeremy D, Peterson, Daniel G, Simpson, Sheron A, Youngblood, Ramey C, Grimwood, Jane, Chougule, Kapeel, Ware, Doreen H, McClung, Anna M, Scheffler, Brian E (March 2021) Gene disruption by structural mutations drives selection in US rice breeding over the last century. PLoS Genetics, 17 (3). e1009389. ISSN 1553-7404

W

Ware, D., Stein, L. (April 2003) Comparison of genes among cereals. Current Opinion in Plant Biology, 6 (2). pp. 121-7. ISSN 1369-5266

Y

Youens-Clark, K., 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., Ware, D. H. (January 2011) Gramene database in 2010: updates and extensions. Nucleic Acids Res, 39. D1085-D1094. ISSN 1362-4962 (Electronic) 0305-1048 (Linking)

Yu, Y., Rambo, T., Currie, J., Saski, C., Kim, H. R., Collura, K., Thompson, S., Simmons, J., Yang, T. J., Nah, G., Patel, A. J., Thurmond, S., Henry, D., Oates, R., Palmer, M., Pries, G., Gibson, J., Anderson, H., Paradkar, M., Crane, L., Dale, J., Carver, M. B., Wood, T., Frisch, D., Engler, F., Soderlund, C., Palmer, L. E., Tetylman, L., Nascimento, L., de la Bastide, M., Spiegel, L., Ware, D., O'Shaughnessy, A., Dike, S., Dedhia, N., Preston, R., Huang, E., Ferraro, K., Kuit, K., Miller, B., Zutavern, T., Katzenberger, F., Muller, S., Balija, V., Martienssen, R. A., Stein, L., Minx, P., Johnson, D., Cordum, H., Mardis, E., Cheng, Z., Jiang, J., Wilson, R., McCombie, W. R., Wing, R. A., Yuan, Q., Ouyang, S., Liu, J., Jones, K. M., Gansberger, K., Moffat, K., Hill, J., Tsitrin, T., Overton, L., Bera, J., Kim, M., Jin, S., Tallon, L., Ciecko, A., Pai, G., van Aken, S., Utterback, T., Reidmuller, S., Bormann, J., Feldblyum, T., Hsiao, J., Zismann, V., Blunt, S., de Vazeilles, A., Shaffer, T., Koo, H., Suh, B., Yang, Q., Haas, B., Peterson, J., Pertea, M., Volfovsky, N., Wortman, J., White, O., Salzberg, S. L., Fraser, C. M., Robin Buell, C., Messing, J., Song, R., Fuks, G., Llaca, V., Kovchak, S., Young, S., Bowers, J. E., Paterson, A. H. (2003) In-depth view of structure, activity, and evolution of rice chromosome 10. Science, 300 (5625). pp. 1566-1569. ISSN 00368075 (ISSN)

Z

Zebell, Sophia (March 2021) Gene body silencing parental alleles for vigorous hybrid rice. Plant Physiology, 186 (2). pp. 822-823. ISSN 0032-0889

Zhou, Yong, Yu, Zhichao, Chebotarov, Dmytro, Chougule, Kapeel, Lu, Zhenyuan, Rivera, Luis F, Kathiresan, Nagarajan, Al-Bader, Noor, Mohammed, Nahed, Alsantely, Aseel, Mussurova, Saule, Santos, João, Thimma, Manjula, Troukhan, Maxim, Fornasiero, Alice, Green, Carl D, Copetti, Dario, Kudrna, David, Llaca, Victor, Lorieux, Mathias, Zuccolo, Andrea, Ware, Doreen, McNally, Kenneth, Zhang, Jianwei, Wing, Rod A (March 2023) Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice. Nature Communications, 14 (1). p. 1567. ISSN 2041-1723