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Jiewei Yu

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20022024

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  • 2007

    Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana: The Rice Annotation Project

    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. & 75 others, 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., Feb 2007, In: Genome Research. 17, 2, p. 175-183 9 p.

    Research output: Contribution to journal › Article › peer-review

    202 Scopus citations

  • Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza

    Ammiraju, J. S. S., Zuccolo, A., Yu, Y., Song, X., Piegu, B., Chevalier, F., Walling, J. G., Ma, J., Talag, J., Brar, D. S., SanMiguel, P. J., Jiang, N., Jackson, S. A., Panaud, O. & Wing, R. A., Oct 2007, In: Plant Journal. 52, 2, p. 342-351 10 p.

    Research output: Contribution to journal › Article › peer-review

    85 Scopus citations

  • Transposable element distribution, abundance and role in genome size variation in the genus Oryza

    Zuccolo, A., Sebastian, A., Talag, J., Yu, Y., Kim, H. R., Collura, K., Kudrna, D. & Wing, R. A., 2007, In: BMC Evolutionary Biology. 7, 152.

    Research output: Contribution to journal › Article › peer-review

    93 Scopus citations
  • 2006

    A global assembly of cotton ESTs

    Udall, J. A., Swanson, J. M., Haller, K., Rapp, R. A., Sparks, M. E., Hatfield, J., Yu, Y., Wu, Y., Dowd, C., Arpat, A. B., Sickler, B. A., Wilkins, T. A., Jin, Y. G., Xiao, Y. C., Scheffler, J., Taliercio, E., Turley, R., McFadden, H., Payton, P. & Klueva, N. & 16 others, Allen, R., Zhang, D., Haigler, C., Wilkerson, C., Suo, J., Schulze, S. R., Pierce, M. L., Essenberg, M., Kim, H. R., Llewellyn, D. J., Dennis, E. S., Kudrna, D., Wing, R., Paterson, A. H., Soderlund, C. & Wendel, J. F., Mar 2006, In: Genome Research. 16, 3, p. 441-450 10 p.

    Research output: Contribution to journal › Article › peer-review

    127 Scopus citations

  • The Oryza bacterial artificial chromosome library resource: Construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza

    Ammiraju, J. S. S., Luo, M., Goicoechea, J. L., Wang, W., Kudrna, D., Mueller, C., Talag, J., Kim, H. R., Sisneros, N. B., Blackmon, B., Fang, E., Tomkins, J. B., Brar, D., MacKill, D., McCouch, S., Kurata, N., Lambert, G., Galbraith, D. W., Arumuganathan, K. & Rao, K. & 7 others, Walling, J. G., Gill, N., Yu, Y., SanMiguel, P., Soderlund, C., Jackson, S. & Wing, R. A., Jan 2006, In: Genome Research. 16, 1, p. 140-147 8 p.

    Research output: Contribution to journal › Article › peer-review

    184 Scopus citations

  • Utilization of a zebra finch BAC library to determine the structure of an avian androgen receptor genomic region

    Luo, M., Yu, Y., Kim, H., Kudrna, D., Itoh, Y., Agate, R. J., Melamed, E., Goicoechea, J. L., Talag, J., Mueller, C., Wang, W., Currie, J., Sisneros, N. B., Wing, R. A. & Arnold, A. P., Jan 2006, In: Genomics. 87, 1, p. 181-190 10 p.

    Research output: Contribution to journal › Article › peer-review

    24 Scopus citations
  • 2005

    Candidate gene database and transcript map for peach, a model species for fruit trees

    Horn, R., Lecouls, A. C., Callahan, A., Dandekar, A., Garay, L., McCord, P., Howad, W., Chan, H., Verde, I., Main, D., Jung, S., Georgi, L., Forrest, S., Mook, J., Zhebentyayeva, T., Yu, Y., Hye, R. K., Jesudurai, C., Sosinski, B. & Arús, P. & 7 others, Baird, V., Parfitt, D., Reighard, G., Scorza, R., Tomkins, J., Wing, R. & Abbott, A. G., May 2005, In: Theoretical and Applied Genetics. 110, 8, p. 1419-1428 10 p.

    Research output: Contribution to journal › Article › peer-review

    68 Scopus citations

  • In-depth sequence analysis of the tomato chromosome 12 centromeric region: Identification of a large CAA block and characterization of pericentromere retrotranposons

    Yang, T. J., Lee, S., Chang, S. B., Yu, Y., de Jong, H. & Wing, R. A., Jul 2005, In: Chromosoma. 114, 2, p. 103-117 15 p.

    Research output: Contribution to journal › Article › peer-review

    46 Scopus citations

  • Large-scale identification of expressed sequence tags involved in rice and rice blast fungus interaction

    Jantasuriyarat, C., Gowda, M., Haller, K., Hatfield, J., Lu, G., Stahlberg, E., Zhou, B., Li, H., Kim, H. R., Yu, Y., Dean, R. A., Wing, R. A., Soderlund, C. & Wang, G. L., 2005, In: Plant physiology. 138, 1, p. 105-115 11 p.

    Research output: Contribution to journal › Article › peer-review

    86 Scopus citations

  • Random sheared fosmid library as a new genomic tool to accelerate complete finishing of rice (Oryza sativa spp. Nipponbare) genome sequence: Sequencing of gap-specific fosmid clones uncovers new euchromatic portions of the genome

    Ammiraju, J. S. S., Yu, Y., Luo, M., Kudrna, D., Kim, H. R., Goicoechea, J. L., Katayose, Y., Matsumoto, T., Wu, J., Sasaki, T. & Wing, R. A., Nov 2005, In: Theoretical and Applied Genetics. 111, 8, p. 1596-1607 12 p.

    Research output: Contribution to journal › Article › peer-review

    30 Scopus citations

  • Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. The Rice Chromosome 3 Sequencing Consortium

    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. & 56 others, 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. R., 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., Soderlund, C., Soderlund, C., Nelson, W., Soderlund, C., De La Bastide, M., Spiegel, L., Nascimento, L., Huang, E., Preston, R., Zutavern, T., Palmer, L., O'haughnessy, A., Dike, S., McCombie, W. R., Minx, P., Cordum, H., Wilson, R., Jin, W., Lee, H. R., Jiang, J. & Jackson, S., Sep 1 2005, In: Genome Research. 15, 9, p. 1284-1291 8 p.

    Research output: Contribution to journal › Article › peer-review

    60 Scopus citations

  • The map-based sequence of the rice genome

    Matsumoto, T., Wu, J., Kanamori, H., Katayose, Y., Fujisawa, M., Namiki, N., Mizuno, H., Yamamoto, K., Antonio, B. A., Baba, T., Sakata, K., Nagamura, Y., Aoki, H., Arikawa, K., Arita, K., Bito, T., Chiden, Y., Fujitsuka, N., Fukunaka, R. & Hamada, M. & 243 others, Harada, C., Hayashi, A., Hijishita, S., Honda, M., Hosokawa, S., Ichikawa, Y., Idonuma, A., Iijima, M., Ikeda, M., Ikeno, M., Ito, K., Ito, S., Ito, T., Ito, Y., Ito, Y., Iwabuchi, A., Kamiya, K., Karasawa, W., Kurita, K., Katagiri, S., Kikuta, A., Kobayashi, H., Kobayashi, N., MacHita, K., Maehara, T., Masukawa, M., Mizubayashi, T., Mukai, Y., Nagasaki, H., Nagata, Y., Naito, S., Nakashima, M., Nakama, Y., Nakamichi, Y., Nakamura, M., Meguro, A., Negishi, M., Ohta, I., Ohta, T., Okamoto, M., Ono, N., Saji, S., Sakaguchi, M., Sakai, K., Shibata, M., Shimokawa, T., Song, J., Takazaki, Y., Terasawa, K., Tsugane, M., Tsuji, K., Ueda, S., Waki, K., Yamagata, H., Yamamoto, M., Yamamoto, S., Yamane, H., Yoshiki, S., Yoshihara, R., Yukawa, K., Zhong, H., Yano, M., Sasaki, T., Yuan, Q., Ouyang, S., Liu, J., Jones, K. M., Gansberger, K., Moffat, K., Hill, J., Bera, J., Fadrosh, D., Jin, S., Johri, S., Kim, M., Overton, L., Reardon, M., Tsitrin, T., Vuong, H., Weaver, B., Ciecko, A., Tallon, L., Jackson, J., Pai, G., Van Aken, S., Utterback, T., Reidmuller, S., Feldblyum, T., Hsiao, J., Zismann, V., Iobst, S., De Vazeille, A. R., Buell, C. R., Ying, K., Li, Y., Lu, T., Huang, Y., Zhao, Q., Feng, Q., Zhang, L., Zhu, J., Weng, Q., Mu, J., Lu, Y., Fan, D., Liu, Y., Guan, J., Zhang, Y., Yu, S., Liu, X., Zhang, Y., Hong, G., Han, B., Choisne, N., Demange, N., Orjeda, G., Samain, S., Cattolico, L., Pelletier, E., Couloux, A., Segurens, B., Wincker, P., D'Hont, A., Scarpelli, C., Weissenbach, J., Salanoubat, M., Quetier, F., Yu, Y., Kim, H. R., Rambo, T., Currie, J., Collura, K., Luo, M., Yang, T. J., Ammiraju, J. S. S., Engler, F., Soderlund, C., Wing, R. A., Palmer, L. E., De La Bastide, M., Spiegel, L., Nascimento, L., Zutavern, T., O'Shaughnessy, A., Dike, S., Dedhia, N., Preston, R., Balija, V., McCombie, W. R., Chow, T. Y., Chen, H. H., Chung, M. C., Chen, C. S., Shaw, J. F., Wu, H. P., Hsiao, K. J., Chao, Y. T., Chu, M. K., Cheng, C. H., Hour, A. L., Lee, P. F., Lin, S. J., Lin, Y. C., Liou, J. Y., Liu, S. M., Hsing, Y. I., Raghuvanshi, S., Mohanty, A., Bharti, A. K., Gaur, A., Gupta, V., Kumar, D., Ravi, V., Vij, S., Kapur, A., Khurana, P., Khurana, P., Khurana, J. P., Tyagi, A. K., Gaikwad, K., Singh, A., Dalal, V., Srivastava, S., Dixit, A., Pal, A. K., Ghazi, I. A., Yadav, M., Pandit, A., Bhargava, A., Sureshbabu, K., Batra, K., Sharma, T. R., Mohapatra, T., Singh, N. K., Messing, J., Nelson, A. B., Fuks, G., Kavchok, S., Keizer, G., Llaca, E. L. V., Song, R., Tanyolac, B., Young, S., Ho, K., Hahn, J. H., Sangsakoo, G., Vanavichit, A., De Mattos, L. A. T., Zimmer, P. D., Malone, G., Dellagostin, O., De Oliveira, A. C., Bevan, M., Bancroft, I., Minx, P., Cordum, H., Wilson, R., Cheng, Z., Jin, W., Jiang, J., Leong, S. A., Iwama, H., Gojobori, T., Itoh, T., Niimura, Y., Fujii, Y., Habara, T., Sakai, H., Sato, Y., Wilson, G., Kumar, K., McCouch, S., Juretic, N., Hoen, D., Wright, S., Bruskiewich, R., Bureau, T., Miyao, A., Hirochika, H., Nishikawa, T., Kadowaki, K. I., Sugiura, M. & Burr, B., Aug 11 2005, In: Nature. 436, 7052, p. 793-800 8 p.

    Research output: Contribution to journal › Article › peer-review

    3173 Scopus citations

  • The Oryza map alignment project: The golden path to unlocking the genetic potential of wild rice species

    Wing, R. A., Ammiraju, J. S. S., Luo, M., Kim, H. R., Yu, Y., Kudrna, D., Goicoechea, J. L., Wang, W., Nelson, W., Rao, K., Brar, D., Mackill, D. J., Han, B., Soderlund, C., Stein, L., SanMiguel, P. & Jackson, S., Sep 2005, In: Plant Molecular Biology. 59, 1, p. 53-62 10 p.

    Research output: Contribution to journal › Article › peer-review

    137 Scopus citations

  • The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications

    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., Singh, N. K., Mohapatra, T., Sharma, T. R., Gaikwad, K., Singh, A., Dalal, V. & Srivastava, S. K. & 79 others, 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, P., Khurana, J. P., Tyagi, A. K., Yuan, Q., Ouyang, S., Liu, J., Zhu, W., Wang, A., Lin, H., Hamilton, J., Haas, B., Wortman, J., Jones, K. M., Kim, M., Overton, L., Tsitrin, T., Fadrosh, D., Bera, J., Weaver, B., Jin, S., 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., Kudrna, D., Mueller, C., Wing, R. A., Kramer, M., Spiegel, L., Nascimento, L., Preston, R., Zutavern, T. & Messing, J., Sep 27 2005, In: BMC biology. 3, 20.

    Research output: Contribution to journal › Article › peer-review

    156 Scopus citations

  • Toward closing rice telomere gaps: Mapping and sequence characterization of rice subtelomere regions

    Yang, T. J., Yu, Y., Chang, S. B., De Jong, H., Oh, C. S., Ahn, S. N., Fang, E. & Wing, R. A., Aug 2005, In: Theoretical and Applied Genetics. 111, 3, p. 467-478 12 p.

    Research output: Contribution to journal › Article › peer-review

    20 Scopus citations
  • 2004

    Sequence composition and genome organization of maize

    Messing, J., Bharti, A. K., Karlowski, W. M., Gundlach, H., Hye, R. K., Yu, Y., Wei, F., Fuks, G., Soderlund, C. A., Mayer, K. F. X. & Wing, R. A., Oct 5 2004, In: Proceedings of the National Academy of Sciences of the United States of America. 101, 40, p. 14349-14354 6 p.

    Research output: Contribution to journal › Article › peer-review

    247 Scopus citations
  • 2003

    Construction and utility of 10-kb libraries for efficient clone-gap closure for rice genome sequencing

    Yang, T. J., Yu, Y., Nah, G., Atkins, M., Lee, S., Frisch, D. A. & Wing, R. A., Aug 1 2003, In: Theoretical and Applied Genetics. 107, 4, p. 652-660 9 p.

    Research output: Contribution to journal › Article › peer-review

    15 Scopus citations

  • In-depth view of structure, activity, and evolution of rice chromosome 10

    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. & 84 others, 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., Johns, M. A., Mao, L., Pan, H. & Dean, R. A., Jun 6 2003, In: Science. 300, 5625, p. 1566-1569 4 p.

    Research output: Contribution to journal › Article › peer-review

    220 Scopus citations
  • 2002

    New genomic resources for the honey bee (Apis mellifera L.): Development of a deep-coverage BAC library and a preliminary STC database

    Tomkins, J. P., Luo, M., Fang, G. C., Main, D., Goicoechea, J. L., Atkins, M., Frisch, D. A., Page, R. E., Guzmán-Novoa, E., Yu, Y., Hunt, G. & Wing, R. A., 2002, In: Genetics and Molecular Research. 1, 4, p. 306-316 11 p.

    Research output: Contribution to journal › Article › peer-review

    14 Scopus citations