h-index: 42, i10-index: 86 by Google Scholar Citations (January 2012)
2012
90. Kodama Y, Mashima J, Kaminuma E, Gojobori T, Ogasawara O, Takagi T, Okubo K, Nakamura Y. (2012) The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments. Nucleic Acids Res., 40, D38-42.
[PubMed: 22110025]
89. Karsch-Mizrachi I, Nakamura Y, Cochrane G; on behalf of the International Nucleotide Sequence Database Collaboration. (2012) The International Nucleotide Sequence Database Collaboration. Nucleic Acids Res., 40, D33-D37.
[PubMed: 22080546]
2011
88. Hakoyama T, Niimi K, Yamamoto T, Isobe S, Sato S, Nakamura Y, Tabata S, Kumagai H, Umehara Y, Brossuleit K, Petersen TR, Sandal N, Stougaard J, Udvardi MK, Tamaoki M, Kawaguchi M, Kouchi H, Suganuma N. (2011) The Integral Membrane Protein SEN1 is Required for Symbiotic Nitrogen Fixation in Lotus japonicus Nodules. Plant Cell Physiol., Nov 28. [Epub ahead of print]
[PubMed: 22123791]
87. Yilmaz P, Gilbert JA, Knight R, Amaral-Zettler L, Karsch-Mizrachi I, Cochrane G, Nakamura Y, Sansone SA, Glöckner FO, Field D. The genomic standards consortium: bringing standards to life for microbial ecology. (2011) ISME J., Apr 7. [Epub ahead of print]
[PubMed: 21472015]
86. Cochrane G, Karsch-Mizrachi I, Nakamura Y; On behalf of the International Nucleotide Sequence Database Collaboration. (2011) The International Nucleotide Sequence Database Collaboration. Nucl. Acids Res., 39, D15-D18.
[PubMed: 21106499]
85. Kaminuma E, Kosuge T, Kodama Y, Aono H, Mashima J, Gojobori T, Sugawara H, Ogasawara O, Takagi T, Okubo K, Nakamura Y. (2011) DDBJ progress report. Nucl. Acids Res., 39, D22-D27.
[PubMed: 21062814]
2010
84. Hirschman L, Sterk P, Field D, Wooley J, Cochrane G, Gilbert J, Kolker E, Kyrpides N, Meyer F, Mizrachi I, Nakamura Y, Sansone SA, Schriml L, Tatusova T, White O, Yilmaz P. Meeting Report: “Metagenomics, Metadata and Meta-analysis” (M3) Workshop at the Pacific Symposium on Biocomputing 2010. (2010) Stand Genomic Sci., 2 (3) 357-360.
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83. Shirasawa K, Isobe S, Hirakawa H, Asamizu E, Fukuoka H, Just D, Rothan C, Sasamoto S, Fujishiro T, Kishida Y, Kohara M, Tsuruoka H, Wada T, Nakamura Y, Sato S, Tabata S. (2010) SNP Discovery and Linkage Map Construction in Cultivated Tomato. DNA Res., 17, 381-391.
[PubMed: 21044984]
82. Inagaki S, Miura-Kamio A, Nakamura Y, Lu F, Cui X, Cao X, Kimura H, Saze H, Kakutani T. (2010) Autocatalytic differentiation of epigenetic modifications within the Arabidopsis genome. EMBO J. 29, 3496-3506.
[PubMed: 20834229]
81. Kodama Y, Kaminuma E, Saruhashi S, Ikeo K, Sugawara H, Tateno Y, Nakamura Y. (2010) Biological Databases at DNA Data Bank of Japan in the Era of Next-Generation Sequencing Technologies. Adv Exp Med Biol., 680, 125-135.
[PubMed: 20865494]
80. Katayama T, Arakawa K, Nakao M, Ono K, Aoki-Kinoshita KF, Yamamoto Y, Yamaguchi A, Kawashima S, Chun HW, Aerts J, Aranda B, Barboza LH, Bonnal RJ, Bruskiewich R, Bryne JC, Fernendez JM, Funahashi A, Gordon PM, Goto N, Groscurth A, Gutteridge A, Holland R, Kano Y, Kawas EA, Kerhornou A, Kibukawa E, Kinjo AR, Kuhn M, Lapp H, Lehvaslaiho H, Nakamura H, Nakamura Y, Nishizawa T, Nobata C, Noguchi T, Oinn TM, Okamoto S, Owen S, Pafilis E, Pocock M, Prins P, Ranzinger R, Reisinger F, Salwinski L, Schreiber M, Senger M, Shigemoto Y, Standley DM, Sugawara H, Tashiro T, Trelles O, Vos RA, Wilkinson MD, York W, Zmasek CM, Asai K, Takagi T. (2010) The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. J Biomed Semantics. Aug 21;1(1):8.
[PubMed: 20727200]
79. Shirasawa, K., Asamizu, E., Fukuoka, H., Ohyama, A., Sato, S., Nakamura, Y., Tabata, S., Sasamoto, S., Wada, T., Kishida, Y., Tsuruoka, H., Fujishiro, T., Yamada, M. and Isobe, S. (2010) An interspecific linkage map of SSR and intronic polymorphism markers in tomato. Theor Appl Genet., 121, 731-739.
[PubMed: 20431859]
78. Kaneko, T., Minamisawa, K., Isawa, T., Nakatsukasa, H., Mitsui, H., Kawaharada, Y., Nakamura, Y., Watanabe, A., Kawashima, K., Ono, A., Shimizu, Y., Takahashi, C., Minami, C., Fujishiro, T., Kohara, M., Katoh, M., Nakazaki, N., Nakayama, S., Yamada, M., Tabata, S. and Sato, S. (2010) Complete Genomic Structure of the Cultivated Rice Endophyte Azospirillum sp. B510. DNA Res., 17, 37-50.
[PMC: PMC2818188]
77. Nakao, M., Okamoto, S., Kohara, M., Fujishiro, T., Fujisawa, T., Sato, S., Tabata, S., Kaneko, T. and Nakamura, Y. (2010) CyanoBase: the cyanobacteria genome database update 2010. Nucleic Acids Res., 38, (Database issue) D379-381.
[PMC: PMC2808859]
76. Kaminuma, E., Mashima, J., Kodama, Y., Gojobori, T., Ogasawara, O., Okubo, K., Takagi, T. and Nakamura, Y. (2010) DDBJ launches a new archive database with analytical tools for next-generation sequence data. Nucleic Acids Res., 38, (Database issue) D33-38.
[PMC: PMC2808917]
2009
75. Hakoyama, T., Niimi, K., Watanabe, H., Tabata, R., Matsubara, J., Sato, S., Nakamura, Y., Tabata, S., Jichun, L., Matsumoto, T., Tatsumi, K., Nomura, M., Tajima, S., Ishizaka, M., Yano, K., Imaizumi-Anraku, H., Kawaguchi, M., Kouchi, H. and Suganuma N. (2009) Host plant genome overcomes the lack of a bacterial gene for symbiotic nitrogen fixation. Nature, 462, 514-517.
[Nature]
74. Ikeda, S., Kaneko, T., Okubo, T., Rallos, L.E., Eda, S., Mitsui, H., Sato, S., Nakamura, Y., Tabata, S. and Minamisawa K. (2009) Development of a bacterial cell enrichment method and its application to the community analysis in soybean stems. Microb Ecol., 58, 703-714.
[PubMed: 19662454]
2008
73. Shimoda, Y., Mitsui, H., Kamimatsuse, H., Minamisawa, K., Nishiyama, E., Ohtsubo, Y., Nagata, Y., Tsuda, M., Shinpo, S., Watanabe, A., Kohara, M., Yamada, M., Nakamura, Y.,Tabata, S. and Sato S. (2008) Construction of signature-tagged mutant library in Mesorhizobium loti as a powerful tool for functional genomics. DNA Res., 15, 297-308.
[PMC: PMC2575893]
72. Sato, S., Nakamura, Y., Kaneko, T., Asamizu, E., Kato, T., Nakao, M., Sasamoto, S., Watanabe, A., Ono, A., Kawashima, K., Fujishiro, T., Katoh, M., Kohara, M., Kishida, Y., Minami, C., Nakayama, S., Nakazaki, N., Shimizu, Y., Shinpo, S., Takahashi, C., Wada, T., Yamada, M., Ohmido, N., Hayashi, M., Fukui, K., Baba, T., Nakamichi, T., Mori, H. and Tabata, S. (2008) Genome Structure of the Legume, Lotus japonicus. DNA Res., 15, 227-239.
[PMC: PMC2575887]
71. Shimoda, Y., Shinpo, S., Kohara, M., Nakamura, Y., Tabata, S. and Sato, S. (2008) A Large Scale Analysis of Protein-Protein Interactions in the Nitrogen-fixing Bacterium Mesorhizobium loti. DNA Res., 15, 13-23.
[PubMed: 18192278]
2007
70. Kinoshita, A., Nakamura, Y., Sasaki, E., Kyozuka, J., Fukuda, H. and Sawa, S. (2007) Gain-of-Function Phenotypes of Chemically Synthetic CLAVATA3/ESR-Related (CLE) Peptides in Arabidopsis thaliana and Oryza sativa. Plant Cell Physiol., 48, 1821-1825.
[PubMed: 17991631]
69. Hisano, H., Sato, S., Isobe, S., Sasamoto, S., Wada, T., Matsuno, A., Fujishiro, T., Yamada, M., Nakayama, S., Nakamura, Y., Watanabe, S., Harada, K. and Tabata, S. (2007) Characterization of the soybean genome using EST-derived microsatellite markers. DNA Res., 14, 271-281.
[PubMed: 118192281]
68. Kaneko, T., Nakajima, N., Okamoto, S., Suzuki, I., Tanabe, Y., Tamaoki, M., Nakamura, Y., Kasai, F., Watanabe, A., Kawashima, K., Kishida, Y., Ono, A., Shimizu, Y., Takahashi, C., Minami, C., Fujishiro, T., Kohara, M., Katoh, M., Nakazaki, N., Nakayama, S., Yamada, M., Tabata, S. and Watanabe, M.M. (2007) Complete genomic structure of the bloom-forming toxic cyanobacterium Microcystis aeruginosa NIES 843. DNA Res., 14, 247-256.
[PubMed: 18192279]
67. Sato, S., Shimoda, Y., Muraki, A., Kohara, M., Nakamura, Y. and Tabata, S. (2007) A Large-scale Protein protein Interaction Analysis in Synechocystis sp. PCC6803. DNA Res., 14, 207-216.
[PubMed: 18000013]
2006
66. Sugiyama, A., Shitan, N., Sato, S., Nakamura, Y., Tabata, S. and Yazaki, K. (2006) Genome-wide analysis of ATP-binding cassette (ABC) proteins in a model legume plant, Lotus japonicus: comparison with Arabidopsis ABC protein family. DNA Res., 13, 205-228.
[PubMed: 17164256]
65. Kanamori, N., Madsen, L.H., Radutoiu, S., Frantescu, M., Quistgaard, E.M., Miwa, H., Downie, J.A., James, E.K., Felle, H.H., Haaning, L.L., Jensen, T.H., Sato, S., Nakamura, Y., Tabata, S., Sandal, N. and Stougaard, J. (2006) A nucleoporin is required for induction of Ca2+ spiking in legume nodule development and essential for rhizobial and fungal symbiosis. Proc Natl Acad Sci U S A., 103, 359-364.
[PubMed: 16407163]
2005
64. Sato, S., Isobe, S., Asamizu, E., Ohmido, N., Kataoka, R., Nakamura, Y., Kaneko, T., Sakurai, N., Okumura, K., Klimenko, I., Sasamoto, S., Wada, T., Watanabe, A., Kohara, M., Fujishiro, T. and Tabata, S. (2005) Comprehensive Structural Analysis of the Genome of Red Clover (Trifolium pratense L.). DNA Res., 12, 301-364.
[PubMed: 16769692]
63. Imaizumi, R., Sato, S., Kameya, N., Nakamura, I., Nakamura, Y., Tabata, S., Ayabe, S. and Aoki, T. (2005) Activation tagging approach in a model legume, Lotus japonicus. J Plant Res., 118, 391-399.
[PubMed: 16273423]
62. Asamizu, E., Nakamura, Y., Sato, S. and Tabata, S. (2005) Comparison of the transcript profiles from the root and the nodulating root of the model legume Lotus japonicus by serial analysis of gene expression. Mol Plant Microbe Interact., 18, 487-498.
[PubMed: 15915647]
61. Buzas, D.M., Lohar, D., Sato, S., Nakamura, Y., Tabata, S., Vickers, C.E., Stiller, J. and Gresshoff, P.M. (2005) Promoter trapping in Lotus japonicus reveals novel root and nodule GUS expression domains. Plant Cell Physiol., 46, 1202-1212.
[PubMed: 15899881]
60. Krusell, L., Krause, K., Ott, T., Desbrosses, G., Kramer, U., Sato, S., Nakamura, Y., Tabata, S., James, E.K., Sandal, N., Stougaard, J., Kawaguchi, M., Miyamoto, A., Suganuma, N. and Udvardi, M.K. (2005) The sulfate transporter SST1 is crucial for symbiotic nitrogen fixation in Lotus japonicus root nodules. Plant Cell., 17, 1625-1636.
[PubMed: 15805486]
2004
59. Miura, K., Yamano, T., Yoshioka, S., Kohinata, T., Inoue, Y., Taniguchi, F., Asamizu, E., Nakamura, Y., Tabata, S., Yamato, K.T., Ohyama, K. and Fukuzawa, H. (2004) Expression profiling-based identification of CO2-responsive genes regulated by CCM1 controlling a carbon-concentrating mechanism in Chlamydomonas reinhardtii. Plant Physiol., 135, 1595-1607.
[PubMed: 15235119]
58. Asamizu, E., Nakamura, Y., Sato, S. and Tabata, S. (2004) Characteristics of the Lotus Japonicus Gene Repertoire Deduced from Large-Scale Expressed Sequence Tag (EST) Analysis. Plant Mol. Biol., 54, 405-414.
[PubMed: 15284495]
57. Obayashi, T., Okegawa, T., Sasaki-Sekimoto, Y., Shimada, H., Masuda, T., Asamizu, E., Nakamura, Y., Shibata, D., Tabata, S., Takamiya, K. and Ohta, H. (2004) Distinctive features of plant organs characterized by global analysis of gene expression in Arabidopsis. DNA Res., 11, 11-25.
[PubMed: 15141942]
[DNA Res (PDF)]
2003
56. Radutoiu, S., Madsen, L.H., Madsen, E.B., Felle, H.H., Umehara, Y., Gronlund, M., Sato, S., Nakamura, Y., Tabata, S., Sandal, N. and Stougaard, J. (2003) Plant recognition of symbiotic bacteria requires two LysM receptor-like kinases. Nature, 425, 585-592.
[PubMed: 1453457]
[nature]
55. Kato, T., Sato, S., Nakamura, Y., Kaneko, T., Asamizu, E. and Tabata, S. (2003) Structural analysis of a Lotus japonicus genome. V. Sequence features and mapping of sixty-four TAC clones which cover the 6.4 Mb regions of the genome. DNA Res., 10, 277-285.
54. Kaneko, T., Nakamura, Y., Sasamoto, S., Watanabe, A., Kohara, M., Matsumoto, M., Shimpo, S., Yamada, M. and Tabata, S. (2003) Structural analysis of four large plasmids harboring in a unicellular cyanobacterium, Synechocystis sp. PCC 6803. DNA Res., 10, 221-228.
[PubMed: 14686584]
[DNA Res (PDF)]
53. Nakamura, Y., Kaneko, T., Sato, S., Mimuro, M., Miyashita, H., Tsuchiya, T., Sasamoto, S., Watanabe, A., Kawashima, K., Kishida, Y., Kiyokawa, C., Kohara, M., Matsumoto, M., Matsuno, A., Nakazaki, N., Shinpo, S., Takeuchi, C., Yamada, M. and Tabata S. (2003) Complete Genome Structure of Gloeobacter violaceus PCC 7421, a Cyanobacterium that Lacks Thylakoids. DNA Res., 10, 181-201.
[PubMed: 14621292]
[DNA Res (PDF)]
(Supplement: DNA Res., 10, 137-145. [DNA Res (PDF)])
52. Asamizu, E., Kato, T., Sato, S., Nakamura, Y., Kaneko, T. and Tabata, S. (2003) Structural analysis of a Lotus japonicus genome. IV. Sequence features and mapping of seventy-three TAC clones which cover the 7.5 Mb regions of the genome. DNA Res., 10, 115-122.
[PubMed: 12886953]
[DNA Res (PDF)]
51. Kaneko, T., Asamizu, E., Kato, T., Sato, S., Nakamura, Y. and Tabata, S. (2003) Structural analysis of a Lotus japonicus genome. III. Sequence features and mapping of sixty-two TAC clones which cover the 6.7 Mb regions of the genome. DNA Res., 10, 27-33.
[PubMed: 12693552]
[DNA Res (PDF)]
2002
50. Kaneko, T., Nakamura, Y., Sato, S., Minamisawa, K., Uchiumi, T., Sasamoto, S., Watanabe, A., Idesawa, K., Iriguchi, M., Kawashima, K., Kohara, M., Matsumoto, M., Shimpo, S., Tsuruoka, H., Wada, T., Yamada, M. and Tabata, S. (2002) Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Res., 9, 189-197
[PubMed: 12597275]
[DNA Res (PDF)]
(Supplement: DNA Res., 9, 225-256. [DNA Res (PDF)])
49. Nakamura, Y., Kaneko, T., Sato,S., Ikeuchi, M., Katoh, H., Sasamoto, S., Watanabe, A., Iriguchi, M., Kawashima, K., Kimura, T., Kishida, Y., Kiyokawa, C., Kohara, M., Matsumoto, M., Matsuno, A., Nakazaki, N., Shinpo, S., Sugimoto, M., Takeuchi, C., Yamada, M. and Tabata S. (2002) Complete genome structure of the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1. DNA Res., 9, 123-130.
[PubMed: 12240834]
[DNA Res (PDF)]
(Supplement: DNA Res., 9, 135-148. [DNA Res (PDF)])
48. Nakamura, Y., Kaneko, T., Asamizu, E., Kato, T., Sato, S. and Tabata, S. (2002) Structural analysis of a Lotus japonicus genome. II. Sequence features and mapping of sixty-five TAC clones which cover the 6.5-Mb regions of the genome. DNA Res., 9, 63-70.
[PubMed: 12056416]
[DNA Res (PDF)]
47. Hanano, S., Amagai, M., Kaneko, T., Kuwata, C., Tsugane, T., Sakurai, N., Nakamura Y., Shibata, D. and Tabata, S. (2002) Analysis of gene expression in Arabidopsis thaliana by array hybridization with genomic DNA fragments aligned along chromosomal regions. Plant J., 30, 247-255.
[PubMed: 12000460]
2001
46. Sato, S., Kaneko, T., Nakamura, Y., Asamizu, E., Kato, T. and Tabata, S. (2001) Structural analysis of a Lotus japonicus genome. I. Sequence features and mapping of fifty-six TAC clones which cover the 5.4 Mb regions of the genome. DNA Res., 8, 311-318.
[PubMed: 11853318]
[DNA Res (PDF)]
45. Kaneko, T., Nakamura, Y., Wolk, C.P., Kuritz, T., Sasamoto, S., Watanabe, A., Iriguchi, M., Ishikawa, A., Kawashima, K., Kimura, T., Kishida, Y., Kohara, M., Matsumoto, M., Matsuno, A., Muraki, A., Nakazaki, N., Shimpo, S., Sugimoto, M., Takazawa, M., Yamada, M., Yasuda, M. and Tabata, S. (2001) Complete genomic sequence of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120. DNA Res., 8, 205-213.
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[DNA Res (PDF)]
(Supplement: DNA Res., 8, 227-253. [DNA Res (PDF)])
44. Sato, S., Kato, T., Kakegawa, K., Ishii, T., Liu, Y.G., Awano, T., Takabe, K., Nishiyama, Y., Kuga, S., Sato, S., Nakamura, Y., Tabata, S. and Shibata, D. (2001) Role of the putative membrane-bound endo-1,4-beta-glucanase KORRIGAN in cell elongation and cellulose synthesis in Arabidopsis thaliana. Plant Cell Physiol., 42, 251-263.
[PubMed: 11266576]
2000
43. Kaneko, T., Nakamura, Y., Sato, S., Asamizu, E., Kato, T., Sasamoto, S., Watanabe, A., Idesawa, K., Ishikawa, A., Kawashima, K., Kimura, T., Kishida, Y., Kiyokawa, C., Kohara, M., Matsumoto, M., Matsuno, A., Mochizuki, Y., Nakayama, S., Nakazaki, N., Shimpo, S., Sugimoto, M., Takeuchi, C., Yamada, M. and Tabata, S. (2000) Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti. DNA Res., 7, 331-338.
[PubMed: 11214968]
[DNA Res (PDF)]
(Supplement: DNA Res., 10, 381-406. [DNA Res (PDF)])
42. Kato, T., Kaneko, T., Sato, S., Nakamura, Y. and Tabata, S. (2000) Complete structure of the chloroplast genome of a legume, Lotus japonicus. DNA Res., 7, 323-330.
[PubMed: 11214967]
[DNA Res (PDF)]
41. Asamizu, E., Miura, K., Kucho, K., Inoue, Y., Fukuzawa, H., Ohyama, K., Nakamura, Y. and Tabata, S. (2000) Generation of expressed sequence tags from low-CO2 and high-CO2 adapted cells of Chlamydomonas reinhardtii. DNA Res., 7, 305-307.
[PubMed: 11089912]
[DNA Res (PDF)]
40. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796-815.
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[Nature]
39. Salanoubat, M., Lemcke, K., Rieger, M., Ansorge, W., Unseld, M., Fartmann, B., Valle, G., Blocker, H., Perez-. Alonso, M., Obermaier, B., Delseny, M., Boutry, M., Grivell, L. A., Mache, R., Puigdomenech, P., De, Simone, V., Choisne, N., Artiguenave, F., Robert, C., Brottier, P., Wincker, P., Cattolico, L., Weissenbach, J., Saurin, W., Quetier, F., Schafer, M., Muller-. Auer, S., Gabel, C., Fuchs, M., Benes, V., Wurmbach, E., Drzonek, H., Erfle, H., Jordan, N., Bangert, S., Wiedelmann, R., Kranz, H., Voss, H., Holland, R., Brandt, P., Nyakatura, G., Vezzi, A., D’Angelo, M., Pallavicini, A., Toppo, S., Simionati, B., Conrad, A., Hornischer, K., Kauer, G., Lohnert, T. H., Nordsiek, G., Reichelt, J., Scharfe, M., Schon, O., Bargues, M., Terol, J., Climent, J., Navarro, P., Collado, C., Perez-Perez, A., Ottenwalder, B., Duchemin, D., Cooke, R., Laudie, M., Berger-. Llauro, C., Purnelle, B., Masuy, D., de Haan, M., Maarse, A. C., Alcaraz, J. P., Cottet, A., Casacuberta, E., Monfort, A., Argiriou, A., flores M., Liguori, R., Vitale, D., Mannhaupt, G., Haase, D., Schoof, H., Rudd, S., Zaccaria, P., Mewes, H. W., Mayer, K. F., Kaul, S., Town, C. D., Koo, H. L., Tallon, L. J., Jenkins, J., Rooney, T., Rizzo, M., Walts, A., Utterback, T., Fujii, C. Y., Shea, T. P., Creasy, T. H., Haas, B., Maiti, R., Wu, D., Peterson, J., Van, Aken, S., Pai, G., Militscher, J., Sellers, P., Gill, J. E., Feldblyum, T. V., Preuss, D., Lin, X., Nierman, W. C., Salzberg, S. L., White, O., Venter, J. C., Fraser, C. M., Kaneko, T., Nakamura, Y., Sato, S., Kato, T., Asamizu, E., Sasamoto, S., Kimura, T., Idesawa, K., Kawashima, K., Kishida, Y., Kiyokawa, C., Kohara, M., Matsumoto, M., Matsuno, A., Muraki, A., Nakayama, S., Nakazaki, N., Shinpo, S., Takeuchi, C., Wada, T., Watanabe, A., Yamada, M., Yasuda, M. and Tabata, S. (European Union Chromosome 3 Arabidopsis Sequencing Consortium, The Institute for Genomic Research and Kazusa DNA Research Institute) (2000) Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana. Nature, 408, 820-822.
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[Nature]
38. Tabata, S., Kaneko, T., Nakamura, Y., Kotani, H., Kato, T., Asamizu, E., Miyajima, N., Sasamoto, S., Kimura, T., Hosouchi, T, Kawashima, K., Kohara, M., Matsumoto, M., Matsuno, A., Muraki, A., Nakayama, S., Nakazaki, N., Naruo, K., Okumura, S., Shinpo, S., Takeuchi, C., Wada, T., Watanabe, A., Yamada, M., Yasuda, M., Sato, S., de la Bastide, M., Huang, E., Spiegel, L., Gnoj, L., O’Shaughnessy, A., Preston, R., Habermann, K., Murray, J., Johnson, D., Rohlfing, T., Nelson, J., Stoneking, T., Pepin, K., Spieth, J., Sekhon, M., Armstrong, J., Becker, M., Belter, E., Cordum, H., Cordes, M., Courtney, L., Courtney, W., Dante, M., Du, H., Edwards, J., Fryman, J., Haakensen, B., Lamar, E., Latreille, P., Leonard, S., Meyer, R., Mulvaney, E., Ozersky, P., Riley, A., Strowmatt, C., Wagner-McPherson, C., Wollam, A., Yoakum, M., Bell, M., Dedhia, N., Parnell, L., Shah, R., Rodriguez, M., See, L.H., Vil, D., Baker, J., Kirchoff, K., Toth, K., King, L., Bahret, A., Miller, B., Marra, M., Martienssen, R., McCombie, W.R., Wilson, R.K., Murphy, G., Bancroft, I., Volckaert, G., Wambutt, R., Dusterhoft, A., Stiekema, W., Pohl, T., Entian, K.D., Terryn, N., Hartley, N., Bent, E., Johnson, S., Langham, S.A., McCullagh, B., Robben, J., Grymonprez, B., Zimmermann, W., Ramsperger, U., Wedler, H., Balke, K., Wedler, E., Peters, S., van Staveren, M., Dirkse, W., Mooijman, P., Lankhorst R.K., Weitzenegger, T., Bothe, G., Rose, M., Hauf, J., Berneiser, S., Hempel, S., Feldpausch, M., Lamberth, S., Villarroel, R., Gielen, J., Ardiles, W., Bents, O., Lemcke, K., Kolesov, G., Mayer, K., Rudd, S., Schoof, H., Schueller, C., Zaccaria, P., Mewes, H.W., Bevan, M. and Fransz, P. (The Kazusa DNA Research Institute, The Cold Spring Harbor and Washington University in St Louis Sequencing Consortium and The European Union Arabidopsis Genome Sequencing Consortium) (2000) Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana. Nature, 408, 823-826.
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[Nature]
37. Nikaido, I., Asamizu, E., Nakajima, M., Nakamura, Y., Saga, N. and Tabata, S. (2000) Generation of 10,154 expressed sequence tags from a leafy gametophyte of a marine red alga, Porphyra yezoensis. DNA Res., 7, 223-227.
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[DNA Res (PDF)]
36. Kaneko, T., Katoh, T., Sato, S., Nakamura, Y., Asamizu, E. and Tabata, S. (2000) Structural analysis of Arabidopsis thaliana chromosome 3. II. Sequence features of the 4,251,695 bp regions covered by 90 P1, TAC and BAC clones. DNA Res., 7, 217-221.
[PubMed: 10907853]
[DNA Res (PDF)]
35. Asamizu, E., Nakamura, Y., Sato, S. and Tabata, S. (2000) A large scale analysis of cDNA in Arabidopsis thaliana: generation of 12,028 non-redundant expressed sequence tags from normalized and size-selected cDNA libraries. DNA Res., 7, 175-180.
[PubMed: 10907847]
[DNA Res (PDF)]
34. Sato, S., Nakamura, Y., Kaneko, T., Katoh, T., Asamizu, E. and Tabata, S. (2000) Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence features of the regions of 4,504,864 bp covered by sixty P1 and TAC clones. DNA Res., 7, 131-135.
[PubMed: 10819329]
[DNA Res (PDF)]
33. Asamizu, E., Nakamura, Y., Sato, S. and Tabata, S. (2000) Generation of 7137 non-redundant expressed sequence tags from a legume, Lotus japonicus. DNA Res., 7, 127-130.
[PubMed: 10819328]
[DNA Res (PDF)]
32. Sato, S., Nakamura, Y., Kaneko, T., Katoh, T., Asamizu, E., Kotani, H. and Tabata, S. (2000) Structural analysis of Arabidopsis thaliana chromosome 5. X. Sequence features of the regions of 3,076,755 bp covered by sixty P1 and TAC clones. DNA Res., 7, 31-63.
[PubMed: 10718197]
[DNA Res (PDF)]
31. Nakamura, Y., Kaneko, T. and Tabata, S. (2000) CyanoBase, the genome database for Synechocystis sp. strain PCC6803: status for the year 2000. Nucleic Acids Res. 28, 72.
[PubMed: 10592184]
30. Nakamura, Y., Gojobori, T. and Ikemura, T. (2000) Codon usage tabulated from international DNA sequence databases: status for the year 2000. Nucleic Acids Res. 28, 292.
[PubMed: 10592250]
1999
29. Asamizu, E., Nakamura, Y., Sato, S., Fukuzawa, H. and Tabata, S. (1999) A large scale structural analysis of cDNAs in a unicellular green alga, Chlamydomonas reinhardtii. I. Generation of 3433 non-redundant expressed sequence tags. DNA Res., 6, 369-373.
[PubMed]
[DNA Res (PDF)]
28. Sato, S., Nakamura, Y., Kaneko, T., Asamizu, E. and Tabata, S. (1999) Complete structure of the chloroplast genome of Arabidopsis thaliana. DNA Res. 6, 283-290.
[PubMed]
[DNA Res (PDF)]
27. Kaneko, T., Katoh, T., Sato, S., Nakamura, Y., Asamizu, E., Kotani, H., Miyajima, N. and Tabata, S. (1999) Structural analysis of Arabidopsis thaliana chromosome 5. IX. Sequence features of the regions of 1,011,550 bp covered by seventeen P1 and TAC clones.
DNA Res. 6, 183-195.
[PubMed:10470850 ]
[DNA Res (PDF)]
26. Nakamura, Y., Kaneko, T., Miyajima, N. and Tabata, S. (1999) Extension of CyanoBase. CyanoMutants: repository of mutant information on Synechocystis sp. strain PCC6803. Nucleic Acids Res.
27, 66-68.
[PubMed: 9847144]
25. Nakamura, Y., Gojobori, T. and Ikemura, T. (1999) Codon usage tabulated from the international DNA sequence databases; its status 1999. Nucleic Acids Res. 27 292.
[PubMed: 9847205]
1998
24. Asamizu, E., Sato, S., Kaneko, T., Nakamura, Y., Kotani, H., Miyajima, N., Tabata, S. (1998) Structural analysis of Arabidopsis thaliana chromosome 5. VIII. Sequence features of the regions of 1,081,958 bp covered by seventeen physically assigned P1 and TAC clones. DNA Res. 5, 379-391.
[PubMed: 10048488]
[DNA Res (PDF)]
23. Nakamura, Y., Sato, S., Asamizu, E., Kaneko, T., Kotani, H., Miyajima, N. and Tabata, S. (1998) Structural analysis of Arabidopsis thaliana chromosome 5.VII. Sequence features of the regions of 1,013,767 bp covered by sixteen physically assigned P1 and TAC clones. DNA Res. 5, 297-308.
[PubMed: 9872454]
[DNA Res (PDF)]
22. Kotani, H., Nakamura, Y., Sato, S., Asamizu, E., Kaneko, T., Miyajima, N. and Tabata, S. (1998) Structural analysis of Arabidopsis thaliana chromosome 5.VI. Sequence features of the regions of 1,367,185 bp covered by 19 physically assigned P1 and TAC clones. DNA Res. 5, 203-216.
[PubMed: 9734815]
[DNA Res (PDF)]
21. Kaneko, T., Kotani, H., Nakamura, Y., Sato, S., Asamizu, E., Miyajima, N. and Tabata, S. (1998) Structural analysis of Arabidopsis thaliana chromosome 5. V. Sequence features of the regions of 1,381,565 bp covered by twenty one physically assigned P1 and TAC clones. DNA Res. 5, 131-145.
[PubMed: 9679202]
[DNA Res (PDF)]
20. Sato, S., Kaneko, T., Kotani, H., Nakamura, Y., Asamizu, E., Miyajima, N. and Tabata, S. (1998) Structural analysis of Arabidopsis thaliana chromosome 5. IV. Sequence features of the regions of 1,456,315 bp covered by nineteen physically assigned P1 and TAC clones. DNA Res. 5, 41-54.
[PubMed: 9628582]
[DNA Res (PDF)]
19. Nakamura, Y., Gojobori, T. and Ikemura, T. (1998) Codon usage tabulated from the international DNA sequence databases. Nucleic Acids Res. 26, 336-337.
[PubMed: 9399868]
18. Nakamura, Y., Kaneko, T., Hirosawa, M., Miyajima, N. and Tabata, S. (1998) CyanoBase, a www database containing the complete nucleotide sequence of the genome of Synechocystis sp. strain PCC6803
Nucleic Acids Res. 26, 63-67.
[PubMed: 9399802]
1997
17. Nakamura, Y. and Tabata, S. (1997) Codon-anticodon assignment and detection of codon usage trends in seven microbial genomes. Microb. Comp. Genomics 2, 299-312.
[PubMed: 9689228]
16. Nakamura, Y., Sato, S., Kaneko, T., Kotani, H., Asamizu, E., Miyajima, N. and Tabata, S. (1997) Structural analysis of Arabidopsis thaliana chromosome 5. III. Sequence features of the regions of 1,191,918 bp covered by seventeen physically assigned P1 clones. DNA Res. 4, 401-414.
[PubMed: 9501997]
[DNA Res (PDF)]
15. Kotani, H., Nakamura, Y., Sato, S., Kaneko, T., Asamizu, E., Miyajima, N. and Tabata, S. (1997) Structural analysis of Arabidopsis thaliana chromosome 5. II. Sequence features of the regions of 1,044,062 bp covered by thirteen physically assigned P1 clones. DNA Res. 4, 291-300.
[PubMed: 9405937]
[DNA Res (PDF)]
14. Sato, S., Kotani, H., Nakamura, Y., Kaneko, T., Asamizu, E., Fukami, M., Miyajima, N. and Tabata, S. (1997) Structural analysis of Arabidopsis thaliana chromosome 5. I. Sequence features of the 1.6 Mb regions covered by twenty physically assigned P1 clones. DNA Res. 4, 291-300.
[PubMed: 9330910]
[DNA Res (PDF)]
13. Sugaya, K., Sasanuma, S., Nohata, J., Kimura, T., Fukagawa, T., Nakamura, Y., Ando, A., Inoko, H., Ikemura, T and Mita, K. (1997) Gene organization of human NOTCH4 and (CTG)n polymorphism in this human counterpart gene of mouse proto-oncogene Int3. Gene. 189, 235-244.
[PubMed: 9168133]
12. Nakamura, Y., Gojibori, T. and Ikemura, T. (1997) Codon usage tabulated from the international DNA sequence databases. Nucleic Acids Res. 25, 244-245.
[PubMed: 9016546]
1996
11. Kaneko, T., Sato, S., Kotani, H., Tanaka, A., Asamizu, E., Nakamura, Y., Miyajima, N., Hirosawa, M., Sugiura, M., Sasamoto, S., Kimura, T., Hosouchi, T., Matsuno, A., Muraki, A., Nakazaki, N., Naruo, K., Okumura, S., Shimpo, S., Takeuchi, C., Wada, T., Watanabe, A., Yamada, M., Yasuda, M. and Tabata, S. (1996) Sequence analysis of the genome of the unicellular Cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res. 3, 109-136.
[PubMed: 8905231]
[DNA Res (PDF)]
(Supplement: DNA Res., 3, 185-209. [DNA Res (PDF)])
10. Nakamura, Y., Wada, K., Wada, Y., Doi, H., Kanaya, S., Gojobori, T. and Ikemura, T. (1996) Codon usage tabulated from the international DNA sequence databases. Nucleic Acids Res. 24, 214-215.
[PubMed: 8594583]
9. Kanaya, S., Kudo, Y., Nakamura, Y. and Ikemura, T. (1996) Detection of genes in Escherichia coli sequences determined by genome projects and prediction of protein production levels, based on multivariate diversity in codon usage. Comput. Appl. Biosci. 12, 213-225.
[PubMed: 8872390]
8. Fukagawa, T., Nakamura, Y., Okumura, K., Nogami, M., Ando, A., Inoko, H., Saitou, N. and Ikemura, T. (1996) Human pseudoautosomal boundary-like sequences: expression and involvement in evolutionary formation of the present-day pseudoautosomal boundary of human sex chromosomes. Hum. Mol. Genet. 5, 23-32.
[PubMed: 8789436]
7. Nakamura, Y., Wada, K., Wada, Y., Doi, H., Kanaya, S., Gojobori, T. and Ikemura, T. (1996) Codon usage tabulated from the international DNA sequence databases. Nucleic Acids Res. 24, 214-215.
[PubMed: 8594583]
1993
6. Ohta, E., Oda, K., Yamato, K., Nakamura, Y., Takemura, M., Nozato, N., Akashi, K., Ohyama, K. and Michel, F. (1993) Group I introns in athe liverwort mitochondrial genome: the gene coding for subunit 1 of cytochrome oxidase shares five intron positions with its fungal counterparts. Nucleic Acids Res. 21, 1297-1305.
[PubMed: 93219095]
1992
5. Oda, K., Yamato, K., Ohta, E., Nakamura, Y., Takemura, M., Nozato, N., Akashi, K. and Ohyama, K. (1992) Transfer RNA genes in the mitochondrial genome from a liverwort, Marchantia polymorpha: the absence of chloroplast-like tRNAs. Nucleic Acids Res. 20, 3773-3777.
[PubMed: 92350681]
4. Takemura, M., Oda, K., Yamato, K., Ohta, E., Nakamura, Y., Nozato, N., Akashi, K. and Ohyama K. (1992) Gene clusters for ribosomal proteins in the mitochondrial genome of a liverwort, Marchantia polymorpha. Nucleic Acids Res. 20, 3199-3205.
[PubMed: 92319654]
3. Oda, K., Yamato, K., Ohta, E., Nakamura, Y., Takemura, M., Nozato, N., Akashi, K. and Ohyama, K. (1992) Complete nucleotide sequence of mitochondrial genome of a liverwort, Marchantia polymorpha. Plant Mol. Biol. Rep. 10, 105-163.
2. Oda, K., Yamato, K., Ohta, E., Nakamura, Y., Takemura, M., Nozato, N., Akashi, K., Kanegae, T., Ogura, Y., Kohchi, T. and Ohyama, K. (1992) Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA. A primitive form of plant mitochondrial genome. J. Mol. Biol. 223, 1-7.
[PubMed: 92114051]
1991
1. Ogura, Y., Yoshida, T., Nakamura, Y., Takemura, M., Oda, K. and Ohyama, K. (1991) Gene encoding a putative zinc finger protein in Synechocystis PCC6803. Agric. Biol. Chem. 55, 2259-2264.
[PubMed: 92118327]