yn/Publications

2017

124. Tokurou Shimizu, Yasuhiro Tanizawa, Takako Mochizuki, Hideki Nagasaki, Terutaka Yoshioka, Atsushi Toyoda, Asao Fujiyama, Eli Kaminuma, Yasukazu Nakamura. (2017) Draft sequencing of the heterozygous diploid genome of Satsuma (Citrus unshiu Marc.) using a hybrid assembly approach. Frontiers in Genetics. in press.

123. Kodama Y, Mashima J, Kosuge T, Kaminuma E, Ogasawara O, Okubo K, Nakamura Y, Takagi T. (2017) DNA Data Bank of Japan: 30th anniversary. Nucleic Acids Res, doi: 10.1093/nar/gkx926.
[PubMed: 29040613]

122. Bowman JL, Kohchi T, Yamato KT, Jenkins J, Shu S, Ishizaki K, Yamaoka S, Nishihama R, Nakamura Y, Berger F, Adam C, Aki SS, Althoff F, Araki T, Arteaga-Vazquez MA, Balasubrmanian S, Barry K, Bauer D, Boehm CR, Briginshaw L, Caballero-Perez J, Catarino B, Chen F, Chiyoda S, Chovatia M, Davies KM, Delmans M, Demura T, Dierschke T, Dolan L, Dorantes-Acosta AE, Eklund DM, Florent SN, Flores-Sandoval E, Fujiyama A, Fukuzawa H, Galik B, Grimanelli D, Grimwood J, Grossniklaus U, Hamada T, Haseloff J, Hetherington AJ, Higo A, Hirakawa Y, Hundley HN, Ikeda Y, Inoue K, Inoue SI, Ishida S, Jia Q, Kakita M, Kanazawa T, Kawai Y, Kawashima T, Kennedy M, Kinose K, Kinoshita T, Kohara Y, Koide E, Komatsu K, Kopischke S, Kubo M, Kyozuka J, Lagercrantz U, Lin SS, Lindquist E, Lipzen AM, Lu CW, De Luna E, Martienssen RA, Minamino N, Mizutani M, Mizutani M, Mochizuki N, Monte I, Mosher R, Nagasaki H, Nakagami H, Naramoto S, Nishitani K, Ohtani M, Okamoto T, Okumura M, Phillips J, Pollak B, Reinders A, Rövekamp M, Sano R, Sawa S, Schmid MW, Shirakawa M, Solano R, Spunde A, Suetsugu N, Sugano S, Sugiyama A, Sun R, Suzuki Y, Takenaka M, Takezawa D, Tomogane H, Tsuzuki M, Ueda T, Umeda M, Ward JM, Watanabe Y, Yazaki K, Yokoyama R, Yoshitake Y, Yotsui I, Zachgo S, Schmutz J. (2017) Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome. Cell, 171(2): 287-304. e15. doi: 10.1016/j.cell.2017.09.030.
[PubMed: 28985561]

121. Mai F. Minamikawa, Keisuke Nonaka, Eli Kaminuma, Hiromi Kajiya-Kanegae, Akio Onogi, Shingo Goto, Terutaka Yoshioka, Atsushi Imai, Hiroko Hamada, Takeshi Hayashi, Satomi Matsumoto, Yuichi Katayose, Atsushi Toyoda, Asao Fujiyama, Yasukazu Nakamura, Tokurou Shimizu and Hiroyoshi Iwata. (2017) Genome-wide association study and genomic prediction in citrus: Potential of genomics-assisted breeding for fruit quality traits. Scientific Reports, 7, Article number: 4721. doi:10.1038/s41598-017-05100-x
[PubMed: 28680114]

120a. Shimura Y, Hirose Y, Misawa N, Wakazuki S, Fujisawa T, Nakamura Y, Kanesaki Y, Yamaguchi H, Kawachi M. (2017) Complete Genome Sequence of a Coastal Cyanobacterium, Synechococcus sp. Strain NIES-970. Genome Announc. 5(14). pii: e00139-17. doi: 10.1128/genomeA.00139-17.
[PubMed: 28385852]

120. Tanizawa Y, Kaminuma E, Sakamoto M, Ohkuma M, Nakamura Y, Arita M, Tohno M. (2017) Genomic characterization reconfirms the taxonomic status of Lactobacillus parakefiri. Biosci Microbiota Food Health, 36(3): 129-134. doi: 10.12938/bmfh.16-026.
[PubMed: 28748134]

119. Takako Mochizuki, Yasuhiro Tanizawa, Takatomo Fujisawa, Tazro Ohta, Naruo Nikoh, Tokurou Shimizu, Atsushi Toyoda, Asao Fujiyama, Nori Kurata, Hideki Nagasaki, Eli Kaminuma and Yasukazu Nakamura. (2017) DNApod: DNA Polymorphism Annotation Database from Next-Generation Sequence Read Archives. PLOS ONE, https://doi.org/10.1371/journal.pone.0172269
[PubMed: 28234924]

118a. Nakaya A, Ichihara H, Asamizu E, Shirasawa S, Nakamura Y, Tabata S, Hirakawa H. (2017) Plant Genome DataBase Japan (PGDBj). Methods Mol Biol., 1533:45-77. Review
[PubMed: 27987164]

2016

118. Nakai R, Fujisawa T, Nakamura Y, Baba T, Nishijima M, Karray F, Sayadi S, Isoda H, Naganuma T, Niki H. (2016) Genome sequence and overview of Oligoflexus tunisiensis Shr3T in the eighth class Oligoflexia of the phylum Proteobacteria. Stand Genomic Sci., 11:90. doi: 10.1186/s40793-016-0210-6.
[PubMed: 27999625]

117. Tokurou Shimizu , Akira Kitajima, Keisuke Nonaka, Terutaka Yoshioka, Satoshi Ohta, Shingo Goto, Atsushi Toyoda, Asao Fujiyama, Takako Mochizuki, Hideki Nagasaki, Eli Kaminuma, Yasukazu Nakamura. (2016) Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes. Pros ONE, http://dx.doi.org/10.1371/journal.pone.0166969
[PubMed: 27902727]

116. Takatomo Fujisawa, Rei Narikawa, Shin-ichi Maeda, Satoru Watanabe, Yu Kanesaki, Koichi Kobayashi, Jiro Nomata, Mitsumasa Hanaoka, Mai Watanabe, Shigeki Ehira, Eiji Suzuki, Koichiro Awai and Yasukazu Nakamura. (2016) CyanoBase: a large-scale update on its 20th anniversary. Nucl. Acids Res., doi: 10.1093/nar/gkw1131
[PubMed: 27899668]

115. Mashima J, Kodama Y, Kosuge T, Fujisawa T, Katayama T, Nagasaki H, Okuda Y, Kaminuma E, Ogasawara O, Okubo K, Nakamura Y, Takagi T. (2016) DNA data bank of Japan (DDBJ) progress report. Nucleic Acids Res., 44(D1): D51-7. doi: 10.1093/nar/gkv1105.
[PubMed: 26578571]

114. Tanizawa Y, Fujisawa T, Kaminuma E, Nakamura Y, Arita M. (2016) DFAST and DAGA: web-based integrated genome annotation tools and resources. Biosci Microbiota Food Health., 35(4): 173-184.
[PubMed: 27867804]

113. Hirose Y, Fujisawa T, Ohtsubo Y, Katayama M, Misawa N, Wakazuki S, Shimura Y, Nakamura Y, Kawachi M, Yoshikawa H, Eki T, Kanesaki Y. (2016) Complete genome sequence of cyanobacterium Fischerella sp. NIES-3754, providing thermoresistant optogenetic tools. J Biotechnol., 220: 45-6. doi: 10.1016/j.jbiotec.2016.01.011.
[PubMed: 26784989]

2015

112. Hirose Y, Fujisawa T, Ohtsubo Y, Katayama M, Misawa N, Wakazuki S, Shimura Y, Nakamura Y, Kawachi M, Yoshikawa H, Eki T, Kanesaki Y. (2015) Complete genome sequence of cyanobacterium Nostoc sp. NIES-3756, a potentially useful strain for phytochrome-based bioengineering. J Biotechnol., 218: 51-52. doi: 10.1016/j.jbiotec.2015.12.002.
[PubMed: 26656223]

111a. Bowman JL, Araki T, Arteaga-Vazquez MA, Berger F, Dolan L, Haseloff J, Ishizaki K, Kyozuka J, Lin SS, Nagasaki H, Nakagami H, Nakajima K, Nakamura Y, Ohashi-Ito K, Sawa S, Shimamura M, Solano R, Tsukaya H, Ueda T, Watanabe Y, Yamato KT, Zachgo S, Kohchi T. (2015) The naming of names: guidelines for gene nomenclature in Marchantia. Plant Cell Physiol., pii: pcv193. Review.
[PubMed: 26644462]

111. Ohyanagi H, Ebata T, Huang X, Gong H, Fujita M, Mochizuki T, Toyoda A, Fujiyama A, Kaminuma E, Nakamura Y, Feng Q, Wang ZX, Han B, Kurata N. (2015) OryzaGenome: Genome Diversity Database of Wild Oryza Species. Plant Cell Physiol., pii: pcv171.
[PubMed: 26578696]

110. Mashima J, Kodama Y, Kosuge T, Fujisawa T, Katayama T, Nagasaki H, Okuda Y, Kaminuma E, Ogasawara O, Okubo K, Nakamura Y, Takagi T. (2015) DNA data bank of Japan (DDBJ) progress report. Nucleic Acids Res., pii: gkv1105.
[PubMed: 26578571]

109. Hirose Y, Suda K, Liu YG, Sato S, Nakamura Y, Yokoyama K, Yamamoto N, Hanano S, Takita E, Sakurai N, Suzuki H, Nakamura Y, Kaneko T, Yano K, Tabata S, Shibata D. (2015) Arabidopsis TAC Position Viewer: a high-resolution map of transformation-competent artificial chromosome (TAC) clones aligned with the Arabidopsis thaliana Columbia-0 genome. Plant J., doi: 10.1111/tpj.12949.
[PubMed: 26227242]

108. Tanizawa Y, Tohno M, Kaminuma E, Nakamura Y, Arita M. (2015) Complete genome sequence and analysis of Lactobacillus hokkaidonensis LOOC260T, a psychrotrophic lactic acid bacterium isolated from silage. BMC Genomics, 16: 240. doi: 10.1186/s12864-015-1435-2.
[PubMed: 25879859]

107. Hiraide Y, Oshima K, Fujisawa T, Uesaka K, Hirose Y, Tsujimoto R, Yamamoto H, Okamoto S, Nakamura Y, Terauchi K, Omata T, Ihara K, Hattori M, Fujita Y. (2015) Loss of Cytochrome cM Stimulates Cyanobacterial Heterotrophic Growth in the Dark. Plant Cell Physiol., 56, 334-345. doi: 10.1093/pcp/pcu165
[PubMed: 25416288]

106. Kodama Y, Mashima J, Kosuge T, Katayama T, Fujisawa T, Kaminuma E, Ogasawara O, Okubo K, Takagi T, Nakamura Y. (2015) The DDBJ Japanese Genotype-phenotype Archive for genetic and phenotypic human data. Nucleic Acids Res., 43, D18-22. doi: 10.1093/nar/gku1120.
[PubMed: 25477381]

105b. Kanesaki Y, Masutani H, Sakanaka M, Shiwa Y, Fujisawa T, Nakamura Y, Yokota A, Fukiya S, Suzuki T, Yoshikawa H. (2015) Complete Genome Sequence of Bifidobacterium longum 105-A, a Strain with High Transformation Efficiency. Genome Announc., 2, pii: e01311-14. doi: 10.1128/genomeA.01311-14.
[PubMed: 25523770]

2014

105a. Tanizawa Y, Fujisawa T, Mochizuki T, Kaminuma E, Nakamura Y, Tohno M. (2014) Draft Genome Sequence of Lactobacillus oryzae Strain SG293T. Genome Announc., 2, pii: e00861-14. doi: 10.1128/genomeA.00861-14.
[PubMed: 25169865]

105. Uchiyama J, Asakura R, Moriyama A, Kubo Y, Shibata Y, Yoshino Y, Tahara H, Matsuhashi A, Sato S, Nakamura Y, Tabata S, Ohta H. (2014) Sll0939 is induced by Slr0967 in the cyanobacterium Synechocystis sp. PCC6803 and is essential for growth under various stress conditions. Plant Physiol Biochem., 81, 36-43. doi: 10.1016/j.plaphy.2014.02.007.
[PubMed: 24629663]

104a. Tanizawa Y, Fujisawa T, Mochizuki T, Kaminuma E, Suzuki Y, Nakamura Y, Tohno M. (2014) Draft genome sequence of Weissella oryzae SG25T isolated from fermented rice grains.Genome Announc., 2, pii: e00667-14. doi: 10.1128/genomeA.00667-14.
[PubMed: 25013139]

104. Hori K, Maruyama F, Fujisawa T, Togashi T, Yamamoto N, Seo M, Sato S, Yamada T, Mori H, Tajima N, Moriyama T, Ikeuchi M, Watanabe M, Wada H, Kobayashi K, Saito M, Masuda T, Sasaki-Sekimoto Y, Mashiguchi K, Awai K, Shimojima M, Masuda S, Iwai M, Nobusawa T, Narise T, Kondo S, Saito H, Sato R, Murakawa M, Ihara Y, Oshima-Yamada Y, Ohtaka K, Satoh M, Sonobe K, Ishii M, Ohtani R, Kanamori-Sato M, Honoki R, Miyazaki D, Mochizuki H, Umetsu J, Higashi K, Shibata D, Kamiya Y, Sato N, Nakamura Y, Tabata S, Ida S, Kurokawa K, Ohta H. (2014) Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation. Nature comm., 5, 3978. doi:10.1038/ncomms4978
[PubMed: 24865297]

103. Iida N, Yamao F, Nakamura Y, Iida T. (2014) Mudi, a web tool for identifying mutations by bioinformatics analysis of whole-genome sequence. Genes to Cells, 19(6): 517-527. doi: 10.1111/gtc.12151.
[PubMed: 24766403]

102. Kobayashi M, Nagasaki H, Garcia V, Just D, Bres C, Mauxion JP, Le Paslier MC, Brunel D, Suda K, Minakuchi Y, Toyoda A, Fujiyama A, Toyoshima H, Suzuki T, Igarashi K, Rothan C, Kaminuma E, Nakamura Y, Yano K, Aoki K. (2014) Genome-Wide Analysis of Intraspecific DNA Polymorphism in ‘Micro-Tom’, a Model Cultivar of Tomato (Solanum lycopersicum). Plant Cell Physiol., 55 (2): 445-454 doi: 10.1093/pcp/pct181.
[PubMed: 24319074]

101. Asamizu E, Ichihara H, Nakaya A, Nakamura Y, Hirakawa H, Ishii T, Tamura T, Fukami-Kobayashi K, Nakajima Y, Tabata S. (2014) Plant Genome DataBase Japan (PGDBj): A Portal Website for the Integration of Plant Genome-Related Databases. Plant Cell Physiol., 55 (1): e8. doi: 10.1093/pcp/pct189.
[PubMed: 24363285]

100. Fukami-Kobayashi K, Nakamura Y, Tamura T, Kobayashi M. (2014) SABRE2: A Database Connecting Plant EST/Full-Length cDNA Clones with Arabidopsis Information. Plant Cell Physiol., 55(1): e5. doi: 10.1093/pcp/pct177.
[PubMed: 24323624]

99. Fujisawa T, Okamoto S, Katayama T, Nakao M, Yoshimura H, Kajiya-Kanegae H, Yamamoto S, Yano C, Yanaka Y, Maita H, Kaneko T, Tabata S, Nakamura Y. (2014) CyanoBase and RhizoBase: databases of manually curated annotations for cyanobacterial and rhizobial genomes. Nucleic Acids Res., 42(1): D666-670. doi: 10.1093/nar/gkt1145.
[PubMed: 24275496]

98. Kosuge T, Mashima J, Kodama Y, Fujisawa T, Kaminuma E, Ogasawara O, Okubo K, Takagi T, Nakamura Y. (2014) DDBJ progress report: a new submission system for leading to a correct annotation. Nucleic Acids Res., 42(1): D44-49. doi: 10.1093/nar/gkt1066.
[PubMed: 24194602]

97a. Scott Federhen, Karen Clark, Tanya Barrett, Helen Parkinson, James Ostell, Yuichi Kodama, Jun Mashima, Yasukazu Nakamura, Guy Cochrane, Ilene Karsch-Mizrachi (2014) Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records. Stand. Genomic Sci., 9(3) doi:10.4056/sigs.4851102 epub-ppub publication date: January 29, 2014. (Editorial/Commentary)
[SIGS]

2013

97. Kasai-Maita H, Hirakawa H, Nakamura Y, Kaneko T, Miki K, Maruya J, Okazaki S, Tabata S, Saeki K, Sato S. (2013) Commonalities and Differences among Symbiosis Islands of Three Mesorhizobium loti Strains. Microbes Environ., 28, 275-278.
[PubMed: 23666538]

96. Nagasaki H, Mochizuki T, Kodama Y, Saruhashi S, Morizaki S, Sugawara H, Ohyanagi H, Kurata N, Okubo K, Takagi T, Kaminuma E, Nakamura Y. (2013) DDBJ Read Annotation Pipeline: A Cloud Computing-Based Pipeline for High-Throughput Analysis of Next-Generation Sequencing Data. DNA Res., 20, 383-390.
[PubMed: 23657089]

95. Kaminuma E, Fujisawa T, Tanizawa Y, Sakamoto N, Kurata N, Shimizu T, Nakamura Y. (2013) H2DB: a heritability database across multiple species by annotating trait-associated genomic loci. Nucleic Acids Res., 41 (D1), D880-884. doi: 10.1093/nar/gks1216.
[PubMed: 23193255]

94. Nakamura Y, Cochrane G, Karsch-Mizrachi I on behalf of the International Nucleotide Sequence Database Collaboration. (2013) The International Nucleotide Sequence Database Collaboration. Nucleic Acids Res., 41 (D1), D21-D24. doi: 10.1093/nar/gks1084.
[PubMed: 23180798]

93. Ogasawara O, Mashima J, Kodama Y, Kaminuma E, Nakamura Y, Okubo K, Takagi T. (2013) DDBJ new system and service refactoring. Nucleic Acids Res., 41 (D1) D25-29. doi: 10.1093/nar/gks1152.
[PubMed: 23180790]

2012

92. Okubo T, Tsukui T, Maita H, Okamoto S, Oshima K, Fujisawa T, Saito A, Futamata H, Hattori R, Shimomura Y, Haruta S, Morimoto S, Wang Y, Sakai Y, Hattori M, Aizawa S, Nagashima KV, Masuda S, Hattori T, Yamashita A, Bao Z, Hayatsu M, Kajiya-Kanegae H, Yoshinaga I, Sakamoto K, Toyota K, Nakao M, Kohara M, Anda M, Niwa R, Jung-Hwan P, Sameshima-Saito R, Tokuda S, Yamamoto S, Yamamoto S, Yokoyama T, Akutsu T, Nakamura Y, Nakahira-Yanaka Y, Takada Hoshino Y, Hirakawa H, Mitsui H, Terasawa K, Itakura M, Sato S, Ikeda-Ohtsubo W, Sakakura N, Kaminuma E, Minamisawa K. (2012) Complete genome sequence of Bradyrhizobium sp. S23321: insights into symbiosis evolution in soil oligotrophs. Microbes Environ. 27, 306-315.
[PubMed: 22452844]

91. The Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485, 635–641. doi:10.1038/nature11119
[PubMed: 22660326]

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]

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. (2012) The Integral Membrane Protein SEN1 is Required for Symbiotic Nitrogen Fixation in Lotus japonicus Nodules. Plant Cell Physiol., 53, 225-236.
[PubMed: 22123791]

2011

87. Yilmaz P, Gilbert JA, Knight R, Amaral-Zettler L, Karsch-Mizrachi I, Cochrane G, Nakamura Y, Sansone SA, Glöckner FO, Field D. (2011) The genomic standards consortium: bringing standards to life for microbial ecology. ISME J., 5, 1565-1567. doi: 10.1038/ismej.2011.39
[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. (2010) Meeting Report: “Metagenomics, Metadata and Meta-analysis” (M3) Workshop at the Pacific Symposium on Biocomputing 2010. Stand Genomic Sci., 2 (3), 357-360.
[PubMed: 21304719]

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. 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

70a. Sato, S., Nakamura, Y., Asamizu, E., Isobe, S. and Tabata, S. (2007) Genome sequencing and genome resources in model legumes. Plant Physiol., 144, 588-593.
[Review]

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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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[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.
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[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.
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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.
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[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.
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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.
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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.
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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
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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.
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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.
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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.
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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.
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[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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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.
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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.
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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.
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[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.
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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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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.
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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.
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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.
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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.
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[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.
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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.
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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.
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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.
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[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.
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[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.
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[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.
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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.
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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.
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[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.
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[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.
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[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.
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[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.
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[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.
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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
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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.
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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.
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[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.
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[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.
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[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.
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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.
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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

1a. Ohyama, K. Ogura, Y., Oda, K., Yamato, K., Ohta, E., Nakamura, Y., Takemura, M., Nozato, N., Akashi, K., Kanegae, T. and Yamada, Y. (1991) Evolution of organellar genomes. in Evolution of Life (Osawa, S. and Honjo, T. eds, Springer-Verlag, Tokyo) pp. 187-198.
review

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]