publications

Our publications of the last 5 years

2017

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 (submitted)

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 (in press)

2016

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. PLOS ONE, http://dx.doi.org/10.1371/journal.pone.0166969
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0166969

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
http://nar.oxfordjournals.org/content/early/2016/11/29/nar.gkw1131.full?keytype=ref&ijkey=vDzkaXzXmXozGE4

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. 2016 Jan 4;44(D1):D51-7. doi: 10.1093/nar/gkv1105. Epub 2015 Nov 17.
[PubMed: 26578571]

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. 2016;35(4):173-184.
[PubMed: 27867804]

Hirose Y, Fujisawa T, Ohtsubo Y, Katayama M, Misawa N, Wakazuki S, Shimura Y, Nakamura Y, Kawachi M, Yoshikawa H, Eki T, Kanesaki Y. Complete genome sequence of cyanobacterium Fischerella sp. NIES-3754, providing thermoresistant optogenetic tools. J Biotechnol. 2016 Feb 20;220:45-6. doi: 10.1016/j.jbiotec.2016.01.011.
[PubMed: 26784989]

2015

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. [Epub ahead of print]
[PubMed: 26656223]

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. [Epub ahead of print] Review.
[PubMed: 26644462]

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. [Epub ahead of print]
[PubMed: 26578696]

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. [Epub ahead of print]
[PubMed: 26578571]

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. [Epub ahead of print]
[PubMed: 26227242]

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, Mar 25;16:240. doi: 10.1186/s12864-015-1435-2.
[PubMed: 25879859]

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]

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]

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

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]

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]

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]

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]

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]

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. Epub 2013 Dec 5.
[PubMed: 24319074]

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. Epub 2013 Dec 19.
[PubMed: 24363285]

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. Epub 2013 Dec 9.
[PubMed: 24323624]

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. Epub 2013 Nov 25.
[PubMed: 24275496]

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. Epub 2013 Nov 4.
[PubMed: 24194602]

2013

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]

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]

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. Epub 2012 Nov 27.
[PubMed: 23193255]

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. Epub 2012 Nov 24.
[PubMed: 23180798]

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. Epub 2012 Nov 24.
[PubMed: 23180790]

See also: http://ynlab.info/members/yn/publications/