Publication List


Nagai, S., K. Hida, S. Urushizaki, Y. Takano, Y. Hongo, T. Kameda, K. Abe (2016). “Massively parallel sequencing-based survey of eukaryotic community structures in Hiroshima Bay and Ishigaki Island.” Gene. 2016 Feb 1;576(2 Pt 1):681-9. DOI:10.1016/j.gene.2015.10.026.
Nagai, S., K. Hida, S. Urushizaki, G. Onitsuka, M. Yasuike, Y. Nakamura, A. Fujiwara, S. Tajimi, K. Kimoto, T. Kobayashi, T. Gojobori, M. Ototake (2016). “Influences of diurnal sampling bias on fixed-point monitoring of plankton biodiversity determined using a massively parallel sequencing-based technique.” Gene. 2016 Feb 1;576(2 Pt 1):667-75. DOI: 10.1016/j.gene.2015.10.025.
Tanabe, A. S., S. Nagai, K. Hida, M. Yasuike, A. Fujiwara, Y. Nakamura, Y, Takano and S. Katakura (2015). “Comparative study of the validity of three regions of the 18S-rRNA gene for massively parallel sequencing-based monitoring of the planktonic eukaryote community.” Mol Eco Resour. 2015 Aug 26. :DOI: 10.1111/1755-0998.12459
Otsuka, Y., A. Muto, R. Takeuchi, C. Okada, M. Ishikawa, K. Nakamura, N. Yamamoto, H. Dose, K. Nakahigashi, S. Tanishima, S. Suharnan, W. Nomura, T. Nakayashiki, W. G. Aref, B. R. Bochner, T. Conway, M. Gribskov, D. Kihara, K. E. Rudd, Y. Tohsato, B. L. Wanner and H. Mori (2015). “GenoBase: comprehensive resource database of Escherichia coli K-12.” Nucleic Acids Res 43(Database issue): D606-617.
Kajitani, R., K. Toshimoto, H. Noguchi, A. Toyoda, Y. Ogura, M. Okuno, M. Yabana, M. Harada, E. Nagayasu, H. Maruyama, Y. Kohara, A. Fujiyama, T. Hayashi and T. Itoh (2014). “Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads.” Genome Res 24(8): 1384-1395.
Gromiha, M. M., Y. Yabuki, S. Kundu, S. Suharnan and M. Suwa (2007). “TMBETA-GENOME: database for annotated beta-barrel membrane proteins in genomic sequences.” Nucleic Acids Res 35(Database issue): D314-316.
Machida, M., K. Asai, M. Sano, T. Tanaka, T. Kumagai, G. Terai, K. Kusumoto, T. Arima, O. Akita, Y. Kashiwagi, K. Abe, K. Gomi, H. Horiuchi, K. Kitamoto, T. Kobayashi, M. Takeuchi, D. W. Denning, J. E. Galagan, W. C. Nierman, J. Yu, D. B. Archer, J. W. Bennett, D. Bhatnagar, T. E. Cleveland, N. D. Fedorova, O. Gotoh, H. Horikawa, A. Hosoyama, M. Ichinomiya, R. Igarashi, K. Iwashita, P. R. Juvvadi, M. Kato, Y. Kato, T. Kin, A. Kokubun, H. Maeda, N. Maeyama, J. Maruyama, H. Nagasaki, T. Nakajima, K. Oda, K. Okada, I. Paulsen, K. Sakamoto, T. Sawano, M. Takahashi, K. Takase, Y. Terabayashi, J. R. Wortman, O. Yamada, Y. Yamagata, H. Anazawa, Y. Hata, Y. Koide, T. Komori, Y. Koyama, T. Minetoki, S. Suharnan, A. Tanaka, K. Isono, S. Kuhara, N. Ogasawara and H. Kikuchi (2005). “Genome sequencing and analysis of Aspergillus oryzae.” Nature 438(7071): 1157-1161.
Koyanagi, K. O., M. Hagiwara, T. Itoh, T. Gojobori and T. Imanishi (2005). “Comparative genomics of bidirectional gene pairs and its implications for the evolution of a transcriptional regulation system.” Gene 353(2): 169-176.
Srinesh Kundu, M. H., Kanako O. Koyanagi, Tadashi Imanishi, Takeshi Itoh (2003). “TTOP: A System for Phylogenetic Tree Editing and Evolutionary Annotation of Genes.” Genome Informatics 14: 583-584.

Selected publication (Acknowledgment)
(関わった論文・発表)
Nishikata, K., RS Cox, 3rd., S. Shimoyama, Y. Yoshida, M. Matsui, Y. Makita and T. Toyoda (2014). “Database construction for PromoterCAD: synthetic promoter design for mammals and plants.” ACS Synth Biol 3(3): 192-196.
Shimoyama, S., RS Cox, 3rd., D. Gifford. and T. Toyoda (2013). “Organizing Scientific Competitions on the Semantic Web.” Database and Expert Systems Applications: pp 311-318.
Cox, R. S., 3rd., K. Nishikata, S. Shimoyama, Y. Yoshida, M. Matsui, Y. Makita and T. Toyoda (2013). “PromoterCAD: Data-driven design of plant regulatory DNA.” Nucleic Acids Res 41(Web Server issue): W569-574.
Shimoyama, S., RS Cox, 3rd., D. Gifford. and T. Toyoda (2013). “A semantic dependency-graph-based approach combining platforms hosting data and applications.” SWWS’13.
Sakurai, N., T. Ara, Y. Ogata, R. Sano, T. Ohno, K. Sugiyama, A. Hiruta, K. Yamazaki, K. Yano, K. Aoki, A. Aharoni, K. Hamada, K. Yokoyama, S. Kawamura, H. Otsuka, T. Tokimatsu, M. Kanehisa, H. Suzuki, K. Saito and D. Shibata (2011). “KaPPA-View4: a metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data.” Nucleic Acids Res 39(Database issue): D677-684.
Hamada, M., K. Tsuda, T. Kudo, T. Kin and K. Asai (2006). “Mining frequent stem patterns from unaligned RNA sequences.” Bioinformatics 22(20): 2480-2487.
Nigel, C., K. Takeuchi and A. Kawazoe (2003). “Open Ontology Forge: An Environment for Text Mining in a Semantic Web World.” In Proc. of the International Workshop on Semantic Web Foundations and Application Technologies.

その他
(学会、和文等)
Nagai, S., S. Urushizaki, H. Chen, A. Fujiwara,  M. Yasuike and S. Katakura. (2016).“Metagenomic approach for HAB monitoring in Japanese coastal waters” The 17th International Conference on Harmful Algae Oct 09-14, 2016 Santa Catarina, Brazil
Nagai, S., S. Urushizaki, H. Chen, Y. Hongo, and S. Katakura. (2016). “Weekly monitoring of eukaryote biodiversity using massively parallel sequencing (MPS)-based technology in Okhotsk Sea in Japan” International Conference on Coastal Zones May 16-18, 2016 Osaka, Japan
岩井祐樹 (2015) PictBioサービスのご紹介 (NGS解析パイプラインパッケージBcMARx) NGS現場の会第四回研究会発表
西典子 (2015) PictBioサービスのご紹介 (NGS解析基礎) NGS現場の会第四回研究会発表
漆崎慎吾 (2015) PictBioサービスのご紹介 (NGS解析サービスPictBio) NGS現場の会第四回研究会発表
陳虹諺, 長井敏, 漆崎慎吾, 山本圭吾, 及川寛, 安池元重, 中村洋路, 田邊晶史, 本郷悠貴, 藤原篤志, 岸野洋久 (2015) Algal bloom and its phylogenetic aggregation 平成27年度日本水産学会春季大会
陳虹諺, 長井敏, 漆崎慎吾, 山本圭吾, 及川寛, 安池元重, 中村洋路, 田邊晶史, 本郷悠貴, 藤原篤志, 岸野洋久 (2015) Algal bloom and its phylogenetic aggregation. 2015年度日本計量生物学会年会
髙野義人, 村澤博基, 漆崎慎吾, 安池元重, 田邊晶史, 藤田大介, 長井敏, 桑原久実 (2015) メタバーコーディング解析による海底礫表面からの海藻種網羅検出の試み 日本藻類学会第39回大会
長井敏, 飛田晃介, 漆崎慎吾, 田邊晶史, 安池元重, 藤原篤志, 髙野義人, 本郷悠貴, 中村洋路, 阿部和雄, 亀田卓彦 (2015) メタゲノミクスによるプランクトンモニタリングの実践(植物プランクトンを中心に) 日本プランクトン学会報 62(1):1–8
Nagai. S, Urushizaki. S, Yasuike. M, Nakamura. Y, Fujiwara. A, Takano. Y, Tanabe. A, Hongo. Y & Katakura. S (2015) Plankton metagenomics in Okhotsk Sea. Proc Int Symp Okhotsk Sea Sea Ice
長井敏, 飛田晃介, 田邊晶史, 安池元重, 藤原篤志 (2014) メタゲノミクスによるプランクトンモニタリングの実践(植物プランクトンを中心に) 日本海洋学会大会
長井敏, 田邊晶史, 飛田晃介, 安池元重, 藤原篤志, 中村洋路, 髙野義人, 片倉靖次 (2014) Comparative study of the validity of three regions of 18S-rRNA gene for massively parallel sequencing-based monitoring of the planktonic eukaryote community 第30回北方圏国際シンポジウム:オホーツク海と流氷
Nagai. S, Hida. K, Yasuike. Y, Fujiwara. M, Nakamura. S (2013) メ​タ​ゲ​ノ​ム​解​析​に​よ​る​海​洋​プ​ラ​ン​ク​ト​ン​の​海​域​特​性​の​解​明​ Proc Int Symp Okhotsk Sea Sea Ice 28:27-30
岩井祐樹 (2013) PictBio NGSデータ解析サービス NGS現場の会第三回研究会発表
西典子 (2013) PictBio NGSデータ解析サービス NGS現場の会第三回研究会発表
漆崎慎吾 (2013) 次世代シーケンサーを用いたいもち病菌菌群間のゲノム構造比較 NGS現場の会第三回研究会発表
西典子 (2012) PictBio NGSデータ解析サービス NGS現場の会第二回研究会発表