Department of Genome Informatics

Subjects:

1. Bioinformatics and molecular evolution analysis of genes and genomes.
2. Analysis of protein 3-D structure information for drug discovery and design.
3. Genome sequencing of disease-causing organisms in collaboration with other laboratories.
4. Development of genome information analysis software, including Next-Generation Sequencing data management and analysis.

Published Papers

1. A comprehensive analysis of reassortment in influenza A virus.

   U Chandimal de Silva, Hokuto Tanaka, Shota Nakamura, Naohisa Goto and Teruo Yasunaga

   Biol Open, 1 (4), 385-390, 2012.
2. Plasmodium cynomolgi genome sequences provide insight into Plasmodium vivax and the monkey malaria clade.

   Shin-Ichiro Tachibana, Steven A Sullivan, Satoru Kawai, Shota Nakamura, Hyunjae R Kim, Naohisa Goto, Nobuko Arisue, Nirianne M Q Palacpac, Hajime Honma, Masanori Yagi, Takahiro Tougan, Yuko Katakai, Osamu Kaneko, Toshihiro Mita, Kiyoshi Kita, Yasuhiro Yasutomi, Patrick L Sutton, Rimma Shakhbatyan, Toshihiro Horii, Teruo Yasunaga, John W Barnwell, Ananias A Escalante, Jane M Carlton and Kazuyuki Tanabe

   Nat Genet, 44 (9), 1051-1055, 2012.
3. Antigenic Analysis of Highly Pathogenic Avian Influenza Virus H5N1 Sublineages Co-Circulating in Egypt.

   Yohei Watanabe, Madiha S Ibrahim, Hany F Ellakany, Norihito Kawashita, Tomo Daidoji, Tatsuya Takagi, Teruo Yasunaga, Takaaki Nakaya and Kazuyoshi Ikuta

   J Gen Virol, 93 (Pt. 10), 2215-2226, 2012.
4. Frequency of D222G and Q223R Hemagglutinin Mutants of Pandemic (H1N1) 2009 Influenza Virus in Japan between 2009 and 2010.

   Mayo Yasugi, Shota Nakamura, Tomo Daidoji, Norihito Kawashita, Ririn Ramadhany, Cheng-Song Yang, Teruo Yasunaga, Tetsuya Iida, Toshihiro Horii, Kazuyoshi Ikuta, Kazuo Takahashi and Takaaki Nakaya

   PLoS One, 7 (2), e30946, 2012.
5. Sharing programming resources between Bio* projects through remote procedure call and native call stack strategies.

   Pjotr Prins, Naohisa Goto, Andrew Yates, Laurent Gautier, Scooter Willis, Christopher Fields and Toshiaki Katayama

   Methods Mol Biol, 856, 513-527, 2012.
6. Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics.

   Raoul J P Bonnal, Jan Aerts, George Githinji, Naohisa Goto, Dan MacLean, Chase A Miller, Hiroyuki Mishima, Massimiliano Pagani, Ricardo Ramirez-Gonzalez, Geert Smant, Francesco Strozzi, Rob Syme, Rutger Vos, Trevor J Wennblom, Ben J Woodcroft, Toshiaki Katayama and Pjotr Prins

   Bioinformatics, 28 (7), 1035-1037, 2012.
7. Structure of the CFA/III major pilin subunit CofA from human enterotoxigenic Escherichia coli determined at 0.90 Å resolution by sulfur-SAD phasing.

   Shunsuke Fukakusa, Kazuki Kawahara, Shota Nakamura, Takaki Iwashita, Seiki Baba, Mitsuhiro Nishimura, Yuji Kobayashi, Takeshi Honda, Tetsuya Iida, Tooru Taniguchi and Tadayasu Ohkubo

   Acta Crystallogr D Biol Crystallogr, 68 (Pt 10), 1418-1429, 2012.
8. Tropism of Pandemic 2009 H1N1 Influenza a Virus.

   Ririn Ramadhany, Mayo Yasugi, Shota Nakamura, Tomo Daidoji, Yohei Watanabe, Kazuo Takahashi, Kazuyoshi Ikuta and Takaaki Nakaya

   Front Microbiol, 3, 128, 2012.
9. Limited cross-reactivity of mouse monoclonal antibodies against Dengue virus capsid protein among four serotypes.

   Megumi Noda, Promsin Masrinoul, Chaweewan Punkum, Chonlatip Pipattanaboon, Pongrama Ramasoota, Chayanee Setthapramote, Tadahiro Sasaki, Mikiko Sasayama, Akifumi Yamashita, Takeshi Kurosu, Kazuyoshi Ikuta and Tamaki Okabayashi

   Biologics, 6, 409-416, 2012.
10. Pyrosequence read length of 16S rRNA gene affects phylogenetic assignment of plant-associated bacteria.

    Takashi Okubo, Seishi Ikeda, Akifumi Yamashita, Kimihiro Terasawa and Kiwamu Minamisawa

    Microbes Environ, 27 (2), 204-208, 2012.
11. Metagenomic analysis of DNA viruses in a wastewater treatment plant in tropical climate.

    Hideyuki Tamaki, Rui Zhang, Florent E Angly, Shota Nakamura, Pei-Ying Hong, Teruo Yasunaga, Yoichi Kamagata and Wen-Tso Liu

    Environ Microbiol, 14 (2), 441-452, 2012.
12. The triple helical structure and stability of collagen model peptide with 4(S)-hydroxyprolyl-Pro-Gly units.

    Daisuke Motooka, Kazuki Kawahara, Shota Nakamura, Masamitsu Doi, Yoshinori Nishi, Yuji Nishiuchi, Young Kee Kang, Takashi Nakazawa, Susumu Uchiyama, Takuya Yoshida, Tadayasu Ohkubo and Yuji Kobayashi

    Biopolymers, 98 (2), 111-121, 2012.
13. Predictive factors for postherpetic neuralgia using ordered logistic regression analysis.

    Yuko Kanbayashi, Keiko Onishi, Keita Fukazawa, Kousuke Okamoto, Hiroshi Ueno, Tatsuya Takagi and Toyoshi Hosokawa

    Clin J Pain, 28 (8), 712-714, 2012.
14. Polydom/SVEP1 is a ligand for integrin α9β1.

    Ryoko Sato-Nishiuchi, Itsuko Nakano, Akio Ozawa, Yuya Sato, Makiko Takeichi, Daiji Kiyozumi, Kiyoshi Yamazaki, Teruo Yasunaga, Sugiko Futaki and Kiyotoshi Sekiguchi

    J Biol Chem, 287 (30), 25615-25630, 2012.
15. Recent Advances in the Development of Small-Molecule Compounds Targeting HIV- 1 gp41 as Membrane Fusion Inhibitors

    Norihito Kawashita, Yu-Shi Tian, U. Chandimal de Silva, Kousuke Okamoto and Tetsuya Takagi

    Mini-Reviews in Organic Chemistry, 9 (1), 20-26, 2012.

Link

http://www.biken.osaka-u.ac.jp/