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. Inhibition of influenza virus infection by targeting genome conserved region with non-natural nucleic acid.

   Tomoya Takahashi, Takuya Ohzawa, Shinjiro Sawada, Nobuo Kato, Naohisa Goto, Shota Nakamura, Teruo Yasunaga and Kunihiro Kaihatsu

   Nucleic Acids Symp Ser (Oxf), (53), 285-286, 2009.
2. Impact of amino acid variations in Gag and protease of HIV type 1 CRF01_AE strains on drug susceptibility of virus to protease inhibitors.

   Piyamat Jinnopat, Panasda Isarangkura-na-ayuthaya, Piraporn Utachee, Yukiko Kitagawa, U Chandimal de Silva, Uamporn Siripanyaphinyo, Yoko Kameoka, Kenzo Tokunaga, Pathom Sawanpanyalert, Kazuyoshi Ikuta, Wattana Auwanit and Masanori Kameoka

   J Acquir Immune Defic Syndr, 52 (3), 320-328, 2009.
3. Clonal dissemination of human isolates of Streptococcus suis serotype 14 in Thailand.

   Anusak Kerdsin, Kazunori Oishi, Saowalak Sripakdee, Nitsara Boonkerd, Pitimol Polwichai, Shota Nakamura, Ryuichi Uchida, Pathom Sawanpanyalert and Surang Dejsirilert

   J Med Microbiol, 58 (Pt 11), 1508-1513, 2009.
4. Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach.

   Shota Nakamura, Cheng-Song Yang, Naomi Sakon, Mayo Ueda, Takahiro Tougan, Akifumi Yamashita, Naohisa Goto, Kazuo Takahashi, Teruo Yasunaga, Kazuyoshi Ikuta, Tetsuya Mizutani, Yoshiko Okamoto, Michihira Tagami, Ryoji Morita, Norihiro Maeda, Jun Kawai, Yoshihide Hayashizaki, Yoshiyuki Nagai, Toshihiro Horii, Tetsuya Iida and Takaaki Nakaya

   PLoS ONE, 4 (1), e4219, 2009.
5. Phenotypic studies on recombinant human immunodeficiency virus type 1 (HIV-1) containing CRF01_AE env gene derived from HIV-1-infected patient, residing in central Thailand.

   Piraporn Utachee, Piyamat Jinnopat, Panasda Isarangkura-Na-Ayuthaya, U Chandimal de Silva, Shota Nakamura, Uamporn Siripanyaphinyo, Nuanjun Wichukchinda, Kenzo Tokunaga, Teruo Yasunaga, Pathom Sawanpanyalert, Kazuyoshi Ikuta, Wattana Auwanit and Masanori Kameoka

   Microbes Infect, 11 (3), 334-343, 2009.
6. Genotypic characterization of CRF01_AE env genes derived from human immunodeficiency virus type 1-infected patients residing in central Thailand.

   Piraporn Utachee, Piyamat Jinnopat, Panasda Isarangkura-Na-Ayuthaya, Udayanga Chandimal de Silva, Shota Nakamura, Uamporn Siripanyaphinyo, Nuanjun Wichukchinda, Kenzo Tokunaga, Teruo Yasunaga, Pathom Sawanpanyalert, Kazuyoshi Ikuta, Wattana Auwanit and Masanori Kameoka

   AIDS Res Hum Retroviruses, 25 (2), 229-236, 2009.
7. Anionic polymer, poly(methyl vinyl ether-maleic anhydride)-coated beads-based capture of human influenza A and B virus.

   Akikazu Sakudo, Koichi Baba, Megumi Tsukamoto, Atsuko Sugimoto, Takashi Okada, Takanori Kobayashi, Norihito Kawashita, Tatsuya Takagi and Kazuyoshi Ikuta

   Bioorg Med Chem, 17 (2), 752-757, 2009.
8. Identification and characterization of a novel type III secretion system in trh-positive Vibrio parahaemolyticus strain TH3996 reveal genetic lineage and diversity of pathogenic machinery beyond the species level.

   Natsumi Okada, Tetsuya Iida, Kwon-Sam Park, Naohisa Goto, Teruo Yasunaga, Hirotaka Hiyoshi, Shigeaki Matsuda, Toshio Kodama and Takeshi Honda

   Infect Immun, 77 (2), 904-913, 2009.
9. Detection of circulating Asian H5N1 viruses by a newly established monoclonal antibody.

   Anariwa Du, Tomo Daidoji, Takaaki Koma, Madiha S Ibrahim, Shota Nakamura, U Chandimal de Silva, Mayo Ueda, Cheng-Song Yang, Teruo Yasunaga, Kazuyoshi Ikuta and Takaaki Nakaya

   Biochem Biophys Res Commun, 378 (2), 197-202, 2009.

Link

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