GOTOH, Osamu


Department of Intelligence Science and Technology
Graduate School of Informatics
Kyoto University
Kyoto 606-8501, Japan

Phone: +81-75-753-9109
Fax: +81-75-753-9110
Office: Engineering Bld. #10, Room #101


Dr. Gotoh graduated from the Department of Physics, Faculty of Science, University of Tokyo and received Dr. Sci. in biophysics from that institution in 1978. He worked as a research scientist in Saitama Cancer Center Research Institute and National Institute of Advanced Industrial Science and Technology before he came to Kyoto. His present major research field is bioinformatics, particularly genome informatics. He is currently involved in development of algorithms and software for analysis of massive genomic sequence data and also interested in application of the methods to uncover important biological signals cryptically encoded in the genome sequences. His group has developed several computer programs that are publicly distributed. The most recent ones are 鉄paln and 鼎galn. The former maps and aligns a large number of transcripts onto a genome very accurately, while the latter can efficiently compare mammalian sized huge genomic sequences on a nominal computer. He is a committee member of classification and nomenclature of cytochrome P450 gene superfamily, which collectively encodes a major class of drug-metabolizing enzymes in both prokaryotes and eukaryotes. He was the president of the Japanese Society for Bioinformatics from 2008 to 2009.

Areas of Interest:

  • Bioinformatics, Genome informatics
    • Genome alignment, comparative genomics
    • Prediction of eukaryotic gene structures
    • Multiple sequence alignment
    • Analysis of alternative splicing and alternative transcription
    • Evolution of gene organizations
  • Biophysics, Biochemistry, and Molecular Biology
    • FESS (Function, Evolution, Sequence, and Structure) analysis of cytochrome P450 gene superfamily
    • Cancer classification based on expression profiles of genes
    • Sequence analysis of transcription factors and their interaction with targets
    • Thermodynamics of helix-coil transition of DNA

Representative Publications:

  • Ichinose, N., Yada, T., Gotoh, O.
    A large-scale motif discovery using a DNA Gray code and equiprobable oligomers
    Bioinformatics, 28, 25-31 (2012).
  • Iwata, H. and Gotoh, O.
    Comparative analysis of information contents relevant to recognition of introns in many species
    BMC Genomics, 12, 45 (2011).
  • Nakato, R. and Gotoh, O.,
    Cgaln: fast and space-efficient whole-genome alignment
    BMC Bioinformatics, 11, 224 (2010).
  • Wang, X. and Gotoh, O.,
    Inference of cancer-specific gene regulatory networks using soft computing rules
    Gene Reg. Sys. Biol., 4, 19-34 (2010).
  • Wang, X. and Gotoh, O.,
    A robust gene selection methods for microarray-based cancer classification,
    Cancer Informatics, 9, 15-30 (2010).
  • Wang, X. and Gotoh, O.,
    Microarray-based cancer prediction using soft computing approach,
    Cancer Informatics, 7, 123-139 (2009).
  • Wang, X. and Gotoh, O.,
    Accurate Molecular Classification of Cancer Using Simple Rules,
    BMC Medical Genomics, 2, 64 (2009).
  • Ohnuma, S., Miura, K., Horii, A., et al.,
    Cancer-associated splicing variants of the CDCA1 and MSMB genes expressed in cancer cell lines and surgically resected gastric cancer tissues,
    Surgery, 145, 57-68 (2009).
  • Ichinose, N., Yada, T., Gotoh, O., and Aihara, K.,
    Reconstruction of transcription-translation dynamics with a model of gene networks,
    J. Theor. Biol., 255 378-386 (2008).
  • Gotoh, O.
    Direct mapping and alignment of protein sequences onto genomic sequence
    Bioinformatics, 24, 2438-244 (2008).
  • Gotoh, O.
    A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence
    Nucleic Acid Res., 36 (8), 2630-2638 (2008).
  • Yamada, S., Gotoh, O., Yamana, H.
    Improvement in speed and accuracy of multiple sequence alignment program PRIME
    IPSJ Trans. Bioinformat., 1, 2-12 (2008).
    Inform. Media Tech., 4, 317-327 (2009).
  • Nakato, R. and Gotoh, O.
    A novel method for reducing computational complexity of whole genome sequence alignment
    in Proceedings of the 6th Asia-Pacific Bioinformatics Conference, Kyoto, p.101-110 (2008).
  • Yamada, S., Gotoh, O., Yamana, H.
    Improvement in accuracy of multiple sequence alignment using novel group-to-group sequence alignment algorithm with piecewise linear gap cost
    BMC Bioinformatics, 7, 524 (2006).
  • Nagasaki, H., Arita, M., Nishizawa, T., Suwa, M., Gotoh, O.
    Automated classification of alternative splicing and transcriptional initiation and construction of a visual database of the classified patterns
    Bioinformatics, 22, 1211-1216 (2006).
  • Gotoh, O., Yamada, S., Yada, T.,
    Multiple Sequence Alignment,
    in Handbook on Computational Molecular Biology, (Aluru, S. ed.) Chapman & Hall/CRC Computer and Information Science Series, (2006)
  • Machida, M., Asai, K., Sano, M., Tanaka, T., Kumagai, T., Terai, G., Kusumoto, K.-I., Arima, T., Akita, O., Kashiwagi, Y., Abe, K., Gomi, K., Horiuchi, H., Kitamoto, K., Kobayashi, T., Takeuchi, M., Denning, D.W., Galagan, J.E., Nierman, W.C., Yu, J., Archer, D.B., Bennett, J.W., Bhatnagar, D., Cleveland, T.E., Fedorova, N.D., Gotoh, O., Horikawa, H., Hosoyama, H., Ichinomiya, M., Igarashi, R., Iwashita, K., Juvvadi, P.R., Kato, M., Kato, Y., Kin, T., Kokubun, A., Maeda, H., Maeyama, N., Maruyama, J.-i., Nagasaki, H., Nakajima, T., Oda, K., Okada, K., Paulsen, I., Sakamoto, K., Sawano, T., Takahashi, M., Takase, K., Terabayashi, Y., Wortman, J.R., Yamada, O., Yamagata, Y., Anazawa, H., Hata, Y., Koide, Y., Komori, T., Koyama, Y., Minetoki, T., Suharnan, S., Tanaka, A., Isono, K., Kuhara, S., Ogasawara, N., Kikuchi, H.,
    Genome sequencing and analysis of Aspergillus oryzae,
    Nature 438, 1157-1161 (2005).
  • Nagasaki, H, Arita, M., Nishizawa, T., Suwa, M., Gotoh, O.,
    Species-specific variation of alternative splicing and transcriptional initiation in six eukaryotes,
    Gene, 364, 53-62 (2005).
  • Sogawa, K., Numayama-Tsuruta, K., Takahashi, T., Matsushita, N., Miura, C., Nikawa, J., Gotoh, O., Kikuchi, Y., Fujii-Kuriyama, Y.,
    A novel induction mechanism of the rat CYP1A2 gene mediated by Ah receptor-Arnt heterodimer,
    Biochem. Biophys. Res. Commun. 318, 746-755 (2004).
  • Kawana, K., Ikuta, T., Kobayashi, Y., Gotoh, O., Takeda, K., Kawajiri, K.,
    Molecular mechanism of nuclear translocation of an orphan nuclear receptor SXR,
    Mol. Pharmacol., 63, 524-531 (2003).
  • Ida-Hosonuma, M., Sasaki, Y., Toyoda, H., Nomoto, A., Gotoh, O., Yonekawa, H., Koike, S.,
    Host range of poliovirus is restricted to simians because of a rapid sequence change of the poliovirus receptor gene during evolution,
    Arch. Virol. 148, 29-44 (2003).
  • Gotoh, O.,
    Homology-based gene structure prediction: simplified matching algorithm using a translated colon (ton) and improved accuracy by allowing for long gaps,
    Bioinformatics, 16, 190-202 (2000).
  • Aoyama, Y., Kudo, M., Asai, K., Okonogi, K., Horiuchi, T., Gotoh, O., Yoshida, Y.,
    Emergence of fluconazole-resistant sterol 14-demethylase P450 (CYP51) in Candida albicans is a model demonstrating the diversification mechanism of P450,
    Arch. Biochem. Biophys., 379, 170-171 (2000).
  • Yoshida, Y., Aoyama, Y., Noshiro, M., and Gotoh, O.,
    Sterol 14-Demethylase P450 (CYP51) provides a breakthrough for the discussion on the evolution of cytochrome P450 gene superfamily,
    Biochem. Biophys. Res. Commun. 273, 799-804 (2000).
  • Kimura, R., Yoshii, H., Nomura, M., Kotomura, N., Mukai, T., Ishihara, S., Ohba, K., Yanase, T., Gotoh, O., Nawata, H., Morohashi, K.,
    Identification of novel first exons in Ad4BP/SF-1 (NR5A1) gene and their tissue- and species-specific usage,
    Biochem Biophys Res Commun. 278, 63-71 (2000).
  • Teramoto, M., Nakamatsu, K., Noshiro, M., Matsuda, Y., Gotoh, O., Shen, M., Tsutsumi, S., Kawamoto, T., Iwamoto, Y., Kato, Y.,
    Gene structure and chromosomal location of a human bHLH transcriptional factor DEC1
    J. Biochem. 129, 391-396 (2000).
  • Gotoh, O.,
    Multiple sequence alignment: algorithms and applications,
    Adv. Biophys. 36, 159-206 (1999)
  • Gotoh, O.,
    Divergent structures of Caenorhabditis elegans cytochrome P450 genes suggest the frequent loss and gain of introns during the evolution of nematodes,
    Mol. Biol. Evol. 15, 1447-1459 (1998).

Academic Degree: Doctor of Philosophy (University of Tokyo)

Academic Society: Bioinformatics Society of Japan, Biophysical Society of Japan, Japanese Biochemical Society, International Society for Computational Biology


  • Graduate Courses:
    Introduction to Computational Biology
  • Undergraduate Courses:
    Primer of Bioinformatics
    Seminar on Introductory Bioinformatics
    Introduction to System Biology

Further Information:

Last Updated: January, 04, 2012