Centers & Labs

RIKEN Center for Integrative Medical Sciences

Laboratory for Medical Science Mathematics

Group Director: Tatsuhiko Tsunoda (Ph.D.)
Tatsuhiko  Tsunoda(Ph.D.)

Medicine, in the very near future, will be able to provide patients with optimized treatments, such as individualized dosage of drugs and therapies. Patient variability with respect to such treatment response arises from variation in both the patients' genomic DNA as well as from environmental interactions. Our research will be directed towards combining genetic factors obtained from genomic sequence variation analysis/detection with gene-expression profiles obtained from microarray experiments; the final goal being their application to diagnoses and genetic therapies. Modern medicine must strive to avoid side effects stemming from the application of inadequate therapies. Towards this goal, one of the most important contributions we could make is genome-wide association studies for identification of disease and/or drug response related genes/variation. Using next-generation sequencer data, we will/have exhaustively explore variation of individuals' genomes and alterations in cancer genomes to a high quality. We will also develop theoretical frameworks and algorithms, and their practical extensions, for handling the ever increasing genetic variation, clinical and gene expression data, investigating disease-causing genes, and clarifying disease etiology.

Main Research Field

Medicine, dentistry, and pharmacy

Related Research Fields

Mathematical and physical sciences

Research Subjects

  • Genome-wide association studies based on linkage disequilibrium and haplotype pattern analyses
  • Theory and algorithms for association studies
  • Analyses of cancer genome
  • Exploration of disease-related genes based on analyses of polymorphisms, gene-expression profiles and pathways
  • Genomic variation analysis based on next generation sequencer data

Selected Publications

  1. Fujimoto, A., Nakagawa, H., Hosono, N., Nakano, K., Abe, T., Boroevich, K.A., Nagasaki, M., Yamaguchi, R., Shibuya, T., Kubo, M., Miyano, S., Nakamura, Y., and Tsunoda, T.:
    "Whole genome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing"
    Nature Genetics, 42, 931-936 (2010).
  2. Fujimoto, A., Totoki, Y., Abe, T., Boroevich, K.A., Hosoda, F., Nguyen, H.H., Aoki, M., Hoshono, N., Kubo, M., Miya, F., Arai, Y., Takahashi, H., Shirakihara, T., Nagasaki, M., Shibuya, T., Nakano, K., Watanabe-Makino, K., Tanaka, H., Nakamura, H., Kusuda, J., Ojima, H., Shimada, K., Okusaka, T., Ueno, M., Shigekawa, Y., Kawakami, Y., Arihiro, K., Ohdan, H., Gotoh, K., Ishikawa, O., Ariizumi, S., Yamamoto, M., Yamada, T., Chayama, K., Kosuge, T., Yamaue, H., Kamatani, N., Miyano, S., Nakagama, H., Nakamura, Y., Tsunoda, T., Shibata, T., and Nakagawa, H.:
    "Whole Genome Sequencing of Liver Cancers Identifies Etiological Influences on Mutation Patterns and Recurrent Mutations in Chromatin Regulators."
    Nature Genetics, 44, 760-764 (2012).
  3. Fujimoto, A., Furuta, M., Shiraishi, Y., Gotoh, K., Kawakami, Y., Arihiro, K., Nakamura, T., Ueno, M., Ariizumi, S., Hai Nguyen, H., Shigemizu, D., Abe T., Boroevich, KA., Nakano, K., Sasaki, A., Kitada, R., Maejima, K., Yamamoto, Y., Tanaka, H., Shibuya, T., Shibata, T., Ojima, H., Shimada, K., Hayami, S., Shigekawa, Y., Aikata, H., Ohdan, H., Marubashi, S., Yamada, T., Kubo, M., Hirano, S., Ishikawa, O., Yamamoto, M., Yamaue, H., Chayama, K., Miyano, S., Tsunoda, T., and Nakagawa, H.:
    "Whole-genome mutational landscape of liver cancers displaying biliary phenotype reveals hepatitis impact and molecular diversity"
    Nature Communications. 6, 6120 (2015).
  4. Kato, M., Nakamura, Y., and Tsunoda, T.:
    "An Algorithm for Inferring Complex Haplotypes in a Region of Copy-Number Variation"
    American Journal of Human Genetics, 83, 157-169 (2008).
  5. Kato, M., Kawaguchi, T., Ishikawa, S., Umeda, T., Nakamichi, R., Shapero, M.H., Jones, K.W., Nakamura, Y., Aburatani, H., and Tsunoda, T.:
    "Population-genetic nature of copy number variations in the human genome"
    Human Molecular Genetics, 19, 761-773 (2010).
  6. Tsunoda, T., Lathrop, G.M., Sekine, A., Yamada, R., Takahashi, A., Ohnishi, Y., Tanaka, T., and Nakamura, Y.:
    "Variation of gene-based SNPs and linkage disequilibrium patterns in the human genome"
    Human Molecular Genetics, 13, 1623-1632 (2004).
  7. Johnson, T.A., Niimura, Y., Tanaka, H., Nakamura, Y. and Tsunoda, T.:
    "hzAnalyzer: Detection, quantification, and visualization of contiguous homozygosity in high-density genotyping datasets."
    Genome Biology, 12, R21 (2011).
  8. The International Cancer Genome Consortium:
    "International network of cancer genome projects"
    Nature, 464, 993-998 (2010).
  9. The International HapMap Consortium:
    "A second generation human haplotype map of over 3.1 million SNPs"
    Nature, 449, 851-862 (2007).
  10. The International HapMap Consortium:
    "A haplotype map of the human genome"
    Nature, 437, 1299-1320 (2005).

Lab Members

Principal Investigator

Tatsuhiko Tsunoda
Group Director

Core Members

Alokanand Sharma
Research Scientist
Artem Lysenko
Postdoctoral Researcher
Takashi Morizono
Technical Staff I
Keith Anthony Boroevich
Technical Staff I

Contact information

North Research Building,
1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama City, Kanagawa,
230-0045, Japan

Email: tatsuhiko.tsunoda [at]

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