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RIKEN Center for Integrative Medical Sciences Laboratory for Systems Genetics

Team Leader: Yukinori Okada (M.D., Ph.D.)

Research Summary

Yukinori Okada(M.D., Ph.D.)

Genome is a blueprint of humans. The goal of our team is to decipher the blueprint and elucidate hidden biology. We focus on large-scale human genome, omics, and phenome data, and underlying high-dimensional network. By developing novel methodologies in statistical genetics and machine learning, we re-define human biology as systems of genetics. Our team aims elucidation of disease biology, novel drug discovery, and implementation of genomic personalized medicine. We welcome for discussion!!

Main Research Fields

  • Medicine, Dentistry & Pharmacy

Related Research Fields

  • Informatics
  • Complex Systems
  • Mathematical & Physical Sciences
  • Biological Sciences
  • Biology
  • System genome science-related
  • Medical biochemistry-related
  • Life, health and medical informatics-related

Keywords

  • Statistical genetics
  • Bioinformatics
  • Artificial intelligence
  • Omics analysis
  • Disease genetics

Selected Publications

  • 1.Sakaue S, Kanai M, Tanigawa Y, Karjalainen J, Kurki M, Koshiba S, Narita A, Konuma T, Yamamoto K, Akiyama M, Ishigaki K, Suzuki A, Suzuki K, Obara W, Yamaji K, Takahashi K, Asai S, Takahashi Y, Suzuki T, Shinozaki N, Yamaguchi H, Minami S, Murayama S, Yoshimori K, Nagayama S, Obata D, Higashiyama M, Masumoto A, Koretsune Y; FinnGen, Ito K, Terao C, Yamauchi T, Komuro I, Kadowaki T, Tamiya G, Yamamoto M, Nakamura Y, Kubo M, Murakami Y, Yamamoto K, Kamatani Y, Palotie A, Rivas MA, Daly MJ, Matsuda K, Okada Y.:
    "A cross-population atlas of genetic associations for 220 human phenotypes."
    Nature Genetics doi:10.1038/s41588-021-00931-x. (2021)
  • 2.Uffelmann E, Huang QQ, Munung NS, de Vries J, Okada Y, Martin AR, Martin HC, Lappalainen T, PosthumaD.:
    "Genome-wide association studies"
    Nature Review Methods Primers. 1:59. (2021)
  • 3.Tomofuji Y, Maeda Y, Oguro-Igashira E, Kishikawa T, Yamamoto K, Sonehara K, Motooka D, Matsumoto Y, Matsuoka H, Yoshimura M, Yagita M, Nii T, Ohshima S, Nakamura S, Inohara H, Takeda K, Kumanogoh A, Okada Y.:
    "Metagenome-wide association study revealed disease-specific landscape of the gut microbiome of systemic lupus erythematosus in Japanese"
    Annals of the Rheumatic Diseases. doi:10.1136/annrheumdis-2021-220687. (2021)
  • 4.COVID-19 Host Genetics Initiative.
    "Mapping the human genetic architecture of COVID-19"
    Nature. doi:10.1038/s41586-021-03767-x. (2021)
  • 5.Naito T, Suzuki K, Hirata J, Kamatani Y, Matsuda K, Toda T, Okada Y.:
    "A deep learning method for HLA imputation and trans-ethnic MHC fine-mapping of type 1 diabetes"
    Nature Communications. 12:1639. (2021)
  • 6.Sakaue S, Hirata J, Kanai M, Suzuki K, Akiyama M, Lai Too C, Arayssi T, Hammoudeh M, Al Emadi S, Masri BK, Halabi H, Badsha H, Uthman IW, Saxena R, Padyukov L, Hirata M, Matsuda K, Murakami Y, Kamatani Y, Okada Y.:
    "Dimensionality reduction reveals fine-scale structure in the Japanese population with consequences for polygenic risk prediction"
    Nature Communications. 11:1569. (2020)
  • 7.Sakaue S, Kanai M, Karjalainen J, Akiyama M, Kurki M, Matoba N, Takahashi A, Hirata M, Kubo M, Matsuda K, Murakami Y; FinnGen, Daly MJ, Kamatani Y, Okada Y.:
    "Trans-biobank analysis with 676,000 individuals elucidates the association of polygenic risk scores of complex traits with human lifespan"
    Nature Medicine. 26:542-548. (2020)
  • 8.Hirata J, Hosomichi K, Sakaue S, Kanai M, Nakaoka H, Ishigaki K, Suzuki K, Akiyama M, Kishikawa T, Ogawa K, Masuda T, Yamamoto K, Hirata M, Matsuda K, Momozawa Y, Inoue I, Kubo M, Kamatani Y, Okada Y.:
    "Genetic and phenotypic landscape of the MHC region in the Japanese population"
    Nature Genetics. 51:470-480. (2019)
  • 9.Sakaue S, Hirata J, Maeda Y, Kawakami E, Nii T, Kishikawa T, Ishigaki K, Terao C, Suzuki K, Akiyama M, Suita N, Masuda T, Ogawa K, Yamamoto Y, Saeki Y, Matsushita M, Yoshimura M, Matsuoka H, Ikari K, Taniguchi A, Yamanaka H, Kawaji H, Lassmann T, Itoh M, Yoshitomi H, Ito H, Ohmura K, Forrest A, Hayashizaki Y, Carninci P, Kumanogoh A, Kamatani Y, de Hoon M, Yamamoto K, Okada Y.:
    "Integration of genetics and miRNA-target gene network identified disease biology implicated in tissue specificity"
    Nucleic Acids Research. 46:11898-11909. (2018)
  • 10.Okada Y, Momozawa Y, Sakaue S, Kanai M, Ishigaki K, Akiyama M, Kishikawa T, Arai Y, Sasaki T, Kosaki K, Suematsu M, Matsuda K, Yamamoto K, Kubo M, Hirose N, Kamatani Y.:
    "Deep whole-genome sequencing reveals recent selection signatures linked to evolution and disease risk of Japanese"
    Nature Communications. 9:1631. (2018)

Events

Publications

Lab Members

Principal investigator

Yukinori Okada
Team Leader

Contact Information

West building (W319),
1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan
Email: yokada [at] riken.jp

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