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RIKEN Information R&D and Strategy Headquarters Medical Data Mathematical Reasoning Team

Team Leader: Eiryo Kawakami (M.D., Ph.D.)

Research Summary

Eiryo  Kawakami(M.D., Ph.D.)

Toward the realization of Society 5.0 society, our laboratory conducts research to understand and predict health/disease state transition by utilizing real-world measurement data obtained from various IoT devices. Since regulatory mechanisms between observed variables are uncertain in the real-world data, we should represent states without relying on specific hypothesis or process model and make predictions considering individuality. Our laboratory flexibly applies various mathematical sciences such as machine learning, network and statistics, aims at understanding health/disease state, and establishing individualized predictive model based on characteristics of each person.

Main Research Fields

  • Biological Sciences

Related Research Fields

  • Informatics
  • Complex Systems
  • Mathematical & Physical Sciences
  • Biology
  • Medicine, Dentistry & Pharmacy
  • Frontiers of informatics
  • Biological Science
  • Basic medicine

Keywords

  • Lifesystem dynamics
  • Machine learning
  • Systems Biology
  • Bioinformatics

Selected Publications

Papers with an asterisk(*) are based on research conducted outside of RIKEN.

  • 1.Kochi Y, Kamatani Y, Kondo Y, Suzuki A, Kawakami E, Hiwa R, Momozawa Y, Fujimoto M, Jinnin M, Tanaka Y, Kanda T, Cooper RG, Chinoy H, Rothwell S, Lamb JA, Vencovský J, Mann H, Ohmura K, Myouzen K, Ishigaki K, Nakashima R, Hosono Y, Tsuboi H, Kawasumi H, Iwasaki Y, Kajiyama H, Horita T, Ogawa-Momohara M, Takamura A, Tsunoda S, Shimizu J, Fujio K, Amano H, Mimori A, Kawakami A, Umehara H, Takeuchi T, Sano H, Muro Y, Atsumi T, Mimura T, Kawaguchi Y, Mimori T, Takahashi A, Kubo M, Kohsaka H, Sumida T, Yamamoto K.:
    “Splicing variant of WDFY4 augments MDA5 signalling and the risk of clinically amyopathic dermatomyositis.”
    Ann Rheum Dis 77, 602-611 (2018)
  • 2.Kawakami E, Adachi N, Senda T, Horikoshi M.:
    “Leading role of TBP in the Establishment of Complexity in Eukaryotic Transcription Initiation Systems.”
    Cell Rep 21, 3941-3956 (2017)
  • 3.Hayatsu N, Miyao T, Tachibana M, Murakami R, Kimura A, Kato T, Kawakami E, Endo TA, Setoguchi R, Watarai H, Nishikawa T, Yasuda T, Yoshida H, Hori S.:
    “Analyses of a Mutant Foxp3 Allele Reveal BATF as a Critical Transcription Factor in the Differentiation and Accumulation of Tissue Regulatory T Cells.”
    Immunity 47, 268-283. e9 (2017)
  • 4.Kawakami E, Nakaoka S, Ohta T, Kitano H.:
    “Weighted enrichment method for prediction of transcription regulators from transcriptome and global chromatin immunoprecipitation data.”
    Nucleic Acids Res 44, 5010-21 (2016)
  • 5.Kawakami E, Singh VK, Matsubara K, Ishii T, Matsuoka Y, Hase T, Kulkarni P, Siddiqui K, Kodilkar J, Danve N, Subramanian I, Katoh M, Shimizu-Yoshida Y, Ghosh S, Jere A, Kitano H.:
    “Network analyses based on comprehensive molecular interaction maps reveal robust control structures in yeast stress response pathways.”
    NPJ Syst Biol Appl 2, 15018 (2016)
  • 6.*Watanabe T, Kawakami E (contributed equally), Shoemaker JE, Lopes TJ, Matsuoka Y, Tomita Y, Kozuka-Hata H, Gorai T, Kuwahara T, Takeda E, Nagata A, Takano R, Kiso M, Yamashita M, Sakai-Tagawa Y, Katsura H, Nonaka N, Fujii H, Fujii K, Sugita Y, Noda T, Goto H, Fukuyama S, Watanabe S, Neumann G, Oyama M, Kitano H, Kawaoka Y.:
    “Influenza virus-host interactome screen as a platform for antiviral drug development.”
    Cell Host Microbe 16, 795-805 (2014)
  • 7.*Imai M, Watanabe T, Hatta M, Das SC, Ozawa M, Shinya K, Zhong G, Hanson A, Katsura H, Watanabe S, Li C, Kawakami E, Yamada S, Kiso M, Suzuki Y, Maher EA, Neumann G, Kawaoka Y.:
    “Experimental adaptation of an influenza H5 HA confers respiratory droplet transmission to a reassortant H5 HA/H1N1 virus in ferrets.”
    Nature 486, 420-8 (2012)
  • 8.*Noda T, Sugita Y, Aoyama K, Hirase A, Kawakami E, Miyazawa A, Sagara H, Kawaoka Y.:
    “Three-dimensional analysis of ribonucleoprotein complexes in influenza A virus.”
    Nat Commun 3, 639 (2012)
  • 9.*Watanabe T, Kiso M, Fukuyama S, Nakajima N, Imai M, Yamada S, Murakami S, Yamayoshi S, Iwatsuki-Horimoto K, Sakoda Y, Takashita E, McBride R, Noda T, Hatta M, Imai H, Zhao D, Kishida N, Shirakura M, de Vries RP, Shichinohe S, Okamatsu M, Tamura T, Tomita Y, Fujimoto N, Goto K, Katsura H, Kawakami E, Ishikawa I, Watanabe S, Ito M, Sakai-Tagawa Y, Sugita Y, Uraki R, Yamaji R, Eisfeld AJ, Zhong G, Fan S, Ping J, Maher EA, Hanson A, Uchida Y, Saito T, Ozawa M, Neumann G, Kida H, Odagiri T, Paulson JC, Hasegawa H, Tashiro M, Kawaoka Y.:
    “Characterization of H7N9 influenza A viruses isolated from humans.”
    Nature 501, 551-5 (2013)
  • 10.*Kawakami E, Watanabe T, Fujii K, Goto H, Watanabe S, Noda T, Kawaoka Y.:
    “Strand-specific real-time RT-PCR for distinguishing influenza vRNA, cRNA, and mRNA.”
    J Virol Methods 173, 1-6 (2011)

Selected Publications

Papers with an asterisk(*) are based on research conducted outside of RIKEN.

  • 1.Kawakami E, Tabata J, Yanaihara N, Ishikawa T, Koseki K, Iida Y, Saito M, Komazaki H, Shapiro JS, Goto C, Akiyama Y, Saito R, Saito M, Takano H, Yamada K, Okamoto A.:
    "Application of Artificial Intelligence for Preoperative Diagnostic and Prognostic Prediction in Epithelial Ovarian Cancer Based on Blood Biomarkers"
    Clinical Cancer Research 25, 3006-3015 (2019)
  • 2.Kochi Y, Kamatani Y, Kondo Y, Suzuki A, Kawakami E, Hiwa R, Momozawa Y, Fujimoto M, Jinnin M, Tanaka Y, Kanda T, Cooper RG, Chinoy H, Rothwell S, Lamb JA, Vencovsky J, Mann H, Ohmura K, Myouzen K, Ishigaki K, Nakashima R, Hosono Y, Tsuboi H, Kawasumi H, Iwasaki Y, Kajiyama H, Horita T, Ogawa-Momohara M, Takamura A, Tsunoda S, Shimizu J, Fujio K, Amano H, Mimori A, Kawakami A, Umehara H, Takeuchi T, Sano H, Muro Y, Atsumi T, Mimura T, Kawaguchi Y, Mimori T, Takahashi A, Kubo M, Kohsaka H, Sumida T, Yamamoto K.:
    "Splicing variant of WDFY4 augments MDA5 signalling and the risk of clinically amyopathic dermatomyositis."
    Annals of the Rheumatic Diseases 77, 602-611 (2018)
  • 3.Kawakami E, Adachi N, Senda T, Horikoshi M.:
    "Leading role of TBP in the Establishment of Complexity in Eukaryotic Transcription Initiation Systems."
    Cell Reports 21, 3941-3956 (2017)
  • 4.Hayatsu N, Miyao T, Tachibana M, Murakami R, Kimura A, Kato T, Kawakami E, Endo TA, Setoguchi R, Watarai H, Nishikawa T, Yasuda T, Yoshida H, Hori S.:
    "Analyses of a Mutant Foxp3 Allele Reveal BATF as a Critical Transcription Factor in the Differentiation and Accumulation of Tissue Regulatory T Cells."
    Immunity 47, 268-283. e9 (2017)
  • 5.Kawakami E, Nakaoka S, Ohta T, Kitano H.:
    "Weighted enrichment method for prediction of transcription regulators from transcriptome and global chromatin immunoprecipitation data."
    Nucleic Acids Research 44, 5010-5021 (2016)
  • 6.Kawakami E, Singh VK, Matsubara K, Ishii T, Matsuoka Y, Hase T, Kulkarni P, Siddiqui K, Kodilkar J, Danve N, Subramanian I, Katoh M, Shimizu-Yoshida Y, Ghosh S, Jere A, Kitano H.:
    "Network analyses based on comprehensive molecular interaction maps reveal robust control structures in yeast stress response pathways."
    npj Systems Biology and Applications 2, 15018 (2016)
  • 7.*Watanabe T, Kawakami E (contributed equally), Shoemaker JE, Lopes TJ, Matsuoka Y, Tomita Y, Kozuka-Hata H, Gorai T, Kuwahara T, Takeda E, Nagata A, Takano R, Kiso M, Yamashita M, Sakai-Tagawa Y, Katsura H, Nonaka N, Fujii H, Fujii K, Sugita Y, Noda T, Goto H, Fukuyama S, Watanabe S, Neumann G, Oyama M, Kitano H, Kawaoka Y.:
    "Influenza virus-host interactome screen as a platform for antiviral drug development."
    Cell Host & Microbe 16, 795-805 (2014)
  • 8.*Imai M, Watanabe T, Hatta M, Das SC, Ozawa M, Shinya K, Zhong G, Hanson A, Katsura H, Watanabe S, Li C, Kawakami E, Yamada S, Kiso M, Suzuki Y, Maher EA, Neumann G, Kawaoka Y.:
    "Experimental adaptation of an influenza H5 HA confers respiratory droplet transmission to a reassortant H5 HA/H1N1 virus in ferrets."
    Nature 486, 420-8 (2012)
  • 9.*Watanabe, T., Kiso, M., Fukuyama, S., Nakajima, N., Imai, M., Yamada, S., Murakami, S., Yamayoshi, S., Iwatsuki-Horimoto, K., Sakoda, Y., Takashita, E., McBride, R., Noda, T., Hatta, M., Imai, H., Zhao, D., Kishida, N., Shirakura, M., de Vries, RP., Shichinohe, S., Okamatsu, M., Tamura, T., Tomita, Y., Fujimoto, N., Goto, K., Katsura, H., Kawakami, E., Ishikawa, I., Watanabe, S., Ito, M., Sakai-Tagawa, Y., Sugita, Y., Uraki, R., Yamaji, R., Eisfeld, AJ., Zhong, G., Fan, S., Ping, J., Maher, EA., Hanson, A., Uchida, Y., Saito, T., Ozawa, M., Neumann, G., Kida, H., Odagiri, T., Paulson, JC., Hasegawa, H., Tashiro, M., Kawaoka, Y.:
    "Characterization of H7N9 influenza A viruses isolated from humans."
    Nature 501, 551-5 (2013)
  • 10.*Kawakami, E., Watanabe, T., Fujii, K., Goto, H., Watanabe, S., Noda, T., Kawaoka, Y.:
    "Strand-specific real-time RT-PCR for distinguishing influenza vRNA, cRNA, and mRNA."
    Journal of Virological Methods 173, 1-6 (2011)

Related Links

Lab Members

Principal investigator

Eiryo Kawakami
Team Leader

Core members

Tetsuo Ishikawa
Research Scientist
Akiko Hanai
Postdoctoral Researcher
Megumi Oya
Postdoctoral Researcher
Pengyu Liu
Postdoctoral Researcher
Manami Kato
Technical Staff II
Keita Koseki
Research Part-time Worker I
Keisuke Chikamoto
Research Part-time Worker I
Akihisa Tateishi
Research Part-time Worker I
Yoshiki Takai
Research Part-time Worker I
Shoichiro Kawauchi
Research Part-time Worker I
Kentaro Hamada
Research Part-time Worker II
Ryo Fujihira
Research Part-time Worker II
Mikiko Nakanishi
Research Part-time Worker II
Shotaro Aoyama
Research Part-time Worker II
Shinji Oguchi
Research Part-time Worker II
Yuina Koi
Research Part-time Worker II
Ayaka Mori
Research Part-time Worker II
Natsumi Yamada
Research Part-time Worker II
Yuta Iida
Research Part-time Worker II
Kohei Osada
Research Part-time Worker II
Shinji Nakaoka
Visiting Scientist
Tazro Ohta
Visiting Scientist
Yuki Goshima
Visiting Scientist
Kyohei Sano
Visiting Scientist
Ayumu Tsuji
Student Trainee
Daigo Kato
Student Trainee
Ryoga Nishimura
Student Trainee

Contact Information

W507/509 West Research Building
1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama City, Kanagawa,
230-0045, Japan
Email: eiryo.kawakami [at] riken.jp

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