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RIKEN Center for Integrative Medical Sciences Laboratory for Comprehensive Genomic Analysis

Team Leader: Yasushi Okazaki (M.D., Ph.D.)

Research Summary

Yasushi  Okazaki(M.D., Ph.D.)

This facility will implement and standardize next generation sequencing applications, with particular focus on analysis of transcriptome, gene regulation network, ncRNA. The platform will provide highly standardized technological and analytical services to the users, in order to minimize the time from sample to data and to deliver high quality data.

Main Research Fields

  • Medicine, Dentistry & Pharmacy

Related Research Fields

  • Informatics
  • Biology

Keywords

  • Mitochondrial Disease
  • Bioinformatics
  • Inherited Disease

Selected Publications

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

  • 1. Ramilowski J, Yip CW, et al.
    "Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping."
    bioRxiv, 700864(2019) doi.org/10.1101/700864
  • 2. Yuuri Yasuoka
    "Enhancer Evolution in Chordates: Lessons from Functional Analyses of Cephalochordate Cis-Regulatory Modules."
    Development, Growth & Differentiation, in press doi: 10.1111/dgd.12684
  • 3. Yuuri Yasuoka
    "Morphogenetic Mechanisms Forming the Notochord Rod: the Turgor Pressure-Sheath Strength Model."
    Development, Growth & Differentiation, in press doi: 10.1111/dgd.12665
  • 4. Yuuri Yasuoka
    "Evolution of cis-regulatory modules for the head organizer gene goosecoid in chordates: comparisons between Branchiostoma and Xenopus."
    Zoological Letters, 5,27 (2019)
  • 5. *Borna NN, Kishita Y, Kohda M, Lim SC, Shimura M, Wu Y, Mogushi K, Yatsuka Y, Harashima H, Hisatomi Y, Fushimi T, Ichimoto K, Murayama K, Ohtake A, Okazaki Y
    "Mitochondrial ribosomal protein PTCD3 mutations cause oxidative phosphorylation defects with Leigh syndrome."
    Neurogenetics 20, 9-25(2019)
  • 6. Hashimoto K, Kouno T, Ikawa T, Hayatsu N, Miyajima Y, Yabukami H, Terooatea T, Sasaki T, Suzuki T, Valentine M, Pascarella G, Okazaki Y, Suzuki H, Shin Y, Minoda A, Taniuchi I, Okano H, Arai Y, Hirose N, Carninci P
    "Single-cell transcriptomics reveals expansion of cytotoxic CD4 T cells in supercentenarians."
    Proc Nat Acad Sci 116, 24242-24251(2019)
  • 7. Yoshida S, Kim S, Wafula EK, Tanskanen J, Kim YM, Honaas L, Yang Z, Spallek T, Conn CE, Ichihashi Y, Cheong K, Cui S, Der JP, Gundlach H, Jiao Y, Hori C, Ishida JK, Kasahara H, Kiba T, Kim MS, Koo N, Laohavisit A, Lee YH, Lumba S, McCourt P, Mortimer JC, Mutuku JM, Nomura T, Sasaki-Sekimoto Y, Seto Y, Wang Y, Wakatake T, Sakakibara H, Demura T, Yamaguchi S, Yoneyama K, Manabe RI, Nelson DC, Schulman AH, Timko MP, dePamphilis CW, Choi D, Shirasu K
    "Genome Sequence of Striga asiatica Provides Insight into the Evolution of Plant Parasitism."
    Curr Biol. 29(18), 3041-3052.e4.(2019) doi: 10.1016/j.cub.2019.07.086.
  • 8. Sriswasdi S, Takashima M, Manabe RI, Ohkuma M, Iwasaki W
    "Genome and transcriptome evolve separately in recently hybridized Trichosporon fungi."
    Commun Biol. 2,263(2019) doi: 10.1038/s42003-019-0515-2.
  • 9. Takashima M, Manabe RI, Ohkuma M
    "Draft Genome Sequences of Basidiomycetous Epiphytic Phylloplane Yeast Type Strains Dioszegia crocea JCM 2961 and Dioszegia aurantiaca JCM 2956."
    Microbiol Resour Announc. 8(26) pii: e01727-18(2019) doi: 10.1128/MRA.01727-18.
  • 10. Takashima M, Manabe RI, Nishimura Y, Endoh R, Ohkuma M, Sriswasdi S, Sugita T, Iwasaki W
    "Recognition and delineation of yeast genera based on genomic data: Lessons from Trichosporonales."
    Fungal Genet Biol. 130, 31-42(2019) doi: 10.1016/j.fgb.2019.04.013.

Related Links

Lab Members

Principal investigator

Yasushi Okazaki
Team Leader

Core members

Kokoro Ozaki
Deputy Team Leader
Tadayuki Takeda
Senior Research Scientist
Riichiroh Manabe
Senior Research Scientist
Michihira Tagami
Senior Technical Scientist
Yuuri Yasuoka
Research Scientist
Norihito Hayatsu
Research Scientist
Hiroko Hagiwara
Research Scientist
Tsugumi Kawashima
Technical Scientist
Shohei Noma
Technical Scientist
Tomoko Hirata
Technical Scientist
Yumiko Yamamoto
Technical Scientist
Hiroo Inaba
Technical Scientist
Chitose Takahashi
Technical Staff I
Hiroko Kinoshita
Technical Staff I
Nozomi Moritsugu
Technical Staff I

Contact Information

West Research Building 4F W403
1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama, Kanagawa,
230-0045, Japan
Tel: +81-(0)45-503-9237
Fax: +81-(0)45-503-9216
Email: LSA-support [at] riken.jp

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