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Yusuke Okazaki (Ph.D.)

Assistant Professor
Ogata Lab., Bioinformatics Center,
Institute for Chemical Research, Kyoto University
ORCiD: http://orcid.org/0000-0001-8770-2774


Career

2010.3 B.Sc at Kyoto University
2012.3 M.Sc at Kyoto University
(Supervisor: Prof. Shin-ichi Nakano, Center for Ecological Research, Kyoto University)
2012.4~2015.3 Mitsubishi Research Institute, Inc
(Worked as a marketing and management consultant)
2015.4~2018.3 Ph.D Student at Kyoto University
(Supervisor: Prof. Shin-ichi Nakano, Center for Ecological Research, Kyoto University)
JSPS Research Fellow (DC1)
2018.4~2020.11 JSPS Research Fellow (PD)
(Host researcher: Dr. Hideyuki Tamaki,
Microbial and Genetic Resources Research Group, Bioproduction Research Institute,
National Institute of Advanced Industrial Science and Technology (AIST) )
2020.12~ Assistant Professor, Chemical Life Science, Bioinformatics Center,
Institute for Chemical Research, Kyoto University

Scientific Grant

(Only those granted as PI are shown. Full list for KAKENHI grant is here )
2015.4~2018.3 KAKENHI Grant-in-Aid for JSPS Fellows "Ecological study of CL500-11, the bacterioplankton lineage dominating in the hypolimnion of Lake Biwa" (2,800,000 JPY)
2017.8~2017.11 The Kyoto University Foundation Overseas' Research Fellowship "Ecology of bacterioplankton in deep freshwater lakes" (863,000 JPY) - Stayed at Limnological Station, University of Zurich
2018.4~2021.3 KAKENHI Grant-in-Aid for JSPS Fellows "Viral, prokaryotic, and eukaryotic microbial ecosystem in deep freshwater lakes revealed by ecogenomics" (3,100,000 JPY)
2020.4~2021.3 Platform for Advanced Genome Science 2020 "Viral, prokaryotic, and eukaryotic microbial ecosystem in deep freshwater lakes revealed by ecogenomics" (Support for sequencing cost)
2021.6~2022.3 The Kyoto University Foundation 2021FY Research promotion grant "Prokaryotic genomic microdiversity revealed through cutting-edge ecogenomics" (1,000,000 JPY)
2021.9~2025.3 Kyoto University 125th Anniversary Fund Kusunoki 125 "Challenging dry questions in environmental microbiology and virology from wet" (5,000,000 JPY)
2022.4~2025.3 KAKENHI Grant-in-Aid for Early-Career Scientists "Who infects whom?: Linking uncultured bacterial and viral genomes " (3,600,000 JPY)
2023.4~2030.3 JST FOREST program "Developing a high-resolution eco-genomics platform through inter-lake comparisons" (50,000,000 JPY)

Award


Skills

  • Microbial sampling in deep freshwater lakes (having a Japanese boat's operator license)
  • Microscopic enumeration of plankton (bacteria, protist, phyto- and zooplankton)
  • Probe construction and specific staining of microbes by CARD-FISH
  • High-throughput bacterial cell counting using flowcytometer
  • Microbial community analysis using SSU rRNA gene amplicon sequencing
  • Shotgun metagenome and metatranscriptome analysis of environmental bacteria and viruses
  • Amplicon and metagenomic analysis using a long-read sequencer
  • Isolation of oligotrophic bacteria using the high-throughput dilution-to-extinction cultivation technique
  • Profiling of microbial genomic microdivesity through metagenomic read mapping

Society


Contributions as a reviewer

Microbes and Environments (4), mSphere (4), Environmental Microbiology (3), Frontiers in Microbiology (2), Limnology (2), Limnology and Oceanography (1), Environmental Microbiology Reports (1), Applied and Environmental Microbiology (1), BMC Microbiology (1), Aquatic Microbial Ecology (1), Aquatic Sciences (1), Scientific Reports (1), Communications Biology (1), Scientific Data (1), Ecological Research (1)


Teaching subjects

  • Kyoto Univ. Faculty of Science; Bioinformatics (team teaching, FY2021-)
  • Kyoto Univ. Graduate School of Science; Advanced Course on Biological Science B (team teaching, FY2022-)
  • Kyoto Univ. Graduate School of Science; Bioinformatics: Advanced Course (team teaching, FY2023-)
  • Kyoto Univ. Liberal Arts and Sciences Courses; Fundamental Chemical Experiments (team teaching, FY2023)

Contact

Chemical Life Science, Bioinformatics Center,
Institute for Chemical Research, Kyoto University
Uji Research Building No.1 CB303, Gokasho, Uji, Kyoto 611-0011, Japan
Tel: +81-774-38-3296
Mail：okazaki*kuicr.kyoto-u.ac.jp
(substitute * by @)