1 Research interest / Develop interest

  • LLM / Image generation
  • Bioinformatics / Computational science / Deep learning
  • R / Bioconductor
  • Medical science / life science
  • Comprehensive image analysis / Electron microscopy

2 Education

  • PhD in Applied Life Science, Osaka Prefecture University (2013)
    • Division of Biological Information Science, Department of Applied Life Sciences, Osaka Prefecture University, Japan.
  • MS in Applied Life Science, Osaka Prefecture University (2010)
    • Division of Biological Information Science, Department of Applied Life Sciences, Graduate school of Life and Environmental Sciences, Osaka Prefecture University, Japan.
  • BS in Agriculture, Obihiro University of Agriculture and Veterinary Medicine (2008)
    • Course of Agriculture (Division of Molecular Life Science), Faculty of Animal Husbandry, Obihiro University of Agriculture and Veterinary Medicine, Japan.

3 Work history

  • Dec 2021 - present : illumina Japan
  • Apr 2020 - Nov 2021 : Osaka Electro-Communication University (OECU)
  • Jan 2016 - Jun 2021 : Kokorotics Inc.
  • Apr 2013 - Mar 2020 : RIKEN
    • 2013-2018 RIKEN Center for Life Science Technologies (CLST)
    • 2014-2020 RIKEN-JEOL Collaboration Center
    • 2016-2020 RIKEN Compass to Healthy Life Research Complex Program (RCH)
    • 2019-2020 RIKEN Center for Biosystems Dynamics Research (BDR)

5 Publications

See Google scholar in detailed.

  1. Satoshi Kume, Issues for Practical Use of Root Nodule Bacteria in Japan. Proceedings of the Seventh National and First International Scientific Convention, Palawan, Philippines, 2007.

  2. Satoshi Kume, et al: Systematic interaction analysis of human lipocalin-type prostaglandin D synthase with small lipophilic ligands, Biochemical Journal 446(2):279-289, 2012.

  3. Satoshi Kume, et al: Fine-tuned broad binding capability of human lipocalin-type prostaglandin D synthase for various small lipophilic ligands. FEBS Letters. 588, 962–969, 2014.

  4. Satoshi Kume, et al: Potential biomarkers of fatigue identified by plasma metabolome analysis in rats, PloS One 10(3):e0120106, 2015.

  5. Satoshi Kume, et al: Development of an Ontology for an Integrated Image Analysis Platform to enable Global Sharing of Microscopy Imaging Data. Proceedings of the 15th International Semantic Web Conference, P23, 2016.

  6. Satoshi Kume, et al: Music Improves Subjective Feelings Leading to Cardiac Autonomic Nervous Modulation: A Pilot Study, Frontiers in Neuroscience. 11:108, 2017.

  7. Yoshiaki Teraoka✝, Satoshi Kume✝, et al: Comprehensive Evaluation of the Binding of Lipocalin-Type Prostaglandin D Synthase to Poorly Water-Soluble Drugs, Molecular Pharmaceutics, 14 (10): 3558–3567, 2017. (✝: equal contribution)

  8. Satoshi Kume✝✝, et al: Development of Semantic Web-Based Imaging Database for Biological Morphome. In: Wang Z., Turhan AY., Wang K., Zhang X. (eds) Semantic Technology. JIST 2017. Lecture Notes in Computer Science, vol 10675. Springer, Cham, 2017. (✝✝: corresponding author)

  9. Norio Kobayashi, Satoshi Kume, et al: RIKEN MetaDatabase: A Database Platform as a Microcosm of Linked Open Data Cloud for Life Sciences, The International Journal on Semantic Web and Information Systems, 14(1) 140-164, 2018.

  10. Yurie Hara, Satoshi Kume, et al: Changes in TCA cycle and TCA cycle-related metabolites in plasma upon citric acid administration in rats, Heliyon 7 (12), E08501, 2021.

  11. Satoshi Kume✝✝, Kouji Kozaki✝✝: Extracting Domain-specific Concepts from Large-scale Linked Open Data, IJCKG’21: The 10th International Joint Conference on Knowledge GraphsDecember 2021 Pages 28–37, doi: https://doi.org/10.1145/3502223.3502227 (✝✝: corresponding author)

  12. Raku Son, Kenji Yamazawa, Akiko Oguchi, Mitsuo Suga, Masaru Tamura, Yasuhiro Murakawa, Satoshi Kume✝✝: Morphomics via Next-generation Electron Microscopy, Journal of Molecular Cell Biology, mjad081, Published: 26 December 2023 (✝✝: corresponding author)

5.1 Japanese Article

  1. 久米慧嗣, 田村勝, 小林紀郎, 村川泰裕: 電子線・X線イメージング技術が織りなす画像ビッグデータ時代の病理学, 病理と臨床「特集 病理形態学の新技術」37 (7), 617-623.

  2. 久米 慧嗣, 村川 泰裕: SEMによる切片の広域撮像技術と生体組織の網羅的形態解析への展望 / Large-Area Imaging Technology of Tissue Sections Using SEM and Prospects for Comprehensive Morphological Analysis of Biological Tissues, 顕微鏡/55 巻 (2020) 1 号/書誌 特集：「切片SEM 法」の基礎と生物学・医学生物学研究への応用.

  3. 小口 綾貴子, 村川 泰裕, 柳田 素子, 久米 慧嗣: 広域電子顕微鏡解析からみる腎病理の未来図 / Large-scale electron microscopy-driven next-generation renal pathology (Japanese), 腎臓内科 = Nephrology 13(4), 502-509, 2021-04, 科学評論社.

  4. 久米慧嗣, 古崎晃司: 材料知識探索のためのオントロジー(第3章 材料設計の知識探索 第6節), データ駆動型材料開発 ～オントロジーとマイニング、計測と実験装置の自動制御～, Nov 2021

6 Presentations

See past presentations in detailed.

This list since 2021

  1. Satoshi Kume: Introduction to Bioimaging Analysis in R, Bioc Asia 2021 workshop, 4th Nov 2021.

7 Committee activity

  • Organizer, BioPackathon (2020 - present)
  • Expert investigator, National Institute of Science and Technology Policy of Japan (2019 - 2021)
  • Organizing Committee Member, BioC Asia 2021 (2021)
  • BioC Asia 2021 Organizing Committee Member (2021)
  • Program Committee Member, 16th Annual Meeting of the Fatigue Society of Japan (2019 - 2020)
  • Ethics Committee Member (Life Science), Kokorotics Research Ethics Committee (2017 - 2020)
  • Member (Data Science), Insurance Innovation Creation Research Group (2018 - 2020)
  • Member (Life Science), the Evaluation Committee for the Database Services of RIKEN Information Technology Center (2016)

8 Scientific community

  • Regular member, The Japanese Society of Microscopy / 日本顕微鏡学会 正会員 (2016-2021)
  • Regular member, The Japanese Society for Artificial Intelligence / 日本人工知能学会 正会員 (2019-2021)

9 Honors

  • The 8th RIKEN Research Incentive Award (23th Mar 2017, RIKEN)
  • The 2nd RIKEN Industry Partnerships Incentive Award (23th Mar 2017, RIKEN)
  • RIKEN CLST Research Incentive Award 2016 (4th Apr 2017, RIKEN CLST)
  • JASSP Short-term Student Exchange Promotion Program (Outbound) Scholarship (Oct 2006, JASSP)

10 Teaching Experience

  • Teaching lecturer, Department of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan. (Jan 2019)

  • Part-time lecturer for science foundation of life, a class of first-degree, Kobe Shoin Women’s University. (Apr 2013 - Jul 2013)

  • Teaching assistant, Department of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan. (Jul 2011 - Mar 2013)

11 Research funding

  1. Prof. Osafune memorial scholarship by the Japanese Society of Microscopy (Principal investigator): Comprehensive Morphological Analysis of Three-Dimensional Cell Images Using Sequential Semantic Segmentation Method of Deep Learning, 2020.

  2. JSPS KAKENHI Challenging Research (Exploratory) (Principal investigator): Construction of next-generation health diagnosis by the health informatics of bioimage information, 2018–2021.

  3. JSPS KAKENHI Grant-in-Aid for Young Scientists (B) (Principal investigator): The Clarification of Molecular Mechanisms of Fatigue Underlying Fatigue Regulation Factors Using Adeno-associated Virus, 2015–2017.

  4. JSPS KAKENHI Grant-in-Aid for Research Activity Start-up (Principal investigator): Metabolic alterations of urea cycle and anti-fatigue effect of ornithine administration in fatigued animals, 2013–2015.