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Koji Ishiya

Affiliation: Sapiens Life Sciences, Evolution and Medicine Research Center, Kanazawa University (concurrent appointment at Institute for the Study of Ancient Civilizations and Cultural Resources)
Job Class: Assistant Professor
Specialty: Bioinformatics、Genomics、Paleogenomics
*Kanazawa University


Research activities

Paleogenomics, the analysis of DNA extracted from archaeological samples, is a powerful approach to uncover valuable biological information about past and even extinct organisms. The rapid progress in this field in recent years has been driven by advancements in bioinformatics, a discipline that analyzes and interprets biological data from an information science perspective. Traditionally, DNA analysis of archaeological samples has faced numerous challenges, including degradation over time, exogenous DNA contamination from other individuals or species, and extremely limited DNA quantities. However, bioinformatics research incorporating cutting-edge technologies such as statistics, machine learning, deep learning, and artificial intelligence has helped overcome these problems. By focusing on bioinformatics development, I aim to deepen our understanding of the origins and evolution of humans, animals, plants, and microorganisms (pathogens) while promoting interdisciplinary research that integrates the sciences and humanities, including archaeological science.


Selected recent papers

  • Koji Ishiya, Fuzuki Mizuno, Jun Gojobori, Masahiko Kumagai, Yasuhiro Taniguchi, Osamu Kondo, Masami Matsushita, Takayuki Matsushita, Li Wang, Kunihiko Kurosaki, Shintaroh Ueda (2024). High-coverage genome sequencing of Yayoi and Jomon individuals shed light on prehistoric human population history in East Eurasia. bioRxiv.
  • Koji Ishiya, Sachiyo Aburatani (2021). Multivariate statistical monitoring system for microbial population dynamics. Physical biology 19(1).
  • Koji Ishiya, Fuzuki Mizuno, Li Wang, Shintaroh Ueda (2019). MitoIMP: A computational framework for imputation of missing data in low-coverage human mitochondrial genome. Bioinformatics and Biology Insights, 13, 1-9.
  • Koji Ishiya, Shintaroh Ueda (2017). MitoSuite: a graphical tool for human mitochondrial genome profiling in massive parallel sequencing. PeerJ, 5.