Assistant Professor ISHIYA, Koji
Faculty, Affiliation
Sapiens Life sciences, Evolution and Medicine Research Center Sapiens Life Sciences, Evolution and Medicine Research Center
College and School Educational Field
Laboratory
Ishiya Laboratory
Academic Background
【Academic background(Doctoral/Master's Degree)】
The university of Tokyo Doctor Graduate School of Science Department of Biological Sciences 201803 Completed
Career
(2015/04-2018/03)
National Institute of Advanced Industrial Science and Technology(2018/04-2020/03)
Waseda University Research Organization for Nano & Life Innovation(2018/07-2020/03)
National Institute of Advanced Industrial Science and Technology Research Scientist(2020/04-2023/09)
Kanazawa University Institute for the Study of Ancient Civilizations and Cultural Resources(2021/06-2025/01)
Waseda University(2021/09-2024/06)
National Institute of Advanced Industrial Science and Technology Senior Research Scientist(2023/10-2024/06)
Kanazawa University Sapiens Life sciences, Evolution and Medicine Research Center Assistant professor(2024/07-)
Year & Month of Birth
Academic Society
SOCIETY OF EVOLUTIONARY STUDIES, JAPAN
THE ANTHROPOLOGICAL SOCIETY OF NIPPON
JAPANESE SOCIETY FOR DNA POLYMORPHISM RESEARCH
European Society for Evolutionary Biology
JAPANESE SOCIETY FOR BIOINFORMATICS
Award
JAPANESE SOCIETY FOR BIOINFORMATICS
JAPANESE SOCIETY FOR BIOINFORMATICS
○若手研究賞(2022/11)
Specialities
Speciality Keywords
Bioinformatics,Genomics,Metagenomics,Paleogenome,Population Genetics,Phylogenetics,Software Development,Machine Learning,Evolution
Research Themes
Books
Papers
- Outlier detection for minor compositional variations in taxonomic abundance data Koji Ishiya,Sachiyo Aburatani Applied Sciences 9 7 1355 2019/03
- Genome sequence of Rhodococcus erythropolis type strain, JCM 3201 Keitaro Yoshida,Wataru Kitagawa,Koji Ishiya,Yasuo Mitania,Nobutaka Nakashima,Sachiyo Aburatani,Tomohiro Tamura Microbiology Resource Announcements 8 14 e01730-18 2019/04
- Scaffold size-dependent effect on the enhanced uptake of antibiotics and other compounds by Escherichia coli and Pseudomonas aeruginosa Kyosuke Yamamoto,Nao Yamamoto,Shotaro Ayukawa,Yoshiaki Yasutake,Koji Ishiya,Nobutaka Nakashima Scientific Reports 12 1 2022/04
- Multivariate statistical monitoring system for microbial population dynamics. Koji Ishiya,Sachiyo Aburatani Physical biology 19 1 2021/12/07
- Disruption of SMC-related genes promotes recombinant cholesterol esterase production in Burkholderia stabilis Kenji Konishi,Yoshiaki Yasutake,Shuji Muramatsu,Satomi Murata,Keitaro Yoshida,Koji Ishiya,Sachiyo Aburatani,Shin-ichi Sakasegawa,Tomohiro Tamura Applied Microbiology and Biotechnology 106 24 8093 2022/12
- MitoIMP: A computational framework for imputation of missing data in low-coverage human mitochondrial genome Koji Ishiya,Fuzuki Mizuno,Li Wang,Shintaroh Ueda Bioinformatics and Biology Insights 13 1 2019/09
- Recognition of differential culture conditions with dimensional reduction approach Koji Ishiya,Takeaki Taniguchi Journal of Physics: Conference Series 2701 1 012139 2024/02
- Bioarchaeological study of ancient Teotihuacans based on complete mitochondrial genome sequences and diet isotopes. Fuzuki Mizuno,Fuyuki Tokanai,Masahiko Kumagai,Koji Ishiya,Saburo Sugiyama,Michiko Hayashi,Kunihiko Kurosaki,Shintaroh Ueda Annals of human biology 50 1 390 2023/10
- Comparative Genome Analysis of Three Komagataeibacter Strains Used for Practical Production of Nata-de-Coco Koji Ishiya,Hideki Kosaka,Takashi Inaoka,Keitarou Kimura,Nobutaka Nakashima Frontiers in Microbiology 12 2022/02
- Comparative Genome Analysis Reveals Accumulation of Single-Nucleotide Repeats in Pathogenic Escherichia Lineages Koji Ishiya,Nobutaka Nakashima Current Issues in Molecular Biology 44 2 498 2022/01/20
- Isolation and characterization of Lipomyces starkeyi mutants with greatly increased lipid productivity following UV irradiation. Hiroaki Takaku,Sayaka Ebina,Kotoha Kasuga,Rikako Sato,Satoshi Ara,Haruka Kazama,Tomohiko Matsuzawa,Katsuro Yaoi,Hideo Araki,Yosuke Shida,Wataru Ogasawara,Koji Ishiya,Sachiyo Aburatani,Harutake Yamazaki Journal of bioscience and bioengineering 131 6 613 2021/02/10
- A biomolecular anthropological investigation of William Adams, the first SAMURAI from England Fuzuki Mizuno,Koji Ishiya,Masami Matsushita,Takayuki Matsushita,Katherine Hampson,Michiko Hayashi,Fuyuki Tokanai,Kunihiko Kurosaki,Shintaroh Ueda Scientific Reports 10 1 21651 2020/12
- Inference of Regulatory System for TAG Biosynthesis in Lipomyces starkeyi. Sachiyo Aburatani,Koji Ishiya,Toshikazu Itoh,Toshihiro Hayashi,Takeaki Taniguchi,Hiroaki Takaku Bioengineering 7 4 2020/11/19
- Evolutionary History of the Risk of SNPs for Diffuse-Type Gastric Cancer in the Japanese Population Risa L. Iwasaki,Koji Ishiya,Hideaki Kanzawa-Kiriyama,Yosuke Kawai,Jun Gojobori,Yoko Satta Genes 11 7 775 2020/07/10
- Citrate-mediated acyl-coa synthesis is required for the promotion of growth and triacylglycerol production in oleaginous yeast lipomyces starkeyi Rikako Sato,Satoshi Ara,Harutake Yamazaki,Koji Ishiya,Sachiyo Aburatani,Hiroaki Takaku Microorganisms 9 8 2021/08
- Novel approach for accurate detection of contaminating human mitochondrial DNA in next-generation sequencing data Koji Ishiya,Shintaroh Ueda Journal of Physics: Conference Series 1391 1 2019/12/13
- MitoSuite: a graphical tool for human mitochondrial genome profiling in massive parallel sequencing Koji Ishiya,Shintaroh Ueda PEERJ 5 2017/05
- Latent semantic analysis reveals time-series gene expression trends in yeast under hypoxic conditions Koji Ishiya,Takeaki Taniguchi AIP Conference Proceedings 2023/01
- LsSpt23p is a regulator of triacylglycerol synthesis in the oleaginous yeast Lipomyces starkeyi Hiroaki Takaku,Haruka Kazama,Rikako Sato,Kazuki Mori,Satoshi Ara,Koji Ishiya,Tomohiko Matsuzawa,Katsuro Yaoi,Hideo Araki,Yosuke Shida,Wataru Ogasawara,Kosuke Tashiro,Satoru Kuhara,Harutake Yamazaki,Sachiyo Aburatani Applied Microbiology and Biotechnology 107 4 1269 2023/01/17
- Advances in Microbial Community Analysis with Bioinformatics Koji Ishiya,Sachiyo Aburatani 60 2 52 2022/02
- High-coverage genome sequencing of Yayoi and Jomon individuals shed light on prehistoric human population history in East Eurasian Koji Ishiya,Fuzuki Mizuno,Jun Gojobori,Masahiko Kumagai,Yasuhiro Taniguchi,Osamu Kondo,Masami Matsushita,Takayuki Matsushita,Li Wang,Kunihiko Kurosaki,Shintaroh Ueda bioRχiv 2024/08
- Identification and characterization of the suppressed lipid accumulation-related gene, SLA1, in the oleaginous yeast Lipomyces starkeyi Rikako Sato,Harutake Yamazaki,Kazuki Mori,Sachiyo Aburatani,Koji Ishiya,Yosuke Shida,Wataru Ogasawara,Kosuke Tashiro,Satoru Kuhara,Hiroaki Takaku Bioscience, Biotechnology, and Biochemistry 2024/07/31
Conference Presentations
- Robust age prediction model based on massive methylation data among multi-tissue(conference：19th International Conference on Systems Biology)(2018/10)
- An introduction to paleogenomics: Challenges in poorly preserved fossil remains(conference：Chile-Japan Academic Forum 2016)(2016/11)
- Evaluating modern-day human contamination based on mitogenomic data(conference：HTSA2014:Practical Course on High-Throughput Sequencing Data Analysis)(2014/10)
- Human biological sex determination using X/Y-linked k-mer signatures(conference：1st Asia & Pacific Bioinformatics Joint Conference (APBJC2024))(2024/10/24)
- Detection of phylogenetically-informative SNPs in human Y-chromosome from next-generation sequencing data(conference：The 2019 Congress of the European Society for Evolutionary Biology)(2019/08)
- A Bioinformatics Strategy for Separating Ancient DNA from Modern DNA Contamination(conference：The 12th KCJ Bioinformatics Training Course and Symposium)(2014/06)
- HuMAP: A comprehensive tool for accessing NGS data on human mitogenome(conference：The 11th International Workshop on Advanced Genomics)(2015/05)
- Time-series Change Detection Approach for Microbial Population Dynamics(conference：11th International Conference on Bioscience, Biochemistry and Bioinformatics)(2021/01/11)
- Application of Latent Semantic Analysis to Metagenomic Data(conference：the 23rd European Conference on Computational Biology)(2024/09)
- Inference of contaminated haplogroup in high-throughput sequencing data(conference：第39回日本分子生物学会年会)(2016/10)
Others
Arts and Fieldwork
○MitoIMP(2019/04-)(result：A computational framework for imputation of missing data in low-coverage human mitochondrial genome)
○MitoSuite(2017/05-)(place：mitosuite.com)(result：MitoSuite is a user-friendly graphical tool for analysis of data from high-throughput sequencing of the human mitochondrial genome.)
Patent
Theme to the desired joint research
Grant-in-Aid for Scientific Research
○「生物考古情報の復元に向けたパレオメタゲノミクス技術の開発 」(2024-2025)
○「メタゲノムを利用した試料属性推定システムの構築 」(2023-2025)
○「半定住狩猟採集民の社会組織と葬制：骨考古学先端技術との連携による先史社会の復元」(2021-2026)
○「古ゲノム分析による日本列島の穀物利用史の解明」(2021-2023)
○「シン・パレオゲノミクスが創る博物館資料群活用の新展開」(2021-2023)
○「パレオゲノミクス解析プラットフォーム開発とその応用」(2020-2025)
○「迅速なDNA多型解析システム開発」(2019-2022)
○「ミトコンドリアゲノム及び核ゲノム情報を用いた古代中国人類集団の遺伝的背景の解明」(2015-2017)
○「遺跡出土古人骨の核DNA保存領域に関する包括的研究」(2025-2028)