Research Summary

Selected Publications

• 1. Kadoya T, Suzuki K, and Terui A
  "Linking energetic instability to compositional changes in biological communities"
  PNAS in press (2025)
• 2. Nobusada T, Yip CW, Agrawal S, Severin J, Abugessaisa I, Hasegawa A, Hon CC, Ide S, Koido M, Kondo A, Masuya H, Oki S, Tagami M, Takada T, Terao C, Thalhath N, Walker S, Yasuzawa K, Shin JW, De Hoon MJL, Carninci P, Kawaji H, and Kasukawa T
  "Update of the FANTOM web resource: enhancement for studying noncoding genomes"
  Nucleic acids research, 53(D1), D419–D424. (2025)
  doi: 10.1093/nar/gkae1047
• 3. Kyoda, K., Itoga, H., Yamagata, Y., Fujisawa, E., Wang, F., Miranda-Miranda, M., Yamamoto, H., Nakano, Y., Tohsato, Y., & Onami, S
  "SSBD: an ecosystem for enhanced sharing and reuse of bioimaging data"
  Nucleic acids research, 53(D1), D1716–D1723. (2025)
  doi:10.1093/nar/gkae860
• 4. Yamagata Y, Kushida T, Onami S and Masuya H
  "Homeostasis imbalance process ontology: a study on COVID-19 infectious processes."
  BMC Medical Informatics and Decision Making, 23 Supplement 4, (2024)
  doi: 10.1186/s12911-024-02516-0
• 5. Yamagata Y, Fukuyama T, Onami S and Masuya H
  "Prototyping an Ontological Framework for Cellular Senescence Mechanisms: A Homeostasis Imbalance Perspective."
  Scientific Data, 11, Article number: 485, (2024)
  doi: 10.1038/s41597-024-03331-y
• 6. Kumaishi K, Usui E, Suzuki K, Kobori S, Sato T, Toda Y, Takanashi H, Shinozaki S, Noda M, Takakura A, Matsumoto K, Yamasaki Y, Tsujimoto H, Iwata H, Ichihashi Y
  "High throughput method of 16S rRNA gene sequencing library preparation for plant root microbial community profiling"
  Scientific Reports, 12(1), 1-10, (2022).
  doi:10.1038/s41598-022-23943-x
• 7. Suzuki K, Matsuzaki SS, Masuya H
  "Decomposing predictability to identify dominant causal drivers in complex ecosystems"
  PNAS, 119 (42) e220440511 (2022)
  doi:10.1073/pnas.2204405119
• 8. Takada T, Fukuta K, Usuda D, Kushida T, Kondo S, Kawamoto S, Yoshiki A, Obata Y, Fujiyama A, Toyoda A, Noguchi H, Shiroishi T, Masuya H
  "MoG+: a database of genomic variations across three mouse subspecies for biomedical research., Mammalian Genome"
  Mammalian Genome. 33, 31-43 (2021)
  doi:10.1007/s00335-021-09933-w
• 9. Suzuki K, Nakaoka S, Fukuda S, Masuya H
  "Energy landscape analysis elucidates the multistability of ecological communities across environmental gradients"
  Ecological Monographs. (2021)
  
• 10. Masuya H, Usuda D, Nakata H, Yuhara N, Kurihara K, Namiki Y, Iwase S, Takada T, Tanaka N, Suzuki K, Yamagata Y, Kobayashi N, Yoshiki A, Kushida T
  "Establishment and application of information resource of mutant mice in RIKEN BioResource Research Center"
  Laboratory Animal Research. 37(6), (2021)

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