Integrated Bioresource Information Division > About us > Publications

Publications

  • Papers and books
  • Press releases
  • Awards
  • Others

Papers and books
  1. Kyoda K, Itoga H, Yamagata Y, Fujisawa E, Wang F, Miranda-Miranda M, Yamamoto H, Nakano Y, Tohsato Y, and Onami S. SSBD: an ecosystem for enhanced sharing and reuse of bioimaging data. Nucleic Acids Research, 2024.
    https://doi.org/10.1093/nar/gkae860 (2024)
  2. Hashimoto K, Hayasaka D, Eguchi Y, Seko Y, Cai J, Suzuki K, Goka K, and Kadoya T. Multifaceted effects of variable biotic interactions on population stability in complex interaction webs. Communications Biology 7:1309, 2024.
    https://doi.org/10.1038/s42003-024-06948-2 (2024)
  3. Khettari O, Nishida N, Liu S, Munne R, Yamagata Y, Quiniou S, Chaffron S, Matsumoto Y. Mention-Agnostic Information Extraction for Ontological Annotation of Biomedical Articles. ACL Anthology, Proceedings of the 23rd Workshop on Biomedical Natural Language Processing, 2024.
    https://doi.org/10.18653/v1/2024.bionlp-1.37 (2024)
  4. Yamagata Y and Yamada R. Survey on large language model annotation of cellular senescence from figures in review articles. Genomics & Informatics, Volume 22 Supplement 1, May 17 2024.
    https://doi.org/10.1186/s44342-024-00011-6 (2024)
  5. Cruz M, Bergmans W, Takada T, Shiroishi T. Type specimens, taxonomic history, and genetic analysis of the Japanese dancing mouse or waltzer, Mus wagneri variety rotans Droogleever Fortuyn, 1912 (Mammalia, Muridae). ZooKeys 1200: 27–39.
    https://doi.org/10.3897/zookeys.1200.118823 (2024)
  6. 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, May 22 2024.
    https://doi.org/10.1186/s12911-024-02516-0 (2024)
  7. 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.
    https://doi.org/10.1038/s41597-024-03331-y (2024)
    Brief overview (YouTube video)
  8. Fujiwara K, Kubo S, Endo T, Takada T, Shiroishi T, Suzuki H, Osada N. Inference of selective forces on house mouse genomes during secondary contact in East Asia. Genome Research.
    https://doi.org/10.1101/gr.278828.123 (2024)
  9. Dohi E, Kushida T, Yamagata Y, Takatsuki T, Shin J, Masuya H, Thomas Liener, and RobertHoehndorf. BioHackJP 2023 Report R1:Improving phenotype ontology interoperability. BioHackrXiv.
    https://doi.org/10.37044/osf.io/d27fw (2024)
  10. Toju H, Fujita H, Ushio M, Suzuki K, Abe MS, Yamamichi M, Iwayama K, Canarini A, Hayashi I, Fukushima K, Fukuda S, Kiers ET. Metagenomic analysis of ecological niche overlap and community collapse in microbiome dynamics. Frontiers in Microbiology, 14, 1261137.
    https://doi.org/10.3389/fmicb.2023.1261137 (2023)
  11. Kushida T, Farias TM, Sima AC, Dessimoz C, Chiba H, Bastian FB, Masuya H. Exploring Disease Model Mouse Using Knowledge Graphs: Combining Gene Expression, Orthology, and Disease Dataset. BioRxiv, August 31, 2023.
    https://doi.org/10.1101/2023.08.30.555283 (2023)
  12. Oestereicher MA, Wotton JM, Ayabe S, About GB, Cheng TK, Choi JH, Clary D, Dew EM, Elfertak L, Guimond A, Mashhadi HH, Heaney JD, Kelsey L, Keskivali-Bond P, Gomez FL, Marschall S, McFarland M, Meziane H, Fuentes VM, Nam KH, Nichtová Z, Pimm D, Bower L, Prochazka J, Rozman J, Santos L, Stewart M, Tanaka N, Ward CS, Willett AME, Wilson R, Braun RE, Dickinson ME, Flenniken AM, Herault Y, Lloyd K, Mallon AM, McKerlie C, Murray SA, Nutter LMJ, Sedlacek R, Seong JK, Sorg T, Tamura M, Wells S, Schneltzer E, Fuchs H, Gailus-Durner V, de Angelis MH, White JK, Spielmann N. Comprehensive ECG reference intervals in C57BL/6N substrains provide a generalizable guide for cardiac electrophysiology studies in mice, Mammalian Genome 34(2), 180–199, June 9, 2023.
    https://doi.org/10.1007/s00335-023-09995-y (2023)
  13. Fujita H, Ushio M, Suzuki K, Abe MS, Yamamichi M, Okazaki Y, Canarini A, Hayashi I, Fukushima K, Fukuda S, Kiers ET, Toju H. Facilitative interaction networks in experimental microbial community dynamics. Frontiers in Microbiology, April 11, 2023.
    https://doi.org/10.3389/fmicb.2023.1153952 (2023)
  14. Okada S, Inabu Y, Miyamoto H, Suzuki K, Kato T, Kurotani A, Taguchi Y, Fujino R, Shiotsuka Y, Etoh T, Tsuji N, Matsuura M, Tsuboi A, Saito A, Masuya H, Kikuchi J, Nagasawa Y, Hirose A, Hayashi T, Ohno H, Takahashi H. Estimation of silent phenotypes of calf antibiotic dysbiosis. Scientific Reports, 13(1), 6359, 2023.
    https://doi.org/10.1038/s41598-023-33444-0 (2023)
  15. Fujita H, Ushio M, Suzuki K, Abe MS, Yamamichi M, Okazaki Y, Canarini A, Hayashi I, Fukushima K, Fukuda S, Kiers ET, Toju H, Facilitative interaction networks in experimental microbial community dynamics. Front. Microbiol. 14:1153952, 2023.
    https://doi.org/10.3389/fmicb.2023.1153952 (2023)
  16. Fujita H, Ushio M, KSuzuki, Abe MS, Yamamichi M, Iwayama K, Canarini A, Hayashi I, Fukushima K, Fukuda S, Kiers ET, Toju H. Alternative stable states, nonlinear behavior, and predictability of microbiome dynamics. Microbiome, 11(1), 1-16, 2023.
    https://doi.org/10.1186/s40168-023-01474-5 (2023)
  17. Yajima D, Fujita H, Hayashi I, Shima G, Suzuki K, Toju H. Core species and interactions prominent in fish-associated microbiome dynamics. Microbiome, 11(1), 53, 2023.
    https://doi.org/10.1186/s40168-023-01498-x (2023)
  18. Yamagata Y, Fukuyama T, Onami S, Masuya H. Ontology for cellular senescence mechanisms. BioRxiv, March 10, 2023.
    https://doi.org/10.1101/2023.03.09.531883 (2023)
  19. Miyamoto H, Kawachi N, Kurotani A, Moriya S, Suda W, Suzuki K, Matsuura M, Tsuji N, Nakaguma T, Ishii C, Tsuboi A, Shindo C, Kato T, Udagawa M, Satoh T, Wada S, Masuya H, Miyamoto H, Ohno H, Kikuchi J. Computational estimation of sediment symbiotic bacterial structures of seagrasses overgrowing downstream of onshore aquaculture. Environmental Research, 115130, 2022.
    https://doi.org/10.1016/j.envres.2022.115130 (2022)
  20. 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. https://doi.org/10.1038/s41598-022-23943-x (2022)
  21. Miura I, Kikkawa Y, Yasuda SP, Shinogi A, Usuda D, Kumar V, Takahashi JS, Tamura M, Masuya H, Wakana S., Characterization of single nucleotide polymorphisms for a forward genetics approach using genetic crosses in C57BL/6 and BALB/c substrains of mice., Exp Anim. 2022 71:240-251.
    https://doi.org/10.1538/expanim.21-0181 (2022)
  22. Suzuki K, Matsuzaki SS, Masuya H, Decomposing predictability to identify dominant causal drivers in complex ecosystems.
    https://doi.org/10.1073/pnas.2204405119 (2022)
  23. Suzuki K, Abe MS, Kumakura D, Nakaoka S, Fujiwara F, Miyamoto H, Nakaguma T, Okada M, Sakurai K, Shimizu S, Iwata H, Masuya H, Nihei N, Ichihashi Y., Chemical-Mediated Microbial Interactions Can Reduce the Effectiveness of Time-Series-Based Inference of Ecological Interaction Networks., International Journal of Environmental Research and Public Health.
    https://doi.org/10.3390/ijerph19031228 (2022)
  24. 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.
    https://doi.org/10.1007/s00335-021-09933-w (2021)
  25. Ninomiya Y, Kuriki S, Shiroishi T, Takada T., A modification of MaxT procedure using spurious correlations., Journal of Statistical Planning and Inference. 214 128-138.
    https://doi.org/10.1016/j.jspi.2021.02.001 (2021)
  26. Li Y, Fujiwara K, Osada N, Kawai Y, Takada T, Kryukov AP, Abe K, Yonekawa H, Shiroishi T, Moriwaki K, Saitou N, Suzuki H. House mouse Mus musculus dispersal in East Eurasia inferred from 98 newly determined complete mitochondrial genome sequences., Heredity. 126 132–147.
    https://doi.org/10.1038/s41437-020-00364-y (2021)
  27. Mizuno-Iijima S, Nakashiba T, Ayabe S, Nakata H, Ike F, Hiraiwa N, Mochida K, Ogura A, Masuya H, Kawamoto S, Tamura M, Obata Y, Shiroishi T, Yoshiki A., Mouse resources at the RIKEN BioResource Research Center and the National BioResource Project core facility in Japan., Mammalian Genome. doi:10.1007/s00335-021-09916-x
    https://doi.org/10.1007/s00335-021-09916-x (2021)
  28. Suzuki K, Nakaoka S, Fukuda S, Masuya H., Energy landscape analysis elucidates the multistability of ecological communities across environmental gradients., Ecological Monographs. doi:10.1002/ecm.1469
    https://esajournals.onlinelibrary.wiley.com/doi/10.1002/ecm.1469 (2021)
  29. Chen Y, Sakurai K, Maeda S, Masui T, Okano H, Dewender J, Seltmann S, Kurtz A, Masuya H, Nakamura Y, Sheldon M, Schneider J, Stacey GN, Panina Y, Fujibuchi W., Integrated Collection of Stem Cell Bank Data, a Data Portal for Standardized Stem Cell Information., Stem Cell Reports. 16(4) 997-1005. doi: 10.1016/j.stemcr.2021.02.014
    https://pubmed.ncbi.nlm.nih.gov/33740463/ (2021)
  30. 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)
    https://labanimres.biomedcentral.com/articles/10.1186/s42826-020-00068-8 (2021)
  31. Matsuzaki SS, Tanaka A, Kohzu A, Suzuki K, Komatsu K, Shinohara R, Nakagawa M, Nohara S, Ueno R, Satake K, Hayashi S., Seasonal dynamics of the activities of dissolved 137Cs and the 137Cs of fish in a shallow, hypereutrophic lake: Links to bottom-water oxygen concentrations., Science of The Total Environment. 77 143257.
    https://doi.org/10.1016/j.scitotenv.2020.143257 (2021)
  32. Suzuki K., Masuya H., A stability landscape concept to understand the compositional stability of microbiota: an introduction from a Lotka-Volterra dynamics., Experimental Medicine. 38(18). https://jglobal.jst.go.jp/en/detailJGLOBAL_ID=202002297639957480 (2020)
  33. Tanaka N, Masuya H., An atlas of evidence-based phenotypic associations across the mouse phenome., Scientific Reports. 10 3957. https://www.nature.com/articles/s41598-020-60891-w (2020)
  34. Hamed Haselimashhadi, Jeremy C Mason, Violeta Munoz-Fuentes, Federico López-Gómez, Kolawole Babalola, Elif F Acar, Vivek Kumar, Jacqui White, Ann M Flenniken, Ruairidh King, Ewan Straiton, John Richard Seavitt, Angelina Gaspero, Arturo Garza, Audrey E Christianson, Chih-Wei Hsu, Corey L Reynolds, Denise G Lanza, Isabel Lorenzo, Jennie R Green, Juan J Gallegos, Ritu Bohat, Rodney C Samaco, Surabi Veeraragavan, Jong Kyoung Kim, Gregor Miller, Helmult Fuchs, Lillian Garrett, Lore Becker, Yeon Kyung Kang, David Clary, Soo Young Cho, Masaru Tamura, Nobuhiko Tanaka, Kyung Dong Soo, Alexandr Bezginov, Ghina Bou About, Marie-France Champy, Laurent Vasseur, Sophie Leblanc, Hamid Meziane, Mohammed Selloum, Patrick T Reilly, Nadine Spielmann, Holger Maier, Valerie Gailus-Durner, Tania Sorg, Masuya Hiroshi, Obata Yuichi, Jason D Heaney, Mary E Dickinson, Wurst Wolfgang, Glauco P Tocchini-Valentini, Kevin C Kent Lloyd, Colin McKerlie, Je Kyung Seong, Herault Yann, Martin Hrabé de Angelis, Steve D M Brown, Damian Smedley, Paul Flicek, Ann-Marie Mallon, Helen Parkinson, Terrence F Meehan., Soft windowing application to improve analysis of high-throughput phenotyping data., Bioinformatics. 36(5) https://doi.org/10.1093/bioinformatics/btz744 (2019)
  35. Yang J, Tsukimi T, Yoshikawa M, Suzuki K, Takeda T, Tomita M, Fukuda S., Cutibacterium acnes (Propionibacterium acnes) 16S rRNA Genotyping of Microbial Samples from Possessions Contributes to Owner Identification., mSystems.4(6) e00594-19. DOI: 10.1128/mSystems.00594-19 https://msystems.asm.org/content/4/6/e00594-19 (2019)
  36. Furuse T, Mizuma H, Hirose Y, Kushida T, Yamada I, Miura I, Masuya H, Funato H, Yanagisawa M, Onoe H, Wakana S., A new mouse model of GLUT1 deficiency syndrome exhibits abnormal sleep-wake patterns and alterations of glucose kinetics in the brain., Disease Models & Mechanisms. 12(9). doi:10.1242/dmm.038828. DOI: https://dmm.biologists.org/content/12/9/dmm038828 (2019)
  37. Tanaka N, Masuya H., Mouse phenome as a biological resource., Impact. 2018(12) 93-95. DOI: https://doi.org/10.21820/23987073.2018.12.93 (2018)
  38. Kobayashi N, Kume S, Lenz K, Masuya H., RIKEN MetaDatabase: A Database Platform for Health Care and Life Sciences as a Microcosm of Linked Open Data Cloud., Int. J. Semantic Web Inf. Syst.   14(1) 140-164 (2018)
  39. Rozman J, Rathkolb B, Oestereicher MA, Schütt C, Ravindranath AC, Leuchtenberger S, Sharma S, Kistler M, Willershäuser M, Brommage R, Meehan TF, Mason J, Haselimashhadi H; IMPC Consortium, Hough T, Mallon AM, Wells S, Santos L, Lelliott CJ, White JK, Sorg T, Champy MF, Bower LR, Reynolds CL, Flenniken AM, Murray SA, Nutter LMJ, Svenson KL, West D, Tocchini-Valentini GP, Beaudet AL, Bosch F, Braun RB, Dobbie MS, Gao X, Herault Y, Moshiri A, Moore BA, Kent Lloyd KC, McKerlie C, Masuya H, Tanaka N, Flicek P, Parkinson HE, Sedlacek R, Seong JK, Wang CL, Moore M, Brown SD, Tschöp MH, Wurst W, Klingenspor M, Wolf E, Beckers J, Machicao F, Peter A, Staiger H, Häring HU, Grallert H, Campillos M, Maier H, Fuchs H, Gailus-Durner V, Werner T, Hrabe de Angelis M., Identification of genetic elements in metabolism by high-throughput mouse phenotyping. Nat Commun. 18;9:288. doi: 10.1038/s41467-017-01995-2. (2018)
  40. Bowl MR, Simon MM, Ingham NJ, Greenaway S, Santos L, Cater H, Taylor S, Mason J, Kurbatova N, Pearson S, Bower LR, Clary DA, Meziane H, Reilly P, Minowa O, Kelsey L; International Mouse Phenotyping Consortium（as a collaborator of the consortium）, Tocchini-Valentini GP, Gao X, Bradley A, Skarnes WC, Moore M, Beaudet AL, Justice MJ, Seavitt J, Dickinson ME, Wur st W, de Angelis MH, Herault Y, Wakana S, Nutter LMJ, Flenniken AM, McKerlie C, Murray SA, Svenson KL, Braun RE, West DB, Lloyd KCK, Adams DJ, White J, Karp N, Flicek P, Smedley D, Meehan TF, Parkinson HE, Teboul LM, Wells S, Steel KP, Mallon AM, Brown SDM., A large scale hearing loss screen reveals an extensive unexplored genetic landscape for auditory dysfunction. Nat Commun. 8 :886. doi: 10.1038/s41467-017-00595-4. (2017)
  41. Karp NA, Mason J, Beaudet AL, Benjamini Y, Bower L, Braun RE, Brown SDM, Chesler EJ, Dickinson ME, Flenniken AM, Fuchs H, Angelis MH, Gao X, Guo S, Greenaway S, Heller R, Herault Y, Justice MJ, Kurbatova N, Lelliott CJ, Lloyd KCK, Mallon AM, Mank JE, Masuya H, McKerlie C, Meehan TF, Mott RF, Murray SA, Parkinson H, Ramirez-Solis R, Santos L, Seavitt JR, Smedley D, Sorg T, Speak AO, Steel KP, Svenson KL; International Mouse Phenotyping Consortium, Wakana S, West D, Wells S, Westerberg H, Yaacoby S, White JK., Prevalence of sexual dimorphism in mamma lian phenotypic traits., Nat Commun. 8:15475. doi: 10.1038/ncomms15475. (2017)
  42. Yamaguchi A, Kozaki K, Yamamoto Y,Masuya H and Kobayashi N, LOD Surfer API: Web API for LOD Surfing Using Class-Class Relationships in Life Sciences., Proceedings of the 10th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4LS 2017), Rome, Italy, December 4-7,  (2017).
  43. Kobayashi N, Kume S, Masuya H, Metadata-driven Interdisciplinary Research Projects Using RIKEN MetaDatabase., Proceedings of the 10th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4LS 2017), Rome, Italy, December 4-7, (2017)
  44. Kobayashi N, Lenz K, Masuya H., RIKEN MetaDatabase: A Database Platform as a Microcosm of Linked Open Data Cloud in the Life Sciences, Semantic Technology:JIST2016, 10055, 99-115 DOI: 10.1007/978-3-319-50112-3_8 (2016)
  45. Yamaguchi A, Kozaki K, Lenz K, Yamamoto Y, Masuya H, Kobayashi N., Semantic Data Acquisition by Traversing Class-Class Relationships over the Linked Open Data, Semantic Technology:JIST2016, 10055, 136-151 DOI: 10.1007/978-3-319-50112-3_11 (2016)
  46. Kimura M, Ichimura S, Sasaki K, Masuya H, Suzuki T, Wakana S, Ikegawa S, Furuichi T., Endoplasmic reticulum stress-mediated apoptosis contributes to a skeletal dysplasia resembling platyspondylic lethal skeletal dysplasia, Torrance type, in a novel Col2a1 mutant mouse line. Biochem Biophys Res Commun. 468:86-91. doi: 10.1016/j.bbrc.2015.10.160. (2015)
  47. Maier H, Schütt C, Steinkamp R, Hurt A, Schneltzer E, Gormanns P, Lengger C, Griffiths M, Melvin D, Agrawal N, Alcantara R, Evans A, Gannon D, Holroyd S, Kipp C, Raj NP, Richardson D, LeBlanc S, Vasseur L, Masuya H, Kobayashi K, Suzuki T, Tanaka N, Wakana S, Walling A, Clary D, Gallegos J, Fuchs H, de Angelis MH, Gailus-Durner V., Principles and application of LIMS in mouse clinics., Mamm Genome. 9-10:467-481. doi: 10.1007/s00335-015-9586-7. Review. (2015)
  48. Karp NA, Meehan TF, Morgan H, Mason JC, Blake A, Kurbatova N, Smedley D, Jacobsen J, Mott RF, Iyer V, Matthews P, Melvin DG, Wells S, Flenniken AM, Masuya H, Wakana S, White JK, Lloyd KC, Reynolds CL, Paylor R, West DB, Svenson KL, Chesler EJ, de Angelis MH, Tocchini-Valentini GP, Sorg T, Herault Y, Parkinson H, Mallon AM, Brown SD., Applying the ARRIVE Guideli nes to an In Vivo Database. PLoS Biol.13:e1002151. doi: 10.1371/journal.pbio.1002151. (2015)
  49. Toki H, Inoue M, Minowa O, Motegi H, Saiki Y, Wakana S, Masuya H, Gondo Y, Shiroishi T, Yao R, Noda T., Novel retinoblastoma mutation abrogating the interaction to E2F2/3, but not E2F1, led to selective suppression of thyroid tumors. Cancer Sci. 105:1360-1368. doi: 10.1111/cas.12495. (2014)
  50. Sarntivijai S, Lin Y, Xiang Z, Meehan TF, Diehl AD, Vempati UD, Schürer SC, Pang C, Malone J, Parkinson H, Liu Y, Takatsuki T, Saijo K, Masuya H, Nakamura Y, Brush MH, Haendel MA, Zheng J, Stoeckert CJ, Peters B, Mungall CJ, Carey TE, States DJ, Athey BD, He Y., CLO: The cell line ontology. J Biomed Semantics. 5:37. doi: 10.1186/2041-1480-5-37. (2014)
  51. Masuya H and Mizoguchi R., The ontology of the genetics, Transactions of the Japanese Society for Artificial Intelligence : AI, 29:311-327, Japanese (2014)
  52. Suzuki T, Furuse T, Yamada I, Motegi H, Kozawa Y, Masuya H, Wakana S., Pheno-Pub: a total support system for the publication of mouse phenotypic data on the web., Mamm Genome. 11-12:473-83. doi: 10.1007/s00335-013-9482-y. (2013)
  53. Makita Y, Kobayashi N, Yoshida Y, Doi K, Mochizuki Y, Nishikata K, Matsushima A, Takahashi S, Ishii M, Takatsuki T, Bhatia R, Khadbaatar Z, Watabe H, Masuya H, Toyoda T., PosMed: Ranking genes and bioresources based on Semantic Web Association Study., Nucleic Acids Res. 41(Web Server issue):W109-114. doi: 10.1093/nar/gkt474. (2013)
  54. Toki H, Inoue M, Motegi H, Minowa O, Kanda H, Yamamoto N, Ikeda A, Karashima Y, Matsui J, Kaneda H, Miura I, Suzuki T, Wakana S, Masuya H, Gondo Y, Shiroishi T, Akiyama T, Yao R, Noda T., Novel mouse model for Gardner syndrome generated by a large-scale N-ethyl-N-nitrosourea mutagenesis program., Cancer Sci. 104:937-944. doi: 10.1111/cas.12161. (2013)
  55. Masuya H., Roles and applications of biomedical ontologies in experimental animal science. Exp Anim. 61:365-73. Review. (2012)
  56. Furuse T, Yamada I, Kushida T, Masuya H, Miura I, Kaneda H, Kobayashi K, Wada Y, Yuasa S, Wakana S., Behavioral and neuromorphological characterization of a novel Tuba1 mutant mouse., Behav Brain Res. 227:167-174. doi: 10.1016/j.bbr.2011.11.002. (2012)
  57. Furuichi T, Masuya H, Murakami T, Nishida K, Nishimura G, Suzuki T, Imaizumi K, Kudo T, Ohkawa K, Wakana S, Ikegawa S., ENU-induced missense mutation in the C-propeptide coding region of Col2a1 creates a mouse model of platyspondylic lethal skeletal dysplasia, Torrance type., Mamm Genome. 22:318-328. doi: 10.1007/s00335-011-9329-3. (2011)
  58. Masuya H, Makita Y, Kobayashi N, Nishikata K, Yoshida Y, Mochizuki Y, Doi K, Takatsuki T, Waki K, Tanaka N, Ishii M, Matsushima A, Takahashi S, Hijikata A, Kozaki K, Furuichi T, Kawaji H, Wakana S, Nakamura Y, Yoshiki A, Murata T, Fukami-Kobayashi K, Mohan S, Ohara O, Hayashizaki Y, Mizoguchi R, Obata Y, Toyoda T., The RIKEN integrated database of mammals., Nuc leic Acids Res. 39(Database issue):D861-870. doi: 10.1093/nar/gkq1078. (2011)
  59. Wada Y, Furuse T, Yamada I, Masuya H, Kushida T, Shibukawa Y, Nakai Y, Kobayashi K, Kaneda H, Gondo Y, Noda T, Shiroishi T, Wakana S., ENU mutagenesis screening for dominant behavioral mutations based on normal control data obtained in home-cage activity, open-field, and passive avoidance tests., Exp Anim. 59:495-510. (2010)
  60. Furuse T, Wada Y, Hattori K, Yamada I, Kushida T, Shibukawa Y, Masuya H, Kaneda H, Miura I, Seno N, Kanda T, Hirose R, Toki S, Nakanishi K, Kobayashi K, Sezutsu H, Gondo Y, Noda T, Yuasa S, Wakana S., Phenotypic characterization of a new Grin1 mutant mouse generated by ENU mutagenesis. Eur J Neurosci. 31:1281-91. doi: 10.1111/j.1460-9568.2010.07164.x. (2010)
  61. Sato H, Suzuki T, Ikeda K, Masuya H, Sezutsu H, Kaneda H, Kobayashi K, Miura I, Kurihara Y, Yokokura S, Nishida K, Tamai M, Gondo Y, Noda T, Wakana S. A monogenic dominant mutation in Rom1 generated by N-ethyl-N-nitrosourea mutagenesis causes retinal degeneration in mice. Mol Vis. 16:378-91. (2010)
  62. Tanaka N, Waki K, Kaneda H, Suzuki T, Yamada I, Furuse T, Kobayashi K, Motegi H, Toki H, Inoue M, Minowa O, Noda T, Takao K, Miyakawa T, Takahashi A, Koide T, Wakana S, Masuya H., SDOP-DB: a comparative standardized-protocol database for mouse phenotypic analyses., Bioinformatics. 26:1133-1134. doi: 10.1093/bioinformatics/btq095. (2010)
  63. Wakana S, Suzuki T, Furuse T, Kobayashi K, Miura I, Kaneda H, Yamada I, Motegi H, Toki H, Inoue M, Minowa O, Noda T, Waki K, Tanaka N, Masuya H, Obata Y., Introduction to the Japan Mouse Clinic at the RIKEN BioResource Center., Exp Anim. 58:443-450. Review. (2009)
  64. Schofield PN, Bubela T, Weaver T, Portilla L, Brown SD, Hancock JM, Einhorn D, Tocchini-Valentini G, Hrabe de Angelis M, Rosenthal N; CASIMIR Rome Meeting participants（as a collaborator of the consortium）., Post-publication sharing of data and tools. Nature. 461:171-173. doi: 10.1038/461171a. (2009)
  65. Yoshida Y, Makita Y, Heida N, Asano S, Matsushima A, Ishii M, Mochizuki Y, Masuya H, Wakana S, Kobayashi N, Toyoda T., PosMed (Positional Medline): prioritizing genes with an artificial neural network comprising medical documents to accelerate positional cloning. Nucleic Acids Res. 37(Web Server issue):W147-152. doi: 10.1093/nar/gkp384. (2009)
  66. Sakuraba Y, Kimura T, Masuya H, Noguchi H, Sezutsu H, Takahasi KR, Toyoda A, Fukumura R, Murata T, Sakaki Y, Yamamura M, Wakana S, Noda T, Shiroishi T, Gondo Y., Identification and characterization of new long conserved noncoding sequences in vertebrates., Mamm Genome. 19:703-12. doi: 10.1007/s00335-008-9152-7. (2008)
  67. Kaminuma E, Masuya H, Miura I, Motegi H, Takahasi KR, Nakazawa M, Matsui M, Gondo Y, Noda T, Shiroishi T, Wakana S, Toyoda T., Objective evaluation measures of genetic marker selection in large-scale SNP genotyping., J Bioinform Comput Biol. 6:905-17. (2008)
  68. Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T, Brazma A, Brinkman RR, Michael Clark A, Deutsch EW, Fiehn O, Fostel J, Ghazal P, Gibson F, Gray T, Grimes G, Hancock JM, Hardy NW, Hermjakob H, Julian RK Jr, Kane M, Kettner C, Kinsinger C, Kolker E, Kuiper M, Le Novère N, Leebens-Mack J, Lewis SE, Lord P, Mall on AM, Marthandan N, Masuya H, McNally R, Mehrle A, Morrison N, Orchard S, Quackenbush J, Reecy JM, Robertson DG, Rocca-Serra P, Rodriguez H, Rosenfelder H, Santoyo-Lopez J, Scheuermann RH, S chober D, Smith B, Snape J, Stoeckert CJ Jr, Tipton K, Sterk P, Untergasser A, Vandesompele J, Wiemann S., Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project., Nat Biotechnol. 26:889-896. doi: 10.1038/nbt.1411. (2008)

Joint press release of RIKEN and JST
SSBD: an ecosystem for enhanced sharing and reuse of bioimaging data
Oct. 31, 2024
https://www.riken.jp/press/2024/20241031_1/index.html(Japanese Only)
Joint press release of Hirosaki Univ., Kinki Univ., RIKEN, and NIG
Multifaceted effects of variable biotic interactions on population stability in complex interaction webs
Oct. 22, 2024
https://web.brc.riken.jp/en/archives/news/20241022_01
Joint press release of Hokkaido Univ., RIKEN, and NIG
Inference of selective forces on house mouse genomes during secondary contact in East Asia
Apr. 19, 2024
https://web.brc.riken.jp/en/archives/news/20240419_01
Joint press release of RIKEN and NIES
Decomposing predictability to identify dominant causal drivers in complex ecosystems
Oct. 17, 2022
https://www.riken.jp/press/2022/20221017_1/index.html (Japanese Only)
Joint press release of RIKEN, Hokkaido Univ. and Keio Univ.
Energy landscape analysis elucidates the multistability of ecological communities
May 18, 2021
https://web.brc.riken.jp/en/archives/news/20210518_01
Joint press release of RIKEN and JST
Toward wider dissemination of large-scale mouse phenotype data
Sep. 20, 2016
http://www.riken.jp/pr/press/2016/20160920_2/ (Japanese Only)


the 28th Miyadi Award of the Ecological Society of Japan
Kenta Suzuki
“Ecosystems, Dynamical Systems, and Complex Systems: Toward an Ecology of Predictive Control”
March. 2024


Best paper award of 6th Joint International Semantic Technology Conference (JIST 2016)
“RIKEN MetaDatabase: A Database Platform as a Microcosm of Linked Open Data Cloud in the Life Sciences”
Nov. 2016


“Long-term recommendations for RIKEN’s life sciences database platform”
The database working group, The RIKEN Advanced Center for Computing and Communication (ACCC)
Oct. 29, 2015
http://metadb.riken.jp/archives/docs/dbwg/LongTermRecommendations_j.pdf (Japanese Only)



 

Comments are closed.