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Integrated Bioresource Information Division

Publications

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Papers
  1. 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)
  2. 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)
  3. 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)
  4. 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)
  5. 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)
  6. 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)
  7. 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).
  8. 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)
  9. 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)
  10. 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)
  11. 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)
  12. 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)
  13. 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)
  14. 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)
  15. 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)
  16. Masuya H and Mizoguchi R., The ontology of the genetics, Transactions of the Japanese Society for Artificial Intelligence : AI, 29:311-327, Japanese (2014)
  17. 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)
  18. 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)
  19. 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)
  20. Masuya H., Roles and applications of biomedical ontologies in experimental animal science. Exp Anim. 61:365-73. Review. (2012)
  21. 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)
  22. 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)
  23. 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)
  24. 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)
  25. 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)
  26. 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)
  27. 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)
  28. 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)
  29. 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)
  30. 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)
  31. 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)
  32. 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)
  33. 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¥
Toward wider dissemination of large-scale mouse phenotype data
Sep. 20, 2016
http://www.riken.jp/pr/press/2016/20160920_2/ (Japanese Only)


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)