{"id":89,"date":"2021-02-08T13:52:05","date_gmt":"2021-02-08T04:52:05","guid":{"rendered":"https:\/\/olsp.riken.jp\/en\/?page_id=89"},"modified":"2026-09-10T17:38:35","modified_gmt":"2026-09-10T08:38:35","slug":"publications","status":"publish","type":"page","link":"https:\/\/olsp.riken.jp\/en\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"<h3>Publications<\/h3>\n<ul>\n<li>Kubo, N., Oguchi, A., Masuya, H., Amano, T., Sakashita, A., Kawaji, H., Kasukawa, T., Oki, S., Ayabe, S., Takada, T., Ogura, A., Inoue, K., Murakawa, Y., Tamura, M., Yoshiki, A., Shiroishi, T.: The future objectives of the International Mouse Phenotyping Consortium (IMPC): functional evaluation of human disease-relevant cis-regulatory elements in the mouse genome. <em>Mamm. Genome<\/em> 37, 93 (2026). [<a href=\"https:\/\/doi.org\/10.1007\/s00335-026-10258-9\" target=\"_blank\" rel=\"noopener\">Open Access<\/a>]<\/li>\n<li>Oota, S., Abe, K., Pan,C.T., Yokota, H., Li, W.H., Ikeo, K.: Reconstruction of cell diversity and cell lineages from somatic mutations in single-cell transcriptomic data, <em>DNA Research<\/em> 33, dsag007 (2026). [<a href=\"https:\/\/doi.org\/10.1093\/dnares\/dsag007\" target=\"_blank\" rel=\"noopener\">Open Access<\/a>]<\/li>\n<li>Miyamoto, H., Takahashi, H., Suda, W., Yamano, H., Inabu, Y., Kodama, H., Nakanishi, Y., Moriya, S., Satoh, T.,\u00a0 Kato, T., Shindo, C., Tsuji, N., Matsuura, M., Ishii, C., Nakaguma, T., Etoh, T., Shiotsuka, Y., Udagawa, M., Kurotani, A., Suzuki, K., Masuya, H., Wada, S., Fukuda, S., Tashiro, Y., Miyamoto, H., Kikuchi, J., Hattori, M., Nishiuch, T., Yamamoto, N., Ohno, H.: Gut-protective metabolic phenotype for diarrhoeal remission caused by an environmental probiotic thermophile. <span class=\"fontItalic\">\u00a0<em>Microbiome<\/em> 14, 194 (2026). [<a href=\"https:\/\/doi.org\/10.1186\/s40168-026-02476-9\" target=\"_blank\" rel=\"noopener\">Open Access<\/a>]<\/span><\/li>\n<li>Okamura-Oho, Y., Shimokawa, K., Oota, S., Yoshiki, A., Morita, M., Nishimura, M., Nakamura, S., Tsujimura, Y., Ishikawa, S., Yokota, H.: Topological modeling of gene expression in the brain with Huntington\u2019s disease reveals selective disruption of co-expression network. <em>Sci. Rep.<\/em>\u00a016, 18328 (2026). [<a href=\"https:\/\/doi.org\/10.1038\/s41598-026-56101-8\" target=\"_blank\" rel=\"noopener\">Open Access<\/a>]<\/li>\n<li>Meharry, S.L., Borensztejn, A., Gaudreault, N., Lucas, J., Medrash, G., Schaefbauer, L., Toloudis, D., Wallace, A., Whitney, B., Wilhelm, L., Ben-Simon, Y., Burel, J.M., Chen, J., Eliceiri, K.W., Gr\u00fcneboom, A., Kyoda, K., Moore, J., Moore, W., Onami, S., Panzeri, D., Rueden, C. T., Tasic, B., Johnson, G. T.: Search, organize, aggregate and share image data with BioFile Finder (BFF). <em>Nat. Methods<\/em> 23<em>,<\/em> 1256-1258. (2026).<\/li>\n<li>Kyoda, K., Okada, H., Onami, S.: A computational framework for extracting mechanistic hypothesis from quantitative data of morphological dynamics. (2026). [<a href=\"https:\/\/doi.org\/10.64898\/2026.06.10.731458\" target=\"_blank\" rel=\"noopener\">bioRxv<\/a>]<\/li>\n<li>Nishida, N., Munne, F.R., Liu, S., Tokunaga, N., Yamagata, Y.,\u00a0Cheng, F., Kozaki, K., Matsumoto, Y.: Dissecting GraphRAG: A Modular Analysis of Knowledge Structuring for Factoid Question Answering. <em>TACL<\/em>. 14, 1-29 (2026).<\/li>\n<li>Nagasaki, M., Katayama, T., Moriya, Y., Sekiya, Y., Kawashima, S., Teraoka, S., Machida, S., Matsubara, T., Hashimoto, H., Asakura, A., Nagano, A., Yamashita, R., Takada, T., Mitsuhashi, N., Kamada, M., Ohkawa, Y., Tokunaga, K., Kawai, Y.: Variant Information Standardization Collegium , JoGo 1.0: the ACTG hierarchical nomenclature and database covering 4.7 million haplotypes across 19,194 human genes, <em>Nucleic Acids Res.<\/em>,\u00a0 gkaf1232 (2025). [<a class=\"extlink\" href=\"https:\/\/doi.org\/10.1093\/nar\/gkaf1232\" target=\"_blank\" rel=\"noopener\">Open Access<\/a>]<\/li>\n<li>Kakuta, N., Takamatsu, T., Hayashi, S., Ikematsu, H., Kadota, T., Soga, K., Yokota, H., Takemura, H.: Development of 490-1600 nm hyperspectral imaging system based on flexible fiberscope. <em>Optics Express<\/em> 33, 43260-43272 (2025). [<a href=\"https:\/\/doi.org\/10.1364\/OE.574001\" target=\"_blank\" rel=\"noopener\">Open Access<\/a>]<\/li>\n<li>Yamashita, N., Koyanagi, Y., Takemura, H., Kusuya, T., Inoue, J., Yokota, H.: Large-scale 3D observation of microstructure around heat-affected zone using 3D internal structure microscopy. <em>Precision Engineering<\/em> 97, 609-623 (2025).[<a href=\"https:\/\/doi.org\/10.1016\/j.precisioneng.2025.09.013\" target=\"_blank\" rel=\"noopener\">Open Access<\/a>]<\/li>\n<li>Moore, J., Rzepka, N., Ratamero, E., Pape, C., Wetzker, C., Moore, W., Lindner, D., Wong, F., Mohamed, K., Ho, K. H. L., Kyoda, K., Sherwood, F., Yoldas, A. K., de Folter, J., Zobel, T., Jones, M. L., Wendt, J., Perlman, E., Stoeter, T., Zoccoler, M. L., Thoennissen, J., Burel, J.-M., Besson, S., Swedlow, J. R., Onami, S., Hartley, M., Huisken, J., Weidtkamp-Peters, S.: Enabling Peta-Scale Federated Repositories through Cloud-Native Formats: Lessons from a fast-paced challenge in the bioimaging community. 2nd Conference on Research Data Infrastructure (CoRDI), Aachen, Germany, <em>Zenodo.<\/em> (2025). [<a href=\"https:\/\/doi.org\/10.5281\/zenodo.16735915\" target=\"_blank\" rel=\"noopener\">Open Access<\/a>].<\/li>\n<li>Yamagata, Y., Kyoda, K., Itoga, H., Fujisawa, E., Onami, S.:\u00a0SSBD Ontology: A Two-Tier Approach for Interoperable Bioimaging Metadata. In<em>: Garijo, D.,\u00a0<\/em><i data-stringify-type=\"italic\">et al.<\/i> T<em>he Semantic Web \u2013 ISWC 2025. ISWC 2025. Lecture Notes in Computer Science<\/em>, vol 16141. Springer, Cham.\u00a0(2025).<\/li>\n<li>Onami, S., Kyoda, K., Yamagata, Y., Itoga, H.: foundingGIDE Deliverable D6.1: Report in metadata model overlap and gaps.<em>\u00a0Zenodo<\/em>. (2025). [<a class=\"wpel-icon-right\" href=\"https:\/\/doi.org\/10.5281\/zenodo.16794787\" target=\"_blank\" rel=\"noreferrer noopener external\" data-wpel-link=\"external\">Open Access<\/a>]<\/li>\n<li>Zakaria, D., Sandri, C., Modesto, M., Spiezio, C., Scarafile, D., Cedras, A., Borruso, L., Manghi, P., Trevisi, P., Segata, N., Mattarelli, P., Arita, M.: Disentangling the gut microbiota of Aldabra giant tortoises of different ages and environments. <em>PeerJ 13, <\/em>e19566 (2025). [<a href=\"https:\/\/doi.org\/10.7717\/peerj.19566\" target=\"_blank\" rel=\"noopener\">Open Access<\/a>]<\/li>\n<li>Takemori, N., Kaulich, P.T., Hahn, J., Schluter, H., Sugiyama, N., Tsumagari, K., Ishihama, Y., Fuchs, S., Iwasaki, M., Muller, F.J., Neusus, C., Jeong, K., Kohlbacher, O., Shimizu, Y., Otsuka, Y., Sato, H., Sasaki, K., Minegishi, Y., Kodera, Y., Fernandez-Cuesta, I., Krichel, B., Araki, N., Tholey, A.: Meeting Report: The Japanese-German Symposium on the &#8220;Advancement and Application of Proteoform-Centric Proteomics&#8221; (Kyoto, Japan, 2024). <em>Proteomics <\/em>25, 6-10 (2025).<\/li>\n<li>Kushida, T., de Farias, T., Sima, A., Dessimoz, C., Chiba, H., Bastian, F.B., Masuya, H.<i>:<\/i> Federated SPARQL query performance evaluation for exploring disease model mouse: combining gene expression, orthology, and disease knowledge graphs. <em>BMC Med Inform Decis Mak<\/em> 25 (Suppl 1), 189 (2025). [<a href=\"https:\/\/doi.org\/10.1186\/s12911-025-03013-8\" target=\"_blank\" rel=\"noopener\">Open Access<\/a>]<\/li>\n<li>Bajcsy, P., Bhattiprolu, S., B\u00f6rner, K., Cimini, B.A., Collinson. L., Ellenberg, J., Fiolka, R., Giger, M., Goscinski, W., Hartley, M., Hotaling, N., Horwitz, R., Jug, F., Kemmer, I., Kreshuk, A., Lundberg, E., Mathur, A., Narayan, K., Onami, S., Plant, A.L., Prior, F., Swedlow, J.R., Taylor, A., Keppler, A. Enabling global image data sharing in the life science. <em> Nature Methods 22, <\/em>672\u2013676. (2025).[<a href=\"https:\/\/doi.org\/10.1038\/s41592-024-02585-z\">Open Access<\/a>]<\/li>\n<li>Fujita, H., Yoshida, S., Suzuki, K.<i>, <\/i>Toji, H<i>.<\/i> Alternative stable states of microbiome structure and soil ecosystem functions. <i>Environmental Microbiome<\/i> 20, 28 (2025).[<a href=\"https:\/\/doi.org\/10.1186\/s40793-025-00688-4\" target=\"_blank\" rel=\"noopener\">Open Access<\/a>]<\/li>\n<li>Miura, H., Cerbus, R. T., Noda, I., Hiratani, I.\u00a0 CWL-Based Analysis Pipeline for Hi-C Data: From FASTQ Files to Matrices. <em>In: Nakato, R. (eds) Computational Methods for 3D Genome Analysis. Methods in Molecular Biology,<\/em> vol 2856. Humana, New York, NY. (2025).<\/li>\n<li>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. <em>Nucleic Acids Research,<\/em> D1716-D1723 (2025). [<a href=\"https:\/\/doi.org\/10.1093\/nar\/gkae860\">Open Access<\/a>]<\/li>\n<li>Nobusada, T., Yip, C.W., Agrawal, S., Severin, J., Abugessaisa, I., Hasegawa, A., Hon, C.C., Ide, S., Koido, M., Kondo, A., Masuya, H., Oki, S., Tagami, M., Takada, T.,Terao, C., Thalhath, N., Walker, S., Yasuzawa, K., Shin, J.W., Hoon, M.D.L., Carninci, P., Kawaji, H., Kasukawa, T. Update of the FANTOM web resource: enhancementfor studying noncoding genomes,<em> Nucleic Acids Research<\/em> 53, 419\u2013D424 (2024). [<a href=\"https:\/\/doi.org\/10.1093\/nar\/gkae1047\" target=\"_blank\" rel=\"noopener\">Open Access<\/a>]<\/li>\n<li>Hashimoto, K., Hayasaka, D., Eguchi, Y., Seko, Y., Cai, J., Suzuki, K., Goka, K., Kadoya, T. Multifaceted effects of variable biotic interactions on population stability in complex interaction webs. <em>Commun Biol <\/em><b>7<\/b>, 1309 (2024).[<a href=\"https:\/\/doi.org\/10.1038\/s42003-024-06948-2\" target=\"_blank\" rel=\"noopener\">Open Access<\/a>]<\/li>\n<li>Yamagata, Y., Yamada, R. Survey on large language model annotation of cellular senescence from figures in review articles. <em>Genomics &amp; Informatics<\/em> 22, 7 (2024) . [<a href=\"https:\/\/doi.org\/10.1186\/s44342-024-00011-6\" target=\"_blank\" rel=\"noopener\">Open Access<\/a>]<\/li>\n<li>Hiraki-Kajiyama, T., Miyasaka, N., Ando, R., Wakisaka, N., Itoga, H., Onami, S., Yoshihara, Y. An atlas and database of neuropeptide gene expression in the adult zebrafish forebrain. <em>The Journal of Comparative Neurology<\/em>, 10.1002\/cne.25619 (2024). [<a class=\"wpel-icon-right\" href=\"https:\/\/doi.org\/10.1002\/cne.25619\" rel=\"external noopener noreferrer\" data-wpel-link=\"external\">Open Access<\/a>]<\/li>\n<li>Agrawal, S., Buyan, A., Severin, J., Koido, M,. Alam, T., Abugessaisa, I., Chang, H.Y., Dostie, J., Itoh, M., Kere, J., Kondo, N., Li, Y., Makeev, V.J., Mendez, M., Okazaki, Y., Ramilowski, J.A., Sigorskikh, A.I., Strug, L.J., Yagi, K,. Yasuzawa, K., Yip, C.W., Hon, C.C., Hoffman, M.M., Terao, C., Kulakovskiy, I.V., Kasukawa, T., Shin, J.W., Carninci, P., De Hoon, M.J. Annotation of nuclear lncRNAs based on chromatin interactions. <em>PLoS One<\/em> 19(5):e0295971 (2024). [<a href=\"https:\/\/doi.org\/10.1371\/journal.pone.0295971\">Open Access<\/a>]<\/li>\n<li>Yamagata, Y., Kushida, T., Onami, S., Masuya, H. Homeostasis imbalance process ontology: a study on COVID-19 infectious processes. <em>BMC Med. Inform. Decis. Mak.<\/em> 23, 301 (2024). [<a class=\"wpel-icon-right\" href=\"https:\/\/doi.org\/10.1186\/s12911-024-02516-0\" rel=\"external noopener noreferrer\" data-wpel-link=\"external\">Open Access<\/a>]<\/li>\n<li>Yamagata, Y., Fukuyama, T., Onami, S., Masuya, H. Prototyping an Ontological Framework for Cellular Senescence Mechanisms: A Homeostasis Imbalance Perspective.<em> Scientific Data<\/em> 11, 485 (2024). [<a href=\"https:\/\/doi.org\/10.1038\/s41597-024-03331-y\" target=\"_blank\" rel=\"noreferrer noopener\">Open Access<\/a>]<\/li>\n<li>Bialy, N., Alber, F., Andrews, B., Angelo, M., Beliveau, B., Bintu, L., Boettiger, A., Boehm, U., Brown, C.M., Bukar, M.M., Chambers, J.J., Cimini, B.A., Eliceiri, K., Errington, R., Faklaris, O., Gaudreault, N., Germain, R.N., Goscinski, W., Grunwald, D., Halter, M., Hanein, D., Hickey, J.W., Lacoste, J., Laude, A., Lundberg, E., Ma, J., Malacrida, L., Moore, J., Nelson, G., Neumann, E.K., Nitschke, R., Onami, S., Pimentel, J.A., Plant, A.L., Radtke, A.J., Sabata, B., Schapiro, D., Sch\u00f6neberg, J., Spraggins, J.M., Sudar, D., Vierdag, W.A.M., Volkmann, N., W\u00e4hlby, C., Siyuan, W., Yaniv, Z., Strambio-De-Castillia, C. Harmonizing the Generation and Pre-publication Stewardship of FAIR Image Data. (2024). [<a class=\"wpel-icon-right\" href=\"https:\/\/doi.org\/10.48550\/arXiv.2401.13022\" target=\"_blank\" rel=\"noreferrer noopener external\" data-wpel-link=\"external\">arXiv<\/a>]<\/li>\n<li>Dohi, E., Kushida, T., Yamagata, Y., Takatsuki, T., Shin, J., Liener, T., Hoehndorf, R. BioHackJP 2023 Report R1:Improving phenotype ontology interoperability. (2024). [<a class=\"wpel-icon-right\" href=\"https:\/\/osf.io\/preprints\/biohackrxiv\/d27fw\" rel=\"external noopener noreferrer\" data-wpel-link=\"external\">BioHackrXiv<\/a>]<\/li>\n<li>Young, T.R., Yamamoto, M., Kikuchi, S.S., Yoshida<i>,<\/i> A.C., Abe, T., Inoue, K., Johansen, J.P., Benucci, A., Yoshimura, Y., Shimogori, T. Thalamocortical control of cell-type specificity drives circuits for processing whisker-related information in mouse barrel cortex. <i>Nature Communications<\/i> 14, 6077. (2023). [<a href=\"https:\/\/doi.org\/10.1038\/s41467-023-41749-x\">Open Access<\/a>]<\/li>\n<li>Kushida, T., de Farias, F.M., Sima, A.,\u00a0 Dessimoz, C., Chiba, H., Bastian, F., Masuya, H. Exploring Disease Model Mouse Using Knowledge Graphs: Combining Gene Expression, Orthology, and Disease Datasets. (2023). [<a href=\"https:\/\/doi.org\/10.1101\/2023.08.30.555283\" target=\"_blank\" rel=\"noopener\">bioRxiv<\/a>]<\/li>\n<li>Moore, J., Basurto-Lozada, D., Besson, S., Bogovic, J., Bragantini, J., Brown, E. M., Burel, JM., Casas, Moreno, X., de Medeiros, G., Diel, E. E., Gault, D., Ghosh, S. S., Gold, I., Halchenko, Y. O., Hartley, M., Horsfall, D., Keller, M. S., Kittisopikul, M., Kovacs, G., K\u00fcpc\u00fc Yolda\u015f, A., Kyoda, K., le Tournoulx, de la Villegeorges, A., Li, T., Liberali, P., Lindner, D., Linkert, M., L\u00fcthi, J., Maitin-Shepard, J., Manz, T., Marconato, L., McCormick, M., Lange, M., Mohamed, K., Moore, W., Norlin, N., \u00d6zdemir, B., Palla, G., Pape, C., Pelkmans, L., Pietzsch, T., Preibisch, S., Prete, M., Rzepka, N., Samee, S., Schaub, N., Sidky, H., Solak, A. C., Stirling, D. R., Striebel, J., Tischer, C., Toloudis, D., Virshup, I., Walczysko, P., Watson, A. M., Wong, F., Yamauchi, K. A., Bayraktar, O., Haniffa, M., Hotaling, N., Onami, S., Royer, L. A., Saalfeld, S., Stegle, O., Theis, F. J., Swedlow, J. R. (2023) .OME-Zarr: a cloud-optimized bioimaging file format with international community support. <em>Histochemistry and Cell Biology <\/em>160, 223-251<em>. <\/em>(2023)<em>.<\/em> [<a href=\"https:\/\/doi.org\/10.1007\/s00418-023-02209-1\">Open Access<\/a>]<\/li>\n<li>\n<div class=\"citation-text\">Koistinen, V., K\u00e4rkk\u00e4inen, O., Keski-Rahkonen, P., Tsugawa, H., Scalbert, A., Arita, M., Wishart, D., &amp; Hanhineva, K. Towards a Rosetta stone for metabolomics: recommendations to overcome inconsistent metabolite nomenclature, <em>Nature metabolism<\/em> (2023). [<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/36890347\/\" target=\"_blank\" rel=\"noopener\">pubmed<\/a>]<\/div>\n<\/li>\n<li>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, <em>Environmental Research<\/em> 219, 115130(2023). [<a href=\"https:\/\/doi.org\/10.1016\/j.envres.2022.115130\" target=\"_blank\" rel=\"noopener\">Open Access<\/a>]<\/li>\n<li>Suzuki, K., Matsuzaki, S.S., Masuya, H. Decomposing predictability to identify dominant causal drivers in complex ecosystems, <em>Proceedings of the National Academy of Sciences <\/em>119 (42), e2204405119 (2022). [<a href=\"https:\/\/doi.org\/10.1073\/pnas.2204405119\" target=\"_blank\" rel=\"noopener\">Open Access<\/a>]<\/li>\n<li>McDonald, J. G., Ejsing, C. S., Kopczynski, D., Hol\u010dapek, M., Aoki, J., Arita, M., Arita, M., Baker, E. S., Bertrand-Michel, J., Bowden, J. A., Br\u00fcgger, B., Ellis, S. R., Fedorova, M., Griffiths, W. J., Han, X., Hartler, J., Hoffmann, N., Koelmel, J. P., K\u00f6feler, H. C., Mitchell, T. W., O\u2019Donnell, V. B., Saigusa, D., Schwudke, D., Schevchenko, A., Ulmer, C. Z., Wenk, M. R., Witting, M., Wolrab, D., Xia, Y., Ahrends, R., Liebisch, G., Ekroos, K. Introducing the Lipidomics Minimal Reporting Checklist, <em>Nature metabolism<\/em> 4(9), 1086\u20131088 (2022). [<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/35934691\/\" target=\"_blank\" rel=\"noopener\">pubmed<\/a>]<\/li>\n<li>Abugessaisa, I., Hasegawa, A., Noguchi, S.,\u00a0 Cardon, M.,\u00a0 Watanabe, K., Takahashi, M., Suzuki, H., Katayama, S., Kere, J., Kasukawa, T. SkewC: Identifying cells with skewed gene body coverage in single-cell RNA sequencing data, <em>iScience<\/em> 25 (2), 103777 (2022). [<a href=\"https:\/\/doi.org\/10.1016\/j.isci.2022.103777\" target=\"_blank\" rel=\"noopener\">Open Access<\/a>]<\/li>\n<li><span class=\"al-author-name-more js-flyout-wrap\">Fukushima<span class=\"delimiter\">, A., <\/span><\/span><span class=\"al-author-name-more js-flyout-wrap\">Takahashi<span class=\"delimiter\">, M.,\u00a0<\/span><\/span><span class=\"al-author-name-more js-flyout-wrap\">Nagasaki<span class=\"delimiter\">, <\/span> <\/span> <span class=\"al-author-name-more js-flyout-wrap\"> H., Aono<span class=\"delimiter\">, Y., <\/span><\/span><span class=\"al-author-name-more js-flyout-wrap\">Kobayashi<span class=\"delimiter\">, M., <\/span><\/span><span class=\"al-author-name-more js-flyout-wrap\">Kusano<span class=\"delimiter\">, M., <\/span><\/span><span class=\"al-author-name-more js-flyout-wrap\">Saito<span class=\"delimiter\">, K., K<\/span><\/span><span class=\"al-author-name-more js-flyout-wrap\">obayashi<span class=\"delimiter\">, N., <\/span><\/span><span class=\"al-author-name-more js-flyout-wrap\">Arita, M. Development of RIKEN Plant Metabolonome MetaDatabase. <em>Plant and Cell Physiology <\/em>63 (3), 433-440 (2021). [<a href=\"https:\/\/doi.org\/10.1093\/pcp\/pcab173\" target=\"_blank\" rel=\"noopener\">Open Access<\/a>]<\/span><\/li>\n<li>Nelson, G., Boehm, U., Bagley, S., Bajcsy, P., Bischof, J., Brown, C.M., Dauphin, A., Dobbie, I.M., Eriksson, J.E., Faklaris, O., Fernandez-Rodriguez, J., Ferrand, A., Gelman, L., Gheisari, A., Hartmann, H., Kukat, C., Laude, A., Mitkovski, M., Munck, S., North, A.J., Rasse, T.M., Resch-Genger, U., Schuetz, L.C., Seitz, A., Strambio-De-Castillia, C., Swedlow, J.R., Alexopoulos, I., Aumayr, K., Avilov, S., Bakker, G.-J., Bammann, R.R., Bassi, A., Beckert, H., Beer, S., Belyaev, Y., Bierwagen, J., Birngruber, K.A., Bosch, M., Breitlow, J., Cameron, L.A., Chalfoun, J., Chambers, J.J., Chen, C.-L., Conde-Sousa, E., Corbett, A.D., Cordelieres, F.P., Nery, E.D., Dietzel, R., Eismann, F., Fazeli, E., Felscher, A., Fried, H., Gaudreault, N., Goh, W.I., Guilbert, T., Hadleigh, R., Hemmerich, P., Holst, G.A., Itano, M.S., Jaffe, C.B., Jambor, H.K., Jarvis, S.C., Keppler, A., Kirchenbuechler, D., Kirchner, M., Kobayashi, N., Krens, G., Kunis, S., Lacoste, J., Marcello, M., Martins, G.G., Metcalf, D.J., Mitchell, C.A., Moore, J., Mueller, T., Nelson, M.S., Ogg, S., Onami, S., Palmer, A.L., Paul-Gilloteaux, P., Pimentel, J.A., Plantard, L., Podder, S., Rexhepaj, E., Royon, A., Saari, M.A., Schapman, D., Schoonderwoert, V., Schroth-Diez, B., Schwartz, S., Shaw, M., Spitaler, M., Stoeckl, M.T., Sudar, D., Teillon, J., Terjung, S., Thuenauer, R., Wilms, C.D., Wright, G.D. and Nitschke, R. QUAREP-LiMi: a community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. <em>Journal of Microscopy <\/em>284, 56-73 (2021). [<a href=\"https:\/\/doi.org\/10.1111\/jmi.13041\" target=\"_blank\" rel=\"noopener\">Open Access<\/a>]<\/li>\n<li>Hirata, T., Tohsato, Y., Itoga, H., Shioi, G., Kiyonari, H., Oka, S., Fujimori, T., Onami, S. NeuroGT: A brain atlas of neurogenic tagging CreER drivers for birthdate-based classification and manipulation of mouse neurons. <em>Cell Reports Methods<\/em> 1, 100012 (2021). [<a href=\"https:\/\/doi.org\/10.1016\/j.crmeth.2021.100012\" target=\"_blank\" rel=\"noopener\">Open Access<\/a>]<\/li>\n<li>Sarkans, U., Chiu, W., Collinson, L., Darrow, M. C., Ellenberg, J., Grunwald, D., H\u00e9rich\u00e9, J. K., Iudin, A., Martins, G. G., Meehan, T., Narayan, K., Patwardhan, A., Russell, M. R. G., Saibil, H. R., Strambio-De-Castillia, C., Swedlow, J. R., Tischer, C., Uhlmann, V., Verkade, P., Barlow, M., Bayraktar, O., Birney, E., Catavitello. C., Cawthorne, C., Wagner-Conrad, S., Duke, E., Paul-Gilloteaux, P., Gustin, E., Harkiolaki, M., Kankaanp\u00e4\u00e4, P., Lemberger, T., McEntyre, J., Moore, J., Nicholls, A. W., Onami, S., Parkinson, H., Parsons, M., Romanchikova, M., Sofroniew, N., Swoger, J., Utz, N., Voortman, L. M., Wong, F., Zhang, P., Kleywegt, G. J., Brazma, A. REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology.\u00a0 <em>Nature Methods <\/em>18, 1418-1422 (2021). [<a href=\"https:\/\/doi.org\/10.1016\/j.crmeth.2021.100012\" target=\"_blank\" rel=\"noreferrer noopener\">Open Access<\/a>]<\/li>\n<li>Suzuki, K., Nakaoka, S., Fukuda, S., Masuya, H. Energy landscape analysis elucidates the multistability of ecological communities across environmental gradients. <em>Ecological Monographs<\/em>. 91, e01469 (2021). [<a href=\"https:\/\/doi.org\/10.1002\/ecm.1469\" target=\"_blank\" rel=\"noopener\">OpenAccess<\/a>]<\/li>\n<li>Swedlow, J. R., Kankaanp\u00e4\u00e4, P., Sarkans, U., Goscinski, W., Galloway, G., Malacrida, L., Sullivan, R. P., H\u00e4rtel, S., Brown, C. M., Wood, C., Keppler, A., Paina, F., Loos, B., Zullino, S., Longo, D. L., Aime, S., Onami, S.\u00a0 A Global view of standards for open image data formats and repositories. <em>Nature Methods <\/em>18, 1440\u20131446\u00a0(2021). [<a href=\"https:\/\/doi.org\/10.1038\/s41592-021-01113-7\" target=\"_blank\" rel=\"noopener\">OpenAccess<\/a>]<\/li>\n<li><span class=\"highwire-citation-authors\"><span class=\"highwire-citation-author first has-tooltip hasTooltip\" data-delta=\"0\" data-hasqtip=\"1\" aria-describedby=\"qtip-1\">Kita<\/span>, Y., <span class=\"highwire-citation-author has-tooltip hasTooltip\" data-delta=\"1\" data-hasqtip=\"2\">Nishibe<\/span>, H., <span class=\"highwire-citation-author has-tooltip hasTooltip\" data-delta=\"2\" data-hasqtip=\"0\">Wang<\/span>, Y., <span class=\"highwire-citation-author\" data-delta=\"3\">Hashikawa<\/span>, T., <span class=\"highwire-citation-author has-tooltip hasTooltip\" data-delta=\"4\" data-hasqtip=\"3\" aria-describedby=\"qtip-3\">Kikuchi<\/span>, S. S., <span class=\"highwire-citation-author has-tooltip hasTooltip\" data-delta=\"5\" data-hasqtip=\"4\" aria-describedby=\"qtip-4\">U<\/span>, M., <span class=\"highwire-citation-author\" data-delta=\"6\">Yoshida<\/span>, A. C., <span class=\"highwire-citation-author has-tooltip hasTooltip\" data-delta=\"7\" data-hasqtip=\"5\">Yoshida<\/span>, C., <span class=\"highwire-citation-author has-tooltip hasTooltip\" data-delta=\"8\" data-hasqtip=\"6\">Kawase<\/span>, T., <span class=\"highwire-citation-author hw-author-orcid-logo-wrapper\" data-delta=\"9\">Ishii<\/span>, S., <span class=\"highwire-citation-author\" data-delta=\"10\">Skibbe<\/span>, H., Shimogori, <span class=\"highwire-citation-author hw-author-orcid-logo-wrapper has-tooltip hasTooltip\" data-delta=\"11\" data-hasqtip=\"7\">T. Cellular-resolution gene expression profiling in the neonatal marmoset brain reveals dynamic species- and region-specific differences. <em><span class=\"highwire-cite-metadata-journal highwire-cite-metadata\">Proceedings of the National Academy of Sciences <\/span><\/em><span class=\"highwire-cite-metadata-date highwire-cite-metadata\">May 2021, <\/span><span class=\"highwire-cite-metadata-volume highwire-cite-metadata\">118 <\/span><span class=\"highwire-cite-metadata-issue highwire-cite-metadata\">(18), <\/span><span class=\"highwire-cite-metadata-pages highwire-cite-metadata\">e2020125118. (2021).<\/span><span class=\"highwire-cite-metadata-doi highwire-cite-metadata\">[<a href=\"https:\/\/doi.org\/10.1073\/pnas.2020125118\" target=\"_blank\" rel=\"noopener\">OpenAccess<\/a>]<\/span><\/span><\/span><\/li>\n<li>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. <em>Laboratory Animal Research <\/em>37, 6 (2021). [<a href=\"https:\/\/doi.org\/10.1186\/s42826-020-00068-8\">OpenAccess<\/a>]<\/li>\n<li>Abugessaisa, I., Ramilowski, JA., Lizio, M., Severin, J., Hasegawa, A., Harshbarger, J., Kondo, A., Noguchi, S., Yip, C., Ooi, J., Tagami, M., Hori, F., Agrawal, S., Hon, C., Cardon, M., Ikeda, S., Ono, H., Bono, H., Kato, M., Hashimoto, K., Bonetti, A., Kato, M., Kobayashi, N., Shin, J., De Hoon, M., Hayashizaki, Y., Carninci, P., Kawaji, H., and Kasukawa, T. FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs.<em> Nucleic Acids Research<\/em> 49 (D1), D892-D898 (2020). [<a href=\"https:\/\/doi.org\/10.1093\/nar\/gkaa1054\" target=\"_blank\" rel=\"noopener\">OpenAccess<\/a>]<\/li>\n<li>Kyoda, K., Okada, H., Itoga, H., Onami, S. Deep collection of quantitative nuclear division dynamics data in RNAi-treated <em>Caenorhabditis elegans<\/em> embryos. (2020).\u00a0 [<a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2020.10.04.325761v1\">bioRxiv<\/a>]<\/li>\n<li>Yamagata, Y., Yamada, H. Ontological approach to the knowledge systematization of a toxic process and toxic course representation framework for early drug risk management.<em> Scientific Reports<\/em> 10, 14581 (2020). [<a href=\"https:\/\/doi.org\/10.1038\/s41598-020-71370-7\">OpenAccess<\/a>]<\/li>\n<li>Kyoda, K., Ho, K.H.L., Itoga, H., Tohsato, Y., Onami, S. BD5: an open HDF5-based data format to represent quantitative biological dynamics data. <em>PLOS ONE<\/em> 15, e0237468 (2020). [<a href=\"https:\/\/doi.org\/10.1371\/journal.pone.0237468\">OpenAccess<\/a>]<\/li>\n<li>Tsugawa, H., Ikeda, K., Takahashi, M., Satoh, A., Mori, Y., Uchino, H., Okahashi, N., Yamada, Y., Tada, I., Bonini, P., Higashi, Y., Okazaki, Y., Zhou, Z., Zhu, Z., Koelmel, J., Cajka, T., Fiehn, O., Saito, K., Arita, M., and Arita, M. A lipidome atlas in MS-DIAL 4. <em>Nature Biotechnology<\/em> 38, 1159\u20131163 (2020). [<a href=\"https:\/\/doi.org\/10.1038\/s41587-020-0531-2\" target=\"_blank\" rel=\"noopener\">OpenAccess<\/a>]<\/li>\n<li>Tanaka, N., and Masuya, H. An atlas of evidence-based phenotypic associations across the mouse phenome. <em>Scientific Reports<\/em> 10, 3957 (2020). [<a href=\"https:\/\/doi.org\/10.1038\/s41598-020-60891-w\" target=\"_blank\" rel=\"noopener\">OpenAccess<\/a>]<\/li>\n<li>Ozaki, H., Hayashi, T., Umeda, M., Nikaido, I<i>.<\/i> Millefy: visualizing cell-to-cell heterogeneity in read coverage of single-cell RNA sequencing datasets.<em> BMC Genomics<\/em> 21, 177 (2020). [<a href=\"https:\/\/doi.org\/10.1186\/s12864-020-6542-z\" target=\"_blank\" rel=\"noopener\">OpenAccess<\/a>]<\/li>\n<li>Matsumoto, H., Hayashi, T., Ozaki, H., Tsuyuzaki, K., Umeda, M., Iida, T., Nakamura, M., Okano, H., Nikaido, I. An NMF-based approach to discover overlooked differentially expressed gene regions from single-cell RNA-seq data. <em>NAR Genomics and Bioinformatics <\/em>2 (1), lqz020 (2020). [<a href=\"https:\/\/doi.org\/10.1093\/nargab\/lqz020\" target=\"_blank\" rel=\"noopener\">OpenAccess<\/a>]<\/li>\n<li>Tsuyuzaki, K., Sato, H., Sato, K., Nikaido, I<i>.<\/i> Benchmarking principal component analysis for large-scale single-cell RNA-sequencing. <em>Genome Biology<\/em> 21, 9 (2020). [<a href=\"https:\/\/doi.org\/10.1186\/s13059-019-1900-3\" target=\"_blank\" rel=\"noopener\">OpenAccess<\/a>]<\/li>\n<li>Kadota, M., Nishimura, O., Miura, H., Tanaka, K., Hiratani, I., Kuraku, S. Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?. <em>GigaScience <\/em>9 (1), giz158 (2020). [<a href=\"https:\/\/doi.org\/10.1093\/gigascience\/giz158\" target=\"_blank\" rel=\"noopener\">OpenAccess<\/a>]<\/li>\n<li>Moore, J., Kobayashi, N., Kunis, S., Onami, S., Swedlow, J. R., the OME Consortium (2019) On bringing bioimaging data into the open (world). <em>Proceedings of 12th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4HCLS 2019)<\/em>, 44-53. [<a class=\"wpel-icon-right\" href=\"http:\/\/ceur-ws.org\/Vol-2849\/paper-06.pdf\" rel=\"external noopener noreferrer\" data-wpel-link=\"external\">Open Access (PDF 693KB)<\/a>]<\/li>\n<li>Morita, M., Shimokawa, K., Nishimura, M., Nakamura, S., Tsujimura, Y., Takemoto, S., Tawara, T., Yokota, H., Wemler, S., Miyamoto, D., Ikeno, H., Sato, A., Furuichi, T., Kobayashi, N., Okumura, Y., Yamaguchi, Y., and Okamura- Oho, Y. ViBrism DB: an interactive search and viewer platform for 2D\/3D anatomical images of gene expression and co-expression networks. <em>Nucleic Acids Research<\/em> 47(D1), D859-D866 (2019). [<a href=\"https:\/\/doi.org\/10.1093\/nar\/gky951\" target=\"_blank\" rel=\"noopener\">OpenAccess<\/a>]<\/li>\n<li>Kobayashi, N., Kume, S., Lenz, K., and Masuya, H. RIKEN MetaDatabase: a database platform for health care and life sciences as a microcosm of linked open data cloud. <em>International Journal on Semantic Web and Information Systems<\/em> 14(1), 140-164 (2018). [<a href=\"https:\/\/doi.org\/10.4018\/IJSWIS.2018010106\" target=\"_blank\" rel=\"noopener\">OpenAccess<\/a>]<\/li>\n<li>Tsuyuzaki K., Nikaido. I. Biological systems as heterogeneous information networks: a mini-review and perspectives. <em>HeteroNAM\u201918<\/em>. WSDM2018 (2018). [<a href=\"https:\/\/arxiv.org\/abs\/1712.08865\" target=\"_blank\" rel=\"noopener\">arXiv<\/a>]<\/li>\n<li>Matsumoto, H., Kiryu, H., Furusawa, C., Ko, MSH., Ko, SBH., Gouda, N., Hayashi, T., Nikaido, I. SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation. <em>Bioinformatics<\/em> 33 (15), 2314\u20132321 (2017). [<a href=\"https:\/\/doi.org\/10.1093\/bioinformatics\/btx194\" target=\"_blank\" rel=\"noopener\">OpenAccess<\/a>]<\/li>\n<li><\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"related\"><\/a><\/p>\n<h3>Related Publications<\/h3>\n<ul class=\"p-rich_text_list p-rich_text_list__bullet\" data-stringify-type=\"unordered-list\" data-indent=\"0\" data-border=\"0\">\n<li data-stringify-indent=\"0\" data-stringify-border=\"0\">Torigoe, M., Islam, T., Kakinuma, H., Fung, C. C. A., Isomura, T., Shimazaki, H., Aoki, T., Fukai, T., Okamoto, H. Zebrafish capable of generating future state prediction error show improved active avoidance behavior in virtual reality. <em>Nature Communications<\/em> 12, 5712 (2021). <a class=\"c-link\" tabindex=\"-1\" href=\"https:\/\/doi.org\/10.1038\/s41467-021-26010-7\" target=\"_blank\" rel=\"noopener noreferrer\" data-stringify-link=\"https:\/\/doi.org\/10.1038\/s41467-021-26010-7\" data-sk=\"tooltip_parent\" data-remove-tab-index=\"true\">[Open Access]<\/a><\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Publications Kubo, N., Oguchi, A., Masuya, H., Amano, T., Sakashita, A., Kawaji, H., Kasukawa, T., Oki, S., Ay [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":5,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-89","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/olsp.riken.jp\/en\/wp-json\/wp\/v2\/pages\/89","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/olsp.riken.jp\/en\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/olsp.riken.jp\/en\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/olsp.riken.jp\/en\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/olsp.riken.jp\/en\/wp-json\/wp\/v2\/comments?post=89"}],"version-history":[{"count":62,"href":"https:\/\/olsp.riken.jp\/en\/wp-json\/wp\/v2\/pages\/89\/revisions"}],"predecessor-version":[{"id":734,"href":"https:\/\/olsp.riken.jp\/en\/wp-json\/wp\/v2\/pages\/89\/revisions\/734"}],"wp:attachment":[{"href":"https:\/\/olsp.riken.jp\/en\/wp-json\/wp\/v2\/media?parent=89"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}