{"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":"2026-04-15T16:04:35","modified_gmt":"2026-04-15T07:04:35","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>Nishida, N., Munne, F.R., Liu, S., Tokunaga, N., <u>Yamagata, Y.<\/u>, Cheng, 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>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. 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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). 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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 Nishida, N., Munne, F.R., Liu, S., Tokunaga, N., Yamagata, Y., Cheng, F., Kozaki, K., Matsumoto,  [&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":55,"href":"https:\/\/olsp.riken.jp\/en\/wp-json\/wp\/v2\/pages\/89\/revisions"}],"predecessor-version":[{"id":691,"href":"https:\/\/olsp.riken.jp\/en\/wp-json\/wp\/v2\/pages\/89\/revisions\/691"}],"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}]}}