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Miura, H., Cerbus, R. T., Noda, I., Hiratani, I. CWL-Based Analysis Pipeline for Hi-C Data: From FASTQ Files to Matrices. In: Nakato, R. (eds) Computational Methods for 3D Genome Analysis. Methods in Molecular Biology, vol 2856. Humana, New York, NY. (2025).
Kyoda, K., Itoga, H., Yamagata, Y., Fujisawa, E., Wang, F., Miranda-Miranda, M., Yamamoto, H., Nakano, Y., Tohsato, Y., Onami, S. SSBD: an ecosystem for enhanced sharing and reuse of bioimaging data. Nucleic Acids Research, gkae860 (2024). [Open Access]
Yamagata, Y., Yamada, R. Survey on large language model annotation of cellular senescence from figures in review articles. Genomics & Informatics 22, 7 (2024) . [Open Access]
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. The Journal of Comparative Neurology, 10.1002/cne.25619 (2024). [Open Access]
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. PLoS One 19(5):e0295971 (2024). [Open Access]
Yamagata, Y., Kushida, T., Onami, S., Masuya, H. Homeostasis imbalance process ontology: a study on COVID-19 infectious processes. BMC Med. Inform. Decis. Mak. 23, 301 (2024). [Open Access]
Yamagata, Y., Fukuyama, T., Onami, S., Masuya, H. Prototyping an Ontological Framework for Cellular Senescence Mechanisms: A Homeostasis Imbalance Perspective. Scientific Data 11, 485 (2024). [Open Access]
Bajcsy, P., Bhattiprolu, S., Borner, K., Cimini, B., Collinson. L., Ellenberg, J., Fiolka, R., Giger, M., Goscinski, W., Hartley, M., Hotaling, N., Horwitz, R., Jug, F., Kreshuk, A., Lundberg, E., Mathur, A., Narayan, K., Onami, S., Plant, A.L., Prior, F., Swedlow, J., Taylor, A., Keppler, A. Enabling Global Image Data Sharing in the Life Sciences. (2024). [arXiv]
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., Schöneberg, J., Spraggins, J.M., Sudar, D., Vierdag, W.A.M., Volkmann, N., Wählby, C., Siyuan, W., Yaniv, Z., Strambio-De-Castillia, C. Harmonizing the Generation and Pre-publication Stewardship of FAIR Image Data. (2024). [arXiv]
Dohi, E., Kushida, T., Yamagata, Y., Takatsuki, T., Shin, J., Liener, T., Hoehndorf, R. BioHackJP 2023 Report R1:Improving phenotype ontology interoperability. (2024). [BioHackrXiv]
Young, T.R., Yamamoto, M., Kikuchi, S.S., Yoshida, 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. Nature Communications 14, 6077. (2023). [Open Access]
Kushida, T., de Farias, F.M., Sima, A., Dessimoz, C., Chiba, H., Bastian, F., Masuya, H. Exploring Disease Model Mouse Using Knowledge Graphs: Combining Gene Expression, Orthology, and Disease Datasets. (2023). [bioRxiv]
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., Küpcü Yoldaş, A., Kyoda, K., le Tournoulx, de la Villegeorges, A., Li, T., Liberali, P., Lindner, D., Linkert, M., Lüthi, J., Maitin-Shepard, J., Manz, T., Marconato, L., McCormick, M., Lange, M., Mohamed, K., Moore, W., Norlin, N., Özdemir, 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. OME-Zarr: a cloud-optimized bioimaging file format with international community support. Histochemistry and Cell Biology 160, 223-251 (2023). [Open Access]
Koistinen, V., Kärkkäinen, O., Keski-Rahkonen, P., Tsugawa, H., Scalbert, A., Arita, M., Wishart, D., & Hanhineva, K. Towards a Rosetta stone for metabolomics: recommendations to overcome inconsistent metabolite nomenclature, Nature metabolism (2023). [pubmed]
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 219, 115130(2023). [Open Access]
Suzuki, K., Matsuzaki, S.S., Masuya, H. Decomposing predictability to identify dominant causal drivers in complex ecosystems, Proceedings of the National Academy of Sciences 119 (42), e2204405119 (2022). [Open Access]
McDonald, J. G., Ejsing, C. S., Kopczynski, D., Holčapek, M., Aoki, J., Arita, M., Arita, M., Baker, E. S., Bertrand-Michel, J., Bowden, J. A., Brügger, B., Ellis, S. R., Fedorova, M., Griffiths, W. J., Han, X., Hartler, J., Hoffmann, N., Koelmel, J. P., Köfeler, H. C., Mitchell, T. W., O’Donnell, 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, Nature metabolism 4(9), 1086–1088 (2022). [pubmed]
Abugessaisa, I., Hasegawa, A., Noguchi, S., Cardon, M., 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, iScience 25 (2), 103777 (2022). [Open Access]
Suzuki, K., Abe, M.S., 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 19, 1228 (2022). [Open Access]
Fukushima, A., Takahashi, M., Nagasaki, H., Aono, Y., Kobayashi, M., Kusano, M., Saito, K., Kobayashi, N., Arita, M. Development of RIKEN Plant Metabolonome MetaDatabase. Plant and Cell Physiology 63 (3), 433-440 (2021). [Open Access]
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. Journal of Microscopy 284, 56-73 (2021). [Open Access]
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. Cell Reports Methods 1, 100012 (2021). [Open Access]
Sarkans, U., Chiu, W., Collinson, L., Darrow, M. C., Ellenberg, J., Grunwald, D., Hériché, 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., Kankaanpää, 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. Nature Methods 18, 1418-1422 (2021). [Open Access]
Suzuki, K., Nakaoka, S., Fukuda, S., Masuya, H. Energy landscape analysis elucidates the multistability of ecological communities across environmental gradients. Ecological Monographs 91, e01469 (2021). [OpenAccess]
Swedlow, J. R., Kankaanpää, P., Sarkans, U., Goscinski, W., Galloway, G., Malacrida, L., Sullivan, R. P., Härtel, S., Brown, C. M., Wood, C., Keppler, A., Paina, F., Loos, B., Zullino, S., Longo, D. L., Aime, S., Onami, S. A Global view of standards for open image data formats and repositories. Nature Methods 18, 1440-1446. (2021). [OpenAccess]
Kita, Y., Nishibe, H., Wang, Y., Hashikawa, T., Kikuchi, S. S., U, M., Yoshida, A. C., Yoshida, C., Kawase, T., Ishii, S., Skibbe, H., Shimogori, T. Cellular-resolution gene expression profiling in the neonatal marmoset brain reveals dynamic species- and region-specific differences. Proceedings of the National Academy of Sciences May 2021, 118 (18), e2020125118. (2021). [OpenAccess]
Masuya, H., Usuda, D., Nakata, H., Yuhara, N., Kurihara, K., Namiki, Y., Iwase, S., Takada, T., Tanaka, N., Suzuki, K., Yamagata, Y., Kobayashi, N., Yoshiki, A., Kushida, T. Establishment and application of information resource of mutant mice in RIKEN BioResource Research Center. Laboratory Animal Research 37, 6 (2021). [OpenAccess]
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. Nucleic Acids Research 49 (D1), D892-D898 (2020). [OpenAccess]
Kyoda, K., Okada, H., Itoga, H., Onami, S. Deep collection of quantitative nuclear division dynamics data in RNAi-treated Caenorhabditis elegans embryos. (2020). [bioRxiv]
Yamagata, Y., Yamada, H. Ontological approach to the knowledge systematization of a toxic process and toxic course representation framework for early drug risk management. Scientific Reports 10, 14581 (2020). [OpenAccess]
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. PLOS ONE 15, e0237468 (2020). [OpenAccess]
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. Nature Biotechnology 38, 1159–1163 (2020). [OpenAccess]
Tanaka, N., and Masuya, H. An atlas of evidence-based phenotypic associations across the mouse phenome. Scientific Reports 10, 3957 (2020). [OpenAccess]
Ozaki, H., Hayashi, T., Umeda, M., Nikaido, I. Millefy: visualizing cell-to-cell heterogeneity in read coverage of single-cell RNA sequencing datasets. BMC Genomics 21, 177 (2020). [OpenAccess]
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. NAR Genomics and Bioinformatics 2 (1), lqz020 (2020). [OpenAccess]
Tsuyuzaki, K., Sato, H., Sato, K., Nikaido, I. Benchmarking principal component analysis for large-scale single-cell RNA-sequencing. Genome Biology 21, 9 (2020). [OpenAccess]
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?. GigaScience 9 (1), giz158 (2020). [OpenAccess]
Moore, J., Kobayashi, N., Kunis, S., Onami, S., Swedlow, J. R., the OME Consortium (2019) On bringing bioimaging data into the open (world). Proceedings of 12th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4HCLS 2019), 44-53. [Open Access (PDF 693KB)]
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. Nucleic Acids Research 47(D1), D859-D866 (2019). [OpenAccess]
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. International Journal on Semantic Web and Information Systems 14(1), 140-164 (2018). [OpenAccess]
Shimogori, T., Abe, A., Go, Y., Hashikawa, T., Kishi, N., Kikuchi, S. S., Kita, Y., Niimi, K., Nishibe, H., Okuno, M., Saga, K., Sakurai, M., Sato, M., Serizawa, T., Suzuki, S., Takahashi, E., Tanaka, M., Tatsumoto, S., Toki, M., U, M., Wang, Y., Windak, K. J., Yamagishi, H., Yamashita, K., Yoda, T., Yoshida, A. C., Yoshida, C., Yoshimoto, T., Okano, H. Digital gene atlas of neonate common marmoset brain, Neuroscience Research 128, 1-13 (2018). [OpenAccess]
Tsuyuzaki K., Nikaido. I. Biological systems as heterogeneous information networks: a mini-review and perspectives. HeteroNAM’18. WSDM2018 (2018). [arXiv]
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. Bioinformatics 33 (15), 2314–2321 (2017). [OpenAccess]