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Publications

  • Song, X., Adachi, T., Kawase, Y., Kimura, T., & Saito, N. (2021). Efficacy of the Wolverine cutting balloon on a simulated calcified coronary lesion: Bench test using a three-dimensional printer and computer simulation with the finite element method. Cardiovasc Interv Ther. Doi: 10.1007 / s12928-020-00739-2

  • Onda, M., Takeuchi, RF, Isobe, K., Suzuki, T., Masaki, Y., Morimoto, N., & Osakada, F. (2021). Temporally multiplexed dual-plane imaging of neural activity with four- dimensional precision. Neurosci Res. doi: 10.1016 / j.neures.2021.02.001

  • Nakao, N., Mori, I., Sunaga, J., & Adachi, T. (2021). Large magnitude of force leads to NO-mediated cell shrinkage in single osteocytes implying an initial apoptotic response. J Biomech, 117, 110245 . doi: 10.1016 / j.jbiomech.2021.110245

  • Kim, J., Ishikawa, K., Sunaga, J., & Adachi, T. (2021). Uniaxially fixed mechanical boundary condition elicits cellular alignment in collagen matrix with induction of osteogenesis. Sci Rep, 11 (1), 9009. doi: 10.1038 / s41598-021-88505-z

  • Ishii, M., Tateya, T., Matsuda, M., & Hirashima, T. (2021). Retrograde ERK activation waves drive base-to-apex multicellular flow in murine cochlear duct morphogenesis. eLife.61092

  • Inoue, YU, Morimoto, Y., Yamada, M., Kaneko, R., Shimaoka, K., Oki, S., ... Inoue, T. (2021). An Optimized Preparation Method for Long ssDNA Donors to Facilitate Quick Knock-In Mouse Generation. Cells, 10 (5). Doi: 10.3390 / cells10051076.

  • Imanishi, A., Ichise, H., Fan, C., Nakagawa, Y., Kuwahara, K., Sumiyama, K., ... Terai, K. (2021). Visualization of Spatially-Controlled Vasospasm by Sympathetic Nerve -Mediated ROCK Activation. Am J Pathol, 191 (1), 194-203. doi: 10.1016 / j.ajpath.2020.09.012

  • Boocock, D., Hino, N., Ruzickova, N., Hirashima, T., & Hannezo, E. (2021). Theory of mechanochemical patterning and optimal migration in cell monolayers. Nature Physics, 17 (2), 267- +. Doi: 10.1038 / s41567-020-01037-7

  • Asakura, Y., Kondo, Y., Aoki, K., & Naoki, H. (2021). Hierarchical modeling of mechano-chemical dynamics of epithelial sheets across cells and tissue. Sci Rep, 11 (1), 4069. doi 10.1038 / s41598-021-83396-6

  • Ando, Y., Okeyo, KO, Sunaga, J., & Adachi, T. (2021). Edge-localized alteration in pluripotency state of mouse ES cells forming topography-confined layers on designed mesh cells. Stem Cell Res, 53, 102352. doi: 10.1016 / j.scr.2021.102352

  • Yoshida, T., Matsuda, M., & Hirashima, T. (2020). Incoherent Feedforward Regulation via Sox9 and ERK Underpins Mouse Tracheal Cartilage Development. Front Cell Dev Biol, 8, 585640. Doi: 10.3389 / fcell.2020.585640

  • Yamada, M., Nagasaki, SC, Suzuki, Y., Hirano, Y., & Imayoshi, I. (2020). Optimization of Light-Inducible Gal4 / UAS Gene Expression System in Mammalian Cells. IScience, 23 (9), 101506. doi: 10.1016 / j.isci.2020.101506

  • Yamada, M., Nagasaki, SC, Ozawa, T., & Imayoshi, I. (2020). Light-mediated control of Gene expression in mammalian cells. Neurosci Res, 152, 66-77. Doi: 10.1016 / j.neures .2019.12.018

  • Watada, M., Hayashi, Y., Watanabe, K., Mizutani, S., Mure, A., Hattori, Y., & Uemura, T. (2020). Divergence of Drosophila species: Longevity and reproduction under different nutrients balances. Genes Cells, 25 (9), 626-636. doi: 10.111 / gtc.12798

  • Watabe, T., Terai, K., Sumiyama, K., & Matsuda, M. (2020). Booster, a Red-Shifted Genetically Encoded Forster Resonance Energy Transfer (FRET) Biosensor Compatible with Cyan Fluorescent Protein / Yellow Fluorescent Protein- Based FRET Biosensors and Blue Light-Responsive Optogenetic Tools. ACS Sens, 5 (3), 719-730. doi: 10.101 / acssensors.9b01941

  • Ueda, Y., Kimura-Yoshida, C., Mochida, K., Tsume, M., Kameo, Y., Adachi, T., ... Matsuo, I. (2020). Intrauterine Pressures Adjusted by Reichert's Membrane Are Crucial for Early Mouse Morphogenesis. Cell Rep, 31 (7), 107637. doi: 10.1016 / j.celrep.2020.107637

  • Takeda, H., Kameo, Y., Inoue, Y., & Adachi, T. (2020). An energy landscape approach to understanding variety and robustness in tissue morphogenesis. Biomech Model Mechanobiol, 19 (2), 471-479. doi: 10.1007 / s10237-019-01222-5

  • Takeda, H., Kameo, Y., & Adachi, T. (2020). Continuum modeling for neuronal mixing during cerebral morphogenesis considering cell migration and tissue growth. Comput Methods Biomech Biomed Engin, 1-7. Doi: 10.1080 / 10255842.2020. 1852554

  • Suzuki, D., Otsubo, H., Adachi, T., Suzuki, T., Nagoya, S., Yamashita, T., & Shino, K. (2020). Functional Adaptation of the Fibrocartilage and Bony Trabeculae at the Attachment Sites of the Anterior Cruciate Ligament. Clin Anat, 33 (7), 988-996. Doi: 10.1002 / ca.23520

  • Shinkai, S., Nakagawa, M., Sugawara, T., Togashi, Y., Ochiai, H., Nakato, R., ... Onami, S. (2020). PHi-C: deciphering Hi-C data into polymer dynamics. NAR Genom Bioinform, 2 (2), lqaa020. doi: 10.1093 / nargab / lqaa020

  • Seymour, PA, Collin, CA, Egeskov-Madsen, AR, Jorgensen, MC, Shimojo, H., Imayoshi, I., ... Serup, P. (2020). Jag1 Modulates an Oscillatory Dll1-Notch-Hes1 Signaling Module to Coordinate Growth and Fate of Pancreatic Progenitors. Dev Cell, 52 (6), 731-747 e738. doi: 10.1016 / j.devcel.2020.01.015

  • Sato, S., Yamashita, T., & Matsuda, M. (2020). Rhodopsin-mediated light-off-induced protein kinase A activation in mouse rod photoreceptor cells. Proc Natl Acad Sci USA, 117 (43), 26996- 27003. doi: 10.1073 / pnas.2009164117

  • Sasaki, F., Hayashi, M., Mouri, Y., Nakamura, S., Adachi, T., & Nakashima, T. (2020). Mechanotransduction via the Piezo1-Akt pathway underlies Sost suppression in osteocytes. Biochem Biophys Res Commun, 521 (3), 806-813. doi: 10.1016 / j.bbrc. 2019.10.174

  • Okunomiya, T., Hioki, H., Nishimura, C., Yawata, S., Imayoshi, I., Kageyama, R., .. .Watanabe, D. (2020). Generation of a MOR-CreER knock-in mouse line to study cells and neural circuits involved in mu opioid receptor signaling. Genesis, 58 (1), e23341. doi: 10.1002 / dvg.23341

  • Nguyen, R., Venkatesan, S., Binko, M., Bang, JY, Cajanding, JD, Briggs, C., ... Kim, JC (2020). Cholecystokinin-Expressing Interneurons of the Medial Prefrontal Cortex Mediate Working Memory Retrieval. J Neurosci, 40 (11), 2314-2331. doi: 10.1523 / JNEUROSCI.1919-19.2020

  • Naoki, H., & Matsui, T. (2020). Somite boundary determination in normal and clock-less vertebrate embryos. Dev Growth Differ, 62 (3), 177-187. doi: 10.111 / dgd.12655
    Matsuda, M., & Terai, K. (2020). Experimental pathology by intravital microscopy and genetically encoded fluorescent biosensors. Pathol Int, 70 (7), 379-390. doi: 10.111 / pin.12925

  • Kumar, V., Leclerc, S., & Taniguchi, Y. (2020). BHi-Cect: a top-down algorithm for identifying the multi-scale hierarchical structure of chromosomes. Nucleic Acids Res, 48 (5), e26. doi: 10.1093 / nar / gkaa004

  • Konagaya, Y., Takakura, K., Sogabe, M., Bisaria, A., Liu, C., Meyer, T., ... Terai, K. (2020). Intravital imaging reveals cell cycle-dependent myogenic cell migration during muscle regeneration. Cell Cycle, 19 (22), 3167-3181. doi: 10.1080 / 15384101.2020.1838779

  • Kobachi, K., Kuno, S., Sato, S., Sumiyama, K., Matsuda, M., & Terai, K. (2020). Biliverdin Reductase-A Deficiency Brighten and Sensitize Biliverdin-binding Chromoproteins. Cell Struct Funct , 45 (2), 131-141. doi: 10.1247 / csf.20010

  • Kinjo, T., Watabe, T., Kobachi, K., Terai, K., & Matsuda, M. (2020). Single-Cell Activation of the cAMP-Signaling Pathway in 3D Tissues with FRET-Assisted Two-Photon Activation of bPAC. ACS Chem Biol, 15 (11), 2848-2853. doi: 10.1021 / acschembio.0c00333

  • Kim, J., & Adachi, T. (2020). Modulation of Sost Gene Expression Under Hypoxia in Three-Dimensional Scaffold-Free Osteocytic Tissue. Tissue Eng Part A. doi: 10.1089 / ten.TEA.2020.0228

  • Kanda, E., Epureanu, BI, Adachi, T., Tsuruta, Y., Kikuchi, K., Kashihara, N., .. .Nitta, K. (2020). Application of explainable ensemble artificial intelligence model to categorization of hemodialysis-patient and treatment using nationwide-real-world data in Japan. PLoS One, 15 (5), e0233491. doi: 10.1371 / journal.pone.0233491

  • Kameo, Y., Sakano, N., & Adachi, T. (2020). Theoretical concept of cortical to cancellous bone transformation. Bone Rep, 12, 100260. Doi: 10.1016 / j.bonr.2020.100260

  • Kameo, Y., Miya, Y., Hayashi, M., Nakashima, T., & Adachi, T. (2020). In silico experiments of bone remodeling explore metabolic diseases and their drug treatment. Sci Adv, 6 (10) , eaax0938. doi: 10.1126 / sciadv.aax0938

  • Inoue, Y., Tateo, I., & Adachi, T. (2020). Epithelial tissue folding pattern in confined geometry. Biomech Model Mechanobiol, 19 (3), 815-822. doi: 10.1007 / s10237-019-01249- 8

  • Imayoshi, I., Tabuchi, S., Matsumoto, M., Kitano, S., Miyachi, H., Kageyama, R., & Yamanaka, A. (2020). Light-induced silencing of neural activity in Rosa26 knock- in and BAC transgenic mice conditionally expressing the microbial halorhodopsin eNpHR3. Sci Rep, 10 (1), 3191. doi: 10.1038 / s41598-020-59984-3

  • Hino, N., Rossetti, L., Marin-Llaurado, A., Aoki, K., Trepat, X., Matsuda, M., & Hirashima, T. (2020). ERK-Mediated Mechanochemical Waves Direct Collective Cell Polarization . Dev Cell, 53 (6), 646-660 e648. doi: 10.1016 / j.devcel.2020.05.011

  • Watanabe, K., Kanaoka, Y., Mizutani, S., Uchiyama, H., Yajima, S., Watada, M., .. .. Hattori, Y. (2019). Interspecies Comparative Analyses Reveal Distinct Carbohydrate-Responsive Systems among Drosophila Species. Cell Rep, 28 (10), 2594-2607 e2597. Doi: 10.1016 / j.celrep. 2019.08.030

  • Terai, K., Imanishi, A., Li, C., & Matsuda, M. (2019). Two Decades of Genetically Encoded Biosensors Based on Forster Resonance Energy Transfer. Cell Struct Funct, 44 (2), 153-169. doi: 10.1247 / csf.18035

  • Tateya, T., Sakamoto, S., Ishidate, F., Hirashima, T., Imayoshi, I., & Kageyama, R. (2019). Three-dimensional live imaging of Atoh1 reveals the dynamics of hair cell induction and organization in the developing cochlea. Development, 146 (21). doi: 10.1242 / dev.177881

  • Sueda, R., Imayoshi, I., Harima, Y., & Kageyama, R. (2019). High Hes1 expression and resultant Ascl1 suppression regulate quiescent vs. active neural stem cells in the adult mouse brain. Genes Dev, 33 ( 9-10), 511-523. doi: 10.1101 / gad.323196.118

  • Ohno, M., Ando, T., Priest, DG, Kumar, V., Yoshida, Y., & Taniguchi, Y. (2019). Sub-nucleosomal Genome Structure Reveals Distinct Nucleosome Folding Motifs. Cell, 176 (3) , 520-534 e525. doi: 10.1016 / j.cell.2018.12.014

  • Naoki, H., Akiyama, R., Sari, DWK, Ishii, S., Bessho, Y., & Matsui, T. (2019). Noise-resistant developmental reproducibility in vertebrate somite formation. PLoS Comput Biol, 15 (2) ), e1006579. doi: 10.1371 / journal.pcbi.1006579

  • Nakao, N., Maki, K., Mofrad, MRK, & Adachi, T. (2019). Talin is required to increase stiffness of focal molecular complex in its early formation process. Biochem Biophys Res Commun, 518 (3), 579 -583. doi: 10.1016 / j.bbrc.2019.08.091

  • Matsuda, A., Li, J., Brumm, P., Adachi, T., Inoue, Y., & Kim, T. (2019). Mobility of Molecular Motors Regulates Contractile Behaviors of Actin Networks. Biophys J, 116 ( 11), 2161-2171. doi: 10.1016 / j.bpj.2019.04.018
    Leclerc, S., Arntz, Y., & Taniguchi, Y. (2019). Proteome-wide Quantification of Labeling Homogeneity at the Single Molecule Level. J Vis Exp (146). Doi: 10.3791/59199

  • Komatsubara, AT, Goto, Y., Kondo, Y., Matsuda, M., & Aoki, K. (2019). Single-cell quantification of the concentrations and dissociation constants of endogenous proteins. J Biol Chem, 294 (15) , 6062-6072. doi: 10.1074 / jbc.RA119.007685

  • Kobayashi, T., Piao, W., Takamura, T., Kori, H., Miyachi, H., Kitano, S., ... Kageyama, R. (2019). Enhanced lysosomal degradation maintains the quiescent state of neural stem cells. Nat Commun, 10 (1), 5446. doi: 10.1038 / s41467-019-13203-4

  • Kinjo, T., Terai, K., Horita, S., Nomura, N., Sumiyama, K., Togashi, K., .. Matsuda, M. (2019). FRET-assisted photoactivation of flavoproteins for in vivo two-photon optogenetics. Nat Methods, 16 (10), 1029-1036. doi: 10.1038 / s41592-019-0541-5

  • Kim, J., & Adachi, T. (2019). Cell Condensation Triggers the Differentiation of Osteoblast Precursor Cells to Osteocyte-Like Cells. Front Bioeng Biotechnol, 7, 288. Doi: 10.3389 / fbioe.2019.00288

  • Kawai, S., Yoshitomi, H., Sunaga, J., Alev, C., Nagata, S., Nishio, M., ... Toguchida, J. (2019). In vitro bone-like nodules generated from patient -derived iPSCs recapitulate pathological bone phenotypes. Nat Biomed Eng, 3 (7), 558-570. doi: 10.1038 / s41551-019-0410-7

  • Kanaoka, Y., Skibbe, H., Hayashi, Y., Uemura, T., & Hattori, Y. (2019). DeTerm: Software for automatic detection of neuronal dendritic branch terminals via an artificial neural network. Genes Cells, 24 (7), 464-472. doi: 10.111 / gtc.12700

  • Inoue, M., Ono, T., Kameo, Y., Sasaki, F., Ono, T., Adachi, T., & Nakashima, T. (2019). Forceful mastication activates osteocytes and builds a stout jawbone. Sci Rep, 9 (1), 4404. Doi: 10.1038 / s41598-019-40463-3

  • Hirashima, T., & Adachi, T. (2019). Polarized cellular mechano-response system for maintaining radial size in developing epithelial tubes. Development, 146 (23). Doi: 10.1242 / dev.181206

  • Chowdhury, S., Hung, CJ, Izawa, S., Inutsuka, A., Kawamura, M., Kawashima, T., ... Yamanaka, A. (2019). Dissociating orexin-dependent and -independent functions of orexin neurons using novel Orexin-Flp knock-in mice. Elife, 8. doi: 10.7545 / eLife.44927

  • Ando, Y., Okeyo, KO, & Adachi, T. (2019). Modulation of adhesion microenvironment using mesh constituting triggers self-organization and primordial germ cell-like differentiation in mouse ES cells. APL Bioeng, 3 (1), 016102 . doi: 10.1063 / 1.5072761

  • Yamaguchi, S., Naoki, H., Ikeda, M., Tsukada, Y., Nakano, S., Mori, I., & Ishii, S. (2018). Identification of animal behavioral strategies by inverse reinforcement learning. PLoS Comput Biol, 14 (5), e1006122. doi: 10.1371 / journal.pcbi.1006122

  • Yamaguchi, S., Naoki, H., Ikeda, M., Tsukada, Y., Nakano, S., Mori, I., & Ishii, S. (2018). Identification of animal behavioral strategies by inverse reinforcement learning. PLoS Comput Biol, 14 (5), e1006122. doi: 10.1371 / journal.pcbi.1006122

  • Yamada, M., Suzuki, Y., Nagasaki, SC, Okuno, H., & Imayoshi, I. (2018). Light Control of the Tet Gene Expression System in Mammalian Cells. Cell Rep, 25 (2), 487- 500 e486. doi: 10.1016 / j.celrep.2018.09.026

  • Toda, K., Isobe, K., Namiki, K., Kawano, H., Miyawaki, A., & Midorikawa, K. (2018). Interferometric temporal focusing microscopy using three-photon excitation fluorescence. Biomed Opt Express, 9 (4), 1510-1519. doi: 10.1364 / BOE.9.001510

  • Sari, DWK, Akiyama, R., Naoki, H., Ishijima, H., Bessho, Y., & Matsui, T. (2018). Time-lapse observation of stepwise regression of Erk activity in zebrafish presomitic mesoderm. Sci Rep , 8 (1), 4335. doi: 10.1038 / s41598-018-22619-9

  • Perron, A., Nishikawa, Y., Iwata, J., Shimojo, H., Takaya, J., Kobayashi, K., ... Uesugi, M. (2018). Small-molecule screening yields a compound that inhibits the cancer-associated transcription factor Hes1 via the PHB2 chaperone. J Biol Chem, 293 (21), 8285-8294. doi: 10.1074 / jbc.RA118.002316

  • Okuda, S., Miura, T., Inoue, Y., Adachi, T., & Eiraku, M. (2018). Combining Turing and 3D vertex models reproduces autonomous multicellular morphogenesis with undulation, tubulation, and branching. Sci Rep, 8 (1), 2386. doi: 10.1038 / s41598-018-20678-6

  • Ohno, M., Priest, DG, & Taniguchi, Y. (2018). Nucleosome-level 3D organization of the genome. Biochem Soc Trans, 46 (3), 491-501. doi: 10.1042 / BST20170388.

  • Muta, Y., Fujita, Y., Sumiyama, K., Sakurai, A., Taketo, MM, Chiba, T., ... Imajo, M. (2018). Composite regulation of ERK activity dynamics underlying tumour-specific traits in the intestine. Nat Commun, 9 (1), 2174. doi: 10.1038 / s41467-018-04527-8

  • Matsumiya, M., Tomita, T., Yoshioka-Kobayashi, K., Isomura, A., & Kageyama, R. (2018). ES cell-derived presomitic mesoderm-like tissues for analysis of synchronized oscillations in the segmentation clock. Development, 145 (4). Doi: 10.1242 / dev.156836

  • Maryu, G., Miura, H., Uda, Y., Komatsubara, AT, Matsuda, M., & Aoki, K. (2018). Live-cell Imaging with Genetically Encoded Protein Kinase Activity Reporters. Cell Struct Funct, 43 (1), 61-74. doi: 10.1247 / csf.18003

  • Marcotti, S., Maki, K., Reilly, GC, Lacroix, D., & Adachi, T. (2018). Hyaluronic acid selective anchoring to the cytoskeleton: An atomic force microscopy study. PLoS One, 13 (10), e0206056. doi: 10.1371 / journal.pone.0206056

  • Maki, K., Han, SW, Hirano, Y., Yonemura, S., Hakoshima, T., & Adachi, T. (2018). Real-time TIRF observation of vinculin recruitment to stretched alpha-catenin by AFM. Sci Rep, 8 (1), 1575. doi: 10.1038 / s41598-018-20115-8

  • Li, WL, Chu, MW, Wu, A., Suzuki, Y., Imayoshi, I., & Komiyama, T. (2018). Adult-born neurons facilitate olfactory bulb pattern separation during task engagement. Elife, 7. doi 10.7554 / eLife.33006

  • Leclerc, S., Arntz, Y., & Taniguchi, Y. (2018). Extending Single Molecule Imaging to Proteome Analysis by Quantitation of Fluorescent Labeling Homogeneity in Complex Protein Samples. Bioconjug Chem, 29 (8), 2541-2549. Doi 10.1021 / acs.bioconjchem.8b00226

  • Komatsu, N., Terai, K., Imanishi, A., Kamioka, Y., Sumiyama, K., Jin, T., .. .. Matsuda, M. (2018). A platform of BRET-FRET hybrid biosensors for optogenetics, chemical screening, and in vivo imaging. Sci Rep, 8 (1), 8984. doi: 10.1038 / s41598-018-27174-x

  • Kikuchi, K., Nakamura, A., Arata, M., Shi, D., Nakagawa, M., Tanaka, T., ... Nakanishi, H. (2018). Map7 / 7D1 and Dvl form a feedback loop that facilitates microtubule remodeling and Wnt5a signaling. EMBO Rep, 19 (7). Doi: 10.15252 / embr.201745471

  • Kaneko, R., Taketsuru, Y., Morita, A., Amano, I., Haijima, A., Imayoshi, I., ... Yanagawa, Y. (2018). Inhibitory neuron-specific Cre-dependent red fluorescent labeling using VGAT BAC-based transgenic mouse lines with identified transgene integration sites. J Comp Neurol, 526 (3), 373-396. doi: 10.1002 / cne.24343

  • Isomura, A., & Kageyama, R. (2018). An Optogenetic Method to Control and Analyze Gene Expression Patterns in Cell-to-cell Interactions. J Vis Exp (133). Doi: 10.3791/57149

  • Imanishi, A., Murata, T., Sato, M., Hotta, K., Imayoshi, I., Matsuda, M., & Terai, K. (2018). A Novel Morphological Marker for the Analysis of Molecular Activities at the Single-cell Level. Cell Struct Funct, 43 (2), 129-140. doi: 10.1247 / csf.18013
     

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