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Miyawaki A, Llopis J, Heim R, McCaffery JM, Adams JA, Ikura M, Tsien RY. (1997) Fluorescent indicators for Ca2+ based on green fluorescent proteins and calmodulin. Nature 388: 882-887.

Miyawaki A, Griesbeck O, Heim R, Tsien RY. (1999) Dynamic and quantitative Ca2+ measurements using improved cameleons. Proc. Natl. Acad. Sci. U S A. 96: 2135 – 2140.

Nagai T, Yamada S, Tominaga T, Ichikawa M, Miyawaki A. (2004) Expanded dynamic range of fluorescent indicators for Ca2+ by circularly permuted yellow fluorescent proteins. Proc. Natl. Acad. Sci. U S A. 101:10554 – 10559.

Mizuno H, Sassa T, Higashijima S, Okamoto H, Miyawaki A. (2013) Transgenic zebrafish for ratiometric imaging of cytosolic and mitochondrial Ca(2+) response in teleost embryo. Cell Calcium, 54 (3): 236-245.

Madisen L, Garner AR, Shimaoka D, Chuong AS, Klapoetke NC, Li L, van der Bourg A, Niino Y, Egolf L, Monetti C, Gu H, Mills M, Cheng A, Tasic B, Nguyen TN, Sunkin SM, Benucci A, Nagy A, Miyawaki A, Helmchen F, Empson RM, Knopfel T, Boyden ES, Reid RC, Carandini M, Zeng H (2015) Transgenic mice for intersectional targeting of neural sensors and effectors with high specificity and performance. Neuron, 85 (5), 942-958.

Nagai T, Sawano A, Park ES, Miyawaki A. (2001) Circularly permuted green fluorescent proteins engineered to sense Ca2+. Proc. Natl. Acad. Sci. U S A. 98: 3197 – 3202.

Miyawaki A. (2006) Ratiometric Pericam. Cell Biology 317-324.

Iwano S, Sugiyama M, Hama H, Watakabe A, Hasegawa N, Kuchimaru T, Tanaka KZ, Takahashi M, Ishida Y, Hata J, Shimozono S, Namiki K, Fukano T, Kiyama M, Okano H, Kizaka-Kondoh S, McHugh TJ, Yamamori T, Hioki H, Maki S, Miyawaki A. (2018) Single-cell bioluminescence imaging of deep tissue in freely moving animals. Scinece, 359 (6378): 935-939.

Watanabe T, Seki T, Fukano T, Sakaue-Sawano A, Karasawa S, Kubota M, Kurokawa H, Inoue K, Akatsuka J, Miyawaki A. (2017) Genetic visualization of protein interactions harnessing liquid phase transitions. Sci. Rep., 7: 46380.

Kumagai A, Ando R, Miyatake H, Greimel P, Kobayashi T, Hirabayashi Y, Shimogori T, Miyawaki A. (2013) A Bilirubin-Inducible Fluorescent Protein from Eel Muscle. Cell 153 (7): 1602-1611.

Shitashima Y, Shimozawa T, Asahi T, Miyawaki A. (2018) A dual-ligand-modulable fluorescent protein based on UnaG and calmodulin. Biochem Biophys Res Commun., 496 (3): 872-879.

Shimozono S, Iimura T, Kitaguchi T, Higashijima S, Miyawaki A. (2013) Visualization of an endogenous retinoic acid gradient across embryonic development, Nature 496: 363-366.

Hama H, Kurokawa H, Kawano H, Ando R, Shimogori T, Noda H, Fukami K, Sakaue-Sawano A, Miyawaki A. (2011) Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain, Nature Neuroscience 14 (11): 1481-1488.

Hama H, Hioki H, Namiki K, Hoshida T, Kurokawa H, Ishidate F, Kaneko T, Akagi T, Saito T, Saido T, Miyawaki A. (2015) ScaleS: an optical clearing palette for biological imaging. Nat. Neuroscience 18 (10): 1518-1529.

Hama H, Hioki H, Namiki K, Hoshida T, Kurokawa H, Ishidate F, Kaneko T, Akagi T, Saito T, Saido T, Miyawaki A. (2016) Deep Imaging of Cleared Brain by Confocal Laser-Scanning Microscopy. Protocol Exchange, doi:10.1038/protex.2016.019.

Sakaue-Sawano A, Kurokawa H, Morimura T, Hanyu A, Hama H, Osawa H, Kashiwagi S, Fukami K, Miyata T, Miyoshi H, Imamura T, Ogawa M, Masai H, Miyawaki A. (2008) Visualizing Spatiotemporal Dynamics of Multicellular Cell Cycle Progression. Cell, 132 (3): 487-498.

Sakaue-Sawano A, Ohtawa K, Hama H, Kawano M, Ogawa M, Miyawaki A. (2008) Tracing the Silhouette of Individual Cells in S/G2/M Phases with Fluorescence. Chemistry & Biology 15: 1243-1248.

Sugiyama M, Sakaue-Sawano A, Iimura T, Fukami K, Kitaguchi T, Kawakami K, Okamoto H, Higashijima S, Miyawaki A. (2009) Illuminating cell-cycle progression in the developing zebrafish embryo. Proc. Natl. Acad. Sci. USA. 106 (49), 20812 – 20817.

Aiba Y, Kometani K, Hamadate M, Moriyama S, Sakaue-Sawano A, Tomura M, Luche H, Fehling HJ, Casellas R, Kanagawa O, Miyawaki A, Kurosaki T. (2010) Preferential localization of IgG memory B cells adjacent to contracted germinal centers. Proc Natl Acad Sci U S A. 107 (27): 12192 – 12197.

Ogura Y, Sakaue-Sawano A, Nakagawa M, Satoh N, Miyawaki A, Sasakura Y. (2011) Coordination of mitosis and morphogenesis: role of a prolonged G2 phase during chordate neurulation. Development 138 (3): 577-587.

Sakaue-Sawano A, Kobayashi T, Ohtawa K, Miyawaki A. (2011) Drug-induced cell cycle modulation leading to cell-cycle arrest, nuclear mis-segregation, or endoreplication. BMC Cell Biology 12:2.

Nakajima YI, Kuranaga E, Sugimura K, Miyawaki A, Miura M. (2011) Non-autonomous Apoptosis is Triggered by Local Cell Cycle Progression during Epithelial Replacement in Drosophila. Mol Cell Biol. 31 (12): 2499 – 2512.

Dan S, Okamura M, Mukai Y, Yoshimi H, Inoue Y, Hanyu A, Sakaue-Sawano A, Imamura T, Miyawaki A, Yamori T. (2011)ZSTK474, a specific phosphatidylinositol 3-kinase inhibitor, induces G1 arrest of the cell cycle in vivo. Eur. J. Cancer 48: 936-943.

Abe T, Sakaue-Sawano A, Kiyonari H, Shioi G, Inoue K, Horiuchi T, Nakao K, Miyawaki A, Aizawa S, Fujimori T. (2012) Visualization of cell cycle in mouse embryos with Fucci2 reporter directed by Rosa26 promoter. Development 140 (1): 237-246.

Nishimura K, Oki T, Kitaura J, Kuninaka S, Saya H, Sakaue-Sawano A, Miyawaki A, Kitamura T. (2013) Targets MgcRacGAP for Destruction in the Late M Phase. PLoS One 8 (5): e63001.

Tomura M, Sakaue-Sawano A, Mori Y, Takase-Utsugi M, Hata A, Ohtawa K, Kanagawa O, Miyawaki A. (2013) Contrasting Quiescent G0 Phase with Mitotic Cell Cycling in the Mouse Immune System. PLoS ONE 8(9): e73801.

Yo M, Sakaue-Sawano A, Noda S, Miyawaki A, Miyoshi H. (2015) Fucci-guided purification of hematopoietic stem cells with high repopulating activity. Biochem. Biophys. Res. Commun., 457 (1): 7-11.

Sakaue-Sawano A, Yo M, Komatsu N, Hiratsuka T, Kogure T, Hoshida T, Goshima N, Matsuda M, Miyoshi H, Miyawaki A.(2017) Genetically Encoded Tools for Optical Dissection of the Mammalian Cell Cycle. Mol. Cell, 68(3), 626–640.

Kogure T, Karasawa S, Araki T, Saito K, Kinjo M, Miyawaki A. (2006) A fluorescent variant of a protein from the stony coral Montipora facilitates dual-color single-laser fluorescence cross-correlation spectroscopy Nature Biotechnology 24: 577-581.

Kawano H, Kogure T, Abe Y, Mizuno H, Miyawaki A. (2008) Two-photon dual-color imaging using fluorescent proteins. Nat. Methods 5(5): 373-374.

Kogure T, Kawano H, Abe Y, Miyawaki A. (2008) Fluorescence imaging using a fluorescent protein with a large Stokes shift. Methods 45: 223-226.

Katayama H, Kogure T, Mizushima N, Yoshimori T, Miyawaki A. (2011) A Sensitive and Quantitative Technique for Detecting Autophagic Events Based on Lysosomal Delivery. Chemistry & Biology, 18 (8): 1042-1052.

Ando R, Mizuno H, Miyawaki A. (2004) Regulated fast nucleocytoplasmic shuttling observed by reversible protein highlighting. Science 306: 1370-1373.

Ando R, Flors C, Mizuno H, Hofkens J, Miyawaki A, (2007) Highlighted generation of fluorescence signals using simultaneous two-color irradiation on Dronpa mutants, Biophysical J., 92: L97-99.

Mizuno H., Abe M., Dedecker P., Makino A., Rocha S., Ohno-Iwashita Y., Hofkens J., Kobayashi T., Miyawaki A. (2011) Fluorescent probes for superresolution imaging of lipid domains on the plasma membrane. Chem. Sci., 2: 1548–1553.

Ando R, Hama H, Yamamoto-Hino M, Mizuno H, Miyawaki A. (2002) An optical marker based on the UV-induced green-to-red photoconversion of a fluorescent protein. Proc. Natl. Acad. Sci. U S A. 99: 12651 – 12656.

Mizuno H, Mal TK, Tong KI, Ando R, Furuta T, Ikura M, Miyawaki A. (2003) Photoinduced peptide cleavage in the green-to-red conversion of a fluorescent protein. Mol. Cell 12: 1051-1058.

Tsutsui H, Jinno Y, Shoda K,Tomita A, Matsuda M,Yamashita E, Katayama H ,Nakagawa A,Miyawaki A. (2015) A Diffraction-Quality Protein Crystal Processed as an Autophagic Cargo, Mol. Cell 58 (1), 186-193.

Tsutsui H, Karasawa S, Shimizu H, Nukina N, Miyawaki A. (2005) Semi-rational engineering of a coral fluorescent protein into an efficient highlighter. EMBO Rep. 6:233-238.

Habuchi S, Tsutsui H, Kochaniak AB, Miyawaki A, van Oijen AM. (2008) mKikGR, a Monomeric Photoswitchable Fluorescent Protein. PloS ONE 3(12):e3944.

Tsutsui H, Shimizu H, Mizuno H, Nukina N, Furuta T, Miyawaki A. (2009) The E1 mechanism in photo-induced β-elimination reactions for green-to red conversion of fluorescent proteins. Chemistry & Biology 16(11):1140-1147.

Karasawa S, Araki T, Yamamoto-Hino M, Miyawaki A. (2003) A green-emitting fluorescent protein from Galaxeidae coral and its monomeric version for use in fluorescent labeling. J. Biol. Chem. 278: 34167 – 34171.

Tsutsui H, Karasawa S, Okamura Y, Miyawaki A. (2008) Improving membrane voltage measurements using FRET with new fluorescent proteins. Nat. Methods 5: 683-685.

Tsutsui H, Higashijima SI, Miyawaki A, Okamura Y. (2010) Visualizing Voltage Dynamics in Zebrafish Heart. J. Physiol. 588 (Pt 12): 2017-2021.

Tsutsui H, Jinno Y, Tomita A, Niino Y, Yamada Y, Mikoshiba K, Miyawaki A, Okamura Y. (2013) Improved detection of electrical activity with a voltage probe based on a voltage-sensing phosphatase. J. Physiol. 591 (Pt 18): 4427 – 4437.

Karasawa S, Araki T, Nagai T, Mizuno H, Miyawaki A. (2004) Cyan-emitting and orange-emitting fluorescent proteins as a donor/acceptor pair for fluorescence resonance energy transfer. Biochem. J. 381:307-312.

Shimozono S, Miyawaki A. (2008) Engineering FRET Constructs Using CFP and YFP. Methods Cell Biol. 85C: 381-393.

Katayama H, Yamamoto A, Yoshimori T, Mizushima N, Miyawaki A. (2008) GFP-like proteins stably accumulation in lysosomes. Cell Struct. Funct. 33: 1-12.

Kitaguchi T, Oya M, Wada Y, Tsuboi T, Miyawaki A. (2013) Extracellular Calcium influx activates Adenylate Cyclase 1 and potentiates Insulin secretion in MIN6 cells.Biochem. J., 450 (2): 365-373.

Shimozono S, Fukano T, Kimura KD, Mori I, Kirino Y, Miyawaki A. (2004) Slow Ca2+ dynamics in pharyngeal muscles in Caenorhabditis elegans during fast pumping.EMBO Rep. 5: 521-526.

Nagai T, Miyawaki A. (2004) A high-throughput method for development of FRET-based indicators for proteolysis. Biochem. Biophys. Res. Commun. 319: 72-77.

Shimozono S; Hosoi H; Mizuno H; Fukano T; Tahara T; Miyawaki A. (2006)Concatenation of Cyan and Yellow Fluorescent Proteins for Efficient Resonance Energy Transfer. Biochemistry 45: 6267 – 6271.

Hama H, Kurokawa H, Kawano H, Ando R, Shimogori T, Noda H, Fukami K, Sakaue-Sawano A, Miyawaki A. (2011) Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain. Nat. Neurosci., 14 (11): 1481-1488.

Kurokawa H, Noda H, Sugiyama M, Sakaue-Sawano A, Fukami K, Miyawaki A. (2012) Software for precise tracking of cell proliferation. Biochem. Biophys. Res. Commun., 417 (3): 1080-1085.

Katayama H., Hama H., Nagasawa K., Kurokawa H., Sugiyama M., Ando R., Funata M., Yoshida N., Homma M., Nishimura T., Takahashi M., Ishida Y., Hioki H., Tsujihata Y., Miyawaki A. (2020) Visualizing and modulating mitophagy for therapeutic studies of neurodegeneration. Cell, 181 (5): 1176-1187.e16.

Yoshioka-Kobayashi K., Matsumiya M., Niino Y., Isomura A., Kori H., Miyawaki A., Kageyama R. (2019) Dynamic control of coupling delay for synchronized oscillations in the segmentation clock. Nature, 538 (7801): 119-123.

Ando R., Sakaue-Sawano A., Shoda K., Miyawaki A. (2020) Two new coral fluorescent proteins of distinct colors for sharp visualization of cell-cycle progression. bioRxiv, 015156.

Ando R., Sakaue-Sawano A., Shoda K., Miyawaki A. (2020) Two new coral fluorescent proteins of distinct colors for sharp visualization of cell-cycle progression. bioRxiv, 015156.