SSBD:database

As Nov 20, 2019 there are 687 BDML files which include 808,372,696 entries, and 4,162 image sets which include 8,745,381 slices of images.

• Bao Z, Murray JI, Boyle T, Ooi SL, Sandel MJ, and Waterston RH, (2006) Automated cell lineage tracing in Caenorhabditis elegans., Proceedings of the National Academy of Sciences of the United States of America, Volume 103, Issue 8, pages 2707-12. [PubMed]
• Kyoda K, Adachi E, Masuda E, Nagai Y, Suzuki Y, Oguro T, Urai M, Arai R, Furukawa M, Shimada K, Kuramochi J, Nagai E, and Onami S, (2013) WDDD: Worm Developmental Dynamics Database., Nucleic acids research, Volume 41, Issue Database issue, pages D732-7. [PubMed]
• Cronin CJ, Mendel JE, Mukhtar S, Kim YM, Stirbl RC, Bruck J, and Sternberg PW, (2005) An automated system for measuring parameters of nematode sinusoidal movement., BMC genetics, Volume 6, pages 5. [PubMed]
• Toyoshima Y, Tokunaga T, Hirose O, Kanamori M, Teramoto T, Jang MS, Kuge S, Ishihara T, Yoshida R, and Iino Y, (2016) Accurate Automatic Detection of Densely Distributed Cell Nuclei in 3D Space., PLoS computational biology, Volume 12, Issue 6, pages e1004970. [PubMed]
• Takayama J and Onami S (2016) The Sperm TRP-3 Channel Mediates the Onset of a Ca(2+) Wave in the Fertilized C. elegans Oocyte., Cell reports, Volume 15, Issue 3, pages 625-637. [PubMed]
• Azuma Y and Onami S (2017) Biologically constrained optimization based cell membrane segmentation in C. elegans embryos., BMC bioinformatics, Volume 18, Issue 1, pages 307. [PubMed]
• Arata Y, Hiroshima M, Pack CG, Ramanujam R, Motegi F, Nakazato K, Shindo Y, Wiseman PW, Sawa H, Kobayashi TJ, Brandão HB, Shibata T, and Sako Y, (2016) Cortical Polarity of the RING Protein PAR-2 Is Maintained by Exchange Rate Kinetics at the Cortical-Cytoplasmic Boundary., Cell reports, Volume 16, Issue 8, pages 2156-2168. [PubMed]
• Ono M, Oshima M, Ogawa M, Sonoyama W, Hara ES, Oida Y, Shinkawa S, Nakajima R, Mine A, Hayano S, Fukumoto S, Kasugai S, Yamaguchi A, Tsuji T, and Kuboki T, (2017) Practical whole-tooth restoration utilizing autologous bioengineered tooth germ transplantation in a postnatal canine model., Scientific reports, Volume 7, pages 44522. [PubMed]
• Inoue S and Kondo S (2016) Suture pattern formation in ammonites and the unknown rear mantle structure., Scientific reports, Volume 6, pages 33689. [PubMed]
• Komatsuzaki A, Ohyanagi T, Tsukasaki Y, Miyanaga Y, Ueda M, and Jin T, (2015) Compact halo-ligand-conjugated quantum dots for multicolored single-molecule imaging of overcrowding GPCR proteins on cell membranes., Small (Weinheim an der Bergstrasse, Germany), Volume 11, Issue 12, pages 1396-401. [PubMed]
• Yasui M, Matsuoka S, and Ueda M, (2014) PTEN hopping on the cell membrane is regulated via a positively-charged C2 domain., PLoS computational biology, Volume 10, Issue 9, pages e1003817. [PubMed]
• Shibata T, Nishikawa M, Matsuoka S, and Ueda M, (2012) Modeling the self-organized phosphatidylinositol lipid signaling system in chemotactic cells using quantitative image analysis., Journal of cell science, Volume 125, Issue Pt 21, pages 5138-50. [PubMed]
• Kamimura Y, Miyanaga Y, and Ueda M, (2016) Heterotrimeric G-protein shuttling via Gip1 extends the dynamic range of eukaryotic chemotaxis., Proceedings of the National Academy of Sciences of the United States of America, Volume 113, Issue 16, pages 4356-61. [PubMed]
• Watabe M, Arjunan SN, Fukushima S, Iwamoto K, Kozuka J, Matsuoka S, Shindo Y, Ueda M, and Takahashi K, (2015) A Computational Framework for Bioimaging Simulation., PloS one, Volume 10, Issue 7, pages e0130089. [PubMed]
• Keller PJ, Schmidt AD, Santella A, Khairy K, Bao Z, Wittbrodt J, and Stelzer EH, (2010) Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy., Nature methods, Volume 7, Issue 8, pages 637-42. [PubMed]
• Kondo T and Hayashi S (2013) Mitotic cell rounding accelerates epithelial invagination., Nature, Volume 494, Issue 7435, pages 125-9. [PubMed]
• Yasugi T, Yamada T, and Nishimura T, (2017) Adaptation to dietary conditions by trehalose metabolism in Drosophila., Scientific reports, Volume 7, Issue 1, pages 1619. [PubMed]
• Keller PJ, Schmidt AD, Wittbrodt J, and Stelzer EH, (2008) Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy., Science (New York, N.Y.), Volume 322, Issue 5904, pages 1065-9. [PubMed]
• Yamada T, Habara O, Kubo H, and Nishimura T, (2018) Fat body glycogen serves as a metabolic safeguard for the maintenance of sugar levels in <i>Drosophila</i>., Development (Cambridge, England), Volume 145, Issue 6, . [PubMed]
• Arjunan SN and Tomita M (2010) A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation., Systems and synthetic biology, Volume 4, Issue 1, pages 35-53. [PubMed]
• Takagi S, Mandai M, Miyamoto N, Nishida A, Hirami Y, Uyama H, Yamamoto M, Takahashi M, Tomita G, and Kurimoto Y, (2017) Incidence of outer retinal tubulation in eyes with choroidal neovascularization under intravitreal anti-vascular endothelial growth factor therapy in a Japanese population., Clinical ophthalmology (Auckland, N.Z.), Volume 11, pages 1219-1225. [PubMed]
• Iraha S, Tu HY, Yamasaki S, Kagawa T, Goto M, Takahashi R, Watanabe T, Sugita S, Yonemura S, Sunagawa GA, Matsuyama T, Fujii M, Kuwahara A, Kishino A, Koide N, Eiraku M, Tanihara H, Takahashi M, and Mandai M, (2018) Establishment of Immunodeficient Retinal Degeneration Model Mice and Functional Maturation of Human ESC-Derived Retinal Sheets after Transplantation., Stem cell reports, Volume 10, Issue 3, pages 1059-1074. [PubMed]
• Nojima S, Susaki EA, Yoshida K, Takemoto H, Tsujimura N, Iijima S, Takachi K, Nakahara Y, Tahara S, Ohshima K, Kurashige M, Hori Y, Wada N, Ikeda JI, Kumanogoh A, Morii E, and Ueda HR, (2017) CUBIC pathology: three-dimensional imaging for pathological diagnosis., Scientific reports, Volume 7, Issue 1, pages 9269. [PubMed]
• Shirai H, Mandai M, Matsushita K, Kuwahara A, Yonemura S, Nakano T, Assawachananont J, Kimura T, Saito K, Terasaki H, Eiraku M, Sasai Y, and Takahashi M, (2016) Transplantation of human embryonic stem cell-derived retinal tissue in two primate models of retinal degeneration., Proceedings of the National Academy of Sciences of the United States of America, Volume 113, Issue 1, pages E81-90. [PubMed]
• Kanemura H, Go MJ, Nishishita N, Sakai N, Kamao H, Sato Y, Takahashi M, and Kawamata S, (2013) Pigment epithelium-derived factor secreted from retinal pigment epithelium facilitates apoptotic cell death of iPSC., Scientific reports, Volume 3, pages 2334. [PubMed]
• Mandai M, Watanabe A, Kurimoto Y, Hirami Y, Morinaga C, Daimon T, Fujihara M, Akimaru H, Sakai N, Shibata Y, Terada M, Nomiya Y, Tanishima S, Nakamura M, Kamao H, Sugita S, Onishi A, Ito T, Fujita K, Kawamata S, Go MJ, Shinohara C, Hata KI, Sawada M, Yamamoto M, Ohta S, Ohara Y, Yoshida K, Kuwahara J, Kitano Y, Amano N, Umekage M, Kitaoka F, Tanaka A, Okada C, Takasu N, Ogawa S, Yamanaka S, and Takahashi M, (2017) Autologous Induced Stem-Cell-Derived Retinal Cells for Macular Degeneration., The New England journal of medicine, Volume 376, Issue 11, pages 1038-1046. [PubMed]
• Sakashita M, Sato M, and Kondo S, (2019) Comparative morphological examination of vertebral bodies of teleost fish using high-resolution micro-CT scans., Journal of morphology, Volume 280, Issue 6, pages 778-795. [PubMed]
• Sugita S, Makabe K, Fujii S, Iwasaki Y, Kamao H, Shiina T, Ogasawara K, and Takahashi M, (2017) Detection of Retinal Pigment Epithelium-Specific Antibody in iPSC-Derived Retinal Pigment Epithelium Transplantation Models., Stem cell reports, Volume 9, Issue 5, pages 1501-1515. [PubMed]
• Bashar MK, Komatsu K, Fujimori T, and Kobayashi TJ, (2012) Automatic extraction of nuclei centroids of mouse embryonic cells from fluorescence microscopy images., PloS one, Volume 7, Issue 5, pages e35550. [PubMed]
• Masumoto KH, Ukai-Tadenuma M, Kasukawa T, Nagano M, Uno KD, Tsujino K, Horikawa K, Shigeyoshi Y, and Ueda HR, (2010) Acute induction of Eya3 by late-night light stimulation triggers TSHβ expression in photoperiodism., Current biology : CB, Volume 20, Issue 24, pages 2199-206. [PubMed]
• Ochiai H, Sugawara T, and Yamamoto T, (2015) Simultaneous live imaging of the transcription and nuclear position of specific genes., Nucleic acids research, Volume 43, Issue 19, pages e127. [PubMed]
• Harima Y, Takashima Y, Ueda Y, Ohtsuka T, and Kageyama R, (2013) Accelerating the tempo of the segmentation clock by reducing the number of introns in the Hes7 gene., Cell reports, Volume 3, Issue 1, pages 1-7. [PubMed]
• Ke MT, Fujimoto S, and Imai T, (2013) SeeDB: a simple and morphology-preserving optical clearing agent for neuronal circuit reconstruction., Nature neuroscience, Volume 16, Issue 8, pages 1154-61. [PubMed]
• Sakakibara Y, Hashimoto S, Nakaoka Y, Kouznetsova A, Höög C, and Kitajima TS, (2015) Bivalent separation into univalents precedes age-related meiosis I errors in oocytes., Nature communications, Volume 6, pages 7550. [PubMed]
• Hirata Y, Oda A, Ohta K, and Aihara K, (2016) Three-dimensional reconstruction of single-cell chromosome structure using recurrence plots., Scientific reports, Volume 6, pages 34982. [PubMed]
• Noguchi M, Sumiyama K, and Morimoto M, (2015) Directed Migration of Pulmonary Neuroendocrine Cells toward Airway Branches Organizes the Stereotypic Location of Neuroepithelial Bodies., Cell reports, Volume 13, Issue 12, pages 2679-86. [PubMed]
• Susaki EA, Tainaka K, Perrin D, Kishino F, Tawara T, Watanabe TM, Yokoyama C, Onoe H, Eguchi M, Yamaguchi S, Abe T, Kiyonari H, Shimizu Y, Miyawaki A, Yokota H, and Ueda HR, (2014) Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis., Cell, Volume 157, Issue 3, pages 726-39. [PubMed]
• Susaki EA, Tainaka K, Perrin D, Yukinaga H, Kuno A, and Ueda HR, (2015) Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging., Nature protocols, Volume 10, Issue 11, pages 1709-27. [PubMed]
• Tainaka K, Kubota SI, Suyama TQ, Susaki EA, Perrin D, Ukai-Tadenuma M, Ukai H, and Ueda HR, (2014) Whole-body imaging with single-cell resolution by tissue decolorization., Cell, Volume 159, Issue 4, pages 911-24. [PubMed]
• Herawati E, Taniguchi D, Kanoh H, Tateishi K, Ishihara S, and Tsukita S, (2016) Multiciliated cell basal bodies align in stereotypical patterns coordinated by the apical cytoskeleton., The Journal of cell biology, Volume 214, Issue 5, pages 571-86. [PubMed]
• Iwata R, Kiyonari H, and Imai T, (2017) Mechanosensory-Based Phase Coding of Odor Identity in the Olfactory Bulb., Neuron, Volume 96, Issue 5, pages 1139-1152.e7. [PubMed]
• Sakaguchi R, Leiwe MN, and Imai T, (2018) Bright multicolor labeling of neuronal circuits with fluorescent proteins and chemical tags., eLife, Volume 7, . [PubMed]
• Minegishi K, Hashimoto M, Ajima R, Takaoka K, Shinohara K, Ikawa Y, Nishimura H, McMahon AP, Willert K, Okada Y, Sasaki H, Shi D, Fujimori T, Ohtsuka T, Igarashi Y, Yamaguchi TP, Shimono A, Shiratori H, and Hamada H, (2017) A Wnt5 Activity Asymmetry and Intercellular Signaling via PCP Proteins Polarize Node Cells for Left-Right Symmetry Breaking., Developmental cell, Volume 40, Issue 5, pages 439-452.e4. [PubMed]
• Ikeda T, Hikichi T, Miura H, Shibata H, Mitsunaga K, Yamada Y, Woltjen K, Miyamoto K, Hiratani I, Yamada Y, Hotta A, Yamamoto T, Okita K, and Masui S, (2018) Srf destabilizes cellular identity by suppressing cell-type-specific gene expression programs., Nature communications, Volume 9, Issue 1, pages 1387. [PubMed]
• Fumoto K, Takigawa-Imamura H, Sumiyama K, Kaneiwa T, and Kikuchi A, (2017) Modulation of apical constriction by Wnt signaling is required for lung epithelial shape transition., Development (Cambridge, England), Volume 144, Issue 1, pages 151-162. [PubMed]
• Kosodo Y, Suetsugu T, Kobayashi TJ, and Matsuzaki F, (2017) Systematic time-dependent visualization and quantitation of the neurogenic rate in brain organoids., Biochemical and biophysical research communications, Volume 483, Issue 1, pages 94-100. [PubMed]
• Higashi T, Tanaka S, Iida T, and Okabe S, (2018) Synapse Elimination Triggered by BMP4 Exocytosis and Presynaptic BMP Receptor Activation., Cell reports, Volume 22, Issue 4, pages 919-929. [PubMed]
• Cornelia Koeberle S, Tanaka S, Kuriu T, Iwasaki H, Koeberle A, Schulz A, Helbing DL, Yamagata Y, Morrison H, and Okabe S, (2017) Developmental stage-dependent regulation of spine formation by calcium-calmodulin-dependent protein kinase IIα and Rap1., Scientific reports, Volume 7, Issue 1, pages 13409. [PubMed]
• Isshiki M, Tanaka S, Kuriu T, Tabuchi K, Takumi T, and Okabe S, (2014) Enhanced synapse remodelling as a common phenotype in mouse models of autism., Nature communications, Volume 5, pages 4742. [PubMed]
• Morita R, Kihira M, Nakatsu Y, Nomoto Y, Ogawa M, Ohashi K, Mizuno K, Tachikawa T, Ishimoto Y, Morishita Y, and Tsuji T, (2016) Coordination of Cellular Dynamics Contributes to Tooth Epithelium Deformations., PloS one, Volume 11, Issue 9, pages e0161336. [PubMed]
• Yamamoto N, Oshima M, Tanaka C, Ogawa M, Nakajima K, Ishida K, Moriyama K, and Tsuji T, (2015) Functional tooth restoration utilising split germs through re-regionalisation of the tooth-forming field., Scientific reports, Volume 5, pages 18393. [PubMed]
• Oshima M, Inoue K, Nakajima K, Tachikawa T, Yamazaki H, Isobe T, Sugawara A, Ogawa M, Tanaka C, Saito M, Kasugai S, Takano-Yamamoto T, Inoue T, Tezuka K, Kuboki T, Yamaguchi A, and Tsuji T, (2014) Functional tooth restoration by next-generation bio-hybrid implant as a bio-hybrid artificial organ replacement therapy., Scientific reports, Volume 4, pages 6044. [PubMed]
• Ogawa M, Oshima M, Imamura A, Sekine Y, Ishida K, Yamashita K, Nakajima K, Hirayama M, Tachikawa T, and Tsuji T, (2013) Functional salivary gland regeneration by transplantation of a bioengineered organ germ., Nature communications, Volume 4, pages 2498. [PubMed]
• Hirayama M, Ogawa M, Oshima M, Sekine Y, Ishida K, Yamashita K, Ikeda K, Shimmura S, Kawakita T, Tsubota K, and Tsuji T, (2013) Functional lacrimal gland regeneration by transplantation of a bioengineered organ germ., Nature communications, Volume 4, pages 2497. [PubMed]
• Bin BH, Bhin J, Takaishi M, Toyoshima KE, Kawamata S, Ito K, Hara T, Watanabe T, Irié T, Takagishi T, Lee SH, Jung HS, Rho S, Seo J, Choi DH, Hwang D, Koseki H, Ohara O, Sano S, Tsuji T, Mishima K, and Fukada T, (2017) Requirement of zinc transporter ZIP10 for epidermal development: Implication of the ZIP10-p63 axis in epithelial homeostasis., Proceedings of the National Academy of Sciences of the United States of America, Volume 114, Issue 46, pages 12243-12248. [PubMed]
• Kamioka Y, Takakura K, Sumiyama K, and Matsuda M, (2017) Intravital Förster resonance energy transfer imaging reveals osteopontin-mediated polymorphonuclear leukocyte activation by tumor cell emboli., Cancer science, Volume 108, Issue 2, pages 226-235. [PubMed]
• Shiura H and Abe K (2019) Xist/Tsix expression dynamics during mouse peri-implantation development revealed by whole-mount 3D RNA-FISH., Scientific reports, Volume 9, Issue 1, pages 3637. [PubMed]
• Nabeshima R, Nishimura O, Maeda T, Shimizu N, Ide T, Yashiro K, Sakai Y, Meno C, Kadota M, Shiratori H, Kuraku S, and Hamada H, (2018) Loss of Fam60a, a Sin3a subunit, results in embryonic lethality and is associated with aberrant methylation at a subset of gene promoters., eLife, Volume 7, . [PubMed]
• Inoue H, Kunida K, Matsuda N, Hoshino D, Wada T, Imamura H, Noji H, and Kuroda S, (2018) Automatic Quantitative Segmentation of Myotubes Reveals Single-cell Dynamics of S6 Kinase Activation., Cell structure and function, Volume 43, Issue 2, pages 153-169. [PubMed]
• Yalikun Y, Aishan Y, Mosha A, Sumiyama K and Yanaka Y, (2018) Oocyte all-surfaces’ imaging method using micro-scale rotational flow, Micro & Nano Letters, Volume 13, Issue 3, pages 306-11. [Link]
• Ueda K, Onishi A, Ito SI, Nakamura M, and Takahashi M, (2018) Generation of three-dimensional retinal organoids expressing rhodopsin and S- and M-cone opsins from mouse stem cells., Biochemical and biophysical research communications, Volume 495, Issue 4, pages 2595-2601. [PubMed]
• Goto S, Onishi A, Misaki K, Yonemura S, Sugita S, Ito H, Ohigashi Y, Ema M, Sakaguchi H, Nishida K, and Takahashi M, (2018) Neural retina-specific Aldh1a1 controls dorsal choroidal vascular development via Sox9 expression in retinal pigment epithelial cells., eLife, Volume 7, . [PubMed]
• Maruyama K, Miyagawa-Tomita S, Mizukami K, Matsuzaki F, and Kurihara H, (2019) Isl1-expressing non-venous cell lineage contributes to cardiac lymphatic vessel development., Developmental biology, Volume 452, Issue 2, pages 134-143. [PubMed]
• Sato Y and Okabe S (2019) Nano-scale analysis of synapse morphology in an autism mouse model with 15q11-13 copy number variation using focused ion beam milling and scanning electron microscopy., Microscopy (Oxford, England), Volume 68, Issue 2, pages 122-132. [PubMed]
• Matsumiya M, Tomita T, Yoshioka-Kobayashi K, Isomura A, and Kageyama R, (2018) ES cell-derived presomitic mesoderm-like tissues for analysis of synchronized oscillations in the segmentation clock., Development (Cambridge, England), Volume 145, Issue 4, . [PubMed]
• Kawaguchi K, Kageyama R, and Sano M, (2017) Topological defects control collective dynamics in neural progenitor cell cultures., Nature, Volume 545, Issue 7654, pages 327-331. [PubMed]
• Jin T, Tuboi S, Komatsuzaki A, Imamura Y, Muranaka Y, Sakata T and Yasuda H, (2016) Enhancement of aqueous stability and fluorescence brightness of indocyanine green using small calix[4]arene micelles for near-infrared fluorescence imaging. MedChemComm, 7(4), 623-631. [Link]
• Tsuboi S, Sasaki A, Sakata T, Yasuda H, and Jin T, (2017) Immunoglobulin binding (B1) domain mediated antibody conjugation to quantum dots for in vitro and in vivo molecular imaging., Chemical communications (Cambridge, England), Volume 53, Issue 68, pages 9450-9453. [PubMed]
• Kinoshita H, Suzuma K, Kaneko J, Mandai M, Kitaoka T, and Takahashi M, (2016) Induction of Functional 3D Ciliary Epithelium-Like Structure From Mouse Induced Pluripotent Stem Cells., Investigative ophthalmology & visual science, Volume 57, Issue 1, pages 153-61. [PubMed]
• Iwasaki Y, Sugita S, Mandai M, Yonemura S, Onishi A, Ito S, Mochizuki M, Ohno-Matsui K, and Takahashi M, (2016) Differentiation/Purification Protocol for Retinal Pigment Epithelium from Mouse Induced Pluripotent Stem Cells as a Research Tool., PloS one, Volume 11, Issue 7, pages e0158282. [PubMed]
• Assawachananont J, Mandai M, Okamoto S, Yamada C, Eiraku M, Yonemura S, Sasai Y, and Takahashi M, (2014) Transplantation of embryonic and induced pluripotent stem cell-derived 3D retinal sheets into retinal degenerative mice., Stem cell reports, Volume 2, Issue 5, pages 662-74. [PubMed]
• Takagi R, Ishimaru J, Sugawara A, Toyoshima KE, Ishida K, Ogawa M, Sakakibara K, Asakawa K, Kashiwakura A, Oshima M, Minamide R, Sato A, Yoshitake T, Takeda A, Egusa H, and Tsuji T, (2016) Bioengineering a 3D integumentary organ system from iPS cells using an in vivo transplantation model., Science advances, Volume 2, Issue 4, pages e1500887. [PubMed]
• Ke MT, Nakai Y, Fujimoto S, Takayama R, Yoshida S, Kitajima TS, Sato M, and Imai T, (2016) Super-Resolution Mapping of Neuronal Circuitry With an Index-Optimized Clearing Agent., Cell reports, Volume 14, Issue 11, pages 2718-32. [PubMed]
• Tanaka Y and Fujita H (2015) Fluid driving system for a micropump by differentiating iPS cells into cardiomyocytes on a tent-like structure, Sensors and Actuators, B: Chemical, Volume 210, pages 267-72. [Link]
• Tanaka Y, Noguchi Y, Yalikun Y and Kamamichi N, (2017) Earthworm muscle driven bio-micropump. Sens Actuators B Chem, 242, 1186-1192. [Link]
• Hayashi K, Tsuchizawa Y, Iwaki M, and Okada Y, (2018) Application of the fluctuation theorem for non-invasive force measurement in living neuronal axons., Molecular biology of the cell, pages mbcE18010022. [PubMed]
• Matsuda K, Gotoh H, Tajika Y, Sushida T, Aonuma H, Niimi T, Akiyama M, Inoue Y, and Kondo S, (2017) Complex furrows in a 2D epithelial sheet code the 3D structure of a beetle horn., Scientific reports, Volume 7, Issue 1, pages 13939. [PubMed]
• Inomata H, Shibata T, Haraguchi T, and Sasai Y, (2013) Scaling of dorsal-ventral patterning by embryo size-dependent degradation of Spemann's organizer signals., Cell, Volume 153, Issue 6, pages 1296-311. [PubMed]
• Suzuki M, Takagi C, Miura S, Sakane Y, Suzuki M, Sakuma T, Sakamoto N, Endo T, Kamei Y, Sato Y, Kimura H, Yamamoto T, Ueno N, and Suzuki KT, (2016) In vivo tracking of histone H3 lysine 9 acetylation in Xenopus laevis during tail regeneration., Genes to cells : devoted to molecular & cellular mechanisms, Volume 21, Issue 4, pages 358-69. [PubMed]
• Ishiwata S, Miyazaki M, Sato K, Nakagome K, Shintani S, Kobirumaki-Shimozawa F, Fukuda N, Suzuki K, Takagi J, Shimamoto Y and Itabashi T, (2017) Dynamic properties of bio-motile systems with a liquid-crystalline structure. Molecular Crystals and Liquid Crystals, 647(1), 127-150. [Link]
• Matsuda M, Koga M, Nishida E, and Ebisuya M, (2012) Synthetic signal propagation through direct cell-cell interaction., Science signaling, Volume 5, Issue 220, pages ra31. [PubMed]
• Matsuda M, Koga M, Woltjen K, Nishida E, and Ebisuya M, (2015) Synthetic lateral inhibition governs cell-type bifurcation with robust ratios., Nature communications, Volume 6, pages 6195. [PubMed]
• Ichimura T, Chiu LD, Fujita K, Machiyama H, Yamaguchi T, Watanabe TM, and Fujita H, (2016) Non-label immune cell state prediction using Raman spectroscopy., Scientific reports, Volume 6, pages 37562. [PubMed]
• Yano T, Matsui T, Tamura A, Uji M, and Tsukita S, (2013) The association of microtubules with tight junctions is promoted by cingulin phosphorylation by AMPK., The Journal of cell biology, Volume 203, Issue 4, pages 605-14. [PubMed]
• Maekawa Y, Onishi A, Matsushita K, Koide N, Mandai M, Suzuma K, Kitaoka T, Kuwahara A, Ozone C, Nakano T, Eiraku M, and Takahashi M, (2016) Optimized Culture System to Induce Neurite Outgrowth From Retinal Ganglion Cells in Three-Dimensional Retinal Aggregates Differentiated From Mouse and Human Embryonic Stem Cells., Current eye research, Volume 41, Issue 4, pages 558-68. [PubMed]
• Inomata K, Kamoshida H, Ikari M, Ito Y, and Kigawa T, (2017) Impact of cellular health conditions on the protein folding state in mammalian cells., Chemical communications (Cambridge, England), Volume 53, Issue 81, pages 11245-11248. [PubMed]
• Uda Y, Goto Y, Oda S, Kohchi T, Matsuda M, and Aoki K, (2017) Efficient synthesis of phycocyanobilin in mammalian cells for optogenetic control of cell signaling., Proceedings of the National Academy of Sciences of the United States of America, Volume 114, Issue 45, pages 11962-11967. [PubMed]
• Makino A, Abe M, Ishitsuka R, Murate M, Kishimoto T, Sakai S, Hullin-Matsuda F, Shimada Y, Inaba T, Miyatake H, Tanaka H, Kurahashi A, Pack CG, Kasai RS, Kubo S, Schieber NL, Dohmae N, Tochio N, Hagiwara K, Sasaki Y, Aida Y, Fujimori F, Kigawa T, Nishibori K, Parton RG, Kusumi A, Sako Y, Anderluh G, Yamashita M, Kobayashi T, Greimel P, and Kobayashi T, (2017) A novel sphingomyelin/cholesterol domain-specific probe reveals the dynamics of the membrane domains during virus release and in Niemann-Pick type C., FASEB journal : official publication of the Federation of American Societies for Experimental Biology, Volume 31, Issue 4, pages 1301-1322. [PubMed]
• Konagaya Y, Terai K, Hirao Y, Takakura K, Imajo M, Kamioka Y, Sasaoka N, Kakizuka A, Sumiyama K, Asano T, and Matsuda M, (2017) A Highly Sensitive FRET Biosensor for AMPK Exhibits Heterogeneous AMPK Responses among Cells and Organs., Cell reports, Volume 21, Issue 9, pages 2628-2638. [PubMed]
• Kunida K, Matsuda M, and Aoki K, (2012) FRET imaging and statistical signal processing reveal positive and negative feedback loops regulating the morphology of randomly migrating HT-1080 cells., Journal of cell science, Volume 125, Issue Pt 10, pages 2381-92. [PubMed]
• Yamao M, Naoki H, Kunida K, Aoki K, Matsuda M, and Ishii S, (2015) Distinct predictive performance of Rac1 and Cdc42 in cell migration., Scientific reports, Volume 5, pages 17527. [PubMed]
• Ito S, Okuda S, Abe M, Fujimoto M, Onuki T, Nishimura T, and Takeichi M, (2017) Induced cortical tension restores functional junctions in adhesion-defective carcinoma cells., Nature communications, Volume 8, Issue 1, pages 1834. [PubMed]
• Yonemura S (2014) Differential sensitivity of epithelial cells to extracellular matrix in polarity establishment., PloS one, Volume 9, Issue 11, pages e112922. [PubMed]
• Takai A, Nakano M, Saito K, Haruno R, Watanabe TM, Ohyanagi T, Jin T, Okada Y, and Nagai T, (2015) Expanded palette of Nano-lanterns for real-time multicolor luminescence imaging., Proceedings of the National Academy of Sciences of the United States of America, Volume 112, Issue 14, pages 4352-6. [PubMed]
• Hayashi S and Okada Y (2015) Ultrafast superresolution fluorescence imaging with spinning disk confocal microscope optics., Molecular biology of the cell, Volume 26, Issue 9, pages 1743-51. [PubMed]
• Aoki K, Kondo Y, Naoki H, Hiratsuka T, Itoh RE, and Matsuda M, (2017) Propagating Wave of ERK Activation Orients Collective Cell Migration., Developmental cell, Volume 43, Issue 3, pages 305-317.e5. [PubMed]
• Bansod S, Kageyama R, and Ohtsuka T, (2017) Hes5 regulates the transition timing of neurogenesis and gliogenesis in mammalian neocortical development., Development (Cambridge, England), Volume 144, Issue 17, pages 3156-3167. [PubMed]
• Aoki K, Kumagai Y, Sakurai A, Komatsu N, Fujita Y, Shionyu C, and Matsuda M, (2013) Stochastic ERK activation induced by noise and cell-to-cell propagation regulates cell density-dependent proliferation., Molecular cell, Volume 52, Issue 4, pages 529-40. [PubMed]
• Tanaka Y (2014) A Peristaltic Pump Integrated on a 100% Glass Microchip Using Computer Controlled Piezoelectric Actuators, Micromachines, Volume 5, Issue 2, pages 289-99. [Link]
• Torisawa T, Taniguchi D, Ishihara S, and Oiwa K, (2016) Spontaneous Formation of a Globally Connected Contractile Network in a Microtubule-Motor System., Biophysical journal, Volume 111, Issue 2, pages 373-385. [PubMed]
• Hihara S, Pack CG, Kaizu K, Tani T, Hanafusa T, Nozaki T, Takemoto S, Yoshimi T, Yokota H, Imamoto N, Sako Y, Kinjo M, Takahashi K, Nagai T, and Maeshima K, (2012) Local nucleosome dynamics facilitate chromatin accessibility in living mammalian cells., Cell reports, Volume 2, Issue 6, pages 1645-56. [PubMed]
• Gessesse B, Nagaike T, Nagata K, Shimizu Y, and Ueda T, (2018) G-Protein Coupled Receptor Protein Synthesis on a Lipid Bilayer Using a Reconstituted Cell-Free Protein Synthesis System., Life (Basel, Switzerland), Volume 8, Issue 4, . [PubMed]
• Fujii M, Ohashi K, Karasawa Y, Hikichi M, and Kuroda S, (2017) Small-Volume Effect Enables Robust, Sensitive, and Efficient Information Transfer in the Spine., Biophysical journal, Volume 112, Issue 4, pages 813-826. [PubMed]