Publications related to the DECODE project


  • Aoyama-Ishiwatari S, et al.
    NUDT21 links mitochondrial IPS-1 to RLR-containing stress granules and activates host antiviral defense.
    The Journal of Immunology 206 (1), 154-163 (2021). doi: 10.4049/jimmunol.2000306

  • Sawai T, et al.
    Mapping the Ethical Issues of Brain Organoid Research and Application
    AJOB Neuroscience (2021) doi: 10.1080/21507740.2021.1896603

  • Yamamoto, K et al.
    Nanofluidic devices and applications for biological analyses
    Analytical Chemistry, 93(1), 332-349 (2021)


  • Alexandr Y, et al.
    A method for automatic tracking of cell nuclei with weakly-supervised mitosis detection in 2D microscopy image sequences.
    Proceedings of the 2020 5th International Conference on Biomedical Signal and Image Processing. Association for Computing Machinery, 67–73 (2020). doi: 10.1145/3417519.3417558

  • Germond A, et al.
    Their Differentiated Progeny, and Cell-State Changes During iPS Reprogramming by Raman Spectroscopy.
    Anal Chem. 92, 14915-14923 (2020). doi: 10.1021/acs.analchem.0c01800

  • Mase S, et al.
    Notch1 and Notch2 collaboratively maintain radial glial cells in mouse neurogenesis.
    Neurosci Res. S0168-0102(20), 30492-2 (2020). doi: 10.1016/j.neures.2020.11.007

  • Nagao Y, et al.
    Robust classification of cell cycle phase and biological feature extraction by image-based deep-learning.
    Mol Biol Cell 31: 1346-1354 (2020). doi: 10.1091/mbc.E20-03-0187

  • Watanabe TM, et al.
    Application of scattering microscopy for evaluation of iPS cell and its differentiated cells.
    Nihon Yakurigaku Zasshi. 155, 312-318 (2020). doi: 10.1254/fpj.20042

  • Yalikun Y, et al.
    Horizontal connection method for glass microfluidic devices
    Micro & Nano Letters. 15(5):333-338 (2020). doi:10.1049/mnl.2019.0603.

  • Yalikun Y, et al.
    Effects of Flow‐Induced Microfluidic Chip Wall Deformation on Imaging Flow Cytometry
    Cytometry:PartA. 97(9):909-920 (2020). doi:10.1002/cyto.a.23944


  • Ali A, Abouleila Y, Germond A.
    An Integrated Raman Spectroscopy and Mass Spectrometry Platform to Study Single-Cell Drug Uptake, Metabolism, and Effects
    JoVE. e60449 (2019). doi:10.3791/60449

  • Ali A, et al.
    Single-Cell Screening of Tamoxifen Abundance and Effect Using Mass Spectrometry and Raman-Spectroscopy
    Anal Chem. 91:2710-2718 (2019). doi:10.1021/acs.analchem.8b04393.

  • Aishan Y, et al.
    Thin glass micro-dome structure based microlens fabricated by accurate thermal expansion of microcavities
    Appl. Phys. Lett. 115, 263501 (2019). doi:10.1063/1.5123186

  • David BG, et al.
    Linking substrate and nucleus via actincytoskeleton in pluripotency maintenance of mouse embryonic stem cells.
    Stem Cell Res. 41:101614 (2019). doi: 10.1016/j.scr.2019.101614

  • Fujita I, et al.
    Endfoot regeneration restricts radial glial state and prevents translocation into the outer subventricular zone in early mammalian brain development
    Nature Cell Biology. 22, 26-37 (2019). doi:10.1038/s41556-019-0436-9

  • Kawaue T, et al.
    Lzts1 controls both neuronal delamination and outer radial glial-like cell generation during mammalian cerebral development
    Nat Commun. 10(1):2780 (2019). 10.1038/s41467-019-10730-y

  • Konnno D, et al.
    Dmrt factors determine the positional information of cerebral cortical progenitors via differential suppression of homeobox genes
    Development. 146: dev174243 (2019). doi: 10.1242/dev.174243

  • Kono K, et al.
    Reconstruction of Par-dependent polarity in apolar cells reveals a dynamic process of cortical polarization
    eLife. 8:e45559 (2019). 10.7554/eLife.45559.039

  • Shimizu Y, et al.
    Metabolome Analysis by Single-Cell Mass Spectrometry. Proteome letters.
    Proteome letters. 4:1-7 (2019). doi:10.14889/jpros.4.1_1

  • Yazaki J, et al.
    HaloTag-based conjugation of proteins to barcoding-oligonucleotides
    Nucleic Acids Research. 48(2):e8 (2019). doi:10.1093/nar/gkz1086

before 2018

  • Nozaki T, et al.
    Dynamic Organization of Chromatin Domains Revealed by Super-Resolution Live-Cell Imaging.
    Molecular Cell Jul 20;67(2):282-293.e7 (2017). doi: 10.1016/j.molcel.2017.06.018

  • Ogawa T, et al.
    The efficacy and further functional advantages of random-base molecular barcodes for absolute and digital quantification of nucleic acid molecules.
    Scientific Reports 7, 13576 (2017). doi:10.1038/s41598-017-13529-3

  • Hayashi S, et al.
    Ultrafast superresolution fluorescence imaging with spinning disk confocal microscope optics
    Molecular Biology of the Cell 26, 1743-1751 (2015). doi:10.1091/mbc.E14-08-1287

  • Ichimura T, et al.
    Visualizing the appearance and disappearance of the attractor of differentiation using Raman spectral imaging.
    Scientific Reports 5, 11358 (2015). doi:10.1038/srep11358

  • Okada Y, Nakagawa S.
    Super-Resolution Imaging of Nuclear Bodies by STED Microscopy in Nuclear Bodies and Noncoding RNAs (Nakagawa S, Hirose T ed)
    Methods in Molecular Biology 1262: 21-35 (2015).

  • Takai A, et al.
    Expanded palette of Nano-lanterns for real-time multicolor luminescence imaging.
    Proc. Natl. Acad. Sci. U S A. 112:4352-6 (2015). doi:10.1073/pnas.1418468112

  • Uno S, et al.
    A spontaneously blinking fluorophore based on intramolecular spirocyclization for live-cell super-resolution imaging.
    Nature Chemistry 6: 681-689 (2014). doi:10.1038/nchem.2002

  • Yaginuma H, et al.
    Diversity in ATP concentrations in a single bacterial cell population revealed by quantitative single-cell imaging.
    Scientific Reports 4, 6522 (2014). doi:10.1038/srep06522

  • Shiroguchi K, et al.
    Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes.
    Proc. Natl. Acad. Sci. USA 109, 1347-1352 (2012). doi:10.1073/pnas.1118018109