Shindo Y, Balachandra S, and Amodeo AA. Visualizing developmental dynamics of nuclear morphology and transport machinery in Drosophila. bioRxiv. https://doi.org/10.1101/2024.10.17.618964.
Bhatt AD, Brown MG, Wackford AB, Shindo Y, Amodeo AA. Local nuclear to cytoplasmic ratio regulates H3.3 incorporation via cell cycle state during zygotic genome activation. bioRxiv. https://doi.org/10.1101/2024.07.15.603602.
Shindo Y, Brown MG, and Amodeo AA. Versatile roles for histones in early development. Current Opinion in Cell Biology. 75, 102069 (2022)
Shindo Y and Amodeo, AA. Modeling the roles for nuclear import dynamics in the early embryonic cell cycle. Biophysical Journal. 120, 4277–4286 (2021)
Shindo Y and Amodeo AA. Excess histone H3 is a competitive Chk1 inhibitor that controls cell-cycle remodeling in the early Drosophila embryo. Current Biology, 31, 2633–2642 (2021)
Shindo Y and Amodeo AA. Dynamics of free and chromatin-bound histone H3 during early embryogenesis. Current Biology, 29, 359–366 (2019)
Shindo Y, Kondo Y, and Sako Y. Inferring a nonlinear biochemical network model from a heterogeneous single-cell time course data. Scientific Reports, 8, 6790 (2018)
Iwamoto K, Shindo Y, and Takahashi K. Modeling cellular noise behind heterogeneous cell responses in epidermal growth factor signaling pathway. PLOS Computational Biology, 12, e1005222 (2016)
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. Cortical Polarity of the RING Protein PAR-2 is Maintained by Exchange Rate Kinetics at the Cortical-Cytoplasm Boundary. Cell Reports, 16, 2156–2168 (2016)
Shindo Y, Iwamoto K, Mouri K, Hibino K, Tomita M, Kosako H, Sako Y, and Takahashi K. Conversion of graded phosphorylation into switch-like nuclear translocation via autoregulatory mechanisms in ERK signalling. Nature Communications, 7, 10485 (2016)
Watabe M, Arjunan SNV, Fukushima S, Iwamoto K, Kozuka J, Matsuoka S, Shindo Y, Ueda M, and Takahashi K. A computational framework for bioimaging simulation. PLOS ONE, 10, e0130089 (2015)
Shindo Y, Nozaki T, Saito R, and Tomita M. Computational analysis of associations between alternative splicing and histone modifications. FEBS Letters, 587, 516–521 (2013)