Search Results - "Shinkai, Soya"

Dynamic Nucleosome Movement Provides Structural Information of Topological Chromatin Domains in Living Human Cells by Shinkai, Soya, Nozaki, Tadasu, Maeshima, Kazuhiro, Togashi, Yuichi

“…The mammalian genome is organized into submegabase-sized chromatin domains (CDs) including topologically associating domains, which have been identified using…”
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PHi-C2: interpreting Hi-C data as the dynamic 3D genome state by Shinkai, Soya, Itoga, Hiroya, Kyoda, Koji, Onami, Shuichi

“…Abstract Summary High-throughput chromosome conformation capture (Hi-C) is a widely used assay for studying the three-dimensional (3D) genome organization…”
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Dissipative Heat Decomposition in Stochastic Energetics: Implication of the Instantaneous Diffusion Coefficient in Nonequilibrium Steady States by Shinkai, Soya

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Microrheology for Hi-C Data Reveals the Spectrum of the Dynamic 3D Genome Organization by Shinkai, Soya, Sugawara, Takeshi, Miura, Hisashi, Hiratani, Ichiro, Onami, Shuichi

“…The one-dimensional information of genomic DNA is hierarchically packed inside the eukaryotic cell nucleus and organized in a three-dimensional (3D) space…”
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Condensed but liquid-like domain organization of active chromatin regions in living human cells by Nozaki, Tadasu, Shinkai, Soya, Ide, Satoru, Higashi, Koichi, Tamura, Sachiko, Shimazoe, Masa A, Nakagawa, Masaki, Suzuki, Yutaka, Okada, Yasushi, Sasai, Masaki, Onami, Shuichi, Kurokawa, Ken, Iida, Shiori, Maeshima, Kazuhiro

“…In eukaryotes, higher-order chromatin organization is spatiotemporally regulated as domains, for various cellular functions. However, their physical nature in…”
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Single-nucleosome imaging reveals steady-state motion of interphase chromatin in living human cells by Iida, Shiori, Shinkai, Soya, Itoh, Yuji, Tamura, Sachiko, Kanemaki, Masato T, Onami, Shuichi, Maeshima, Kazuhiro

“…Dynamic chromatin behavior plays a critical role in various genome functions. However, it remains unclear how chromatin behavior changes during interphase,…”
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Bridging the dynamics and organization of chromatin domains by mathematical modeling by Shinkai, Soya, Nozaki, Tadasu, Maeshima, Kazuhiro, Togashi, Yuichi

“…The genome is 3-dimensionally organized in the cell, and the mammalian genome DNA is partitioned into submegabase-sized chromatin domains. Genome functions are…”
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1/f$ Spectrum and 1-Stable Law in One-Dimensional Intermittent Map with Uniform Invariant Measure and Nekhoroshev Stability by Shinkai, Soya, Aizawa, Yoji

“…We investigate ergodic properties of a one-dimensional intermittent map that has not only an indifferent fixed point but also a singular structure such that a…”
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Toward understanding the dynamic state of 3D genome by Shinkai, Soya, Onami, Shuichi, Nakato, Ryuichiro

“…The three-dimensional (3D) genome organization and its role in biological activities have been investigated for over a decade in the field of cell biology…”
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4D Genome Analysis Using PHi-C2 by Shinkai, Soya, Onami, Shuichi

“…Hi-C methods reveal 3D genome features but lack correspondence to dynamic chromatin behavior. PHi-C2, Python software, addresses this gap by transforming Hi-C…”
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Generalized Lyapunov exponent as a unified characterization of dynamical instabilities by Akimoto, Takuma, Nakagawa, Masaki, Shinkai, Soya, Aizawa, Yoji

“…The Lyapunov exponent characterizes an exponential growth rate of the difference of nearby orbits. A positive Lyapunov exponent (exponential dynamical…”
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Dissipative Heat Decomposition in Stochastic Energetics: Implication of the Instantaneous Diffusion Coefficient in Nonequilibrium Steady States by Shinkai, Soya

“…We give a decomposition expression for dissipative heat using the instantaneous diffusion coefficient in a nonequilibrium steady state. The dissipative heat…”
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Quantitative Theory of Active Diffusion Trajectories by Instantaneous Diffusion Coefficient by Shinkai, Soya, Togashi, Yuichi

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The Lempel-Ziv complexity of non-stationary chaos in infinite ergodic cases by SHINKAI, Soya, AIZAWA, Yoji

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Centromere/kinetochore is assembled through CENP-C oligomerization by Hara, Masatoshi, Ariyoshi, Mariko, Sano, Tomoki, Nozawa, Ryu-Suke, Shinkai, Soya, Onami, Shuichi, Jansen, Isabelle, Hirota, Toru, Fukagawa, Tatsuo

“…Kinetochore is an essential protein complex required for accurate chromosome segregation. The constitutive centromere-associated network (CCAN), a subcomplex…”
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Distributional Behavior of Time Averages of Non-L1 Observables in One-dimensional Intermittent Maps with Infinite Invariant Measures by Akimoto, Takuma, Shinkai, Soya, Aizawa, Yoji

“…In infinite ergodic theory, two distributional limit theorems are well-known. One is characterized by the Mittag-Leffler distribution for time averages of L 1…”
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Single‐molecule tracking of Nanog and Oct4 in living mouse embryonic stem cells uncovers a feedback mechanism of pluripotency maintenance by Okamoto, Kazuko, Fujita, Hideaki, Okada, Yasushi, Shinkai, Soya, Onami, Shuichi, Abe, Kuniya, Fujimoto, Kenta, Sasaki, Kensuke, Shioi, Go, Watanabe, Tomonobu M

“…Nanog and Oct4 are core transcription factors that form part of a gene regulatory network to regulate hundreds of target genes for pluripotency maintenance in…”
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1/f Spectrum and 1-Stable Law in One-Dimensional Intermittent Map with Uniform Invariant Measure and Nekhoroshev Stability by Shinkai, Soya, Aizawa, Yoji

“…We investigate ergodic properties of a one-dimensional intermittent map that has not only an indifferent fixed point but also a singular structure such that a…”
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PHi-C: deciphering Hi-C data into polymer dynamics by Shinkai, Soya, Nakagawa, Masaki, Sugawara, Takeshi, Togashi, Yuichi, Ochiai, Hiroshi, Nakato, Ryuichiro, Taniguchi, Yuichi, Onami, Shuichi

“…Abstract Genomes are spatiotemporally organized within the cell nucleus. Genome-wide chromosome conformation capture (Hi-C) technologies have uncovered the 3D…”
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Distributional behavior of time averages of Non-[L.sup.1] observables in one-dimensional intermittent maps with infinite invariant measures by Akimoto, Takuma, Shinkai, Soya, Aizawa, Yoji

“…In infinite ergodic theory, two distributional limit theorems are well-known. One is characterized by the Mittag-Leffler distribution for time averages of…”
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