業　績　＜Publications＞

2020.4～2021.3
原著論文 （Refereed original papers)

  • T. Kohsokabe and K. Kaneko. Dynamical Systems Approach to Evolution-Development Congruence: Revisiting Haeckel’s Recapitulation Theory. J Exp. Zoology B, 2021;1–14. (2021)

  • Q-Y. Tang, T.Hatakeyama, K. Kaneko. Functional Sensitivity and Mutational Robustness of Proteins. Physical Review Research 2 (3), 033452 (2020)

  • A. Sakata and K. Kaneko. Dimensional reduction in evolving spin-glass model: correlation of phenotypic responses to environmental and mutational changes. Phys.Rev.Lett. 124, 218101 (2020)

  • T. Kurikawa, O. Barak, K. Kaneko. Repeated sequential learning increases memory capacity via effective decorrelation in a recurrent neural network. Phys. Rev. Research 2, 023307 (2020)

  • Y. Matsushita, & K. Kaneko. Homeorhesis in Waddington's Landscape by Epigenetic Feedback Regulation. Phys. Rev. Research 2, 023083 (2020)

  • J.F. Yamagishi and K. Kaneko. Chaos with a High-dimensional Torus. Physical Review Research 2, 023044 (2020)

  • K. Itao and K. Kaneko. Reply to Read and Parkin: Our model correctly expresses the ethnographic nature of the cultural incest taboo and kinship structures. Proceedings of National Academy of Sciences (USA), Letter 117, 9167-9168 (2020)

  • C. Furusawa and N. Irie:Toward understanding of evolutionary constraints: experimental and theoretical approaches, Biophys. Rev. 12(5):1155-1161 (2020).

  • T. Horinouchi, C. Furusawa: Understanding metabolic adaptation by using bacterial laboratory evolution and trans-omics analysis, Biophys. Rev., 12(3):677-682 (2020).

  • R. Ohbayashi, S. Hirooka, R. Onuma, Y. Kanesaki, Y. Hirose, Y. Kobayashi, T. Fujiwara, C. Furusawa, S-Y Miyagishima: Evolutionary changes in DnaA-dependent chromosomal replication in Cyanobacteria, Front. Microbiol., 11, 786 (2020).

  • T. Horinouchi, T. Maeda, H. Kotani, C. Furusawa: Suppression of antibiotic resistance evolution by single-gene deletion, Sci. Rep., 10(1):4178 (2020).

  • T. Maeda, J. Iwasawa, H. Kotani, N. Sakata, M. Kawada, T. Horinouchi, A. Sakai, K. Tanabe, C. Furusawa: High-throughput laboratory evolution and evolutionary constraints in Escherichia coli, Nature Communications, 11(1):5970 (2020).

  • Y. Himeoka, N. Mitarai: When to wake up? The optimal waking-up strategies for starvation-induced persistence, PLoS Comp. Biol., 17(2):e1008655 (20201).

  • S Aoyama-Ishiwatari, T Okazaki, S Iemura, T Natsume, Y Okada, Y Gotoh, NUDT21 links mitochondrial IPS-1 to RLR-containing stress granules and activates host antiviral defense. The Journal of Immunology 206 (1), 154-163, 2021 (Grant: ABISのみ)　DOI: https://doi.org/10.4049/jimmunol.2000306

  • Nagao Y, Sakamoto M, Chinen T, Okada Y, Takao D. 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

  • Fujioka Y, Alam JM, Noshiro D, Mouri K, Ando T, Okada Y, May AI, Knorr RL, Suzuki K, Ohsumi Y, Noda NN. Phase separation organizes the site of autophagosome formation., Nature 578(7794) 301-305, 2020 DOI: 10.1038/s41586-020-1977-6

  • Nakagama Y, Takeda N, Ogawa S, Takeda H, Furutani Y, Nakanishi T, Sato T, Hirata Y, Oka A, Inuzuka R. Noonan syndrome-associated biallelic LZTR1 mutations cause cardiac hypertrophy and vascular malformations in zebrafish. Mol Genet Genomic Med. 8(3):e1107 (2020)

  • Christopher B M., Nishiyama A, Ryan J, Nakamura R, Yiğit M, Glück IM, Trummer C, Qin W, Bartoschek MD, Traube FR, Parsa E, Ugur E, Modic M, Acharya A, Stolz P, Ziegenhain C, Wierer M, Enard W, Carell T, Lamb DC, Takeda H, Nakanashi M, Bultmann S & Leonhardt H. Recent Evolution of a TET-Controlled and DPPA3/STELLA-Driven Pathway of Passive DNA Demethylation in Mammals. Nature Communications 11(1):5972(2020)

  • S. Nakayama, T. Yano , T. Namba, S. Konishi, M. Takagishi, E. Herawati, T. Nishida, Y. Imoto, S. Ishihara, M. Takahashi, K. Furuta, K. Oiwa, A. Tamura, S. Tsukita. Planar cell polarity induces local microtubule bundling for coordinated ciliary beating. J. Cell Biol. 220 (7), e20201003 (2021)

  • M. Tateno and S. Ishihara, Interfacial-curvature-driven coarsening in mass-conserved reaction-diffusion systems. Phys. Rev. Res. in press

  • Giachello ANG, Zarin AA, Kohsaka H, Fan YN, Nose A, Landgraf M, Baines RA. Electrophysiological validation of premotor interneurons monosynaptically connected to the aCC motoneuron in the Drosophila larval CNS. bioRxiv, (2020) doi: 10.1101/2020.06.17.156430

  • Sun X, Liu Y, Liu C, Mayumi K, Ito K, Nose A, Kohsaka H. A neuromechanical model and kinematic analyses for Drosophila larval crawling based on physical measurements. bioRxiv, (2020) doi: 10.1101/2020.07.17.208611

  • Matsuo Y, Nose A, Kohsaka H. Interspecies variation of larval locomotion kinematics in the genus Drosophila and its relation to habitat temperature. bioRxiv, (2020) doi: 10.1101/2020.11.06.371120

  • Hiramoto A, Jonaitis J, Niki S, Kohsaka H, Fetter RD, Cardona A, Pulver SR, Nose A, Regulation of coordinated muscular relaxation by a pattern-regulating intersegmental circuit, Nat. Commun. 12:2943 (2021) doi: 10.1038/s41467-021-23273-y

  • Zeng X, Kawasaki T, Inada K, Kazama H, Nose A. An electrically-coupled pioneer circuit enables motor development via proprioceptive feedback, invited revision in preparation for Curr. Biol.; preprint published on SSRN (2021) doi: 10.2139/ssrn.3787889

  • Takuya Fujiwara, Takahiro Ito, Takashi Funatsua, Makoto Tsunoda. Analysis of intracellular α-keto acids by HPLC with fluorescence detection. Anal. Methods. 12: 2555-2559 (2020)

  • Masaru Kato, Yumi Fujita, Takuya Iizuka, Kyohei Nozaki, Sho Takano, Takashi Funatsu, Yoshihiro Sano, Shuhei Murayama, Koji Karasawa. Extraction of urinary cell-free DNA by using triamine-modified silica particles for liquid biopsy. Anal. Bioanal. Chem. 412(23): 5647-5652 (2020)

  • Beob Soo Kim, Mitsuru Naito, Rimpei Kamegawa, Hyun Jin Kim, Ryo Iizuka, Takashi Funatsu, Shingo Ueno, Takanori Ichiki, Akihiro Kishimura, Kanjiro Miyata. Photo-reactive oligodeoxynucleotide-embedded nanovesicles (PROsomes) with switchable stability for efficient cellular uptake and gene knockdown. Chem. Commun (Camb). 56(66): 9477-9480 (2020)

  • Masatoshi Wakamori, Kohki Okabe, Kiyoe Ura, Takashi Funatsu, Masahiro Takinoue, Takashi Umehara. Quantification of the effect of site-specific histone acetylation on chromatin transcription rate. Nucleic Acids Res. 48(22): 12648-12659 (2020)

  • Takuya Fujiwara, Takashi Funatsu, Makoto Tsunoda. Fast analysis using pillar array columns: Quantification of branched-chain a-keto acids in human plasma samples. J. Pharm. Biomed. Anal. 198: 114019 (2021)

  • Masanari Shimada, Hideyuki Mizuno, Ludovic Berthier, and Atsushi Ikeda. Low-frequency vibrations of jammed packings in large spatial dimensions. Physical Review E, 101, 052906(1-8) (2020).

  • Kumpei Shiraishi, Hideyuki Mizuno, and Atsushi Ikeda. Mechanical and Vibrational Properties of Three-Dimensional Dimer Packings Near the Jamming Transition. Journal of the Physical Society Japan, 89, 074603(1-11) (2020).

  • Masanari Shimada, Hideyuki Mizuno, and Atsushi Ikeda. Vibrational spectrum derived from local mechanical response in disordered solids, Soft Matter, 16, 7279-7288 (2020).

  • Hideyuki Mizuno, Hua Tong, Atsushi Ikeda, and Stefano Mossa. Intermittent rearrangements accompanying thermal fluctuations distinguish glasses from crystals. The Journal of Chemical Physics, 153, 154501(1-13) (2020).

  • Masanari Shimada, Hideyuki Mizuno, and Atsushi Ikeda. Novel elastic instability of amorphous solids in finite spatial dimensions. Soft Matter, 17, 346-364 (2021).

  • A.Seita, H.Nakaoka, R.Okura, Y.Wakamoto. Intrinsic growth heterogeneity of mouse leukemia cells underlies differential susceptibility to a growth-inhibiting anticancer drug. PLoS ONE. 16(2): e0236534. (2021)

  • Fengyun Zhu, Rubin Wang, Kazuyuki Aihara, and Xiaochuan Pan: Energy-efficient Firing Patterns with Sparse Bursts in the Chay Neuron Model, Nonlinear Dynamics, Vol.100, pp.2657-2672 (2020).

  • Hiroshi Yamashita, Kazuyuki Aihara, and Hideyuki Suzuki: Timescales of Boolean Satisfiability Solver using Continuoustime Dynamical System,'' Communications in Nonlinear Science and Numerical Simulation, Vol.84, Article No.105183 (2020).

  • Siyang Leng, Huanfei Ma, Jurgen Kurts, Ying-Cheng Lai, Wei Lin, Kazuyuki Aihara, and Luonan Chen: Partial Cross Mapping Eliminates Indirect Causal Influences,'' Nature Communications, Vol.11, Article No.2632, pp.1-9 (2020).

  • Chuan Chen, Rui Li, Lin Shu, Zhiyu He, Jining Wang, Chengming Zhang, Huanfei Ma, Kazuyuki Aihara, and Luonan Chen: Predicting future dynamics from short-term time series using an Anticipated Learning Machine, National Science Review, Vol.7, No.6, pp.1079-1091 (2020).

  • Huu Hoang, Eric J. Lang, Yoshito Hirata, Isao T. Tokuda, Kazuyuki Aihara, Keisuke Toyama, Mitsuo Kawato, and Nicolas Schweighofer: Electrical Coupling Controls Dimensionality and Chaotic Firing of Inferior Olive Neurons, PLOS Biology, Vol.16, No.7, e1008075, pp.1-26 (2020).

  • Siyang Leng, and Kazuyuki Aihara: Common Stochastic Inputs Induce Neuronal Transient Synchronization with Partial Reset, Neural Networks, Vol.128, pp,13-21 (2020).

  • Keiichi Koizumi, Makito Oku, Shusaku Hayashi, Akiko Inujima, Naotoshi Shibahara, Luonan Chen, Yoshiko Igarashi, Kazuyuki Tobe, Shigeru Saito, Makoto Kadowaki, and Kazuyuki Aihara: Suppression of Dynamical Network Biomarker Signals at the Predisease State (Mibyou) beforeMetabolic Syndrome inMice by a Traditional Japanese Medicine (Kampo Formula) Bofutsushosan, Evidence-Based Complementary and Alternative Medicine, Vol.2020, Article No. 9129134, pp.1-9 (2020).

  • Keiichi Koizumi, Makito Oku, Shusaku Hayashi, Akiko Inujima, Naotoshi Shibahara, Luonan Chen, Yoshiko Igarashi, Kazuyuki Tobe, Shigeru Saito, Makoto Kadowaki, and Kazuyuki Aihara: Suppression of Dynamical Network Biomarker Signals at the Predisease State (Mibyou) beforeMetabolic Syndrome inMice by a Traditional Japanese Medicine (Kampo Formula) Bofutsushosan, Evidence-Based Complementary and Alternative Medicine, Vol.2020, Article No. 9129134, pp.1-9 (2020).

  • Chiyori T. Urabe, Gouhei Tanaka, Takahiro Oshima, Aya Maruyama, Takako Misaki, Nobuhiko Okabe, and Kazuyuki Aihara: Comparing Catch-up Vaccination Programs based on Analysis of 2012-13 Rubella Outbreak in Kawasaki City, Japan, PLoS ONE, Vol.15, No.8, e0237312, pp.1-20 (2020).

  • Md Abdus Samad Kamal, Makito Oku, Tomohisa Hayakawa, Jun-ichi Imura, and Kazuyuki Aihara: Early Detection of a Traffic Flow Breakdown in the Freeway Based on Dynamical Network Markers, International Journal of Intelligent Transportation Systems Research, Vol.18, No.3, pp.422-435 (2020).

  • Pei Chen, Rui Liu, Kazuyuki Aihara, and Luonan Chen: Autoreservoir Computing for Multistep Ahead Prediction based on the Spatiotemporal Information Transformation, Nature Communications, Vol.11, Article No.4568, pp.1-15 (2020).

  • Xiaoyan Wang, Tianjiao Tang, Lang Cao, Kazuyuki Aihara, and Qian Guo: Inferring Key Epidemiological Parameters and Transmission Dynamics of COVID-19 based on a Modified SEIR Model, Mathematical Modelling of Natural Phenomena, Vol.15, Article No.74, pp.1-13 (2020).

  • Yoshito Hirata and Kazuyuki Aihara: Deep Learning for Nonlinear Time Series: Examples for Inferring Slow Driving Forces, International Journal of Bifurcation and Chaos, Vol.30, No.15, 2050226, pp.1-13 (2020).

  • Seiji Uenohara and Kazuyuki Aihara: Time-Domain Digital-to-Analog Converter for Spiking Neural Network Hardware, Circuits, Systems, and Signal Processing, doi: 10.1007/s00034-020-01597-2 (2020).

  • Yusuke Sakemi, Kai Morino, Timothée Leleu, and Kazuyuki Aihara: Model-size reduction for reservoir computing by concatenating internal states through time, Scientific Reports, Vol.10, Article No.21794, pp.1-13 (2020).

  • Daisuke Inoue, Akihisa Okada, Tadayoshi Matsumori, Kazuyuki Aihara, Hiroaki Yoshida: Traffic Signal Optimization on a Square Lattice with Quantum Annealing, Scientific Reports, Vol.11, Article No.3303, pp.1-12 (2021).

  • Jifan Shi, Kazuyuki Aihara, Luonan Chen: Dynamics-based data Science in Biology, National Science Review, doi: 10.1093/nsr/nwab029 (2021).

  • Mikio Hasegawa, Hirotake Ito, Hiroki Takesue, Kazuyuki Aihara (Invited Paper): Optimization by Neural Networks in the Coherent Ising Machine and its Application to Wireless Communication Systems, IEICE Transactions on Communications, Vol.E104-B, No.3, pp.210--216 (2021).

  • Shunya Okuno, Koji Ikeuchi, Kazuyuki Aihara: Practical Data‐Driven Flood Forecasting Based on Dynamical Systems Theory, Water Resources Research, Vol.57, No.3, e2020WR028427, pp.1--18 (2021--3).

  • Kwang Su Kim, Keisuke Ejima, Shoya Iwanami, Yasuhisa Fujita, Hirofumi Ohashi, Yoshiki Koizumi, Yusuke Asai, Shinji Nakaoka, Koichi Watashi, Kazuyuki Aihara, Robin N. Thompson, Ruian Ke, Alan S. Perelson and Shingo Iwami: A quantitative model used to compare within-host SARS-CoV-2, MERS-CoV and SARS-CoV dynamics provides insights into the pathogenesis and treatment of SARS-CoV-2, PLOS Biology, Vol.19, No.3, e3001128, pp.1-19 (2021).

  • Rui Liu, Jiayuan Zhong, Renhao Hong, Ely Chen, Kazuyuki Aihara, Pei Chen, and Luonan Chen: Predicting Local COVID-19 Outbreaks and Infectious Disease Epidemics based on Landscape Network Entropy, Science Bulletin, doi: 10.1016/j.scib.2021.03.022 (2021).

  • Nakamura T., Harada K., Kamiya T., Takizawa M., Küppers J., Nakajima K., Gütschow M., Kitaguchi T., Ohta K., Kato T., Tsuboi T. Glutamine-induced signaling pathways via amino acid receptors in enteroendocrine L cell lines. J. Mol. Endocrinology64: 133-143, (2020)

  • Yamada T., Yamada S., Ding D-Q., Fujita Y., Takaya E., Hiraoka Y., Murakami H., Ohta K. Maintenance of meiotic crossover against reduced double-strand break formation in fission yeast lacking histone H2A. Z. Gene 743: 144615, (2020)

  • Tanaka H., Muramoto N., Sugimoto H., Oda A., Ohta K. Extended‐TAQing system for large‐scale plant genome reorganization. The Plant Journal 103: 2139-2150, (2020)

  • Seo H., Masuda H., Asagoshi K., Uchiki T., Kawata S., Sasaki G., Yabuki T., Miyai S., Takahashi N., Hashimoto S., Sawada A., Takaiwa A., Koyama C., Tamai K., Kurosawa K., Lin K-Y., Ohta K., and Nakazaki Y. Streamlined human antibody generation and optimization by exploiting designed immunoglobulin loci in a B cell line. Cellular & Mol. Immunology (2020)

  • Fujiwara Y., Horisawa-Takada Y., Inoue E., Tani N., Shibuya H., Fujimura S., Kariyazono R., Sakata T., Ohta K., Araki K., Okada Y, Ishiguro K-I. Meiotic cohesins mediate initial loading of HORMAD1 to the chromosomes and coordinate SC formation during meiotic prophase. PLoS Genetics ,16 (9), e1009048 (2020)

  • Takamura N., Seo H., Ohta K. TET3 dioxygenase modulates gene conversion at the avian immunoglobulin variable region via demethylation of non-CpG sites in pseudogene templates. Genes Cells. 26 (3), 121-135 (2021)

  • Senmatsu S., Asada R., Oda A., Hoffman CS., Ohta K., Hirota K. lncRNA transcription induces meiotic recombination through chromatin remodelling in fission yeast. Commun. Biol. 4 (1), 295 (2021)

  • Hiroki Kojima, Dominique Chen, Mizuki Oka and Takashi Ikegami. Analysis and Design of Social Presence in a Computer-Mediated Communication System Frontiers in Psychology, Human-Media Interaction,Front. Psychol., 24 May 2021

  • Hiroki Kojima, Yuzuru Mitsui and Takashi Ikegami. Spatial and Temporal Taylor's Law in 1-Dim Chaotic Maps Chaos: An Interdisciplinary Journal of Nonlinear Science,Chaos 31, 033111, 2021

  • Atsushi Masumori, Norihiro Maruyama and Takashi Ikegami. Personogenesis through Imitating Human Behaviors in a Humanoid Robot Alter3 Frontiers in Robotics and AI7 p.165. 2020

  • Atsushi Masumori, Lana Sinapayen, Norihiro Maruyama, Takeshi Mita, Douglas Bakkum, Urs Frey, Hirokazu Takahashi and Takashi Ikegami. Neural Autopoiesis: Organizing Self-Boundaries by Stimulus Avoidance in Biological and Artificial Neural Networks. Artificial Life, 2020

  • Broadfield, L. A., Goncalves Duarte, J. A., Schmieder, R., Broekaert, D., Veys, K., Planque, M., Vriens, K., Karasawa, Y., Napolitano, F., Fujita, S., Fujii, M., Eto, M., Holvoet, B., Vangoitsenhoven, R., Fernandez-Garcia, J., Van Elsen, J., Dehairs, J., Zeng, J., Dooley, J., Alba Rubio, R., van Pelt, J., Grunewald, T. G. P., Liston, A., Mathieu, C., Deroose, C. M., Swinnen, J. V., Lambrechts, D., di Bernardo, D., Kuroda, S., De Bock, K., and Fendt, S. M. Fat Induces Glucose Metabolism in Nontransformed Liver Cells and Promotes Liver Tumorigenesis. Cancer Res 81(8), 1988-2001(2021)

  • Egami, R., Kokaji, T., Hatano, A., Yugi, K., Eto, M., Morita, K., Ohno, S., Fujii, M., Hironaka, K., Uematsu, S., Terakawa, A., Bai, Y., Pan, Y., Tsuchiya, T., Ozaki, H., Inoue, H., Uda, S., Kubota, H., Suzuki, Y., Matsumoto, M., Nakayama, K.I., Hirayama, A., Soga, T., Kuroda, S. Trans-omic analysis reveals obesity-associated dysregulation of inter-organ metabolic cycles between the liver and skeletal muscle. iScience 24(3), 102217 (2021)

  • Kokaji, T., Hatano, A., Ito, Y., Yugi, K., Eto, M., Morita, K., Ohno, S., Fujii, M., Hironaka, K., Egami, R., Terakawa, A., Tsuchiya, T., Ozaki, H., Inoue, H., Uda, S., Kubota, H., Suzuki, Y., Ikeda, K., Arita, M., Matsumoto, M., Nakayama, K. I., Hirayama, A., Soga, T., and Kuroda, S. Transomics analysis reveals allosteric and gene regulation axes for altered hepatic glucose-responsive metabolism in obesity. Sci. Signal 13(660), eaaz1236 (2020)

  • Hoshino, D., Kawata, K., Kunida, K., Hatano, A., Yugi, K., Wada, T., Fujii, M., Sano, T., Ito, Y., Furuichi, Y., Manabe, Y., Suzuki, Y., Fujii, N. L., Soga, T., and Kuroda, S. Trans-omic Analysis Reveals ROS-Dependent Pentose Phosphate Pathway Activation after High-Frequency Electrical Stimulation in C2C12 Myotubes. iScience 23(10), 101558 (2020)

  • Ohno, S., Quek, L.-E., Krycer, J. R., Yugi, K., Hirayama, A., Ikeda, S., Shoji, F., Suzuki, K., Soga, T., James, D.E., and Kuroda, S. Kinetic Trans-omic Analysis Reveals Key Regulatory Mechanisms for Insulin-Regulated Glucose Metabolism in Adipocytes. iScience 23(9), 101479 (2020)

  • Wada, T., Hironaka, K., Wataya, M., Fujii, M., Eto, M., Uda, S., Hoshino, D., Kunida, K., Inoue, H., Kubota, H., Takizawa, T., Karasawa, Y., Nakatomi H., Saito N., Hamaguchi, H., Furuichi, Y., Manabe, Y., Fujii, N.L., and Kuroda, S., Single-Cell Information Analysis Reveals That Skeletal Muscles Incorporate Cell-to-Cell Variability as Information Not Noise. Cell Rep 32(9), 108051 (2020)

  • Matsuda, N., Hironaka, K., Fujii, M., Wada, T., Kunida, K., Inoue, H., Eto, M., Hoshino, D., Furuichi, Y., Manabe, Y., Fujii, N.L., Noji, H., Imamura, H, and Kuroda, S., Monitoring and mathematical modeling of mitochondrial ATP in myotubes at single-cell level reveals two distinct population with different kinetics. Quant Biol 8(3), 228-237 (2020)

  • So Nakashima, Yuki Sughiyama, Tetsuya J. Kobayashi Lineage EM Algorithm for Inferring Latent States from Cellular Lineage Trees Bioinformatics Bioinfo. 36(9),2829-2838 (2020)

  • Tetsuya J. Kobayashi Bayesian gates for reliable logical operations under noisy condition Physical Review E Phys. Rev. E, 101, 042205 (2020)

  • Yuta Tokuoka, Takahiro G Yamada, Noriko F Hiroi, Tetsuya J Kobayashi, Kazuo Yamagata, Akira Funahashi 3D convolutional neural networks-based segmentation to acquire quantitative criteria of the nucleus during mouse embryogenesis npj Systems Biology and Applications npj Syst. Biol. App., 6, 32 (2020)

  • Takuya Kato, Tetsuya J. Kobayashi Understanding adaptive immune system as reinforcement learning Physical Review Research Phys Rev Res., 3, 013222 (2021)

  • Kento Nakamura, Tetsuya J. Kobayashi Connection between bacterial chemotactic network and optimal filtering Physical Review Letters Phys. Rev. Lett., 126,12,128102 (2021)

  • Visualization and molecular characterization of whole-brain vascular networks with capillary resolution Miyawaki T., Morikawa S., Susaki E.A., Nakashima A., Takeuchi H., Yamaguchi S., Ueda H.R., Ikegaya Y. Nat. Commun. 11, 1104 (2020)

  • Imoto, D., Saito, N., Nakajima, A., Gen Honda, G., Ishida, M., Sugita, T, Ishihara, S., Katagiri, K., Okimura, C., Iwadate, Y., Sawai, S.* (submitted in revision) Comparative mapping of crawling-cell morphodynamics in deep learning-based feature space.　投稿中

  • Wakai, M. K., Nakamura, M.J.,Sawai, S., Hotta, K., Oka, K.*, Two-Round Ca 2+ transient in papillae by mechanical stimulation induces metamorphosis in the ascidian Ciona intestinalis type A. Proc Biol Sci. 288(1945), 20203207 - 20203207 (2021) 10.1098/rspb.2020.3207

  • Ishihara S, Sato T, Du G, Guardavaccaro D, Nakajima A, Sawai S, Kataoka T, Katagiri K*, Phosphatidic acid-dependent localization and basal de-phosphorylation of RA-GEFs regulate lymphocyte trafficking. BMC biol. 18(1), 75 - 75 (2020) 10.1186/s12915-020-00809-0

  • Y. Kurashina, M. Tsuchiya, A. Sakai, T. Maeda, Y. Jung Heo, F. Rossi, N. Choi, M. Yanagisawa, H. Onoe, Simultaneous crosslinking induces macroscopically phase-separated microgel from a homogeneous mixture of multiple polymers. Applied Materials Today, 22:100937 (2021) (doi: 10.1016/j.apmt.2021.100937)

  • K. Harusawa, C. Watanabe, Y. Kobori, K. Tomita, A. Kitamura, M. Kinjo, M. Yanagisawa. Membrane surface modulates slow diffusion in small crowded droplets. Langmuir, 37:437–444 (2021) (doi: 10.1021/acs.langmuir.0c03086)

  • S. Fujiwara, K. Shoji, C. Watanabe, R. Kawano, M. Yanagisawa. Microfluidic formation of honeycomb-patterned droplets bounded by interface bilayers via bimodal molecular adsorption. Micromachines, 11:701 (2020) (doi: 10.3390/mi11070701)

  • A. Sakai, Y. Murayama, M. Yanagisawa. Cyclic micropipette aspiration reveals viscoelastic change of a gelatin microgel prepared inside a lipid droplet. Langmuir, 36:5186–5191 (2020) (doi: 10.1021/acs.langmuir.0c00428)

  • C. Watanabe, A. Oda, Aoki, M. Yanagisawa. Liposomal adhesion via electrostatic interactions and osmotic deflation increases membrane tension and lipid diffusion coefficient. Soft Matter, 16:4549-4554 (2020) (doi: 10.1039/D0SM00416B)

  • S. Hayasaki, M. Shimizu, Y. Katsurada, A. Sakai, M. Yanagisawa, Y. Atomi, T. Watanabe, Visualizing Molecular Chaperone Controlled Resilient Cell Traction Force by Micropost Arrays Fabricated by Two-photon Initiated Polymerization, Journal of Fiber Science and Technology,76 (9), 288-295 (2020)

  • C. Watanabe+, Y. Kobori+, J. Yamamoto, M. Kinjo, M. Yanagisawa, (+ equally contributed) Quantitative Analysis of Membrane Surface and Small Confinement Effects on Molecular Diffusion, The Journal of Physical Chemistry (J. Phys. Chem.), 124: 1090-1098 (2020)

  • Shogo Nagata, Fumisato Ozawa, Minghao Nie, and Shoji Takeuchi: 3D culture of functional human iPSC-derived hepatocytes using a core-shell microfiber, PLOS ONE, 15(6): e0234441, 2020

  • Keisuke Sugahara, Yuya Morimoto, Sho Takamori, Shoji Takeuchi: A dynamic microarray device for pairing and electrofusion of giant unilamellar vesicles, Sensors and Actuators B: Chemical, Vol.311, 127922, 2020

  • Yuya Morimoto, Hiroaki Onoe, and Shoji Takeuchi: Biohybrid robot with skeletal muscle tissue covered with a collagen structure for moving in air, APL Bioengineering, Volume BHM2020, Issue 1, APL Bioeng. 4, 026101, 2020

  • Hironori Sugiyama, Toshihisa Osaki, Shoji Takeuchi, Taro Toyota: Hydrodynamic accumulation of small molecules and ions into cell-sized liposomes against a concentration gradient, Communications Chemistry, Vol. 3, No.32, (2020)

  • M. Matsuo, Y. Hirata, K. Kurihara, T. Toyota, T. Miura, K. Suzuki, T. Sugawara, “Environment-Sensitive Intelligent Self-Reproducing Artificial Cell with a Modification-Active Lipo-Deoxyribozyme”, Micromachines, 11, 606 (18pages) (2020).

  • H. Sugiyama, T. Osaki, S. Takeuchi, T. Toyota, “Perfusion Chamber for Observing Liposome-based Cell Model Prepared by Water-in-oil Emulsion Transfer Method”, ACS Omega, 5, 19429-19436 (2020).

  • Ai Shima, Akane Itou, Shoji Takeuchi: Cell fibers promote proliferation of co-cultured cells on a dish,Scientific Reports, Vol. 10, No. 1, 288 (7 pages), 2020

  • Wei Sun, Binil Starly, Andrew C Daly, Jason A Burdick, Jürgen Groll, Gregor Skeldon, Wenmiao Shu, Yasuyuki Sakai, Marie Shinohara, Masaki Nishikawa, Jinah Jang, Dong-Woo Cho, Minghao Nie, Shoji Takeuchi, Serge Ostrovidov, Ali Khademhosseini, Roger D Kamm, Vladimir Mironov, Lorenzo Moroni, and Ibrahim T Ozbolat: The bioprinting roadmap, Biofabrication, Vol. 12, No. 2, 022002, 2020 (review paper)

  • Yongxin Li, Akihito Omori, Rachel Flores, Sheri Satterfield, Christine Nguyen, Tatsuya Ota, Toko Tsurugaya, Tetsuro Ikuta, Kazuho Ikeo, Mani Kikuchi, Jason Leong, Adrian Reich, Meng Hao, Wenting Wan, Yang Dong, Yandong Ren, Si Zhang, Tao Zeng, Masahiro Uesaka, Yui Uchida, Xueyan Li, Tomoko Shibata, Takahiro Bino, Kota Ogawa, Shuji Shigenobu, Mariko Kondo, Fayou Wang, Luonan Chen, Gary Wessel, Hidetoshi Saiga, Robert Cameron, Brian Livingston, Cynthia Bradham, Wen Wang*, Naoki Irie* Genomic insights of body plan transitions from bilateral to pentameric symmetry in Echinoderms Communications Biology 3, Article number: 371 (2020)

  • John D. Hogan, Jessica L. Keenan, Lingqi Luo, Dakota Y. Hawkins, Jonas Ibn-Salem, Arjun Lamba, Daphne Schatzberg, Michael L. Piacentino, Daniel T. Zuch, Amanda B. Core, Carolyn Blumberg, Bernd Timmermann, José Horacio Grau, Emily Speranza, Miguel A. Andrade-Narravo, Naoki Irie, Albert J. Poustka, Cynthia A. Bradham The developmental transcriptome for Lytechinus variegatus exhibits temporally punctuated gene expression changes Developmental Biology Vol. 460, Issue 2, 139-154 (2020)

  • Mizuuchi, R.*, Ichihashi, N. Translation-coupled RNA replication and parasitic replicators in membrane-free compartments Chemical communications, 56, 13453-13456 (2020)

  • Furubayashi, T., Ueda, K., Bansho, Y., Motooka, D., Nakamura, S., Mizuuchi, R., Ichihashi, N.* Emergence and diversification of a host-parasite RNA ecosystem through Darwinian evolution. eLIFE 9:e56038 (2020)

  • Okauchi, H., Sakatani,Y., Ohtsuka, K., Ichihashi, N.* Minimization of elements for isothermal DNA replication by an evolutionary approach ACS Synthetic Biology 9, 1771–1780 (2020)

  • K. Yoshimura, and S. Ito, Information geometric inequalities of chemical thermodynamics Physical Review Research 3, 013175 (2021).

  • S. Otsubo, S. Ito, A. Dechant, and T. Sagawa Estimating entropy production by machine learning of short-time fluctuating currents Physical Review E 101, 062106 (2020).

  • S. Ito, and A. Dechant Stochastic Time Evolution, Information Geometry, and the Cramér-Rao Bound PHYSICAL REVIEW X 10, 021056 (2020).

  • S. Ito, M. Oizumi, and S-i. Amari Unified framework for the entropy production and the stochastic interaction based on information geometry Physical Review Research 2, 033048 (2020).

  • M. Meijers, S. Ito, and P. R. ten Wolde Behavior of information flow near criticality Phys. Rev. E 103, L010102 (2021).

  • Seohyun Lee, Hyuno Kim, Hideo Higuchi and Masatoshi Ishikawa. Visualization Method for the Cell-Level Vesicle Transport Using Optical Flow and a Diverging Colormap. Sensors 2021, 21, 522, 1-13　(2021).

  • Seine A. Shintani, Takumi Washio and Hideo Higuchi. Mechanism of Contraction Rhythm Homeostasis for Hyperthermal Sarcomeric Oscillations of Neonatal Cardiomyocytes.Sci. Rep.10:20468, 1-12　(2020)

  • Seohyun Lee, Hyuno Kim, Hideo Higuchi, Masatoshi Ishikawa. Visualization and Data Analysis for Intracellular Transport using Computer Vision Techniques. 2020 IEEE Sensors Applications Symposium. IEEE Xplore 20055684, 1-6 (2020)

  • Seohyun Lee, Hyuno Kim, Hideo Higuchi. Extended Dual-Focus Microscopy for Ratiometric-Based 3D Movement Tracking. Appl.Sci. 10,6243;1-12 (2020).

  • Kohsuke Gonda, Hiroshi Negishi, Mayumi Takano-Kasuya, Narufumi Kitamura, Naoko Furusawa, Yasushi Nakano, Yoh Hamada, Masayuki Tokunaga, Hideo Higuchi, Hiroshi Tada, Takanori Ishida. Heterogeneous drug efficacy of an antibody-drug conjugate visualized using simultaneous imaging of its delivery and intracellular damage in living tumor tissues. Translational Oncology. 13, 100764,1-11 (2020).


会議録 （Conference proceedings)
  • Alexandr Yu. Kondratiev, Hideyuki Yaginuma, Yasushi Okada, Andrey S. Krylov, and Dmitry V. Sorokin. 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, New York, NY, USA, 67–73. DOI:https://doi.org/10.1145/3417519.3417558 "
  • Hiroshi Yamashita, Hideyuki Suzuki and Kazuyuki Aihara: "Representation and Destabilization of Local Minima in Continuous-Time Boolean Satisfiability Solver," Proceedings of the 2020 International Symposium on Nonlinear Theory and its Applications (NOLTA2020), pp. 258-261 (2020).
  • Kohei Homma, Norihiro Maruyama, Atsushi Masumori, Takashi Ikegami Cognitive map and subjective time compression generated by Hierarchical RNNn Interactive Session on jsai2020 online-2-33 "
  • Atsushi Masumori, Itsuki Doi, John Smith, Ryuta Aoki and Takashi Ikegami. Evolving Acoustic Niche Differentiation and Soundscape Complexity Based on Intraspecific Sound Communication The 2020 Conference on Artificial Life, pp.465-472 Palin Choviwatana, Shota Ejima, Mizuki Oka and Takashi Ikegami. Web as an evolutionary ecosystem: Emergence of keystone species. The 2020 Conference on Artificial Life, pp.230-238
  • Hiroki Sato, Itsuki Doi, Yasuhiro Hashimoto, Mizuki Oka, Takahashi and Takashi Ikegami. Selection and Accelerated Divergence in Hashtag Evolution on a Social Network Service. The 2020 Conference on Artificial Life, pp.535-540
  • C. Watanabe and M. Yanagisawa, "Unique phase behavior in cell size space: Synergetic effect of molecular crowding and confinement", Biophysical Reviews, 12 (2), 385-386 (2020)

総説解説 （Reviews)
  • 古澤力, 前田智也, 芝井厚: 大腸菌進化実験の表現型・遺伝子型解析：微生物生態系進化の予測と制御へ向けて, 実験医学, 38(18):3072 (2020).
  • 斉藤 稔, 井元大輔, 澤井 哲「深層学習による細胞形状解析」実験医学 38(20), 3461 – 3466 (2020)
  • 高尾大輔、岡田康志、「細胞画像のわずかな違いをとらえて分類するAI―細胞画像の見分け方をAIに教えてもらおう」、実験医学増刊「機械学習を生命科学に使う!」、羊土社(2020)
  • 岡田康志、「生きている系の統計力学」、パリティ編集委員会編、物理科学,この1年2020、丸善出版(2020)
  • 石原秀至, 杉村薫「組織変形の定量化手法と多階層連続体モデル」特集：細胞や個体の集団が生み出すかたち，パターンとダイナミクス, 生物物理 60 pp. 37-43 (2020)
  • 能瀬聡直、高坂洋史　「ショウジョウバエ行動制御回路の構造と機能解剖」　生物物理 60(6):319-324 (2020) doi: 10.2142/biophys.60.319
  • 若本祐一　「ラマン分光を用いた細胞内の遺伝子発現の推定」実験医学増刊 Vol.38 No.20, 3376（2020）
  • 合原一幸：「人工知能の現在と未来 ー疾病動態への数理的アプローチを例にしてー」，臨床血液，Vol.61, No.5, pp.549-553 (2020).
  • 合原一幸：「未病の数学的定義に基づく超早期精密医療に向けて」，糖尿病・内分泌代謝科, Vol.52, No.2, pp.137-141 (2021).
  • 太田邦史,　小田有沙「多部位ゲノム再編成系TAQingシステムによる生物機能の改良」（株）技術情報協会「ゲノム編集技術を応用した製品開発とその実用化」（2021）
  • 小林 徹也 生命科学における機械学習の応用とその課題 数理科学 58,7,43-49 (2020)"
  • Molecular Mechanisms of REM Sleep,Yamada R.G., Ueda H.R.,Front. Neurosci. 13, 1402 (2020)
  • Tissue clearing and its applications in neuroscience,Ueda H.R., Ertürk A., Chung K., Gradinaru V., Chédotal A., Tomancak P., Keller P.J. Nat. Rev. Neurosci. doi:10.1038/s41583-019-0250-1 (2020)
  • 渡邊千穂, 柳澤実穂. 「化粧品のDDSに貢献するリポソームの開発と応用」コスメティックステージ, Vol. 14 (3), (2020)
  • 島亜衣: 広辞苑を3倍楽しむ（第106回）「筋肉」, 科学（岩波書店）, 2020.1
  • Masahiro Uesaka*, Shigeru Kuratani, Naoki Irie,The developmental hourglass model and recapitulation: An attempt to integrate the two models. Journal of Experimental Zoology, part B (2021) https://doi.org/10.1002/jez.b.23027 "
  • Shigeru Kuratani*, Masahiro Uesaka, Naoki Irie,How can recapitulation be reconciled with modern concepts of evolution? Journal of Experimental Zoology, part B (2021) https://doi.org/10.1002/jez.b.23020 "
  • Chikara Furusawa*, Naoki Irie* Toward understanding of evolutionary constraints: experimental and theoretical approaches Biophysical Reviews DOI: 10.1007/s12551-020-00708-2 (2020)"
  • Mizuuchi, R.*, Ichihashi, N.* Primitive Compartmentalization for the Sustainable Replication of Genetic Molecules. Life 11, 191(2021).
  • 市橋伯一　「原始生命の細胞構造を探る」地學雑誌　129巻6号871-880 (2020)
  • 市橋伯一　「物質から生命への進化の鍵は寄生体との共進化にあった?!」化学　75巻　46-49 (2020)
  • 芦田 慶太, 設樂 久志, 岡 浩太郎「食物欠乏は線虫の走化性行動を変化させる」生物物理60, 346-348 (2020)
  • 伊藤創祐「物理学と情報幾何学 - ゆらぐ系の熱力学の視点から」数理科学 Ｎｏ.689 2020年11月号 (2020)
  • T. Toyota, H. Sugiyama, S. Hiroi, H. Ito, H. Kitahata, Chemically Artificial Rovers Based on Self-propelled Droplets in Micrometer-scale Environment, Current Opinion in Colloid and Interface Science, 49, 60-68 (2020).
  • 豊田太郎, 森田雅宗，ジャイアントベシクルを利用したバイオ分析, ぶんせき, Vol.7, 255-260 (2020).

著書 （Books)
  • 金子 邦彦, 澤井 哲, 高木 拓明, 古澤 力 「細胞の理論生物学: ダイナミクスの視点から」東京大学出版会 (2020)
  • Nobuhito Yamamoto and Yasushi Okada, ed. Single Molecule Microscopy in Neurobiology, Springer 2020, ISBN: 978-0716-0531-8
  • 小川（西秋） 葉子/是永 論/太田 邦史　編著「モビリティーズのまなざし―ジョン・アーリの思想と実践」丸善出版（2020）
  • 小鍛治俊哉、幡野敦、柚木克之、黒田真也 「マウス肝臓における肥満特異的な代謝制御トランスオミクスネットワーク構築」実験医学(羊土社）、38(8)：1289-1294 (2020)
  • 小林徹也, 杉村薫, 舟橋啓 (編著), 実験医学増刊号「機械学習を生命科学に使う！ 」羊土社 (2020)
  • 島亜衣, 竹内昌治: 培養肉研究の現状と展望, 臨床栄養, Vol.136, No.7, pp.962-963, 2020.6
  • 山田哲也, 大崎寿久, 竹内昌治: 第4章 人工細胞膜を利用したセンサ開発, 膜たんぱく質工学ハンドブック, pp.504-509, 2020.4
  • T. Toyota, (J. Čejková, ed.), Samoreprodukce chemického modelu buňky, Robot 100 - Sto rozumů, Vysoká škola chemicko-technologická v Praze, pp.319-322 (in Czech, 2020年11月).