業　績　＜Publications＞

2019.4～2020.3
原著論文 （Refereed original papers)
  • K Ashida, H Shidara, K Hotta, K Oka. Optical dissection of synaptic plasticity for early adaptation in Caenorhabditis elegans. Neuroscience. 428, 112-12 (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)

  • A. Ikeda, T. Kawasaki, L. Berthier, K. Saitoh and T. Hatano. Universal relaxation dynamics of sphere packings below jamming Phys. Rev. Lett. 124, 058001-1-6 (2020)

  • H. Mizuno, M. Shimada and A. Ikeda. Anharmonic properties of vibrational excitations in amorphous solids Phys. Rev. Research 2, 013215-1-13 (2020)

  • K. Saitoh, T. Hatano, A. Ikeda and B. P. Tighe. Stress relaxation above and below the jamming transition Phys. Rev. Lett. 124, 118001-1-5 (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)

  • 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)

  • Advantage of Leakage of Essential Metabolites for Cells”, J. F. Yamagishi, N. Saito, K. Kaneko, Phys. Rev. Lett., 124(4):048101 (2020)

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

  • H. Sugiyama, T. Osaki, S. Takeuchi, T. Toyota, “Hydrodynamic condensation of small molecules and ions into cell-sized liposomes”, Communications Chemistry, 3, 32 (2020)

  • Mikihisa Muta, Mikihisa Muta, Ryo Iizuka, Tatsuya Niwa, Yuanfang Guo, Hideki Taguchi, Takashi Funatsu. Nascent SecM chain interacts with outer ribosomal surface to stabilize translation arrest. Biochem. J. 477 (2): 557-566 (2020)

  • M.K. Kajita, K. Aihara, and T.J. Kobayashi: "Reliable Target Ligand Detection by Noise-induced Receptor Cluster Formation," Chaos: An Interdisciplinary Journal of Nonlinear Science, Vol.30, No.1, 011104-1-6 (2020)

  • Masashi K. Kajita, Kazuyuki Aihara, Tetsuya J. Kobayashi、 Reliable target ligand detection by noise-induced receptor cluster formation .Chaos (2020)

  • So Nakashima, Yuki Sughiyama, Tetsuya J. Kobayashi. Lineage EM Algorithm for Inferring Latent States from Cellular Lineage Trees. Bioinformatics. Accepted (2020)

  • Tetsuya J. Kobayashi. Bayesian gates for reliable logical operations under noisy condition. Physical Review E. accepted (2020)

  • Qian-YuanTang and Kunihiko Kaneko. Long-range Correlation in Protein Dynamics: Confirmation by Structural Data and Normal Mode Analysis. PLoS Comp. Biol., 16 (2), e1007670 (2020)

  • T.U. Sato, K. Kaneko. Evolutionary dimension reduction in phenotypic space. Phys. Rev. Research, 2 (1), 013197 (2020)

  • K.Itao, K. Kaneko. Evolution of Kinship Structures Driven by Marriage Tie and Competition. PNAS, 117 (5), 2378-2384 (2020)

  • J.F. Yamagishi, N. Saito and K. Kaneko. Advantage of Leakage of Essential Metabolites for Cells. Phys. Rev. Lett. 124, 048101 (2020)

  • Y. Himeoka, K. Kaneko. Epigenetic Ratchet: Spontaneous Adaptation via Stochastic Gene Expression. Scientific Reports, 10, 459 (2020)

  • T.S. Hatakeyama, K. Kaneko. Transition in relaxation paths in allosteric molecules: Enzymatic kinetically constrained model. Phys. Rev. Research 2, 012005(R) (2020)

  • Shun Otsubo, Sosuke Ito, Andreas Dechant and Takahiro Sagawa ”Estimating entropy production by machine learning of short-time fluctuating currents” arXiv:2001.07460 (2020). [Preprint]

  • Sosuke Ito, Masafumi Oizumi and Shun-ichi Amari ”Unified framework for the entropy production and the stochastic interaction based on information geometry” arXiv:1810.09545v5 (2020). [Preprint]

  • Ninomiya H, Intoh A, Ishimine H, Onuma Y, Ito Y, Michiue T, Tazaki A, Kato M. Application of a human mesoderm tissue elongation system in vitro derived from human induced pluripotent stem cells to risk assessment for teratogenic chemicals. Chemosphere. (2020)

  • Satoshi Ishida, Naohiro Terasaka, Takayuki Katoh & Hiroaki Suga,An aminoacylation ribozyme evolved from a natural tRNA-sensing T-box riboswitch, Nature Chemical Biology (2020)

  • Kato Y., Kuroda T., Huang Y., Ohta R., Goto Y., Suga H.,Chemoenzymatic Posttranslational Modification Reactions for the Synthesis of Ψ[CH2NH]-Containing Peptides,Angewandte Chemie - International Edition(2020)

  • Goto Y., Suga H.,In Vitro Biosynthesis of Peptides Containing Exotic Azoline Analogues,ChemBioChem(2020)

  • C. Tsiamantas; S. Kwon; J.M. Rogers; C. Douat; I. Huc; H. Suga,Ribosomal Incorporation of Aromatic Oligoamides as Peptide Sidechain Appendages.,Angew Chem Int Edit, (2020)

  • S.R. Fleming; P.M. Himes; S.V. Ghodge; Y. Goto; H. Suga; A.A. Bowers,Exploring the Post-Translational Enzymology of PaaA by mRNA Display.,J Am Chem Soc, (2020)

  • T. Katoh; H. Suga,Ribosomal Elongation of Cyclic γ-Amino Acids using a Reprogrammed Genetic Code.",J Am Chem Soc, (2020)

  • Quek LE, Krycer JR, Ohno S, Yugi K, Fazakerley DJ, Scalzo R, Elkington SD, Dai Z, Hirayama A, Ikeda S, Shoji F, Suzuki K, Locasale JW, Soga T, James DE, Kuroda S.Dynamic 13C Flux Analysis Captures the Reorganization of Adipocyte Glucose Metabolism in Response to Insulin.iScience. 23(2):100855, (2019)

  • Tottori, T., Fujii, M., Kuroda, S.Robustness against additional noise in cellular information transmissionPhys.Rev.E100, 042403, (2019)

  • Tetsuya J. Kobayashi, Yuki Sughiyama. Fitness Gain of Individually Sensed Information by Cells. Entropy. 21(10), 1002 (2019)

  • Kazumasa B. Kaneko, Ryosuke Tateishi, Takahisa Miyao, Yuki Takakura, Nobuko Akiyama, Ryo Yokota, Taishin Akiyama, Tetsuya J. Kobayashi. Quantitative Analysis Reveals Reciprocal Regulations Underlying Recovery Dynamics of Thymocytes and Thymic Environment in Mice. Communication Biology. 11(2), 444 (2019)

  • N. Takeuchi, K. Kaneko. The origin of the central dogma through conflicting multilevel selection. Proc. R. Soc. B. 286: 20191359 (2019)

  • Y.Fujimoto, K. Kaneko. Emergence of Exploitation as Symmetry Breaking in Iterated Prisoner's Dilemma. Phys.Rev.Research.1, 033077（2019）

  • A. Kamimura, K. Kaneko. Molecular Diversity and Network Complexity in Growing Protocells. Life. 9, 53 (2019)

  • A. Kamimura, Y.J. Matsubara, K. Kaneko, and N. Takeuchi. Horizontal transfer between loose compartments stabilizes replication of fragmented ribozymes. PLoS Comp. Biol. e15, e1007094 (2019)

  • Toshinori Namba and Shuji Ishihara, "Cytoskeleton polarity is essential in determining orientational order in basal bodies of multi-ciliated cells", PLoS Comput Biol 16(2): e1007649 (2020)

  • E.Nakamura and K. Kaneko. Statistical Evolutionary Laws in Music Styles. Scientific Reports, vol. 9, No. 15993, pp. 1-11, (2019)

  • Senmatsu S, Asada R, Abe T, Hoffman CS, Ohta K, Hirota K. lncRNA transcriptional initiation induces chromatin remodeling within a limited range in the fission yeast fbp1 promoter. Sci Rep. 9: 299 (2019).

  • Kariyazono R, Oda A, Yamada T, Ohta K. Conserved HORMA domain-containing protein Hop1 stabilizes interaction between proteins of meiotic DNA break hotspots and chromosome axis. Nucl. Acids Res. 47: 10166-10180 (2019).

  • 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 in press.

  • Abe K, Shimada A, Tayama S, Nishikawa H, Kaneko T, Tsuda S, Karaiwa A, Matsui T, Ishitani T, Takeda H. Horizontal Boundary Cells, a Special Group of Somitic Cells, Play Crucial Roles in the Formation of Dorsoventral Compartments in Teleost Somite. Cell Reports 27(3), 928 - 939 (2019)

  • Fukushima HS, Takeda H, & Nakamura R. Targeted in vivo epigenome editing of H3K27me3. Epigenetics & Chromatin, 12(1):17(2019)

  • Takashi Ikegami, Yasuhiro Hashimoto and Mizuki Oka. Open-Ended Evolution and a Mechanism of Novelties in Web Services. Artificial Life, 25:2, pp.168-177 (2019)

  • Norihiro Maruyama,Daichi Saito, Yasuhiro Hashimoto, Takashi Ikegami. Dynamic organization of flocking behaviors in a large-scale boids model. Journal of Computational Social Science, pp.1-8 (2019)

  • Otto E Rossler, Lisa-Ruth Vial, Frank Kuske, August Nitschke, Takashi Ikegami and Andrei Ujica. Brain Equation and Personogenesis. Clinics in Pediatrics, vol.2, pp.1-11 (2019)

  • Olaf WItkowski and Takashi Ikegami. How to Make Swarms Open-Ended? Evolving Collective Intelligence Through a Constricted Exploration of Adjacent Possibles. [in press] arXiv:1903.08228 (2019)

  • Y. Li, H. Kokubu, and K. Aihara. Explicit Transversality Conditions and Local Bifurcation Diagrams for Bogdanov - Takens Bifurcation on Center Manifolds. Physica D, Vol.39, pp.52-65 (2019)

  • T. Miyaji, N. Sviridova, K. Aihara, T. Zhao, and A. Nakano. Human Photoplethysmogram through the Morse Graph: Searching for the Saddle Point in Experimental Data, Chaos, Vol.29, No.4, 043121 (2019)

  • K. Koizumi, M. Oku, S. Hayashi, A. Inujima, N. Shibahara, L. Chen, Y. Igarashi, K. Tobe, S. Saito, M. Kadowaki, and K. Aihara. Identifying Pre-disease Signals before Metabolic Syndrome in Mice by Dynamical Network Biomarkers, Scientific Reports, Vol.9, Article No.8767, pp.1-11 (2019)

  • H. Tamura, Y. Katori, K. Aihara. Possible Mechanism of Internal Visual Perception: Context-dependent Processing by Predictive Coding and Reservoir Computing Network, Journal of Robotics, Networking and Artificial Life, Vol.6, No.1, pp.42-47 (2019)

  • T. Kanamaru and K. Aihara: "Acetylcholine-mediated Top-down Attention Improves the Response to Bottom-up Inputs by Deformation of the Attractor Landscape," PLOS ONE, Vol.14, No.10, e0223592, pp.1-23 (2019)

  • T. Matsumori, H. Sakai, and K. Aihara: "Early-warning Signals using Dynamical Network Markers Selected by Covariance," Physical Review E, Vol.100, No.5, 052303, pp.1-9 (2019)

  • J. Shi, T. Li, L. Chen, and K. Aihara: "Quantifying Pluripotency Landscape of Cell Differentiation from scRNA-seq Data by Continuous Birth-death Process," PLOS Computational Biology, Vol.15, No.11, pp.1-17 (2019)

  • K. Tokuda, Y. Katori, and K. Aihara: "Chaotic Dynamics as a Mechanism of Rapid Transition of Hippocampal Local Field Activity between Theta and Non-theta States," Chaos, Vol.29, No.11, 113115, pp.1-16 (2019)

  • K. Shiraishi, H. Mizuno and A. Ikeda. Vibrational properties of two-dimensional dimer packings near the jamming transition Phys. Rev. E 100, 012606-1-16 (2019).

  • N. Oyama, T. Kawasaki, H. Mizuno and A. Ikeda. Glassy dynamics of a model of bacterial cytoplasm with metabolic activities Phys. Rev. Research 1, 032038-1-6(R) (2019)

  • H. Senoo, Y. Kamimura, R. Kimura, A. Nakajima, S. Sawai, H. Sesaki and M. Iijima, Phosphorylated Rho–GDP directly activates mTORC2 kinase towards AKT through dimerization with Ras–GTP to regulate cell migration. Nature Cell Biology 21, 867-878 (2019) doi: 10.1038/s41556-019-0348-8

  • Y. Yoon, J. Park, A. Taniguchi, H. Kohsaka, K. Nakae, S. Nonaka, S. Ishii and A. Nose. System level analysis of motor-related neural activities in larval Drosophila. J Neurogenet. 33, 179-189. (2019)

  • *H. Kohsaka, M. Zwart, A. Fushiki, R. Fetter, J. Truman, A. Cardona and *A. Nose. Regulation of forward and backward locomotion through intersegmental feedback circuits in Drosophila larvae. Nat. Commun. 10(1):2654. (2019)

  • David BG, Fujita H, Yasuda K, Okamoto K, Panina Y, Ichinose J, Sato O, Horie M, Ichimura T, Okada Y, Watanabe TM. Linking substrate and nucleus via actin cytoskeleton in pluripotency maintenance of mouse embryonic stem cells., Stem cell research 41 101614-101614, (2019)

  • Kaneshiro J, Okada Y, Shima T, Tsuji M, Imada K, Ichimura T, Watanabe TM. Second harmonic generation polarization microscopy as a tool for protein structure analysis. Biophys Physbiol. 16: 147-157, (2019)

  • Wang C, Taki M, Sato Y, Tamura Y, Yaginuma H, Okada Y, Yamaguchi S. A photostable fluorescent marker for the superresolution live imaging of the dynamic structure of the mitochondrial cristae. Proc Natl Acad Sci U S A. 116(32):15817-15822, (2019)

  • Tanaka H, Okazaki T, Aoyama S, Yokota M, Koike M, Okada Y, Fujiki Y, Gotoh Y. Peroxisomes control mitochondrial dynamics and the mitochondrion-dependent apoptosis pathway. J Cell Sci. 132: jcs224766, (2019)

  • Kono K, Yoshiura S, Fujita I, Okada Y, Shitamukai A, Shibata T, Matsuzaki F. Reconstruction of Par-dependent polarity in apolar cells reveals a dynamic process of cortical polarization. eLife 8: e45559, (2019)

  • Lu CH, Tang WC, Liu YT, Chang SW, Wu FCM, Chen CY, Tsai YC, Yang SM, Kuo CW, Okada Y, Hwu YK, Chen P, Chen BC. Lightsheet localization microscopy enables fast, large-scale, and three-dimensional super-resolution imaging. Commun Biol. 2:177, (2019)

  • Theoretical modeling reveals that regulatory T cells increase T-cell interaction with antigen-presenting cells for stable immune tolerance, T. Yamaguchi, S. Teraguchi, C. Furusawa, H Machiyama, T. M. Watanabe, H. Fujita, S. Sakaguchi, T. Yanagida, Int. Immunol., 31(11):743-753 (2019)

  • “Complete Genome Sequence of a Radioresistant Bacterial Strain, Deinococcus grandis ATCC 43672”, A.Shibai, K. Satoh, M. Kawada, I. Narumi, C. Furuswa, Microb. Res. Announc., 8(45):e01226 (2019)

  • “Complete Genome Sequences of Three Star-Shaped Bacteria, Stella humosa, Stella vacuolata, and Stella Species ATCC 35155”, A.Shibai, T. Maeda, M. Kawada, H. Kotani, N. Sakata, C. Furusawa, Microb. Res. Announc., 8(32):e00719 (2019)

  • “Development of an Automated UV Irradiation Device for Microbial Cell Culture”, A.Shibai, S. Tsuru, T. Yomo, SLAS Technol., 24(3):342-348 (2019)

  • “High-throughput identification of the sensitivities of an Escherichia coli ΔrecA mutant strain to various chemical compounds”, T. Maeda*, T. Horinouchi, N. Sakata, A. Sakai, C. Furusawa, Jour. Antibiot., 72(7):566-573 (2019)

  • C. Watanabe and M. Yanagisawa, "Unique phase behavior in cell size space: Synergetic effect of molecular crowding and confinement", Biophysical Reviews (Biophys. Rev.), in press (DOI: 10.1007/s12551-020-00656-x).

  • 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, in press.

  • D. Ishikawa, Y. Suzuki, C. Kurokawa, M. Ohara, M. Tsuchiya, M. Morita, M. Yanagisawa, M. Endo, R. Kawano, M. Takinoue*, “DNA origami nanoplate-based emulsion with designed nanopore function”, Angew. Chem. Int. Ed., 58:15299-15303 (2019)

  • S. Kohyama, N. Yoshinaga*, M. Yanagisawa, K. Fujiwara*, N. Doi, "Cell-sized confinement controls generation and stability of a protein wave for spatiotemporal regulation in cells"., eLife, 8:e44591 (2019).

  • A. Sakai, N. Hiro-oka, S. Sasaki, S. Kidoaki, M. Yanagisawa*, “Lipid membrane effect on the elasticity of gelatin microgel prepared inside lipid microdroplets”, Journal of the Society of Rheology Japan (Nihon Reoroji Gakkaishi), vol. 47, p. 55-59(2019)

  • K. Koyanagi, K. Kudo, M. Yanagisawa*, , “Sol–Gel coexisting phase of polymer microgels triggers spontaneous buckling”, （雑誌サプリメンタルカバーに選出）, Langmuir, vol. 35, p. 2283-2288(2019)

  • Hasegawa S., Susaki E.A., Tanaka T., Komaba H., Wada T., Fukagawa M., Ueda H.R., Nangaku M. Comprehensive three-dimensional analysis (CUBIC-kidney) visualizes abnormal renal sympathetic nerves after ischemia/reperfusion injury. Kidny Int. 96, 129-138 (2019)

  • Puelles V.G., Fleck D., Ortz L., Papadouri S., Strieder T., Böhner A.M.C., van der Wolde J.W., Vogt M., Saritas T., Kuppe C., Fuss A., Menzel S., Klinkhammer B.M., Müller-Newen G., Heymann F., Decker L., Braun F., Kretz O., Moeller M.J. Novel 3D analysis using optical tissue clearing documents the evolution of murine rapidly progressive glomerulonephritis. Kidny Int. 96, 505-516 (2019)

  • Advanced CUBIC tissue clearing for whole-organ cell profiling Matsumoto K., Mitani T.T., Horiguchi S.A., Kaneshiro J., Murakami T.C., Mano T., Fujishima H., Konno A., Watanabe T.M., Hirai H., Ueda H.R.Nat. Protoc. 14, 3506-3537 (2019)

  • Next-generation human genetics for organism-level systems biology Ukai H., Sumiyama K., Ueda H.R.Curr. Opin. Biotechnol. 58, 137-145 (2019)

  • H Mori, K Ashida, H Shidara, T Nikai, K Hotta, K Oka. Serotonin modulates behavior-related neural activity of RID interneuron in Caenorhabditis elegans. PLoS One, 14, e0226044 (2019).

  • Matthijs Meijers, Sosuke Ito, and Pieter Rein ten Wolde ”Behavior of information flow near criticality” arXiv:1906.00787 (2019). [Preprint]

  • Sosuke Ito ”Thermodynamics of information geometry as a generalization of the Glansdorff-Prigogine criterion for stability” arXiv:1908.09446 (2019). [Preprint]

  • "Recapitulation-like developmental transitions of chromatin accessibility in vertebrates Masahiro Uesaka, Shigeru Kuratani, Hiroyuki Takeda & Naoki Irie Zoological Letters volume 5, Article number: 33 (2019)

  • Visualizing dynamic actin cross-linking processes driven by the actin-binding protein anillin,Matsuda K., Sugawa M., Yamagishi M., Kodera N., Yajima FEBS Letters(2019)

  • Takumi Washio, Seine A. Shintani, Hideo Higuchi, Seiryo Sugiura and Toshiaki Hisada. Effect of myofibril passive elastic properties on the mechanical communication between motor proteins on adjacent sarcomeres. Scientific Reports 9:9355 (2019)

  • K. Sasaki, M. Kaya, J. Watoson and H. Higuchi. A unified walking model for dimeric motor proteins Biophys. J.115, 1-12 (2019)

  • "Christos Tsiamantas, Sunbum Kwon, Ce´line Douat, Ivan Huc *band Hiroaki Suga,Optimizing aromatic oligoamide foldamer side-chains for ribosomal translation initiation,Chem. Commun(2019)

  • Hirose H., Hideshima T., Katoh T., Suga H,A Case Study on the Keap1 Interaction with Peptide Sequence Epitopes Selected by the Peptidomic mRNA Display,ChemBioChem(2019)

  • Fujino T., Kondo T., Suga H., Murakami H.,Exploring the Minimal RNA Substrate of Flexizymes,ChemBioChem(2019)

  • Tsiamantas C., Otero-Ramirez M.E., Suga H.,Discovery of Functional Macrocyclic Peptides by Means of the RaPID System,Methods in Molecular Biology(2019)

  • "Mickal Nawatha1,5, Joseph M. Rogers 2,5, Steven M. Bonn3, Ido Livneh4, Betsegaw Lemma3,Sachitanand M. Mali1, Ganga B. Vamisetti1, Hao Sun1, Beatrice Bercovich4, Yichao Huang 2,Aaron Ciechanover4, David Fushman3, Hiroaki Suga2* and Ashraf Brik,De novo macrocyclic peptides that specifically modulate Lys48-linked ubiquitin chains,Nature Chemistry(2019)

  • Toby Passioura, Wenyu Liu, Daniel Dunkelmann, Takashi Higuchi, Hiroaki Suga,Correction to “Display Selection of Exotic Macrocyclic Peptides Expressed Under a Radically Reprogrammed 23 Amino Acid Genetic Code”,Journal of the American Chemical Society (2019)

  • Hisaaki Hirose1, Christos Tsiamantas1, Takayuki Katoh and Hiroaki Suga,In vitro expression of genetically encoded non-standard peptides consisting of exotic amino acid building blocks,Current Opinion in Biotechnology(2019)

  • Tran STP, Hipolito CJ, Suzuki H, Xie R, Kim Tuyen HD, Dijke PT, Terasaka N, Goto Y, Suga H, Kato M, Generation of non-standard macrocyclic peptides specifically binding TSC-22 homologous gene-1.Biochem Biophys Res Commun. (2019)

  • Y. Huang; M.M. Wiedmann; H. Suga,RNA Display Methods for the Discovery of Bioactive Macrocycles.,Chemical reviews(2019)

  • Yizhen YinNobuaki OchiTimothy W. CravenDavid BakerNagio TakigawaHiroaki Suga,De Novo Carborane-Containing Macrocyclic Peptides Targeting Human Epidermal Growth Factor Receptor,J. Am. Chem. Soc. (2019)

  • Rumit Maini,Hiroyuki Kimura,Ryo Takatsuji,Takayuki Katoh,Yuki Goto,Hiroaki Suga,Ribosomal Formation of Thioamide Bonds in Polypeptide Synthesis,J. Am. Chem. Soc. (2019)

会議録 （Conference proceedings)
  • K. F. Kamei, K. J. Kobayashi-Kirschvink, H. Nakaoka, Y. Wakamoto. Bacterial proteomes are predictable from cellular Raman spectra. APS March Meeting, Online presentation, (2020)

  • Koya Sato, Mizuki Oka, Yasuhiro Hashimoto, Takashi Ikegami and Kazuhiko Kato. How the Nature of Web Services Drive Vocabulary Creation in Social Tagging. Proc. of the 2nd International Conference on Information Science and System, [in press] (2019)

  • Norihiro Maruyama, Daichi Saito and Takashi Ikegami. Emergence of Superorganisms in a Large Scale Boids Model, 2019 IEEE Symposium on Artificial Life, [in press] (2019)

  • Daichi Saito, Norihiro Maruyama, Takashi Ikegami and Yasuhiro Hashimoto, Visualization of Dynamic Structure in Flocking Behavior, THE 3RD INTERNATIONAL SYMPOSIUM ON SWARM BEHAVIOR AND BIO-INSPIRED ROBOTICS (SWARM 2019), pp.94-100, (2019)

  • Yuma Kajihara, Takashi Ikegami, and Kenji Doya. Model-based empowerment computation for dynamical agents. 2019 IEEE Symposium Series on Computational Intelligence (SSCI), pp. 255-261, (2019.)

  • Atsushi Masumori, Takashi Ikegami and Lana Sinapayen, Predictive Coding as Stimulus Avoidance in Spiking Neural Networks, 2019 IEEE Symposium Series on Computational Intelligence (SSCI), pp. 271-277, (2019)

  • Norihiro Maruyama, Daichi Saito, and Takashi Ikegami, Emergence of Superorganisms in a Large Scale Boids Model, 2019 IEEE Symposium Series on Computational Intelligence (SSCI), pp. 299-305, (2019)

  • Shotaro Tsuji and Kazuyuki Aihara. A Fast Method of Computing Persistent Homology of Time Series Data, Proceedings of 2019 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP 2019), pp.3462-3466 (2019)

  • Farad Khoyratee, Stephany Mai Nishikawa, Zhongyue Luo, Soo Hyeon Kim, Sylvain Saighi, Teruo Fujii, Yoshiho Ikeuchi, Kazuyuki Aihara, Timothee Levi. Biomimetic Spiking Neural Network (SNN) Systems for 'in vitro' Cells Stimulation,'' Proceedings of IEEE International Symposium on Circuits and Systems, 18880988, pp.1-5 (2019)

  • Hiroshi Yamashita, Hideyuki Suzuki, Zoltan Toroczkai, and Kazuyuki Aihara. Bounded Continuous-Time Satisfiability Solver, Proceedings of the 2019 International Symposium on Nonlinear Theory and Its Applications (NOLTA2019), pp.436-439 (2019)

  • Komei Kurasawa, Hirotake Ito, Jing Ma, Toshimori Honjo, Takahiro Inagaki, Kensuke Inaba, Takuya Ikuta, Hiroki Takesue, Kazuyuki Aihara, and Mikio Hasegawa. Experimental Study on Coherent Ising Machine Applied to Hopfield-Tank Neural Network-based Optimization, Proceedings of the 2019 International Symposium on Nonlinear Theory and Its Applications (NOLTA2019), pp.274-277 (2019)

  • Huanfei Ma, Siyang Leng, Kazuyuki Aihara, and Luonan Chen. Analysis of High-dimensional Short-term Time Series Data, Proceedings of the 2019 International Symposium on Nonlinear Theory and Its Applications (NOLTA2019), p.531 (2019)

  • Takahiro Omi, Naonori Ueda, and Kazuyuki Aihara. Fully Neural Netowk based Model for General Temporal Point Processes, Advances in Neural Information Processing Systems, Vol.32, pp.2120-2129 (2019)

  • Hiroki R. Ueda, 「全身全細胞解析の実現にむけて」, 第107回　日本泌尿器科学会, 名古屋, (2019)

  • Hiroki R. Ueda, 「組織透明化技術「CUBIC」のヒト病理組織診断への応用 」, 第108回　日本病理学会　スイーツセミナー, 名古屋, (2019)

  • Hiroki R. Ueda, 「全身透明化の先に見えるもの～死因解明への応用に向けて～」, 死因研究シンポジウム, 大阪, (2019)

  • Hiroki R. Ueda, 「全脳全細胞解析の実現にむけて」, 第35回電子顕微鏡技術学会学術講演会の ワークショップ , 名古屋, (2019)

  • Hiroki R. Ueda, Systems Biology of Mammalian Sleep/Wake Cycles Toward Molecular definition of NREM and REM sleeps, 第42回　日本神経科学大会 (Neuro 2019), 新潟(2019)

  • Hiroki R. Ueda, 「全身全細胞解析の実現にむけて」, 第7回　がんと代謝研究会, 仙台, (2019)

  • Hiroki R. Ueda, 「全身全細胞解析の実現に向けて」, 第51回 日本臨床分子形態学会 総会・学術集会, 福岡, (2019)

  • Hiroki R. Ueda, Systems Biology of Mammalian Sleep/Wake ～Cycles　Phosphorylation Hypothesis of Sleep～, The 4th Symposium of the Inter-University Research Network for Trans-Omics Medicine Trans-Omics for Advanced Medical Sciences, 徳島, (2019)

  • Hiroki R. Ueda, Whole-body/organ Imaging with Single-cell Resolution Toward Organism-level Systems Biology, 3rd QST International Symposium ""Quantum Life Science"", 奈良, (2019)

総説解説 （Reviews)
  • Yuri Takiguchi, Ryo Kariyazono, Kunihiro Ohta "Detection of DNA Damage-Induced DSBs by the Contour-Clamped Homogeneous Electric Field (CHEF) System in Mammalian Cells." Methods Mol Biol. 2119:101-109. (2020)

  • Takatomi Yamada,Hiroshi Murakami,Kunihiro Ohta "Pulsed-Field Gel Electrophoresis for Detecting Chromosomal DNA Breakage in Fission Yeast." Methods Mol Biol.2119:135-143.(2020)

  • 田中剛平，合原一幸「ネットワークと脳科学」数理科学, No.680, pp.59-65 (2020)

  • 年吉 洋, 曹 良, 合原一幸　「中国COVID-19統計データに見られる特異現象」生産研究, Vol.72, No.2, pp.139-140 (2020)

  • 藤原直哉, 翁長朝功, 和田崇之, 合原一幸　「感染抑制政策の最終規模への影響」 生産研究, Vol.72, No.2, pp.141-143 (2020)

  • Kohsaka H. and Nose A. Interneurons for specific animal behavior. Cytologia, 85(1):1-2 (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)

  • 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)

  • 小林鉱石, 亀井健一郎, 中岡秀憲, 若本祐一 「ラマンスペクトルから細胞の遺伝子発現を推定する」生物物理60, 108-110 (2020)

  • 池田昌司　「ガラスの不思議とその科学」現代化学 2019年10月号, 52-58 (2019)

  • S. Takagi and A. Nose. Circuit architecture for somatotopic action selection in invertebrates. Neurosci Res. 2019 Mar;140:37-42. doi:10.1016/j.neures.2018.08.008. Epub (2018)

  • 高坂洋史「同一の神経回路網が相異なる運動出力を生み出すネットワーク機構」月刊細胞、51(14):31-33 (2019)

  • 岡田康志「蛍光イメージングによる網羅的シングルセル解析」実験医学 37(20) 3527-3532, (2019)

  • 岡田康志「超解像顕微鏡の原理と応用」病理と臨床37: 580-587, (2019)

  • 「適応と進化におけるマクロ現象論―表現型変化の低次元拘束と揺らぎ?応答関係」, 金子邦彦, 古澤力, 日本物理学会誌, 74(3), 137-147 (2019)

  • 「微生物進化実験の定量解析：予測・制御・細胞状態論へ向けて」, 古澤力, 堀之内貴明, 生物物理, 59(5), 262-265 (2019)

  • 渡邊千穂, 柳澤実穂．「リポソームの応用における基本課題と対策：膜構造と閉じ込め」膜誌, 44, 234-238 (2019)

  • 渡邊千穂，柳澤実穂. 「高分子混雑とミクロな閉じ込めが導く分子拡散」 C&I Commun. 44, 1 (2019)

  • 亀井健一郎, 小林鉱石, 中岡秀憲, 若本祐一 「細胞のラマンスペクトルから遺伝子発現プロファイルを推定する新手法」バイオサイエンスとインダストリー77(1), 17-21 (2019)

著書 （Books)
  • 金子邦彦.　普遍生物学: 物理に宿る生命、生命の紡ぐ物理. 東京大学出版会 (2019)

  • 池上高志、分担執筆、「東京大学駒場スタイル」、東京大学教養学部(2019)