2018.4～2019.3
原著論文 （Refereed original papers)

• A. Germond, T. Ichimura, T. Horinouchi, H. Fujita, C. Furusawa, T. M. Watanabe,
  Raman spectral signature reflects transcriptomic features of antibiotic resistance in Escherichia coli”,
  Communications Biology, 1:85 (2018)
  
  
• K. Okamoto, A. Germond, H. Fujita, C. Furusawa, Y. Okada, T. M. Watanabe,
  “Single cell analysis reveals a biophysical aspect of collective cell-state transition in embryonic stem cell differentiation”,
  Sci. Rep., 8(1):11965 (2018)
  
  
• C. Furusawa and K. Kaneko,
  “Formation of dominant mode by evolution in biological systems”,
  Phys. Rev. E, 97(4), 042410 (2018)
  
  
• K. Tokuyama, Y. Toya, T. Horinouchi, C. Furusawa, F. Matsuda, *H. Shimizu,
  “Application of adaptive laboratory evolution to overcome a flux limitation in an Escherichia coli production strain.”,
  Biotechnol. Bioeng., 115(6):1542-1551 (2018)
  
  
• C. Furusawa, T. Horinouchi, T. Maeda,
  “Toward prediction and control of antibiotic-resistance evolution”,
  Curr. Opin. Biotechonl., 54, 45-59 (2018)
  
  
• T. Hirasawa, M. Saito, K. Yoshikawa, C. Furusawa, H. Shimizu,
  "Integrated Analysis of the Transcriptome and Metabolome of Corynebacterium glutamicum during Penicillin-Induced Glutamic Acid Production”,
  Biotechnol. Jour., 1700612 (2018)
  
  
• T. Maeda, T. Horinouchi, N. Sakata, A. Sakai, C. Furusawa,
  “High-throughput identification of the sensitivities of an Escherichia coli ΔrecA mutant strain to various chemical compounds”,
  Jour. Antibiot., in press
  
  
• Y. Fujimoto, K. Kaneko.
  Functional Dynamics by Intention Recognition in Iterated Games.
  New J. Phys. 21, 023025 (2019)
  
  
• M. Inoue, K. Kaneko.
  Cooperative reliable response from sloppy gene-expression dynamics.
  EPL, 124, 38002(2018)
  
  
• Y. J. Matsubara and K. Kaneko.
  Kinetic selection of template polymer with complex sequences.
  Phys. Rev. Lett. 121, 118101 (2018)
  
  
• A.Kamimura　and K. Kaneko.
  Exponential growth for self-reproduction in a catalytic reaction network: relevance of a minority molecular species and crowdedness.
  New J. Phys. 20, 035001 (2018)
  
  
• T.Kohsokabe and K. Kaneko.
  Boundary-Induced Pattern Formation from Uniform Temporal Oscillation.
  Chaos 28, 045110 (2018)
  
  
• K. Kaneko and C. Furusawa.
  Macroscopic Theory for Evolving Biological Systems Akin to Thermodynamics.
  Ann. Rev. Biophys, 47, 273-290 (2018)
  
  
• V. Nier, G. Peyret, J. d’Alessandro, S. Ishihara, B. Ladoux, and P. Marcq.
  Kalman inversion stress microscopy.
  Biophys. J. 115, 1808-1816 (2018)
  
  
• Shima T, Morikawa M, Kaneshiro J, Kambara T, Kamimura S, Yagi T, Iwamoto H, Uemura S, Shigematsu H, Shirouzu M, Ichimura T, Watanabe TM, Nitta R, Okada Y, Hirokawa N.
  Kinesin-binding-triggered conformation switching of microtubules contributes to polarized transport.
  J Cell Biol. 217:4164-4183, 2018 Oct 8. pii: jcb.201711178. doi: 10.1083/jcb.201711178. [Epub ahead of print] PubMed PMID: 30297389.
  
  
• Hayashi K, Tsuchizawa Y, Iwaki M, Okada Y.
  Application of the fluctuation theorem for non-invasive force measurement in living neuronal axons.
  Mol Biol Cell, 29:3017-3025, 2018 Oct 3:mbcE18010022. doi: 10.1091/mbc.E18-01-0022. [Epub ahead of print] PubMed PMID: 30281391.
  
  
• Gzrybowski M, Taki M, Senda K, Sato Y, Ariyoshi T, Okada Y, Kawakami R, Imamura T, Yamaguchi S.
  A highly photostable near-infrared labeling agent based on a phospha-rhodamine for long-term and deep imaging.
  Angew. Chem. 57:10137-10141, 2018. doi:10.1002/anie.201804731
  
  
• komatsu N, Terai K, Imanishi A, Kamioka Y, Sumiyama K, Jin T, Okada Y, Nagai T, Matsuda M.
  A platform of BRET-FRET hybrid biosensors for optogenetics, chemical screening, and in vivo imaging.
  Scientific Reports 8: 8984, 2018.>
  
  
• K. Sasaki, M. Kaya, and H. Higuchi.
  A unified walking model for dimeric motor proteins Biophys. J.115, 1-12 (2018)
  
  
• 3,Yoshimi Kinoshita1, Taketoshi Kambara1, 2, Kaori Nishikawa1, Motoshi Kaya1 and Hideo Higuchi1*.
  Step Sizes and Rate Constants of Single-headed Cytoplasmic Dynein Measured with Optical Tweezers.
  Sci. Rep. 16333 (2018.11)
  
  
• 4. Seohyun Lee, Hyuno Kim, Hideo Higuchi.
  Numerical method for vesicle movement analysis in a complex cytoskeleton network.
  Opt. Express 26, 16236-16239 (2018)
  
  
• S. Yamamoto, Y. Iwamaru, Y. Shimizu, Y. Ueda, M. Sato, K. Yamaguchi and J. Nakanishi,
  “Epidermal growth factor-nanoparticle conjugates change the activity from anti-apoptotic to pro-apoptotic at membrane rafts”
  Acta Biomater., 88, 383-391 (2019). DOI: 10.1016/j.actbio.2019.02.026.
  
  
• K. Fushimi, T. Miyazaki, Y. Kuwasaki, T. Nakajima, T. Yamamoto, K. Suzuki, Y. Ueda, K. Miyake, Y. Takeda, J.-H. Choi, H. Kawagishi, E. Y. Park, M. Ikeuchi, M. Sato and R. Narikawa,
  “Rational conversion of chromophore selectivity of cyanobacteriochromes to accept mammalian intrinsic biliverdin”
  Proc. Natl. Acad. Sci. USA, accepted.
  
  
• Ryo Nishihara, Ramasamy Paulmurugan, Takahiro Nakajima, Eiji Yamamoto, Arutselvan Natarajan, Rayhaneh Afjei, Yuki Hiruta, Naoko Iwasawa, Shigeru Nishiyama, Daniel Citterio, Moritoshi Sato, Sung Bae Kim and Koji Suzuki,
  Highly bright and stable NIR-BRET with blue-shifted coelenterazine derivatives for deep-tissue imaging of molecular events in vivo,
  Theranostics online date 2019-2-14; doi:10.7150/thno.32219; in press
  
  
• K. J. Kobayashi-Kirschvink, H. Nakaoka, A. Oda, K. F. Kamei, K. Nosho, H. Fukushima, Y. Kanesaki, S. Yajima, H. Masaki, K. Ohta, Y. Wakamoto.
  Linear Regression Links Transcriptomic Data and Cellular Raman Spectra.
  Cell Systems 7(1), 104-117.E4 (2018)
  
  
• Hiroshi Yamaguchi, Toshiyuki Oda, Masahide Kikkawa, & Hiroyuki Takeda,
  Systematic studies of all PIH proteins in zebrafish reveal their distinct roles in axonemal dynein assembly.
  eLife, 2018 May 9;7. pii: e36979. doi: 10.7554/eLife.36979.
  
  
• Yui Uchida Y, Masahiro Uesaka, Takayoshi Yamamoto, Hiroyuki Takeda & Naoki Irie,
  Embryonic lethality is not sufficient to explain hourglass-like conservation of vertebrate embryos.
  EvoDevo, 9(7)(2018)
  
  
• Inoue Y., Kumagai M., Zhang X., Saga T., Wang D., Koga A. & Takeda H.
  Fusion of piggyBac-like transposons and herpesviruses occurs frequently in teleosts.
  Zoological Letters, 4:6 (2018)
  
  
• Naoki Irie*, Noriyuki Satoh, Shigeru Kuratani.
  The phylum Vertebrata: a case for zoological recognition.
  Zoological Letters 4:32 (2018)
  
  
• Umeda M., Tsunekawa C., Senmatsu S., Asada R., Abe T., Ohta K., Hoffman CS., Hirota K.
  Histone Chaperone Asf1 Is Required for the Establishment of Repressive Chromatin in Schizosaccharomyces pombe fbp1 Gene Repression.
  Mol Cell Biol. 38(18) pii: e00194-18 (2018).
  
  
• Kobayashi-Kirschvink KJ, Nakaoka H., Oda A., Kamei KF., Nosho K., Fukushima H., Kanesaki Y., Yajima S., Masaki H, Ohta K., *Wakamoto Y.
  　Transcriptomes and Raman spectra are linked linearly through a shared low-dimensional subspace.
  　Cell Systems 7:104-117.e4. (2018)
  
  
• Muramoto N., *Oda A., Tanaka H., Nakamura T., Kugou K., Suda K., Kobayashi A., Yoneda S., Ikeuchi A., Sugimoto H., Kondo S., Ohto C., Shibata T., *Mitsukawa N., Ohta K.
  Phenotypic diversification by enhanced genome restructuring after induction of multiple DNA double-strand breaks
  Nature Commun., 9: 1995 (2018)
  
  
• Yamada S., Kugou K., Ding DQ., Fujita Y., Hiraoka Y., Murakami H., Ohta K., *Yamada T.
  The conserved histone variant H2A.Z illuminates meiotic recombination initiation.
  Curr. Genetics 64: 1015-1019 (2018)
  
  
• Okamoto Y, Iwasaki WM, Kugou K, Takahashi KK, Oda A, Sato K, Kobayashi W, Kawai H, Sakasai R, Takaori-Kondo A, Yamamoto T, Kanemaki MT, Taoka M, Isobe T, Kurumizaka H, Innan H, Ohta K, Ishiai M, *Takata M.
  Replication stress induces accumulation of FANCD2 at central region of large fragile genes.
  Nucleic Acids Res., 46: 2932-2944 (2018)
  
  
• Yamada S., Kugou K., Ding DQ., Fujita Y., Hiraoka Y., Murakami H., Ohta K., *Yamada T.
  The histone variant H2A.Z promotes initiation of meiotic recombination in fission yeast.
  Nucleic Acids Res., 46: 609-620 (2018)
  
  
• Adachi A., Senmatsu S., Asada R., Abe T., Hoffman C.S., Ohta K. *Hirota K.
  Interplay between ADCRs and histone acetylation regulates the formation of accessible chromatin in fission yeast fbp1 upstream regulatory region.
  Genes & Genetic Systems, 92: 267-276 (2018)
  
  
• Goto T, Ito Y, Michiue T.
  Roles of Xenopus chemokine ligand CXCLh (XCXCLh) in early embryogenesis.
  Dev. Growth Differ. 60: 226-238. (2018)
  
  
• Hirano S, Yamamoto T, Michiue T.
  FRET-based tension measurement across actin-associated mechanotransductive structures using Lima1.
  Int. J. Dev. Biol. 62:631-636. (2018)
  
  
• Watanabe T, Yamamoto T, Tsukano K. Hirano S. Horikawa A, Michiue T.
  Fam46a regulates BMP-dependent pre-placodal ectoderm differentiation in Xenopus.
  Development 145: pii:dev166710. (2018)
  
  
• Soeda S, Yamada-Nomoto K, Michiue T, Ohsugi M.
  RSK/MASTL pathway delays meiotic exit in mouse zygotes to ensure paternal chromosome stability.
  Dev. Cell. 47: 363-376. (2018)
  
  
• T. Fujimori, A. Nakajima, N. Shimada and S. Sawai.
  Tissue self-organization based on collective cell migration by contact activation of locomotion and chemotaxis.
  PNAS In press (2019) DOI: 10.1073/pnas.1815063116
  
  
• K. Nishio; R. Belle; T. Katoh; A. Kawamura; T. Sengoku; K. Hanada; N. Ohsawa; M. Shirouzu; S. Yokoyama; H. Suga
  "Thioether Macrocyclic Peptides Selected against TET1 Compact Catalytic Domain Inhibit TET1 Catalytic Activity."
  Chembiochem : a European journal of chemical biology, 19, 979-985 (2018)
  
  
• T. Passioura; B. Bhushan; A. Tumber; A. Kawamura; H. Suga　
  "Structure-activity studies of a macrocyclic peptide inhibitor of histone lysine demethylase 4A."
  Bioorganic & medicinal chemistry, 26, 1225-1231 (2018)
  
  
• J.M. Rogers; S. Kwon; S.J. Dawson; P.K. Mandal; H. Suga; I. Huc
  "Ribosomal synthesis and folding of peptide-helical aromatic foldamer hybrids."
  Nature chemistry, 10, 405-412 (2018)
  
  
• T. Katoh; H. Suga
  "Ribosomal Incorporation of Consecutive beta-Amino Acids."
  Journal of the American Chemical Society, 140, 12159-12167 (2018)
  
  
• J.M. Bacusmo; A.B. Kuzmishin; W.A. Cantara; Y. Goto; H. Suga; K. Musier-Forsyth
  "Quality control by trans-editing factor prevents global mistranslation of non-protein amino acid alpha-aminobutyrate."
  RNA Biol, 15, 576-585 (2018)
  
  
• T.E. McAllister; T.L. Yeh; M.I. Abboud; I.K.H. Leung; E.S. Hookway; O.N.F. King; B. Bhushan; S.T. Williams; R.J. Hopkinson; M. Munzel; N.D. Loik; R. Chowdhury; U. Oppermann; T.D.W. Claridge; Y. Goto; H. Suga; C.J. Schofield; A. Kawamura
  "Non-competitive cyclic peptides for targeting enzyme-substrate complexes."　
  Chemical science, 9, 4569-4578 (2018) 　
  
  
• H. Suga
  "Max-Bergmann award lecture:A RaPID way to discover bioactive nonstandard peptides assisted by the flexizyme and FIT systems."
  Journal of peptide science : an official publication of the European Peptide Society, 24, (2018)
  
  
• K. Tajima; T. Katoh; H. Suga
  "Genetic code expansion via integration of redundant amino acid assignment by finely tuning tRNA pools."
  Current opinion in chemical biology, (2018)
  
  
• N.K. Bashiruddi; U. Matsunaga; M. Nagano; J. Takagi; H. Suga
  "Facile Synthesis of Dimeric Thioether-Macrocyclic Peptides with Antibody-like Affinity against Plexin-B1."
  Bioconjugate Chem, 29, 1847-1851 (2018)
  
  
• Y. Goto; H. Suga
  "Engineering of RiPP pathways for the production of artificial peptides bearing various non-proteinogenic structures."
  Current opinion in chemical biology, 46, 82-90 (2018)
  
  
• T. Passioura; W. Liu; D. Dunkelmann; T. Higuchi; H. Suga
  "Display Selection of Exotic Macrocyclic Peptides Expressed under a Radically Reprogrammed 23 Amino Acid Genetic Code."
  Journal of the American Chemical Society, 140, 11551-11555 (2018)
  
  
• T. Passioura; K. Watashi; K. Fukano; S. Shimura; W. Saso; R. Morishita; Y. Ogasawara; Y. Tanaka; M. Mizokami; C. Sureau; H. Suga; T. Wakita
  "De Novo Macrocyclic Peptide Inhibitors of Hepatitis B Virus Cellular Entry."
  Cell chemical biology, 25, 906-+ (2018)
  
  
• T. Kusakizako; Y. Tanaka; C.J. Hipolito; H. Suga; O. Nureki
  "Crystallographic Analysis of MATE-Type Multidrug Exporter with Its Inhibitors."
  Methods Mol Biol, 1700, 37-57 (2018)
  
  
• Y. Iwane; T. Katoh; Y. Goto; H. Suga
  "Artificial Division of Codon Boxes for Expansion of the Amino Acid Repertoire of Ribosomal Polypeptide Synthesis."
  Methods Mol Biol, 1728, 17-47 (2018)
  
  
• Y. Goto; H. Suga
  "Artificial In Vitro Biosynthesis Systems for the Development of Pseudo-Natural Products." B Chem Soc Jpn, 91, 410-419 (2018)
  
  
• J.M. Rogers; T. Passioura; H. Suga
  "Nonproteinogenic deep mutational scanning of linear and cyclic peptides."
  Proc Natl Acad Sci USA, 115, 10959-10964 (2018)
  
  
• W. Miao; K. Sakai; R. Imamura; K. Ito; H. Suga; T. Sakuma; T. Yamamoto; K. Matsumoto
  "MET Activation by a Macrocyclic Peptide Agonist that Couples to Biological Responses Differently from HGF in a Context-Dependent Manner."
  Int J Mol Sci, 19, 3141 (2018)
  
  
• K. W. Decoene; W. Vannecke; T. Passioura; H. Suga; A. Madder
  "Pyrrole-Mediated Peptide Cyclization Identified through Genetically Reprogrammed Peptide Synthesis."
  Biomedicines, 6, 99 (2018)
  
  
• Y. Huang; M. M. Wiedmann; H. Suga
  "RNA Display Methods for the Discovery of Bioactive Macrocycles."
  Chem Rev, XX, XXX (2018)
  
  
• W. Miao; K. Sakai; N. Ozawa; T. Nishiuchi; Y. Suzuki; K. Ito; T. Morioka; M. Umitsu; J. Takagi; H. Suga; K. Matsumoto
  "Cellular signaling and gene expression profiles evoked by a bivalent macrocyclic peptide that serves as an artificial MET receptor agonist"
  Sci Rep, 8, 16492 (2018)
  
  
• H. Hirose; C. Tsiamantas; T. Katoh; H. Suga
  "In vitro expression of genetically encoded non-standard peptides consisting of exotic amino acid building blocks."
  Curr Opin Biotechnol, 58, 28-36 (2018)
  
  
• M.E. Otero-Ramirez; T. Passioura; H. Suga
  "Structural Features and Binding Modes of Thioether-Cyclized Peptide Ligands."
  Biomedicines, 6, (2018)
  
  
• S.R. Fleming; T.E. Bartges; A.A. Vinogradov; C.L. Kirkpatrick; Y. Goto; H. Suga; L.M. Hicks; A.A. Bowers
  "Flexizyme-enabled benchtop biosynthesis of thiopeptides."
  Journal of the American Chemical Society (2019)
  
  
• T.P. Christoph Nitsche, Paul Varava, Mithun C. Mahawaththa, Mila M. Leuthold, Christian D. Klein, Hiroaki Suga and Gottfried Otting
  "De Novo Discovery of Nonstandard Macrocyclic Peptides as Noncompetitive Inhibitors of the Zika Virus NS2B-NS3 Protease."
  ACS Med. Chem. Lett., (2019)
  
  
• R. Takatsuji; K. Shinbara; T. Katoh; Y. Goto; T. Passioura; R. Yajima; Y. Komatsu; H. Suga
  "Ribosomal synthesis of backbone-cyclic peptides compatible with in vitro display."
  Journal of the American Chemical Society, (2019)
  
  
• Y. Yin; Q. Fei; W. Liu; Z. Li; H. Suga; C. Wu
  "Chemical and Ribosomal Synthesis of Topologically Controlled Bicyclic and Tricyclic Peptide Scaffolds Primed by Selenoether Formation."
  Angewandte Chemie, (2019)
  
  
• A.A. Vinogradov; Y. Yin; H. Suga
  "Macrocyclic Peptides as Drug Candidates: Recent Progress and Remaining Challenges."
  Journal of the American Chemical Society, (2019)
  
  
• T. Watahiki, T. Nomoto, L. Chiari, T. Toyota, and M. Fujinami.
  Experimental investigation of the self-propelled motion of a sodium oleate tablet and boat at an oil-water interface.
  Langmuir 34, 5487-5494 (2018)
  
  
• S. Honda and T. Toyota.
  Photocontrolled network formation and dissociation with coumarin end-functionalized branched poly(dimethyl siloxane)s.
  Polymer 148, 211-216 (2018)
  
  
• S. Konno, T. Banno, H. Takagi, S. Honda and T. Toyota.
  Irreversible Aggregation of Alternating Tetra-Block-Like Amphiphile in Water.
  PLOS ONE 13, e0202816 (2018).
  
  
• Yohsuke Fukai, Masaki Sano
  Large-scale flow out of spatiotemporal chaos in electroconvection of cholesteric liquid crystal
  2019/3/5 Bulletin of the American Physical Society American Physical Society
  
  
• Takaki Yamamoto, Masaki Sano
  Hydrodynamic rotlet dipole driven by spinning chiral liquid crystal droplets
  2019/2/25 Physical Review E American Physical Society
  
  
• Kawata, K., Yugi, K., Hatano, A., Kokaji, T., Tomizawa, Y., Fujii, M., Uda, S., Kubota, H., Matsumoto, M., Nakayama, K.I., and Kuroda, S.
  Reconstruction of global regulatory network from signaling to cellular functions using phosphoproteomic data
  Genes to Cells 24, 82–93. (2018) doi: 10.1111/gtc.12655
  
  
• Inoue, H., Kunida, K., Matsuda, N., Hoshino, D., Wada, T., Imamura, H., Noji, H., and Kuroda, S.
  Automatic Quantitative Segmentation of Myotubes Reveals Single-cell Dynamics of S6 Kinase Activation
  Cell Struct. Funct. 43, 153-169 (2018) doi: 10.1247/csf.18012
  
  
• Kubota, H., Uda, S., Matsuzaki, F., Yamauchi, Y., and Kuroda, S.
  In Vivo Decoding Mechanisms of the Temporal Patterns of Blood Insulin by the Insulin-AKT Pathway in the Liver
  Cell Sys. 7, 1-11 (2018) doi:10.1016/j.cels.2018.05.013
  
  
• J. Park, S. Kondo, H. Tanimoto, H. Kohsaka and A. Nose.
  Data-driven analysis of motor activity implicates 5-HT2A neurons in backward locomotion of larval Drosophila.
  Sci Rep. 2018 Jul 9;8(1):10307 (2018)
  
  
• Norihiro Maruyama,Daichi Saito, Yasuhiro Hashimoto, Takashi Ikegami,
  Dynamic organization of flocking behaviors in a large-scale boids model,
  journal of Computational Social Science, 2019 pp 1–8
  
  
• John Brumley, Charles Taylor, Reiji Suzuki, Takashi Ikegami, Victoria Vesna, Hiroo Iwata,
  Bird Song Diamond in Deep Space 8k.
  AI & Society, September 2018. DOI, 10.1007/s00146-018-0862-4.
  
  
• Otto E Rossler, Lisa-Ruth Vial, Frank Kuske, August Nitschke, Takashi Ikegami and Andrei Ujica,
  Brain Equation and Personogenesis,
  Clinics in Pediatrics, vol.2 2019, pp.1-11.
  
  
• Y.Nakanishi-Ohno and K.Hukushima,
  Data-driven diagnosis for compressed sensing with cross validation,
  Physical Review E, 98, 052120 (2018)
  
  
• R.Tamura and K.Hukushima,
  Bayesian optimization for computationally extensive probability distributions,
  PloS one 13 (3), e0193785 (2018)
  
  
• Y.Mizuno and K.Hukushima,
  Power-law decay in the nonadiabatic photodissociation dynamics of alkali halides due to quantum wavepacket interference,
  J. Chem. Phys. 149 (17), 174313(2018)
  
  
• S.Takabe, T.Maehara and K.Hukushima,
  Typical approximation performance for maximum coverage problem,
  Physical Review E 97 (2), 022138 (2018)
  
  
• J.F. Yamagishi , N. Saito, and K. Kaneko.
  The advantage of leakage of essential metabolites and resultant symbiosis of diverse species,
  arXiv:1811.10172
  
  
• T. Komori, A. Shibai, H. Saito, Y. Akeno, A. Germond, T. Horinouchi, C. Furusawa and S. Tsuru.
  Enhancement of K‐strategy evolution in histidine utilization using a container with compartments,
  Volume23, Pages 893-903 (2018)
  
  
• Tetsuya Hiraiwa and Roland Netz,
  ”Systematic bottom-up theory for the viscoelastic response of worm-like-chain networks”,
  Europhysics Letters Vol.123, p.58002 (2018).
  
  
• Tetsuya Hiraiwa,
  “Two types of exclusion interactions for self-propelled objects and collective motion induced by their combination”,
  Physical Review E Vol.99, p.012614 (2019).v
  
  

会議録 （Conference proceedings)

• Alexandr Yu. Kondratiev ; Hideyuki Yaginuma ; Yasushi Okada ; Dmitry V. Sorokin.
  A Method for Automatic Tracking of Cell Nuclei in 2D Epifluorescence Microscopy Image Sequences.
  Eighth International Conference on Image Processing Theory, Tools and Applications (IPTA). 2018
  
  
• Seohyun Lee, Hyuno Kim, Masatoshi Ishikawa, and Hideo Higuchi.
  3D Nanoscale Tracking Data Analysis for Intracellular Organelle Movement using Machine Learning Approach.
  International conference on Artificial Intelligence in Information and Communication. 181-184 (2019)
  
  
• Doi, D., & Ikegami, T.
  "Endogenous and Exogenous Bursts in a Honey Bee Hive."
  Artificial Life Conference Proceedings. One Rogers Street, Cambridge, MA 02142-1209 USA journals-info@ mit. edu: MIT Press, 2018.
  
  
• Masumori, A., Sinapayen, L., Maruyama, N., Mita, T., Bakkum, D., Frey, U., ... & Ikegami, T.
  (2018, July). Autonomous Regulation of Self and Non-Self by Stimulation Avoidance in Embodied Neural Networks.
  In Artificial Life Conference Proceedings (pp. 163-170).
  One Rogers Street, Cambridge, MA 02142-1209 USA journals-info@ mit. edu: MIT Press.
  
  
• Ikegami, T., Virgo, N., Witkowski, O., Oka, M., Suzuki, R. and Iizuka, H.
  (2018).Beyond AI: A New Epistemology for Artificial Life and Complex Systems, an Introduction to the 2018 ALIFE conference.
  In Artificial Life Conference Proceedings (pp. 1-4).
  One Rogers Street, Cambridge, MA 02142-1209 USA journals-info@mit.edu: MIT Press.
  
  

総説解説 （Reviews)

• K. Kaneko, C. Furusawa,
  "Macroscopic Theory for Evolving Biological Systems Akin to Thermodynamics",
  Annual Rev. Biophys., 47, 273-290 (2018)
  
  
• T. Horinouchi, T. Maeda, C. Furusawa,
  "Understanding and engineering alcohol-tolerant bacteria using OMICS technology”,
  World Jour. Microb. Biotech., 34(11), 157 (2018)
  
  
• 金子邦彦, 古澤力, "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", 日本生物物理学会誌, 74(3), 137-145 (2019)
  
  
• 金子邦彦, 古澤力　「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」日本物理学会誌, 第74巻 第3号, 137 (2019)
  
  
• 樋口秀男　「ファイマンラチェット-生体分子の運動の理解にむけて-」数理科学56 , 34-39 (2019)
  
  
• 佐藤守俊「バイオ医薬品創出の基盤技術であるゲノム編集を自由自在に光操作する」
  
  
• 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, 17-21 (2019)
  
  
• 入江直樹　「動物学の百科事典」　公益社団法人日本動物学会 , 3-20, ファイロティピック段階 (2018)
  
  
• 小田有沙、太田邦史、『制限酵素を用いた新しいゲノム改良技術　〜大規模ゲノムシャフリング 「TAQing システム」』、バイオサイエンスとインダストリーVol.76 No.5 (2018年)
  
  
• 神野圭太　近藤洋平　澤井哲　「スケール不変な細胞間シグナリング」生物物理58(6) 316-318 (2018)
  
  
• 本多 智, 豊田太郎「光で流動・非流動状態を制御する高分子材料－ナマコをヒントに生みだされた次世代の新素材」化学 73, 40-44 (2018)
  
  
• 豊田太郎「ジャイアントベシクルの基礎と細胞構成系・再構成系への展開」Molecular Electronics and Bioelectronics 29, 12-15 (2018)
  
  
• H. Sugiyama and T. Toyota. Toward Experimental Evolution with Giant Vesicles. Life 8, 53 (2018)
  
  
• 髙木優、能瀬聡直　「ショウジョウバエ幼虫の行動制御回路」　月刊臨床神経科学36(8), 903-906 (2018)
  
  
• 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 Aug 18.
  
  
• 永井健、平岩徹也、太田隆夫 「アクティブソフトマターの動的秩序」固体物理 (8月号 通巻630号) 423-434頁 (2018) .
  
  
• 平岩徹也「アクトミオシン細胞骨格のダイナミクスと力学の数値シミュレーション」
  分子シミュレーション研究会会誌「アンサンブル」20, (No. 3, 7月号 通巻83号) 167-172頁 (2018).
  
  
• Tetsuya Hiraiwa, Fu-Lai Weng, Tatsuo Shibata and Erina Kuranaga,
  “Mathematical Modeling of Tissue Folding and Asymmetric Tissue Flow during Epithelial Morphogenesis”,
  Symmetry Vol.11, p.113 (2019).
  
  

著書 （Books)

• 分担執筆, 定量生物学（小林徹也 編）, 化学同人, 2018
  
  
• 金子邦彦（分担執筆）、第13章　生命システムの物理ーゆらぎ、安定性、可塑性ー（『現代物理の展望』放送大学教育振興会（2019））
  
  
• 杉村薫, 石原秀至「組織の力・応力の定量生物学」小林徹也編　定量生物学 第７章(2018年8月)化学同人
  
  
• 金本理奈, 石原秀至「弱点克服 物理数学」東京図書(2019)
  
  
• 岡田康志、超解像・一分子イメージングによる分子動態の計測、森泰生、尾藤晴彦編、脳神経化学、第30章、319－329、化学同人、2018
  
  
• H. Higuchi and C. Shingyoji.
  Measuring the Motile Properties of Single Dynein Molecules. Chaper 5 In Handbook of dynein 2nd eds. Hirose and Amos ed.
  Pan Stanford Publishing.　In press (2019)
  
  
• 若本 祐一 （分担執筆）, 細胞成長・増殖の定量生物学. 第5章 In 定量生物学 - 生命現象を定量的に理解するために. 化学同人 (2018)
  
  
• 太田邦史 「生命多元性原理」入門　講談社メチエ (2018)
  
  
• 澤井哲 中島昭彦
  「這いまわる細胞の走化性に関する定量生物学」『定量生物学 －生命現象を定量的に理解するために－』（小林徹也 編）第6章p.93-107.
  化学同人 (2018)
  
  
• T. Toyota, T. Banno and K. Asakura.
  Synthetic approaches to control self-propelled motion of micrometre-sized oil droplets in aqueous solution.
  Chapter 5 In Self-organized Motion: Physicochemical Design based on Nonlinear Dynamics. Nakata, Pimienta, Lagzi, Kitahata,
  Suematsu ed. RSC Publishing (2018)
  
  
• 池上高志、分担執筆、iHuman 有機体‐人間‐機械の未来、学芸みらい社 2019年3月
  
  

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