論文発表 2017年3月まで


Abe S, Tabe H, Ijiri H, Yamashita K, Hirata K, Atsumi K, Shimoi T, Akai M, Mori H, Kitagawa S, Ueno T. Crystal Engineering of Self-Assembled Porous Protein Materials in Living Cells, ACS Nano, 11(3), 2410–2419, 2017. DOI: 10.1021/acsnano.6b06099, PMID: 28094987 

Arimura T, Do JH, Tanaka F. Electrochemically Switchable Molecular-Tweezers, J. Oleo Sci. 66(4), 419-423, 2017. DOI: 10.5650/jos.ess17027, PMID: 28381789

Bao HL, Ishizuka T, Sakamoto T, Fujimoto K, Uechi T, Kenmochi N, Xu Y. Characterization of human telomere RNA G-quadruplex structures in vitro and in living cells using 19F NMR spectroscopy, Nucleic Acids Res. In press, 2017. DOI:10.1093/nar/gkx109, PMID: 28180296

Higashino T, Nakatsuji H, Fukuda R, Okamoto H, Imai H, Matsuda T, Tochio H, Shirakawa M, Tkachenko NV, Hashida M, Murakami T, Imahori H. Hexaphyrin as a potential theranostic dye for photothermal therapy and 19F magnetic resonance imaging, ChemBioChem, 10, cover picture, 2017. DOI:10.1002/cbic.201700071, PMID: 28198587

Hiratani M, Ohara M, Kawano R. Amplification and quantification of an antisense oligonucleotide from target microRNA using programmable DNA and a biological nanopore, Anal Chem. 89(4), 2312-2317, 2017. DOI: 10.1021/acs.analchem.6b03830 

Islam MS, Kuribayashi-Shigetomi K, Kabir AMR, Inoue D, Sada K, Kakugo A. Role of Confinement in the Active Self-organization of Kinesin-driven Microtubules, Sensors and Actuators B: Chemical, 247, 53-60, 2017. DOI: 10.1016/j.snb.2017.03.006 

Kashida H. 樫田啓、浅沼浩之 DNA二重鎖の高い安定性と直交性をもつ疑似塩基対の開発, 高分子論文集. 2017. DOI: 10.1295/koron.2017-0009 

Kawano R, Horike N, Hijikata Y, Kondo M, Carné-Sánchez A, Larpent P, Ikemura S, Osaki T, Kamiya K, Kitagawa S, Takeuchi S, Furukawa S. Metal-organic cuboctahedra for synthetic ion channels with multiple conductance states, Chem (Cell press), 2(3), 393-403, 2017. DOI: 10.1016/j.chempr.2017.02.002

Kawashima H, Mayama H, Nakamura Y, Fujii S. Hydrophobic polypyrroles synthesized by aquesous chemical oxidative polymerization and their use as light-responsive liquid marble stabilizers, Polymer Chemistry, 8, 2609-2618, 2017. DOI: 10.1039/C7PY00158D 

Kobayashi S, Terai T, Yoshikawa Y, Ohkawa R, Ebihara M, Hayashi M, Takiguchi K, Nemoto N. In vitro Selection of Random Peptides against Artificial Lipid Bilayers: A Potential Tool to Immobilize Molecules on Membranes, Chem Commun (Camb), 53, 3458-3461, 2017. DOI: 10.1039/C7CC00099E, PMID: 28271115

Kojima K,  Matsutani Y,  Yamashita T,  Yanagawa M,  Imamoto Y,  Yamano Y,  Wada A,  Hisatomi O,  Nishikawa K,  Sakurai K, Y. Shichida Y. Adaptation of cone pigments found in green rods for scotopic vision through a single amino acid mutation. Proc. Natl. Acad. Sci. USA, 114(21), 2017, 5437-5442.  DOI: 10.1073/pnas.1620010114, PMID: 28484015

Kojima K, Yamashita T,  Imamoto Y,  Kusakabe TG,  Tsuda M,  Shichida Y. Evolutionary Steps Involving Counterion Displacement in a Tunicate Opsin. Proc. Natl. Acad. Sci. USA, 114(23), 2017, 6028-6033. DOI: 10.1073/pnas.1701088114,  PMID: 28533401

Kurokawa C, Fujiwara K, Morita M, Kawamata I, Murata S, Takinoue M, Yanagisawa M, DNA cytoskelton for stabilizing artificial cells. Proc. Nat. Ac. Sci., 114(28), 2017, 7228–7233. DOI: 10.1073/pnas.1702208114

Maity B, Abe S, Ueno T. Observation of gold sub-nanocluster nucleation within a crystalline protein cage, Nat. Commun. 8, 14820, 2017. DOI:10.1038/ncomms14820

Maity B, Ueno T. Design of Bioinorganic Materials At the Interface of Coordination and Biosupramolecular Chemistry, Chem. Rec. Volume 17, Issue 4, April 2017 , 383–398, 2017.  DOI:10.1002/tcr.201600122 

Mizukami S, Kashibe M, Matsumoto K, Hori Y, Kikuchi K. Enzyme-Triggered Compound Release using Functionalized Antimicrobial Peptide Derivatives, Chem. Sci. 8, 3047-3053, 2017. DOI: 10.1039/C6SC04435B

Mizukami S. Targetable Fluorescent Sensors for Advanced Cell Function Analysis, J. Photochem. Photobiol. C, in press, 2017. DOI: 10.1016/j.jphotochemrev.2017.01.003

Murayama K, Asanuma, H. Effect of Methyl Group on Acyclic Serinol Scaffold for Tethering Dyes on DNA Duplex stability, ChemBioChem, 18, 142-149, 2017. DOI: 10.1002/cbic.201600558 

Nakamura Y, Yamada S, Nishikawa S, Matsuura K. DNA-modified Artificial Viral Capsids self-assembled from DNA-conjugated beta-Annulus Peptide, J. Pept. Sci. in press,  2017. DOI: 10.1002/psc.2967 

Ogasawara S. Duration Control of Protein Expression In Vivo by Light-Mediated Reversible Activation of Translation, ACS CHEM BIOL. 12, 351-356, 2017. DOI:10.1021/acschembio.6b00684 

Ohara M, Takinoue M, Kawano R, Nanopore Logic Operation with DNA to RNA Transcription in a Droplet System, ACS Synthetic Biology, 6(7), 2017, 1427-1432, DOI: 10.1021/acssynbio.7b00101 PMID: 28414903

Oi H, Fujita D, Suzuki Y, Sugiyama H, Endo M, Matsumura S, Ikawa Y. Programmable formation of catalytic RNA triangles and squares by assembling modular RNA enzymes, The Journal of Biochemistry, 161 (5): 451-462, 2017. DOI: 10.1093/jb/mvw093, PMID: 28096453 

Okitsu T, Matsuyama T, Yamashita T, Ishizuka T, Yawo H, Imamoto Y, Shichida Y, Wada A. Alternative Formation of Red-Shifted Channelrhodopsins: Noncovalent Incorporation with Retinal-Based Enamine-Type Schiff Bases and Mutated Channelopsin, Chem Pharm Bull (Tokyo), 65(4), 356-358, 2017. DOI: 10.1248/cpb.c17-00054 

Saito A, Farhana TI, Kabir AMR, Inoue D, Konagaya A, Sada K, Kakugo A. Understanding the emergence of collective motion of microtubules driven by kinesins: role of concentration of microtubules and depletion force, RSC Adv. 7, 13191-13197, 2017. DOI:10.1039/C6RA27449H 

Sato Y, Hiratsuka Y, Kawamata I, Murata S, Nomura SM. Micrometer-sized molecular robot changes its shape in response to signal molecules, Science Robotics. 2(4), eaal3735, 2017. DOI: 10.1126/scirobotics.aal3735 

Shrestha P, Jonchhe S, Emura T, Hidaka K, Endo M, Sugiyama H, Mao H. Confined Space Dramatically Facilitates G-quadruplex Formation, Nature Nanotechnology, 12, 2017. DOI:10.1038/nnano.2017.29 

Suzuki Y, Taniguchi E. Molecular Artificial Intelligence by using DNA reactions, Proc. Of International Conference on Artificial Life and Robotics, 591-594, 2017.

Suzuki Y. Neural Networks by using Self-Reinfocement Reactions, Proc. Of International Conference on Artificial Life and Robotics, 595-598, 2017.

Suzuki Y. Artificial Chemistry by Sound Waves, Proc. Of International Conference on Artificial Life and Robotics, 599-602, 2017.

Takabatake F, Kawamata I, Sugawara K, Murata S. Discretization of Chemical Reactions in a Periodic Cellular Space, New Generation Computing, 1-11, 2017. DOI: 10.1007/s00354-017-0009-z 

Takahashi K, Sunohara M, Terai T, Kumachi S, Nemoto N. Enhanced mRNA-protein fusion efficiency of a single-domain antibody by selection of mRNA display with additional random sequences in the terminal translated regions, Biophys Physicobiol.  14, 23-28, 2017. DOI: 10.2142/biophysico.14.0_23, PMID: 28275529 

Tominaga Y, Usui K, Hirata A, Kitagawa A, Ito H, Nokihara K. Development of Peptide Microarray to Detect the Protein in Saliva for Periodontal Disease Test, Peptide Science 2016,  131-132, 2017.

Yang Y, Tashiro R, Suzuki Y, Emura T, Hidaka K, Sugiyama H, Endo M. A Photoregulated DNA-Based Rotary System And Direct Observation of Its Rotational Movement, Chemistry, A European Journal, 23(16), 3979-3985, 2017. DOI: 10.1002/chem.201605616 

Yasuda S, Hayakawa M, Onoe H, Takinoue M. Twisting microfluidics in a planetary centrifuge, Soft Matter, 13(11), 2141-2147, 2017. DOI: 10.1039/C6SM02695H 

Yasui M, Ikuta K. Modeling and measurement of curing properties of a photocurable polymer containing magnetic particles and microcapsules. Microsystems & Nanoengineering,  3, 17035, 2017. DOI:10.1038/micronano.2017.35.

Yue WW, Frederiksen R, Ren X, Luo DG, YamashitaT, Shichida Y, Cornwall MC, anYau KW. Spontaneous activation of visual pigments in relation to openness/closedness of chromophore-binding pocket. Elife, 6, e18492, 2017. DOI:10.7554/eLife.18492, PMID: 28186874 



Aasanuma H, Niwa R, Akahane M, Murayama K, Kashida H, Kamiya Y. Strand-invading linear probe combined with unmodified PNA, Bioorg. Med. Chem. 24, 4129-4137, 2016. DOI:10.1016/j.bmc.2016.06.055

Abe S, Maity B, Ueno T. Design of a Confined Environment using a Protein Cage and Crystals in Development of Biohybrid Materials, Chem. Commun. 52, 6496-6512, 2016. DOI:10.1039/C6CC01355D

Asada Y, Ooshita F, Inoue M. An efficient silent self-stabilizing 1-maximal matching algorithm in anonymous networks, Journal of Graph Algorithms and Applications, 20, 59-78, 2016. DOI:10.7155/jgaa.00384

Asanuma H, Murayama K, Kamiya Y, Kashida H. Design of photo-functional oligonucleotide by “copolymerization” of natural nucleobases with base-surrogate prepared from acyclic scaffold, Polym. J. 49, 279-289, 2016. DOI: 10.1038/pj.2016.120 

Azuma S, Owaki K, Shinohara N, Sugie T. Performance Analysis of Chemotaxis Controllers: Which Has Better Chemotaxis Controller, Escherichia coli or Paramecium caudatum? IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 13,No. 4,pp. 730–741. 2016. DOI:10.1109/TCBB.2015.2474397

Azuma S, Yoshida T, Sugie T. Structural Monostability of Activation-Inhibition Boolean Networks. IEEE Transactions on Control of Network Systems, to appear (2017). DOI:10.1109/TCNS.2015.2485440

Azuma S, Kure T, Sugie T. Structural Bistability Analysis of Boolean Networks, 55th IEEE Conference on Decision and Control, 2016, DOI: 10.1109/CDC.2016.7799007

Azuma S, Yoshida T, Sugie T. Designability of Multi-attractor Boolean Networks with a Fixed Network Structure, “IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences” E99-A, 423-425, 2016. DOI:10.1587/transfun.E99.A.423

Basterretxea A, Haga Y, Sanchez-Sanchez A, Isik M, Irusta L, Tanaka M, Fukushima K, Sardon H. Biocompatibility and hemocompatibility evaluation of polyether urethanes synthesized using DBU organocatalyst, EUR POLYM J. 84, 750-758, 2016. DOI: 10.1016/j.eurpolymj.2016.08.008

Das S, Flocchini P, Prencipe G, Santoro N, Yamashita M. Autonomous mobile robots with lights. THEOR. COMPUT. SCI. Volume 609, Part 1, 171-184, 2016. DOI: 10.1016/j.tcs.2015.09.018 

Doi T, Kawai H, Murayama K, Kashida H, Asanuma H. Visible Light-Triggered Crosslinking of DNA Duplex by Reversible [2+2] Photocycloaddition of Styrylpyrene. Chem. Eur. J.  22, 10533-10538, 2016. DOI: 10.1002/chem.201602006

Endo K, Hayashi K, Saito H. High-resolution Identification and Separation of Living Cell Types by Multiple microRNA-responsive Synthetic mRNAs. Sci. Rep. 6, 21991, 2016. DOI:10.1038/srep21991

Endo M. 遠藤 政幸, DNAオリガミの応用 構造から機能へ, 現代化学, No. 544, 2016, 40-45.

Flocchini P, Santoro N, Viglietta G, Yamashita M. Universal Systems of Oblivious Mobile Robots. SIROCCO 2016, 242-257, 2016. DOI: 10.1007/978-3-319-48314-6_16 

Fujimoto K, Furusawa M, Nakamura S, Sakamoto T. UVA responsive anticancer prodrugs based on photo induced electron injection into oligonucleotide having 5-halouracils, Chem. Lett. 45(9), 1078–1080, 2016. DOI:10.1246/cl.160492

Fujimoto K, Toyosato K, Nakamura S, Sakamoto T. RNA fluorescence in situ hybridization using 3-cyanovinylcarbazole modified oligodeoxyribonucleotides as photo-cross-linkable probes, BIOORG MED CHEM LETT, 26(21), 5312–5314, 2016. DOI:10.1016/j.bmcl.2016.09.035, PMID: 27680586 

Fujita K, Tanaka Y, Abe S, Ueno T. A Photoactive CO Releasing Protein Cage for Dose-Regulated Delivery in Living Cells, Anger. Chem. Int. Ed. 55, 1056-1060, 2016. DOI:10.1002/anie.201506738. PMID: 26332099

Fujita S, Matsuura K. Encapsulation of CdTe Quantum Dots in Synthetic Viral Capsids, Chem. Lett. 45 (8), 922-924, 2016. DOI: 10.1246/cl.160396 

Fujiwara K, Doi N. Biochemical preparation of cell extract for cell-free protein synthesis without physical disruption. PLOS ONE. 11(4): e0154614. 2016. DOI:10.1371/journal.pone.0154614. PMID: 27128597.

Fukushima K. Biodegradable functional biomaterials exploiting substituted trimethylene carbonates and organocatalytic transesterification, Polym. J. 48, 1103-1114, 2016. DOI: 10.1038/pj.2016.80 

Fukushima K. Poly(trimethylene carbonate)-based polymers engineered for biodegradable functional biomaterials, Biomater. Sci. 4, 9-24, 2016. DOI: 10.1039/C5BM00123D, PMID: 26323327 

Godonoga M, LinTY, Oshima A, Sumitomo K, Tang MS, Cheung YW, Kinghorn AB, Dirkzwager RM, Zhou C, Kuzuya A, Tanner JA, Heddle JG. A DNA aptamer recognising a malaria protein biomarker can function as part of a DNA origami assembly. Scientific Reports. 6: 21266. 2016. DOI:10.1038/srep21266. PMID26891622

Guégan R, Sueyoshi K, Anraku S, Yamamoto S, Miyamoto N. Sandwich organization of non-ionic surfactant liquid crystalline phases as induced by large inorganic K4Nb6O17 nanosheets. Chem. Commun. 52: 1594-1597. 2016. DOI: 10.1039/C5CC08948D.

Hagiya M, Aubert-Kato N, Wang S, Kobayashi S. Molecular computers for molecular robots as hybrid systems. Theoretical Computer Science. 632: 4–20. 2016. DOI:10.1016/j.tcs.2015.11.002.

Hasan M, Nishimoto A, Ohgita T, Hama S, Kashida H, Asanuma H, Kogure K. Faint electric treatment-induced rapid endosomal escape for efficient delivery of functional macromolecules into the cytoplasm. J. Control Release. Vol.228: 20-25. 2016. DOI:10.1016/j.jconrel.2016.02.048.

Hayakawa M, Nagai KH, Onoe H, Takinoue M. Influence of asymmetry and driving forces on the propulsion of bubble-propelled catalytic micromotors, Micromachines. 7(12), 229, 2016. DOI:10.3390/mi7120229. 

Hayakawa M, Onoe H, Nagai KH,  Takinoue M. Complex- shaped three- dimensional multi- compartmental microparticles generated by diffusional and Marangoni microflows in centrifugally discharged droplets. Sci. Rep. vol. 6. 20793. 2016. DOI:10.1038/srep20793. PMID:26861767.

Hayashi M, Nishiyama M, Kazayama Y, Toyota T, Harada Y, Takiguchi K. Reversible Morphological Control of Tubulin-Encapsulating Giant Liposomes by Hydrostatic Pressure. Langmuir.  32(15): 3794-3802. 2016. DOI:10.1021/acs.langmuir.6b00799.  PMID: 27023063

Hiratani M, Ohara M, Kawano R. Recognition of microRNA Expression Pattern in Serum Using Programmable Droplet System for Cancer Diagnosis, Proc microTAS, 1244-1245, 2016.

Ikeda M, Kabumoto M. Chemically Caged Nucleic Acids, Chem. Lett, 46(5), 634-640, 2016. DOI:10.1246/cl.161063 

Ikeda M, Kamimura M, Hayakawa Y, Shibata A, Kitade Y. Reduction-responsive guanine incorporated into G-quadruplex-forming DNA, ChemBioChem. 17, 1304-1307, 2016. DOI:10.1002/cbic.201600164, PMID: 27124306

Inoue D, Nitta T, Rashedul Kabir AM, Sada K, Gong JP, Konagaya A, Kakugo A. Sensing surface mechanical deformation using active probes driven by motor proteins.  Nature Communications, 7. 2016. DOI:10.1038/ncomms12557.

Ishikawa D, Suzuki Y, Kurokawa C, Ohara M, Morita M, Yanagisawa M, Kawano R, Endo M, Takinoue M. Self-Assembled Microcapsule of Amphiphilic Janus DNA Nanoplates at the Water-Oil Interface, Proc microTAS, 116-117, 2016.

Isokawa T, Pepper F, Kawamata I, Matsui N, Murata S, Hagiya M. Universal Totalistic Asynchonous Cellular Automaton and Its Possible Implementation by DNA, Lecture Notes in Computer Science UCNC 2016, 182-195, 2016. DOI:10.1007/978-3-319-41312-9_15 

Ito H, Higuchi Y, Shimokawa N. Coarse-grained molecular dynamics simulation of charged lipid membranes: Phase separation and morphological dynamics, Physical Review E, 94, 042611, 1-11, 2016. DOI:https://doi.org/10.1103/PhysRevE.94.042611 

Ito M, Ishiwata T, Anan S, Kokado K, Inoue D, Kabir AMR, Kakugo A, Sada K. Construction and Gilding of Metal-Organic Frameworks and Microtubule Conjugates, Chemistry Select, 1(16), 5358-5362, 2016. DOI: 10.1002/slct.201601431

Ito M, Kabir AMR, Islam MS, Inoue D, Wada S, Sada K, Konagaya A, Kakugo A. Mechanical Oscillation of Dynamic Microtubule Rings, RSC Adv. 6, 69149-69155, 2016. DOI: 10.1039/c6ra16613j 

Kabir AMR, Ito M, Uenishi K, Anan S, Konagaya A, Sada K, Sugiura M, Kakugo A. A Photoregulated ATP Generation System for In Vitro Motility Assay, Chem. Lett. 46, 178-180, 2016. DOI: 10.1246/cl.160903 

Kamachia Y, Bastakotia BP, Alshehric SM, Miyamoto N, Nakato T, Yamauchi Y. Thermo-responsive hydrogels containing mesoporous silica toward controlled and sustainable releases. Materials Letters. 168: 176-179. 2016. DOI:10.1016/j.matlet.2015.12.132.

Kandatsu D, Cervantes-Salguero K, Kawamata I, Hamada S, Nomura SM, Fujimoto K, Murata S. Reversible Gel‐Sol Transition of Photo‐Responsive DNA Gel, ChemBioChem, 17(12), 1118–1121, 2016. DOI:10.1002/cbic.201600088, PMID: 27123549

Kashida H, Asanuma H. Development of pseudo base-pairs on D-threoninol which exhibit various functions, Bull. Chem. Soc. Jpn. 90(5), 475-484, 2016 DOI: 10.1246/bcsj.20160371 

Kashida H, Morimoto K, Asanuma H. A linear probe using spontaneous pairing between Cy3 and quencher for RNA detection. Sci. Technol. Adv. Mater. in press. 2016.

Kashida H, Morimoto K, Asanuma, H. A stem-less probe using spontaneous pairing between Cy3 and quencher for RNA detection. Sci. Technol. Adv. Mater. in press. 2016. DOI:10.1080/14686996.2016.1182412.

Kashida H, Murayama K, Asanuma H. Acyclic artificial nucleic acids with phosphodiester bonds exhibit unique functions. Polymer J. in press. 2016. DOI: 10.1038/pj.2016.39.

Kato M, Sugiyama T, Sakai K, Yamashita T, Fujita H, Sato K, Tomonari S, Shichida Y, Ohuchi H. Two Opsin 3-Related Proteins in the Chicken Retina and Brain: A TMT-Type Opsin 3 Is a Blue-Light Sensor in Retinal Horizontal Cells, Hypothalamus, and Cerebellum. PLoS One, 11, e0163925, 2016. DOI:10.1371/journal.pone.0163925, PMID: 27861495 

Kawamata I, Hosoya T, Takabatake F, Sugawara K, Nomura SM, Isokawa T, Peper F, Hagiya M, Murata S. Pattern Formation and Computation by Autonomous Chemical Reaction Diffusion Model Inspired by Cellular Automaton, The Frouth International Symposium on Computing and Networking, 2016. DOI: 10.1109/CANDAR.2016.0046 

Kawamata I, Yoshizawa S, Takabatake F, Sugawara K, and Murata SDiscrete DNA Reaction-Diffusion Model for Implementing Simple Cellular Automaton, Lecture Notes in Computer Science UCNC 2016, 168-181, 2016. DOI:10.1007/978-3-319-41312-9_14 

Kawasaki S, Muraoka T, Hamada T, Shigyou K, Nagatsugi F, Kinbara K. Synthesis and Thermal Responses of Polygonal Poly (ethylene glycol) Analogues, Chemistry-An Asian Journal, 11, 1028-1035, 2016. DOI:10.1002/asia.201501381, PMID: 26864823 

Kim H, Okamoto H, Felber AE, Polomska A, Morone N, Heuser JE, Leroux JC, Murakami T. Polymer-coated pH-responsive high-density lipoproteins, J. Control. Release. 228, 132–140, 2016. DOI:10.1016/j/jconrel.2016.03.005, PMID: 26959846 

Kudo A, Sato M, Sawaguchi H, Hotta J, Mayama H, Nonomura Y. Adhesion and Disintegration Phenomena on Fractal Agar Gel Surfaces. J. Oleo Sci. 65, 909-912, 2016. DOI:10.5650/jos.ess16085 

Kumachi S, Husimi Y, Nemoto N. An RNA Binding Peptide Consisting of Four Types of Amino Acid by in Vitro Selection Using cDNA Display, ACS Omega, 1, 52–57, 2016. DOI: 10.1021/acsomega.6b00015 

Kuzyk A, Yang Y, Duan X, Stoll S, Govorov AO, Sugiyama H, Endo M, Liu N. A light-driven 3D plasmonic nanosystem that translates molecular motion into reversible chiroptical function, Nat. Commun. 7, 10591, 2016. DOI:10.1038/ncomms10591, PMID: 26830310 

Lamani A, Yamashita M. Realization of Periodic Functions by Self-stabilizing Population Protocols with Synchronous Handshakes. Proceedings of 5th International Conference on Theory and Practice of Natural Computing (TPNC2016) TPNC 2016, 21-33, 2016. DOI: 10.1007/978-3-319-49001-4_2 

Madhu R, Veeramani V, Chen SM, Veerakumar P, Liu SB, Miyamoto N. Functional Porous Carbon–ZnO Nanocomposites for High-Performance Biosensors and Energy Storage Applications, Phys. Chem. Chem. Phys. 18, 16466-16475, 2016. DOI: 10.1039/C6CP01285J 

Maeda H, Kowada T, Kikuta J, Furuya M, Shirazaki M, Mizukami S, Ishii M, Kikuchi K. Real-time intravital imaging of pH variation associated with osteoclast activity, Nat. Chem. Biol. 12, 579–585. 2016. DOI:10.1038/nchembio.2096 

Maity B, Fukumori K, Abe S, Ueno T. Immobilization of two organometallic complexes into a single cage to construct protein-based microcompartment, Chem. Commun. 52, 5463-5466, 2016. DOI: 10.1039/c6cc00679e, PMID: 27021005 

Malgras V, Kamachi Y, Nakato T, Yamauchi Y, Miyamoto N. Perspective: Recent Developments in Hybrid Hydrogels Containing Inorganic Nanomaterials, Nanosci. Nanotechnol. Lett. 8, 355-359, 2016. DOI: 10.1166/nnl.2016.2140 

Masuda K, Ripley B, Nyati K, Dubey P, Zaman M, Hanieh H, Hoga M, Yamashita K, Standley D, Mashima T, Katahira M, Okamoto T, Matsuura Y, Takeuchi O, Kishimoto T, Arid5a regulates naive CD4+ T cell fate through selective stabilization of Stat3 mRNA, Journal of Experimental Medicine, 213, 2016, 605-619. DOI: 10.1084/jem.20151289

Matsumoto K, Kawamura A, Miyata T. Conformationally Regulated Molecular Binding and Release of Molecularly Imprinted Polypeptide Hydrogels That Undergo Helix-Coil Transition, Macromolecules, 50(5), 2136-2144, 2016. DOI:10.1021/acs.macromol.6b02688

Matsumoto K, Tiu BDB, Kawamura A, Advincula RC, Miyata T. QCM Sensing of Bisphenol A Using Molecularly Imprinted Hydrogel/Conducting Polymer Matrix, Polym. J, 48, 525-532, 2016. DOI:10.1038/pj.2016.23 

Matsuura K. 松浦和則. 人工ペプチドによる自己集合性材料―ウイルスキャプシドと光誘起ナノファイバー. 生物物理. 324: 94-97. 2016. DOI:10.2142/biophys.56.094.

Matsuura K, Mizuguchi Y, Kimizuka N. Peptide Nanospheres Self-Assembled from a Modified beta-Annulus Peptide of Sesbania Mosaic Virus, Biopolymers: Peptide Science, 106(4), 470–475, 2016. DOI:10.1002/bip.22774, PMID: 26573103

Matsuura K, Nakamura T, Watanabe K, Noguchi T, Minamihata K, Kamiya N, Kimizuka N. Self-assembly of Ni-NTA-modified beta-Annulus Peptides into Artificial Viral Capsids and Encapsulation of His-tagged Proteins, Org. Biomol. Chem. 14(33), 7869–7874, 2016. DOI: 10.1039/C6OB01227B, PMID: 27386944 

Miyamoto N, Yamamoto S. Inorganic Nanosheet Liquid Crystals: Self-Assembled Structures in Dispersions of Two-Dimensional Inorganic Polymers (in Japanese), Koubunshi Ronbunshu, 73, 262-280, 2016. DOI:10.1295/koron.2015-0075

Miyata T. 宮田隆志,乗岡智沙. 特定分子に応答して膨潤収縮するゲル:分子応答性ゲル, ネットワークポリマー, 37, 61-72, 2016. DOI:10.11364/networkpolymer.37.61 

Mizukami S. 水上進、菊地和也. ラベル化分子設計に基づくタンパク質の可視化と機能制御, 薬学雑誌, 136, 21-27, 2016. DOI: 10.1248/yakushi.15-00225-4 

Morita M, Yamashita H, Hayakawa M, Onoe H, Takinoue M. Capillary- based Centrifugal Microfluidic Device for Size- controllable Formation of Monodisperse Microdroplets. J. Vis. Exp. issue 108: e53860. 2016. DOI:10.3791/53860. PMID: 26967046

Morooka T, Murakawa S, Konomi A, Goto D, Sagara T. Potential-dependent morphological change of n-hexadecane small droplets on a Au(1 1 1) electrode in aqueous solution: A voltammetric and electrochemical fluorescence microscopic study. J. Electroanal. Chem. 779: 25-33. 2016. DOI: 10.1016/j.jelechem.2016.05.040.

Mukai M, Do JH, Miyamoto N, Arimura T. A Belousov–Zhabotinsky Oscillator Driven by a Water-Soluble Metalloporphyrin. Chemistry Select. vol1: 877–878. 2016. DOI: 10.1002/slct.201600308.

Murata S, Kawamata I, Nomura SM. How to Develop Students’ Creativity? ~A Case of Student Competition of Biomolecular Design, Proceeding of IEEE-ICCSE2016, Aug 13-20, 2016.

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Onoe H, Inamori K, Takinoue M, Takeuchi S. Centrifuge-based cell encapsulation in hydrogel microbeads using sub-microliter sample solution. RSC Advances, vol.4:30480–30484. 2014. DOI: 10.1039/C4RA02773F

Ooshita F, Kawai S, Kakugawa H, Masuzawa T. Randomized gathering of mobile agents in anonymous unidirectional ring networks, IEEE Transactions on Parallel and Distributed Systems, 25, 1289-1296, 2014. DOI:10.1109/TPDS.2013.259

Osada E, Suzuki Y, Hidaka K, Ohno H, Sugiyama H, Endo M, Saito H. Engineering RNA-protein complexes with different shapes for imaging and therapeutic applications. ACS Nano. 8(8):8130-40. 2014. DOI:10.1021/nn502253c   PMID: 25058166  .

Owaki T, Shimizu T, Yamato M, Okano T. Cell sheet engineering for regenerative medicine: current challenges and strategies. Biotechnol J., 9(7):904-14. 2014. PMID: 24964041

Park SJ, Umemoto T, Saito-Adachi M, Shiratsuchi Y, Yamato M, Nakai K. Computational promoter modeling identifies the modes of transcriptional regulation in hematopoietic stem cells. PLoS One. 7;9(4):e93853. 2014. PMID: 24710559

Pirraco RP, Iwata T, Yoshida T, Marques AP, Yamato M, Reis RL, Okano T. Endothelial cells enhance the in vivo bone-forming ability of osteogenic cell sheets. Lab Invest. 94(6):663-73. 2014. PMID: 24709778

Rajendran A, Endo M, Hidaka K, Shimada N, Maruyama A, Sugiyama H. A lock-and-key mechanism for the controllable fabrication of DNA origami structures. Chem Commun (Camb)., 50(63):8743-6. 2014.  DOI:10.1039/c4cc02244k   PMID: 24965040  .

Rajendran A, Endo M, Hidaka K, Sugiyama H. Direct and single-molecule visualization of the solution-state structures of G-hairpin and G-triplex intermediates. Angew Chem Int Ed Engl., 53(16):4107-12. 2014.PMID: 24623581

Rajendran A, Endo M, Hidaka K, Tran PLT, Teulade-Fichou MP, Mergny JL, Sugiyama H. G-quadruplex-binding ligand-induced DNA synapsis inside a DNA origami frame, RSC Adv. 4(12), 6346-6355. 2014. DOI: 10.1039/C3RA45676E 

Rajendran A, Endo M, Sugiyama H. State-of-the-art high-speed atomic force microscopy for investigation of single-molecular dynamics of proteins. Chem Rev., 114(2):1493-520. 2014. PMID: 24215590

Saito AC, Ogura T, Fujiwara K, Murata S, Nomura SM. Introducing micrometer-sized artificial objects into live cells: a method for cell-giant unilamellar vesicle electrofusion. PLoS One., 9(9):e106853. 2014. DOI:10.1371/journal.pone.0106853 PMID: 25229561

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Saito H. RNA-protein nanotechnology & synthetic biology. Seikagaku, 86(1), 81-85, 2014. PMID: 24693704 

Sakai M, Suzuki Y. Evolution of Chemical Signals in ecological system evoked by the “cry-wolf” plants.  Artificial Life 14, 983-986, 2014.  DOI: http://dx.doi.org/10.7551/978-0-262-32621-6-ch160. 

Sakamoto T, Shigeno A, Ohtaki Y, Fujimoto K. Photo-regulation of constitutive gene expression in living cells by using ultrafast photo-cross-linking oligonucleotides. Biomaterials Science, 2, 9: 1154-1157. 2014.DOI: 10.1039/C4BM00117F

Sakuma M, Kumashiro Y, Nakayama M, Tanaka N, Umemura K, Yamato M, Okano T. Control of cell adhesion and detachment on Langmuir-Schaefer surface composed of dodecyl-terminated thermo-responsive polymers. J Biomater Sci Polym Ed., 25(5):431-43. 2014. PMID: 24328952

Sasagawa T, Shimizu T, Sekiya S, Yamato M, Okano T. Comparison of angiogenic potential between prevascular and non-prevascular layered adipose-derived stem cell-sheets in early post-transplanted period. J Biomed Mater Res A., 102(2):358-65. 2014.PMID: 23533096

Sasaki R, Matsumine H, Watanabe Y, Takeuchi Y, Yamato M, Okano T, Miyata M, Ando T. Electrophysiologic and functional evaluations of regenerated facial nerve defects with a tube containing dental pulp cells in rats. Plast Reconstr Surg., 134(5):970-8. 2014.PMID: 25347632

Sasaki R, Matsumine H, Watanabe Y, Yamato M, Ando T. Surgical anatomy of the hypoglossal nerve for facial nerve reconstruction research in Swine. J Reconstr Microsurg., 30(8):585-8. 2014.PMID: 24683132

Sato M, Yamato M, Hamahashi K, Okano T, Mochida J. Articular cartilage regeneration using cell sheet technology. Anat Rec (Hoboken) . 297(1):36-43. 2014.PMID: 24293096

Sato R, Obonai T, Tsumura R, Tsumoto K, Koga Y, Yasunaga M, Matsumura Y. Preparation and characterization of anti-tissue factor single-chain variable fragment antibody for cancer diagnosis. Cancer Sci., 105(12):1631-7. 2014. PMID: 25311092

Shima T, Muraoka T, Hamada T, Morita M, Takagi M, Fukuoka H, Inoue Y, Sagawa T, Ishijima A, Omata Y, Yamashita T, Kinbara K. Micrometer-Size Vesicle Formation Triggered by UV Light, Langmuir, 30, 7289-7295, 2014. DOI:10.1021/1a5008022

Shimada N, Kidoaki S, Maruyama A. Smart hydrogels exhibiting UCST-type volume changes under physiologically relevant conditions, RSC Adv. 94, 52346–52348, 2014. DOI: 10.1039/c4ra10612a

Shimada N, Song W, Maruyama A. DNA strand exchange reaction activated by cationic comb-type copolymers having ureido groups, Biomater. Sci. 2,  1480-1485, 2014. DOI: 10.1039/c4bm00207e

Shimizu R, Kamei N, Adachi N, Hamanishi M, Kamei G, Mahmoud EE, Nakano T, Nakano T, Iwata T, Yamato M, Okano T, Ochi M. Repair Mechanism of Osteochondral Defect Promoted by Bioengineered Chondrocyte Sheet. Tissue Eng Part A., 2014 Nov 14. PMID: 25396711

Shiraga T, Yamauchi Y, Kijima S, Yamashita M. L∞-Discrepancy Analysis of Polynomial-Time Deterministic Samplers Emulating Rapidly Mixing Chains. COCOON, 25-36. 2014.

Sugawara K, Correll N, Reishus D. Object Transportation by Granular Convection Using Swarm Robots, Distributed Autonomous Robotic Systems: The 11th Intemational Symposium. 135-147, 2014. DOI:10.1007/978-3-642-55146-8_10 

Sugiyama H, Yamato M, Nishida K, Okano T. Evidence of the survival of ectopically transplanted oral mucosal epithelial stem cells after repeated wounding of cornea. Mol Ther., 22(8):1544-55. 2014. PMID: 24769908

Suzuki A, Maeda S, Hara Y, Hashimoto S. Design and motion control of self-propelled droplets. Proceedings of The 27th IEEE International Conference on Micro Electro Mechanical Systems MEMS, 310-313. 2014. DOI:10.1109/MEMSYS.2014.6765638

Suzuki N, Kamachi Y, Takai K, Kiba S, Kotani T, Sakka Y, Miyamoto N, Yamauchi Y. Effective Use of Mesoporous Silica Filler: Comparative Study on Thermal Stability and Transparency of Silicone Rubbers Loaded with Various Kinds of Silica Particles Eur. J. Inorg. Chem. 2014(17):2773-2778, 2014. DOI:10.1002/ejic.201301615

Suzuki R, Aruga A, Kobayashi H, Yamato M, Yamamoto M. Development of a novel in vivo cancer model using cell sheet engineering. Anticancer Res., 34(9):4747-54. 2014. PMID: 25202053

Suzuki Y, Endo M, Cañas C, Ayora S, Alonso JC, Sugiyama H, Takeyasu K. Direct analysis of Holliday junction resolving enzyme in a DNA origami nanostructure. Nucleic Acids Res., 42(11):7421-8. 2014. DOI:10.1093/nar/gku320  PMID: 24792171

Suzuki Y, Endo M, Katsuda Y, Ou K, Hidaka K, Sugiyama H. DNA origami based visualization system for studying site-specific recombination events. J Am Chem Soc., 136(1):211-8. 2014. PMID: 24328161

Suzuki Y, Endo M, Yang Y, Sugiyama H. Dynamic assembly/disassembly processes of photoresponsive DNA origami nanostructures directly visualized on a lipid membrane surface. J Am Chem Soc. 136(5):1714-7. 2014. PMID: 24428846

Takagi R, Yamato M, Okano T. Regenerative medicine by cell sheet technology: the regeneration for stratified epithelial tissues. Arerugi., 63(9):1223-8. 2014. Japanese. No abstract available. PMID: 25492877

Takahashi H, Shimizu T, Nakayama M, Yamato M, Okano T. Anisotropic Cellular Network Formation in Engineered Muscle Tissue through the Self-Organization of Neurons and Endothelial Cells. Adv Healthc Mater., 2014 Aug 21. PMID:25146917

Takenaka T, Endo M, Suzuki Y, Yang Y, Emura T, Hidaka K, Kato T, Miyata T, Namba K, Sugiyama H. Photoresponsive DNA nanocapsule having an open/close system for capture and release of nanomaterials. Chemistry, 20(46):14951-4. 2014. DOI:10.1002/chem.201404757 PMID: 25223393

Takeuchi R, Kuruma Y, Sekine H, Dobashi I, Yamato M, Umezu M, Shimizu T, Okano T. In vivo vascularization of cell sheets provided better long-term tissue survival than injection of cell suspension. J Tissue Eng Regen Med., 2014 Jan 28. PMID: 24470393

Takinoue M. 瀧ノ上正浩, 「マイクロ流体工学による非平衡人工細胞」, 生体の科学・増大特集「生命動態システム科学」, vol.65, no.5:502-503. 2014.

Takinoue M. 瀧ノ上正浩, 「細胞に見立てた水滴のふるまいから,生命の物理的な原理を探る」(生命の最先端研究・生命の物理学(1)), Newton別冊「やさしくわかる 生命の科学」, 102-103 2014.

Takinoue M, 瀧ノ上正浩, 「細胞スケールの非平衡系における自己秩序化:自律運動と自律振動反応」, 高分子, vol.63, no.6:388-389. 2014.

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Toyota T, Banno T, Nitta S, Takinoue M, Nomoto T, Natsume Y, Matsumura S, Fujinami M. Molecular building blocks and their architecture in biologically/environmentally compatible soft matter chemical machinery. J Oleo Sci., 63(11):1085-98. 2014. PMID: 25341502

Toyota T, Fujito H, Suganami A, Onoue K, Aoki A, Muraki Y, Madono T, Fujinami M, Tamura Y, Hayashi H. Near-infrared-fluorescence imaging of lymph nodes by using liposomally formulated indocyanine green derivatives, Bioorg. Med. Chem. 22, 721-727, 2014. DOI: 10.1016/j.bmc.2013.12.026, PMID: 24393719

Ueno Y, Ito S, Konagaya A. Implementing a modeling software for animated protein-complex interactions using a physics simulation library. J Bioinform Comput Biol., 12(6):1442003. 2014. DOI:10.1142/S0219720014420037 PMID: 25385079

Umeda N, Takahashi H, Kamiya M, Ueno T, Komatsu T, Terai T, Hanaoka K, Nagano T, Urano Y. Boron Dipyrromethene As a Fluorescent Caging Group for Single- Photon Uncaging with Long-Wavelength Visible Light, ACS CHEM BIOL, 9,  2242-2246, 2014. DOI: 10.1021/cb500525p,  PMID: 25140990

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Wang S, Imai K, Hagiya M. On the Composition of Signals in Gellular Automata. Second International Symposium on Computing and Networking (CANDAR) 499-502, 2014. DOI:10.1109/CANDAR.2014.71

Washio K, Kuroda H, Iwata T, Yoshida T, Yamato M, Okano T. Improved enzymatic treatment for accurate cell counting from extracellular matrix-rich periodontal ligament cell sheets. Int J Oral Maxillofac Implants., 29(1):e117-21. 2014. PMID: 24451879

Watanabe Y, Sasaki R, Matsumine H, Yamato M, Okano T. Undifferentiated and differentiated adipose-derived stem cells improve nerve regeneration in a rat model of facial nerve defect. J Tissue Eng Regen Med., 2014 Jun 1. PMID: 24889763

Yamamoto S, De D, Hidaka K, Kim KK, Endo M, Sugiyama H. Single molecule visualization and characterization of Sox2-Pax6 complex formation on a regulatory DNA element using a DNA origami frame. Nano Lett ., 14(5):2286-92. 2014. DOI:10.1021/nl4044949  PMID: 24660747

Yamamoto Y, Hyodo I, Takigahira M, Koga Y, Yasunaga M, Harada M, Hayashi T, Kato Y, Matsumura Y. Effect of combined treatment with the epirubicin-incorporating micelles (NC-6300) and 1,2-diaminocyclohexane platinum (II)-incorporating micelles (NC-4016) on a human gastric cancer model. Int J Cancer., 135(1):214-23. 2014. PMID: 24353132

Yamashita H, Morita M, Sugiura H, Fujiwara K, Onoe H, Takinoue M. Generation of monodisperse cell-sized microdroplets using a centrifuge-based axisymmetric co-flowing microfluidic device. J Biosci Bioeng., vol.119, no.4:492-495 2014. DOI: 10.1016/j.jbiosc.2014.09.018.  PMID: 25454697

Yamashita Y, Yanagisawa M, Tokita M. Sol-gel transition and phase separation in ternary system of gelatin-water; poly (ethylene glycol) oligomer, Journal of Molecular Liquids, 200,  47-51, 2014. DOI:10.1016/j.molliq.2014.03.016 

Yamauchi Y, Yamashita M. Randomized Pattern Formation Algorithm for Asynchronous Oblivious Mobile Robots. Proceedings of the 28th International Symposium on Distributed Computing (DISC2014). LNCS8784. 137-151. 2014. DOI: 10.1007/978-3-662-45174-8_10

Yamazaki T, Heddle JG, Kuzuya A, Komiyama M. Orthogonal enzyme arrays on a DNA origami scaffold bearing size-tunable wells. Nanoscale, 6(15):9122-6. 2014. DOI:10.1039/C4NR01598C PMID: 24974892

Yanagisawa M, Nigorikawa S, Sakaue T, Fujiwara K, Tokita M. Multiple patterns of polymer gels in microspheres due to the interplay among phase separation, wetting, and gelation, Proceedings of the National Academy of Sciences of the United States of America, 111,  15894-15899, 2014. DOI:10.1073/pnas.1416592111,  PMCID: PMC4234581 

Yanagisawa M, Yamashita Y, Mukai S, Annaka M, Tokita M. Phase separation in binary polymer solution: Gelatin/Poly (ethylene glycol) system, Journal of Molecular Liquids, 200,  2-6, 2014. DOI: 10.1016/j.molliq.2013.12.035

Yang Y, Endo M, Suzuki Y, Hidaka K, Sugiyama H. Direct observation of the dual-switching behaviors corresponding to the state transition in a DNA nanoframe. Chem Commun (Camb)., 50(32):4211-3. 2014. PMID: 24626780

Yasuda S. 安田翔也, 早川雅之,瀧ノ上正浩 .「二重らせん構造を有するマイクロゲルファバーの生成手法の構築.」 化学とマイクロ・ナノシステム . vol.13, no.2: 40-41. 2014.

Yasunaga M, Matsumura Y. Role of SLC6A6 in promoting the survival and multidrug resistance of colorectal cancer. Sci Rep. 4:4852. 2014. PMID: 24781822

Yokomori T, Okubo F. Recent developments on reaction automata theory: A survey, in “Recent Advances in Natural Computing” (Selected results from the IWNC 7 Symposium). Series: Mathematics for Industry, vol.9 (Y.Suzuki and M.Hagiya, eds.) ,pp.1-22, Springer, 2014.

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Yoshimitsu K, Muragaki Y, Maruyama T, Yamato M, Iseki H. Development and initial clinical testing of “OPECT”: an innovative device for fully intangible control of the intraoperative image-displaying monitor by the surgeon. Neurosurgery. 10 Suppl 1:46-50; discussion 50. 2014. DOI:10.1227/NEU.0000000000000214. PMID: 24141478

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Cooper C, Elsaesser R, Ono H, Radzik T. Coalescing Random Walks and Voting on Connected Graphs, SIAM J. Discrete Math. 27(4),  1748-1758, 2013. DOI: 10.1137/120900368

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Dhakal S, Mao H, Rajendran A, Endo M, Sugiyama H. G-quadruplex nanostructures probed at the single molecular level by force-based methods, Guanine quartets: Structure and application, 1: 73-85, 2013, DOI: 10.1039/9781849736954-00073

Endo K, Hayashi K, Inoue T, Saito H. A versatile cis-acting inverter module for synthetic translational switches, Nat. Commun. 4, 2393, 2013. DOI: 10.1038/ncomms3393, PMID: 23999119

Endo K, Stapleton JA, Hayashi K, Saito H, Inoue T. Quantitative and simultaneous translational control of distinct mammalian mRNAs, Nucleic Acids Res. 41(13), e135, 2013. DOI: 10.1093/nar/gkt347, PMID: 23685611 

Endo M, Inoue M, Suzuki Y, Masui C, Morinaga H, Hidaka K, Sugiyama H. Regulation of B–Z Conformational Transition and Complex Formation with a Z-Form Binding Protein by Introduction of Constraint to Double-Stranded DNA by using a DNA Nanoscaffold, Chemistry, A European Journal, 19 (50),   16887-16890. 2013. DOI: 10.1002/chem.201303830, PMID: 24194496 

Endo M, Yang Y, Sugiyama H. DNA origami technology for biomaterials applications, Biomater. Sci. 1 (4), 347-360. 2013. DOI: 10.1039/c2bm00154c 

Endo M, Yamamoto S, Tatsumi K, Emura T, Hidaka K, Sugiyama H. RNA-templated DNA origami structures, Chemical Communications, 49, 2879-2881, 2013. DOI: 10.1039/c3cc38804b  PMID: 23446278

Flocchini P, Santoro N, Viglietta G, Yamashita M. Rendezvous of Two Robots with Constant Memory. Proceedings of the 20th International Colloquium on Structural Information and Communication Complexity LNCS、 8179: 189-200, 2013. DOI:10.1007/978-3-319-03578-9_16

Fujimoto K, Yamada A, Yoshimura Y, Tsukaguchi T, Sakamoto T. Details of the ultra-fast DNA photocrosslinking reaction of 3-cyanovinylcarbazole nucleoside; Cistrans isomeric effect and the application for SNP based genotyping. J. Am. Chem. Soc., 135: 16161-16167, 2013. DOI: 10.1021/ja406965f   PMID: 24087918

Fujimoto K, Futamura D, Sakamoto T. Diamine Derivatives Accelerate Photochemical C→U Transition in DNA Double Strand. Chem. Lett., 42: 289-291, 2013.  DOI:10.1246/cl.2013.289

Fujimoto K, Kishi S, Sakamoto T. Geometric Effect on the Photocrosslinking Reaction between 3-Cyanovinylcarbazole Nucleoside and Pyrimidine Base in DNA/RNA Heteroduplex. Photochemistry and Photobiology, 89: 1095-1099, 2013.  DOI:10.1111/php.12118  PMID: 23789821

Fujimoto K, Yoshinaga H, Yoshio Y, Sakamoto T. Quick and Reversible Photocrosslinking Reaction of 3-Cyanovinylcarbazole Nucleoside in DNA Triplex. Organic & Biomolecular Chemistry, 11: 5065-5068, 2013.  DOI:10.1039/C3OB40915E  PMID: 23764762

Fujimoto K, Konishi-Hiratsuka K, Sakamoto T. Quick, Selective and Reversible Photocrosslinking Reaction between 5-Methylcytosine and 3-Cyanovinylcarbazole in DNA Double Strand. Int. J. Mol. Sci. , 14(3): 5765-5774, 2013. DOI: 10.3390/ijms14035765  PMID: 23481638

Fujimoto K, Sawai S. A design principle of group-level decision making in cell populations. PLoS Comp. Biol. 9(6),  e1003110, 2013. DOI:10.1371/journal.pcbi.1003110

Fujiwara K, Aoi KB, Nomura SM. A bacterial salt sensor created by multiplying phenotypes of GroE-depleted Escherichia coli. Analytical Methods, 5: 5918-5922, 2013. DOI: 10.1039/C3AY41092G

Fujiwara K, Katayama T, Nomura SM. Cooperative working of bacterial chromosome replication proteins generated by a reconstituted protein expression system. Nucleic Acid Research, 41(14): 7176-7183, 2013.  DOI: 10.1093/nar/gkt489  PMID: 23737447

Fujiwara K, Nomura SM. Condensation of an Additive-Free Cell Extract to Mimic the Conditions of Live Cells. PLoS ONE, 8(1): e54155, 2013. DOI: 10.1371/journal.pone.0054155   PMID: 23326590

Geng F, Ma R, Nakamura A, Akatsuka K, Ebina Y, Yamauchi Y, Miyamoto N, Tateyama Y, Sasaki T. Unusually stable ~100-fold reversible and instantaneous swelling of inorganic layered materials. Nature Commun., 1632,  2013.   DOI: 10.1038/ncomms2641 PMID: 23535653

Hagiya M, Kawamata I. Towards Co-evolution of Information, Life and Artificial Life, Natural Computing and Beyond. Proceedings in Information and Communications Technology, 6: 39-48, 2013. DOI:10.1007/978-4-431-54394-7_4

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Hara Y, Mayama H, Yamaguchi Y, Takenaka Y, Fukuda R. Direct Observation of Periodic Swelling and Collapse of Polymer Chain Induced by the Belousov-Zhabotinsky Reaction. Journal OF Physical Chemistry B, 117(46): 14351-14357, 2013. DOI:10.1021/jp408417h  PMID: 24147635

Hirose E, Mayama H, Miyauchi A. Does the aquatic invertebrate nipple array prevent bubble adhesion?: an experiment using nanopillar sheets, Biology Letters, 9,  20130552, 2013. DOI: 10.1098/rsbl2013.0552

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Ishikawa J, Furuta H, Ikawa Y. RNA Tectonics (tectoRNA) for RNA nanostructure design and its application in synthetic biology. WIREs RNA, 4,  651-664, 2013. DOI:10.1002/wrna.1185

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Ito M, Kabir AMR, Inoue D, Torisawa T, Toyoshima Y, Sada K, Kakugo A. Formation of Ring-Shaped Microtubule Assemblies through Active Self-Organization on Dynein. Polymer Journal, 46: 220–225. 2013. DOI:10.1038/pj.2013.89

Kabir MH, Gong J, Watanabe Y, Makino M, Furukawa H. Hard-to-soft transition of transparent shape memory gels and the first observation of their critical temperature studied with scanning microscopic light scattering, Materials Letters, 108,  239-242, 2013. DOI:10.1016/j.matlet.2013.07.002 

Kabir MH, Watanabe Y, Gong J, Furukawa H. Characterization of shape memory gels using scanning microscopic light scattering, SPIE Proceedings, 8691,  1D1-1D7, 2013.  DOI:10.1117/12.2009098

Kamiya Y, Ito A, Ito H, Urushihara M, Takai J, Fujii T, Liang XG, Kashida H, Asanuma H. Selective labeling of mature RISC using a siRNA carrying fluorophore-quencher pair. Chem. Sci., 4: 4016-4021, 2013. DOI: 10.1039/c3sc51197a

Kashida H, Doi T, Sakakibara T, Hayashi T, Asanuma H. p-Stilbazole Moieties As Artificial Base Pairs for Photo-Cross-Linking of DNA Duplex. J. Am. Chem. Soc., 135: 7960-7966, 2013. DOI: 10.1021/ja401835j  PMID: 23642021

Keller R, Dörr A, Tabira A, Funahashi A, Ziller MJ, Adams R, Rodriguez N, Le Novère N, Hiroi N, Planatscher H, Zell A, Dräger A. The systems biology simulation core algorithm, BMC Systems Biology. 7(55), 2013. DOI: 10.1186/1752-0509-7-55, PMID: 23826941

Kobayashi S. Enumeration Approach to Computing Chemical Equilibria. Theoretical Computer Science, 499: 51-87, 2013. DOI:10.1016/j.tcs.2013.05.017

Kohara K, Yamamoto S, Seinberg L, Murakami T, Tsujimoto M, Ogawa T, Kurata H, Kageyama H, Takano M. Caboxylated SiO2-coated alpha-Fe nanoparticles: towards a versatile platform for biomedical applications, Chem. Commun. 49 (25), 2563-2565, 2013. DOI: 10.1039/c3cc39055a.  PMID: 23423558

Komatsu D, Fujiwara K, Nomura SM. Construction of a remote-controlled supramolecular micro-crawler. ADVANCES IN ARTIFICIAL LIFE, 208-209, 2013.

Kuzuya A, Watanabe R, Hashizume M, Kaino M, Minamida S, Kameda K, Ohya Y. Precise structure control of three-state nanomechanical DNA origami devices. Methods, 637-664, 2013. DOI: 10.1016/j.ymeth.2013.11.003  PMID: 24270064

Lee JW, Hamada S, Hwang SU, Amin R, Son JY, Dugasani SR, Murata S. Park SH. Quantitative analysis of molecular-level DNA crystal growth on a 2D surface, Sci. Rep. vol. 3, 2013. DOI:10.1038/srep02115 

Liang X, Zhou M, Kato K, Asanuma H. Photoswitch Nucleic Acid Catalytic Activity by Regulating Topological Structure with a Universal Supraphotoswitch. ACS Synth. Biol., 2: 194-202, 2013. DOI: 10.1021/sb300120n PMID: 23656478

Maeda Y, Higo J, Amagai Y, Matsui J, Ohkubo K, Yoshigoe Y, Hashimoto M, Eguchi K, Yamada M, Hasegawa T, Sato Y, Zhou J, Lu J, Miyashita T, Fukuzumi S, Murakami T, Tohji K, Nagase S, Akasaka S. Helicity-selective photoreaction of single-walled carbon nanotubes with organosulfur compounds in the presence of oxygen, J. Am. Chem. Soc. 135,  6356-6362, 2013. DOI:10.1021/ja402199n.

Maruyama K, Tanaka Y, Toda T, Kashida H, Asanuma H. Highly Stable Duplex Formation by Artificial Nucleic Acids Acyclic Threoninol Nucleic Acid (aTNA) and Serinol Nucleic Acid (SNA) with Acyclic Scaffolds. Chem. Eur. J., 19: 14151-14158, 2013.  DOI: 10.1002/chem.201301578 PMID: 24038212

Mathew S, Murakami T, Nakatsuji H, Okamoto H, Morone N, Heuser JE, Hashida M, Imahori H. Exclusive photothermal heat generation by a bis(naphthalocyanine) complex and inclusion into modified high-density lipoprotein nanocarriers for therapeutic applications, ACS Nano, 7,  8908-8916, 2013. DOI: 10.1021/nn403384k.  PMID: 24053139

Miyamoto N, Shintate M, Hoshida Y, Motokawa R, Annaka M. Liquid Crystalline Inorganic Nanosheets for Facile Synthesis of Polymer Hydrogels with Anisotropies in Optical Property, Structure, Swelling/Deswelling, and Ion Transport/Fixation, Chem. Commun., 1082-1084, 2013. DOI: 10.1039/c2cc36654a  PMID: 23283288

Miyamoto N. 宮元 展義. 「粘土鉱物ナノシートコロイドの液晶性.」 日本化学会研究会「低次元系光機能材料研究会」ニュースレター 4: 11-14, 2013.

Morita T, Narita T, Mukai S, Yanagisawa M, Tokita M. Phase behaviors of agarose gel, AIP Advance, 3, 042128 (13 pages) 2013. DOI: http://dx.DOI.org/10.1063/1.4802968 

Murata S, Konagaya A, Kobayashi S, Saito H, Hagiya M. Molecular Robotics: A New Paradigm for Artifacts New Generation Computing, 31: 27-45, 2013. Ohmsha, Ltd. and Springer, 2013. DOI:10.1007/s00354-012-0121-z

Naito T, Yamamoto H, Okuda K, Konishi K, Mayama H, Yamaguchi D, Koizumi S, Kubo K, Nakamura T. Magnetic ordering of spin systems having fractal dimensions, Eur. Phys. J. B, 85,  410-418, 2013. DOI:10.11400/eljb/e2013-40353-3.

Nakata A, Nomoto T, Toyota T, Fujinami M. Tip-enhanced Raman spectroscopy of lipid bilayers in water: Fluidity effect to the TERS spectra by liquid crystal phase membrane, ANAL SCI, 29, 865-870, 2013. PMID: 24025569

Natsume Y, Toyota T. Giant vesicles containing microspheres with high volume fraction prepared by water-in-oil emulsion centrifugation, Chem. Lett. 42, 295-297, 2013. DOI: http://dx.doi.org/10.1246/cl.2013.295 

Nishikawa N, Sakiyama S, Yamazoe S, Kojima Y, Nishihara E, Tsujioka T, Mayama H, Yokojima S, Nakamura S, Uchida K. Photoinduced Self-Epitaxial Crystal Growth of a Diarylethene Derivative with Antireflection Moth-Eye and Superhydrophobic Lotus Effect, Langmuir, 29 (25), 8164-8169, 2013. DOI:10.1021/la4014834, PMID: 23734978 

Nomura SM, Sato Y, Fujiwara K. Molecular robotics approach for constructing an artificial cell model. ADVANCES IN ARTIFICIAL LIFE, 488-491, 2013.

Nonomura Y, Seino E, Abe S. Mayama H. Preparation and Characterization of Fractal Elastomer Surfaces, J. Oleo Sci, 62,  587-590, 2013. PMID: 23985488 

Ohara K, Kohno M, Hamada T, Kawakami K. Entry of a cationic lytic-type peptide into the cytoplasm via endocytosis-dependent and -independent pathways in human glioma U251 cells, Peptides, 50,  28-35, 2013. DOI:10.1016/j.peptides.2013.09.015,  PMID: 24095870

Oyama T, Mayama H, Nonomura Y. Wetting Dynamics of Oil-in-Water Emulsion on Agar Gel Surfaces, Chem. Lett, 42,  871-872, 2013. DOI:10.1246/cl.130307

Phan HTT, Hata T, Morita M, Yoda T, Hamada T, Vestergaard MC, Takagi M. The effect of oxysterols on the interaction of Alzheimer’s amyloid beta with model membranes, Biochim. Biophys. Acta, Biomembr. 1828 (11), 2487-2495, 2013. DOI: 10.1016/j.bbamem.2013.06.021,  PMID: 23800382

Rajendran A, Endo M, Hidaka K, Sugiyama H. Control of the two-dimensional crystallization of DNA origami with various loop arrangements, Chemical Communications, 49: 686-688, 2013. DOI: 10.1039/c2cc37257f  PMID: 23223152

Rajendran A, Endo M, Hidaka K, Tran PLT, Mergny JL, Sugiyama H. Controlling the stoichiometry and strand polarity of a tetramolecular G-quadruplex structure by using a DNA origami frame. Nucleic Acids Res. 41 (18), 8738-8747. 2013. DOI: https://doi.org/10.1093/nar/gkt592, PMID: 23863846

Rajendran A, Endo M, Hidaka K, Tran PLT, Mergny JL, R.J. Gorelick RJ, Sugiyama H. HIV-1 nucleocapsid proteins as molecular chaperones for tetramolecular antiparallel g-quadruplex formation, Journal of the American Chemical Society, 135 (49),  18575-18585. 2013. DOI: 10.1021/ja409085j, PMID: 24224650

Rajendran A, Endo M, Hidaka K, Sugiyama H. Direct and real-time observation of rotary movement of a DNA nanomechanical device, Journal of the American Chemical Society, 135: 1117-1123, 2013. DOI:10.1021/ja310454k  PMID: 23311576

Simion AM, Arimura T, Simion C. Reaction of cinnamaldehyde and derivatives with Raney Ni-Al alloy and Al powder in water. Reduction or oxido-reduction? Comptes Rendus Chimie. Volume 16, Issue 5: 476–481, DOI: 10.1016/j.crci.2012.11.022

Sugawara K. An Object Manipulation by Swarm Robots Inspired by Granular Convection Phenomenon. Proc. of 2013 IEEE/ SICE International Symposium on System Integration, 700-705, 2013. DOI:10.1109/SII.2013.6776708

Sugawara K. Object Transportation by Simple Robots: Application of Brazil Nut Effect Proc. of SICE Annual Conference, 2613-2618, 2013.

Suzuki Y. Harness the Nature for Computation, Natural Computing and Beyond (Springer Verlag) , 6: 47-70, 2013. DOI:10.1007/978-4-431-54394-7_5

Suzuki Y, Sakai M. Modeling “info-chemical” Mediated Ecological System by using Multi Agent System, Fifth International Conference on Agents and Artificial Intelligence, ICAART, 1: 318-323, 2013.

Takahashi T, Nomura F, Yokoyama Y, Tanaka-Takiguchi Y, Homma M, Takiguchi K. Multiple Membrane Interactions and Versatile Vesicle Deformations Elicited by Melittin. Toxins, 5: 637-664, 2013.  DOI:10.3390/toxins5040637  PMID: 23594437

Takizawa H, Nakamura K, Tabira A, Chikahara Y, Matsui T, Hiroi N, Funahashi ALibSBMLSim: a reference implementation of fully functional SBML simulator, Bioinformatics, 29(11), 1474-1476, 2013. DOI: 10.1093/bioinformatics/btt157, PMID: 23564843

Tanaka-Takiguchi Y, Itoh T, Tsujita K, Yamada S, Yanagisawa M, Fujiwara K, Yamamoto A, Ichikawa M, Takiguchi K.  Physicochemical Analysis from Real-Time Imaging of Liposome Tubulation Reveals the Characteristics of Individual F‑BAR Domain Proteins, Langmuir, 29: 328-336, 2013. DOI:10.1021/la303902q PMID: 23199228

Xu X, Yamauchi Y, Kijima S, Yamashita M. Space Complexity of Self-Stabilizing Leader Election in Population Protocol Based on k-interaction. Proceedings of the 15th International Symposium on Stabilization, Safety, and Security of Distributed Systems LNCS, 8255: 86-97, 2013. DOI:10.1007/978-3-319-03089-0_7

Yamauchi Y, Yamashita M. Pattern Formation by Mobile Robots with Limited Visibility. Proceedings of the 20th International Colloquium on Structural Information and Communication Complexity LNCS, 8179: 201-212, 2013. DOI:10.1007/978-3-319-03578-9_17

Yanagisawa M, Yoshida T, Furuta M, Nakata S, Tokita M. Adhesive force between paired microdroplets coated with lipid monolayers, Soft matter, 9, 5891-5897, 2013. DOI:10.1039/C3SM50938A 

Yoshida K, Maeda K, Kusuhara H, Konagaya A. Estimation of feasible solution space using Cluster Newton Method: application to pharmacokinetic analysis of irinotecan with physiologically-basedmodelspharmacokinetic. BMC Systems Biology, 2013 7 (Suppl 3): S3, 2013. DOI:10.1186/1752-0509-7-S3-S3 PMID: 24555857



Endo M, Miyazaki R, Emura T, Hidaka K, Sugiyama H. Transcription Regulation System Mediated by Mechanical Operation of DNA Nanostructure, Journal of the American Chemical Society, 134: 2852−2855, 2012. DOI:10.1021/ja2074856  PMID: 22283546

Endo M, Tatsumi K, Terushima K, Katsuda Y, Hidaka K, Harada Y, Sugiyama H. Direct Visualization of the Movement of a Single T7 RNA Polymerase and Transcription on a DNA Nanostructure, Angewandte Chemie, International Edition, 51: 8778–8782, 2012.  DOI:10.1002/anie.201201890  PMID: 22848002

Endo M, Yang Y, Suzuki Y, Hidaka K, Sugiyama H. Single-Molecule Visualization of the Hybridization and Dissociation of Photoresponsive Oligonucleotides and Their Reversible Switching Behavior in a DNA Nanostructure, Angewandte Chemie, International Edition, 51: 10518-10522, 2012. DOI:10.1002/anie.201205247 PMID: 22965475

Endo M, Yang Y, Sugiyama H. DNA origami technology for biomaterials applications, Biomaterials Science, 1: 347-360, 2013, DOI: 10.1039/c2bm00154c First published on the web 7th December 2012.

Fujimoto K, Hiratsuka-Konishi K, Sakamoto T, Ohtake T, Shinohara K, Yoshimura Y. Specific and reversible photochemical labeling of plasmid DNA using photoresponsive oligonucleotides containing 3-cyanovinylcarbazole, Molecular BioSystems, 8 (2): 491 – 494, 2012. DOI:10.1039/c2mb05422a  PMID: 22183016

Fujinaga N, Yamauchi Y, Kijima S, Yamashita M. Asynchronous pattern formation by anonymous oblivious mobile robots, Proceedings of the 26th International Symposium on Distributed Computing(DISC 2012) , 1: 312–325, 2012.  DOI:10.1007/978-3-642-33651-5_22

Furukawa M, Suzuki Y. Honey Bee Optimization Based on Mimicry of Threshold Regulation in Honey Bee Foraging, Smart Innovation, systems and technologies, 14: 307-316, 2012, DOI: 10.1007/978-3-642-29934-6_30

Furukawa M, 古川 まき, 鈴木 泰博. 「蜜蜂の蜜源選択における閾値調整機能を模した 最適化アルゴリズム.」 日本知能情報ファジー学会誌 24: 1090-1103, 2012.

Hamada S, Murata S. Theoretical Model of Substrate-Assisted Self-Assembly of DNA Nanostructures, RSC Advances, 2: 7406-7412, 2012. DOI:10.1039/C2RA20764H

Hara Y, Jahan RA. Activation Energy of Aggregation-Disaggregation Self-Oscillation of Polymer Chain, Int. J. Mol. Sci. , 13(12): 16281-16290, 2012.  DOI:10.3390/ijms131216281  PMID: 23208370

Hayashi Y, Yuki M, Sugawara K, Kikuchi T, Tsuji K. Rhythmic Behavior of Social Insects from Single to Multibody, Robotics and Autonomous Systems, 60 (5), 714-721, 2012. DOI:10.1016/j.robot.2011.06.016 

Hirabayashi M, Kawamata I, Hagiya M, Kojima H, Oiwa K. In Silico Design Control of the Trade-Off Balance in Robustness and Fragility of Logical Circuits Using DNA Nanostructures, Nanotechnology (IEEE-NANO) , 2012 12th IEEE Conference on 1: 1-6, DOI:10.1109/NANO.2012.6321946

Kashida S, Inoue T, Saito H. Three-dimensionally designed protein-responsive RNA devices for cell signaling regulation, Nucleic Acids Reseach, 40(18), 9369-9378, 2012.  DOI: 10.1093/nar/gks668  PMID: 22810207

Kawamata I, Aubert N, Hamano M, Hagiya M. Abstraction of Graph-Based Models of Bio-Molecular Reaction Systems for Efficient Simulation, Lecture Notes in Bioinformatics, 7605: 187-206, 2012. DOI:10.1007/978-3-642-33636-2_12

Lee JW, Hamada S, Amin R, Kim SH, Kulkarni A, KimTS, Roh YH, Murata S, Ha Park SH. Size-Controllable DNA Rings with Copper-Ion Modification, Small, Vol.8, no.3 374-377, 2012, DOI:10.1002/smll.201101561. PMID: 22180079

Miyamoto N, Nakato T. Liquid Crystalline Inorganic Nanosheet Colloids Derived from Layered Materials, Israel J. Chem, 881-894, 2012.  DOI: 10.1002/ijch.201200033

Mohri K, Nishikawa M, Takahashi N, Matsuoka N, Endo M, Hidaka K, Sugiyama H, Takahashi Y, Takakura Y. Design and development of nano-sized DNA assemblies in polypod-like structures as efficient vehicle for immunostimulatory CpG motifs to immune cells. ACS Nano, 6: 5931–5940, 2012. DOI: 10.1021/nn300727j PMID: 22721419

Nakamura S, Ogasawara S, Matuda S, Saito I, Fujimoto K. Template Directed Reversible Photochemical Ligation of Oligodeoxynucleotides, Molecules, 17: 163-178, 2012. DOI: 10.3390/molecules17010163  PMID: 22202805

Nakata E, Liew FF, Uwatoko C, Kiyonaka S, Mori Y, Katsuda Y, Endo M, Sugiyama H, Morii T. Zinc finger proteins as the adaptor for locating proteins at specific addresses of DNA origami, Angewandte Chemie, International Edition, 51, 2421-2424, 2012. DOI:10.1002/anie.201108199   PMID: 22287266

Okubo F, Kobayashi S, Yokomori T. On the properties of language classes defined by bounded reaction automata, Theoretical Computer Science, 454: 206-221, 2012.

Rajendran A, Endo M, Sugiyama H. Single-Molecule Analysis Using DNA Origami, Angewandte Chemie, International Edition, 51, 874-890, 2012.  DOI:10.1002/anie.201102113  PMID: 22121063

Rajendran A, Endo M, Sugiyama H. Structure and Functional Analysis of Proteins by High-Speed Atomic Force Microscopy, Advances in Protein Chemistry and Structural Biology, 87: 5-55, 2012. DOI:10.1016/B978-0-12-398312-1.00002-0 PMID: 22607751

Rajendran A, Endo M, Sugiyama H. DNA Origami: Synthesis and Self-Assembly, Current Protocols in Nucleic Acid Chemistry, 48, 12.9.1-12.9.18, 2012. DOI:10.1002/0471142700.nc1209s48  PMID: 22395964

Shigeno A, Sakamoto T, Yoshimura Y, Fujimoto K. Quick Regulation of mRNA Functions by a Few Seconds of Photoirradiation, Organic & Biomolecular Chemistry, 10(38), 7820-7825, 2012. DOI:10.1039/c2ob25883h  PMID: 22918386

Shinya K, Gao Y, Cilloniz C, Suzuki Y, Fujie M, Deng G, Zhu Q, Fan S, Makino A, Muramoto Y, Fukuyama S, Tamura D, Noda T, Eisfeld AJ, Katze MG, Chen H, Kawaoka Y. Integrated Clinical, Pathologic, Virologic, and Transcriptomic Analysis of H5N1 Influenza Virus-Induced Viral Pneumonia in the Rhesus Macaque, Journal of Virology, 86: 6055-6066, 2012. DOI:10.1128/JVI.00365-12  PMID: 22491448

Stapleton JA, Endo K, Fujita Y, Hayashi K, Takinoue M, Saito H, Inoue T. Feedback Control of Protein Expression in Mammalian Cells by Tunable Synthetic Translational Inhibition, ACS Synthetic Biology, 1(3): 83-88, 2012.DOI:10.1021/sb200005w  PMID: 23651072

Suzuki Y. Behaviors of Chemical Reactions with Small Number of Molecules, Lecture Notes in Computer Science, 5777: 394-401, 2012. DOI:10.1007/978-3-642-21283-3_49

Wickham SF, Bath J, Katsuda Y, Endo M, Hidaka K, Sugiyama H, Turberfield AJ. A DNA-based molecular motor that can navigate a network of tracks, Nature Nanotechnology, 7, 169-173, 2012. DOI:10.1038/nnano.2011.253  PMID: 22266636

Yamazaki T, Aiba Y, Yasuda K, Sakai Y, Yamanaka Y, Kuzuya A, Ohya Y, Komiyama M. Clear-cut observation of PNA invasion using nanomechanical DNA origami devices. Chem. Commun. 48, 11361-11363.  2012. DOI: 10.1039/C2CC36358E  PubMed: 23073563

Yang Y, Endo M, Hidaka K, Sugiyama H. Photo-controllable DNA Origami Nanostructures Assembling into Predesigned Multiorientational Patterns, Journal of the American Chemical Society, 134, 20645-20653, 2012. DOI:10.1021/ja307785r  PMID: 23210720

Yoshidome T, Endo M, Kashiwazaki G, Hidaka K, Bando T, Sugiyama H. Sequence-Selective Single-Molecule Alkylation with a Pyrrole-Imidazole Polyamide Visualized in a DNA Nanoscaffold, Journal of the American Chemical Society, 134: 4654−4660, 2012. DOI:10.1021/ja209023u  PMID: 22320236


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