Journal Publications


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, to appear (2016).

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. in press. 2016.

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.

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.

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.

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

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.

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.

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.

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.

Oda Y, Sadakane K, Yoshikawa Y, Imanaka T, Takiguchi K, Hayashi M, Kenmotsu T, Yoshikawa K. Highly Concentrated Ethanol Solutions: Good Solvents for DNA as Revealed by Single-Molecule Observation. Chem Phys Chem.  17: 471-473.   2016. DOI:10.1002/cphc.201500988. PMID: 26891092

Sugawara K, Doi Y. Collective Construction of Dynamic Equilibrium Structure Through Interaction of Simple Robots with Semi-active Blocks. Distributed Autonomous Robotic Systems: The 12th Intemational Symposium. 165-176. 2016. DOI:10.1007/978-4-431-55879-8_12.

Yasuga H, Kawano R, Takinoue M, Tsuji Y, Osaki T, Kamiya K, Miki N, Takeuchi S. Logic Gate Operation by DNA Translocation through Biological Nanopores. PLOS ONE. vol. 11, e0149667. 2016. DOI: 10.1371/journal.pone.0149667. PMID: 26890568

Yonamine Y, Cervantes-Salguero K, Minami K, Kawamata I, Nakanishi W, Hill JP, Murata S, Ariga K. Supramolecular 1-D polymerization of DNA origami through a dynamic process at the 2-dimensionally confined air-water interface. Phys Chem Chem Phys 18: 12576-12581. 2016. DOI:10.1039/c6cp01586g. PMID:27091668


Asanuma H, Akahane M, Niwa R, Kashida, H, Kamiya, Y. Highly sensitive and robust linear probe for detection of mRNA in cells. Angew. Chem. Int. Ed., 54, 4315-4319, 2015. DOI: 10.1002/anie.201411000

Bastakoti BP, Li Y, Imura M, Miyamoto N, Nakato T, Sasaki T, Yamauchi Y. Polymeric Micelle Assembly with Inorganic Nanosheets for Construction of Mesoporous Architectures with Crystallized Walls. Angew. Chem. Int. Ed., 54, 4222-4225, 2015. DOI:10.1002/anie.201410942  PMID:25737396 

Cervantes-Salguero K, Hamada S, Nomura SM, Murata S. Polymorphic Ring-Shaped Molecular Clusters Made of Shape-Variable Building Blocks. Nanomaterials., 5(1), 208-217, 2015. DOI:10.3390/nano5010208

Doi T, Kashida H, Asanuma H. Efficiency of [2+2] photodimerization of various stilbene derivatives within the DNA duplex scaffold. Org. Biomol. Chem., 2015, DOI: 10.1039/C4OB02520B PMID: 25689316

Fujinaga N, Yamauchi Y, Ono H, Kijima S, Yamashita M. Pattern Formation by Oblivious Asynchronous Mobile Robots. Molecular Robotics News Letter No. 13. 14, 2015

Furutani M, Uemura A, Shigenaga A, Komiya C, Otaka A, Matsuura K. A
photoinduced growth system of peptide nanofibres addressed by DNA hybridization. Chem Commun (Camb). 2015 May 11;51(38):8020-2. DOI: 10.1039/c5cc01452b. Epub 2015 Mar 17.  PMID: 25778790

Gaudreau P. Improvements to the Cluster Newton Method for Underdetermined Inverse Problems. Molecular Robotics News Letter No.12. 13, 2015

Goldau T, Murayama K, Brieke C, Steinwand S, Mondal P, Biswas M, Burghardt I,
Wachtveitl J, Asanuma H, Heckel A. Reversible photoswitching of RNA hybridization at room temperature with an azobenzene C-nucleoside. Chemistry. 2015 Feb 9;21(7):2845-54. DOI: 10.1002/chem.201405840. Epub 2014 Dec 23. DOI: 10.1002/chem.201405840 PMID:25537843

Kabir AMR, Inoue D, Kishimoto Y, Hotta J, Sasaki K, Kitamura N, Gong JP, Mayama H, Kakugo A. Drag force on micron-sized objects with different surface morphologies in a flow with a small Reynolds number. Polymer Journal. 2015, 1-7. DOI:10.1038/pj.2015.29

Kamiya Y, Takagi T, Ooi H, Ito H, Liang X, Asanuma H. Synthetic gene involving
azobenzene-tethered T7 promoter for the photocontrol of gene expression by visible light. ACS Synth Biol. 2015 Apr 17;4(4):365-70. DOI: 10.1021/sb5001092. Epub 2014 Aug 27. PubMed PMID: 25144622

Kato N, Ishijima A, Inaba T, Nomura F, Takeda S, Takiguchi K. Effects of lipid composition and solution conditions on the mechanical properties of membrane vesicles. Membranes (Basel), 2015 Jan 20;5(1):22-47. DOI: 10.3390/membranes5010022. PMID:25611306

Kim J, Lee J, Hamada S, Murata S, Ha Park S. Self-replication of DNA rings.
Nat Nanotechnol. 2015 Jun;10(6):528-33. DOI: 10.1038/nnano.2015.87. Epub 2015 May 11. PubMed PMID: 25961509

Kimura T, Shintate M, Miyamoto N. In Situ Observation of the Evaporation-Induced Self-Assembling Process of Ps-B-Peo Diblock Copolymers for the Fabrication of Titania Films by Confocal Laser Scanning Microscopy. Chem. Commun. , 2015, 51, 1230-1233.  DOI:10.1039/C4CC08497G  PMID: 25472911

Lamani A. Self-Stabilizing Oscillation in Population Protocol. Molecular Robotics News Letter No. 13. 15, 2015

Morimoto N, Muramatsu K, Nomura SM, Suzuki M. Trading polymeric microspheres: Exchanging DNA molecules via microsphere interaction. Colloids Surf B Biointerfaces.,2015 Feb 17;128C:94-99. DOI:10.1016/j.colsurfb.2015.02.014  PMID: 25731098

Murayama K, Kashida H, Asanuma H. Acyclic L-Threoninol Nucleic Acid (L-aTNA) with Suitable Structural Rigidity Cross-pairs with DNA and RNA. Chem. Commun. , 51, 6500-6503, 2015. DOI: 10.1039/c4cc09244a

Nagai KH, Hayakawa M, Takinoue M. Self-propelled particle with rotationally asymmetric shape. Current Physical Chemistry. Vol.5, issue4, 2015. 1-9. DOI: 10.2174/1877946805999150430123824

Nakamura S,  Fujimoto KPhoto-cross-linking using trifluorothymidine and 3-cyanovinylcarbazole induced a large shifted 19F MR signal. Chem. Commun., 51, 11765-11768, 2015. DOI: 10.1039/C5CC02972D

Nishiyama H, Kobayashi Y, Yamauchi Y, Kijima S, Yamashita M. The Parity Hamiltonian Cycle Problem. CoRR., abs/1501.06323 (2015)

Ohno H, Osada E, Saito H. Design, assembly, and evaluation of RNA-protein nanostructures. Methods Mol Biol.   1297,   197-211.  2015. DOI: 10.1007/978-1-4939-2562-9_14  PMID: 25896005

Saito H. Synthetic RNA technologies to control functions of mammalian cells. Yakugaku Zasshi . 135(3), 399-404 , 2015. DOI: 10.1248/yakushi.14-00240-4.  PMID: 25759049

Shibata T, Suzuki Y, Sugiyama H, Endo M, Saito H. Folding RNA-Protein Complex into Designed Nanostructures. Methods Mol Biol.  1316, 169-179. 2015.  DOI: 10.1007/978-1-4939-2730-2_14.  PMID: 25967061

Suzuki Y, Endo M, Sugiyama H. Lipid-bilayer-assisted two-dimensional self-assembly of DNA origami nanostructures. Nature Communications 6, Article number: 8052. 2015. DOI:10.1038/ncomms9052.

Takiguchi K, Negishi M, Tanaka-Takiguchi Y, Hayashi M, Yoshikawa K. Specific Transformation of Assembly with Actin Filaments and Molecular Motors in a Cell-Sized Self-Emerged Liposome. Orig Life Evol Biosph., 2015 Jan 15.  DOI:10.1007/s11084-014-9395-0  PMID:25585806

Wada S, Kabir AMR, Kawamura R, Ito M, Inoue D, Sada K, Kakugo A. Controlling the bias of rotational motion of ring-shaped microtubule assembly. Biomacromolecules., 2015 Jan 12;16(1):374-8.  DOI:10.1021/bm501573v  PMID: 25474594

Wada S, Rashedul Kabir AMR, Ito M, Inoue D, Sada K, Kakugo A. Effect of length and rigidity of microtubules on the size of ring-shaped assemblies obtained through active self-organization. Soft Matter., 2015 Jan 5. DOI:10.1039/C4SM02292K  PMID: 25557641

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., 2015 Apr;116(4):492-5.  DOI:10.1016/j.jbiosc.2014.09.018  PMID: 25454697


Abe H, Hara Y, Maeda S, Hashimoto S. Adhesion of Gels by silica particle. Journal OF Physical Chemistry B., 118(9), 2518-2522,   DOI:10.1021/jp410367v  PMID: 24490795

Ahmed N, Murosaki T, Kurokawa T, Kakugo A, Yashima S, Nogata Y, Gong JP. Prolonged morphometric study of barnacles grown on soft substrata of hydrogels and elastomers. Biofouling., 2014;30(3):271-9. PMID: 24447274

Ahn J, Miura Y, Yamada N, Chida T, Liu X, Kim A, Sato R, Tsumura R, Koga Y, Yasunaga M, Nishiyama N, Matsumura Y, Cabral H, Kataoka K. Antibody fragment-conjugated polymeric micelles incorporating platinum drugs for targeted therapy of pancreatic cancer. Biomaterials., 2015 Jan;39:23-30. PMID: 25477168

Akimoto J, Arauchi A, Nakayama M, Kanaya R, Iwase Y, Takagi S, Yamato M, Okano T. Facile cell sheet manipulation and transplantation by using in situ gelation method. J Biomed Mater Res B Appl Biomater., 2014 Nov;102(8):1659-68. PMID: 24665017

Aoki Y, Hayami K, Sterck HD, Konagaya A. Cluster Newton Method for Sampling Multiple Solutions of Underdetermined Inverse Problems: Application to a Parameter Identification Problem in Pharmacokinetics. SIAM J. Scientific Computing., 36 (1), B14-B44, 2014. DOI:10.1137/120885462

Arimura T, Mukai M. Self-Oscillating Gel Actuator Driven by Ferroin. Chemical Communications, 50, 5861-5863, 2014.  DOI:10.1039/C4CC01613K  PMID: 24740701 

Asanuma H, Kashida H, Kamiya Y. De novo design of functional oligonucleotides with acyclic scaffolds. Chem Rec., 2014 Dec;14(6):1055-69.   DOI:10.1002/tcr.201402040  PMID: 25171046

Aubert N, Mosca C, Fujii T, Hagiya M, Rondelez Y. Computer Assisted Design for Scaling Up Systems based on DNA Reaction Networks. Journal of the Royal Society Interface, 11, 2014. PMID: 24451393

Aubert N, Rondelez Y, Fujii T, Hagiya M. Enforcing delays in DNA computing systems. Natural Computing. 13, 559-572, 2014. DOI:10.1007/s11047-014-9450-9

Baccouche A, Montagne K, Padirac A, Fujii T, Rondelez Y. Dynamic DNA-toolbox reaction circuits: a walkthrough. Methods, 2014 May 15;67(2):234-49. PMID: 24495737

Bastakoti BP, Li Y, Imura M, Miyamoto N, Nakato T, Sasaki T, Yamauchi Y. Gigantic Swelling of Inorganic Layered Materials: A Bridge to Molecularly Thin Two-Dimensional Nanosheets. J. Am. Chem. Soc. 136, 5491-5500, 2014. DOI:10.1021/ja501587y

Bastakoti BP, Li Y, Miyamoto N, Ye J, Srinivasu P, Yamauchi Y. Polymeric Micelle Assembly for Direct Synthesis of Functionalized Mesoporous Silica with Fully Accessible Pt Nanoparticles toward Improved Co Oxidation Reaction. Chem. Commun., 50, 9101-9104, 2014. DOI:10.1039/C4CC02556C.

Chen FQ, Yamauchi Y, Kijima S, Yamashita M. Locomotion of Metamorphic Robotic System Based on Local Information (Extended Abstract). SRDS Workshops, 2014: 40-45.

Endo K, Parr C, Saito H. Expanding the synthetic ribonucleoprotein world in cells. Nat Methods.  11(11), 1105-1106, 2014.
DOI: 10.1038/nmeth.3148  PMID: 25357239

Endo M, Yamamoto S, Emura T, Hidaka K, Morone N, Heuser JE, Sugiyama H. Helical DNA origami tubular structures with various sizes and arrangements. Angew Chem Int Ed Engl., 2014 Jul 14;53(29):7484-90.  DOI:10.1002/anie.201402973  PMID: 24888699

Endo M, Takeuchi Y, Emura T, Hidaka K, Sugiyama H. Preparation of chemically modified RNA origami nanostructures. Chemistry, 2014 Nov 17;20(47):15330-3. DOI:10.1002/chem.201404084  PMID: 25313942

Endo M, Sugiyama H. Single-molecule imaging of dynamic motions of biomolecules in DNA origami nanostructures using high-speed atomic force microscopy. Acc Chem Res., 2014 Jun 17;47(6):1645-53. DOI:10.1021/ar400299m  PMID: 24601497

Fujimoto K, Takematsu YK, Shigeno A, Furusawa M, Sakamoto T. Short oligonucleotide prodrug having 5-fluoro and 5-iodouracil inhibits the proliferation of cancer cells in a photo-responsive manner. Bioorg Med Chem Lett.
2014 Aug 15;24(16):3736-8. DOI: 10.1016/j.bmcl.2014.07.002. Epub 2014 Jul 14 PMID: 25080163.

Fujiwara K, Yanagisawa M, Nomura SM. Reconstitution of intracellular environments in vitro and in artificial cells. BIOPHYSICS, Vol.10, pp. 43-48 (2014) DOI:10.2142/biophysics.10.43

Geng F, Ma R, Ebina Y, Yamauchi Y, Miyamoto N, Sasaki T. Gigantic Swelling of Inorganic Layered Materials: A Bridge to Molecularly Thin Two-Dimensional Nanosheets. J. Am. Chem. Soc., 136, 5491-5500, 2014. PMID: 24635385

Goldau T, Murayama K, Brieke C, Steinwand S, Mondal P, Biswas M, Burghardt I, Wachtveitl J, Asanuma H, Heckel A. Reversible Photoswitching of RNA Hybridization at Room Temperature with an Azobenzene C-Nucleoside. Chemistry, 2014 Dec 23. PMID: 25537843

Gutmann G,  Inoue D,  Kakugo AKonagaya A. Real-time 3D Microtubule Gliding Simulation.  Proc. of LSMS & ICSEE 2014, 461, pp13-22. Shanghai, Sep. 20-23, China (2014) DOI:10.1007/978-3-662-45283-7_2

Hagiya M, Konagaya A, Kobayashi S, Saito H, Murata S. Molecular robots with sensors and intelligence. Acc Chem Res. 47(6) 1681-1690, 2014. DOI:10.1021/ar400318d  PMID: 24905779

Hagiya M, Wang S, Kawamata I, Murata S, Isokawa T, Peper F, Imai K.  On DNA-Based Gellular Automata. Lecture Notes in Computer Science.  8553,  177-189 , 2014. DOI: 10.1007/978-3-319-08123-6_15

Han Y,  Inoue D,  Kakugo AKonagaya A. Tracking single microtubules by using B-spline curves and Hausdorff Distance.  Proc. of Int. Conf. on Image Processing Theory, Tools and Applications (IPTA2014) pp1-6., Oct. 14-17, Paris, France (2014) DOI:10.1109/IPTA.2014.7001957

Hara Y. Activation energy of autonomous polymer chain with high LCST. Advanced Materials Research. 2014. 941.1212-1215., DOI: 10.4028/

Hara Y. A self-oscillating polymer chain with high LCST. Advanced Materials Research. 2014. 941. 1208-1211., DOI: 10.4028/

Hara Y. Function and Autonomous Behavior of Self-Oscillating Polymer Systems. Polymers. 2014. 6. 1958-1971., DOI: 10.3390/polym6071958

Hara Y, Mayama H, Yamaguchi Y, Fujimoto K. Activation energy of the Belousov-Zhabotinsky reaction in a gel with Fe(bpy)3 catalyst. Chemistry Letters, 43(5), 673-675, 2014. DOI:10.1246.cl131175

Hara Y, Mayama H, Yamaguchi Y. Generative Force of Self-oscillating Gel. Journal OF Physical Chemistry B, 118(9), 2576-2581, 2014. PMID: 24524539

Hara Y, Mayama H, Fujimoto K. Influence of Belousov-Zhabotinsky substrate concentrations on autonomous oscillation of polymer chains with Fe(bpy)3 catalyst. J. Phys Chem B. 2014 Jun 19; 118(24):6931-6. PMID: 24853126

Hara Y, Yamaguchi Y, Mayama H. Switching the BZ Reaction with a Strong-Acid-Free Gel. Journal OF Physical Chemistry B, 118(2), 634-638, 2014. PMID: 24354341

Hara Y, Fujimoto K, Mayama H. Self-Oscillation of Polymer Chains with an Fe(bpy)3 Catalyst Induced by the Belousov-Zhabotinsky Reaction. Journal OF Physical Chemistry B, 118(2), 608-612, 2014. PMID: 24359086

Haraguchi Y, Shimizu T, Matsuura K, Sekine H, Tanaka N, Tadakuma K, Yamato M, Kaneko M, Okano T. Cell sheet technology for cardiac tissue engineering. Methods Mol Biol., 2014;1181:139-55. PMID: 25070334

Huy DQ, Aubert N, Noman N, Fujii T, Rondelez Y, Iba H. An Effective Method for Evolving Reaction Network in Synthetic Biochemical Systems. IEEE Transaction on Evolutionary Computations. DOI:10.1109/TEVC.2014.2326863(2014).

Inadomi T, Ikeda S, Okumura Y, Kikuchi H, Miyamoto N. Anomalous Thermo- and Photo-Responsive Anisotropic Deformation of Poly (N-Isopropylacrylamide) Gel Hybridized with Liquid Crystalline Inorganic Nanosheets Aligned by Electric Field Macromol. Rapid Commun., 35, 1741-1746, 2014. DOI:10.1002/marc.201400333

Itoga K, Kobayashi J, Yamato M, Okano T. Micropatterning with a liquid crystal display (LCD) projector. Methods Cell Biol. , 2014;119:141-58. PMID: 24439283

Iwata T, Yamato M, Ishikawa I, Ando T, Okano T. Tissue engineering in periodontal tissue. Anat Rec (Hoboken) . 2014. Jan;297(1):16-25. PMID: 24343910

Iwayama D, Yamato M, Tsubokura T, Takahashi M, Okano T. Cell/tissue processing information system for regenerative medicine. J Tissue Eng Regen Med., 2014 Apr 3. PMID: 24700532

Kabir AMR, Inoue D, Hamano Y, Mayama H, Sada K, Kakugo A. Biomolecular motor modulates mechanical property of microtubule. Biomacromolecules, 2014 May 12;15(5):1797-805.  DOI:10.1021/bm5001789  PMID: 24697688

Kameishi S, Sugiyama H, Yamato M, Sado Y, Namiki H, Kato T, Okano T. Remodeling of epithelial cells and basement membranes in a corneal deficiency model with long-term follow-up. Lab Invest. 2014 Dec 22. PMID: 25531563.

Kamiya Y, Takai J, Ito H, Murayama K, Kashida H, Asanuma H. Enhancement of stability and activity of siRNA by terminal substitution with serinol nucleic acid (SNA). ChemBioChem., 2014 Nov 24;15(17):2549-55.  DOI:10.1002/cbic.201402369  PMID: 25233814

Kamiya Y, Asanuma H. Light-driven DNA nanomachine with a photoresponsive molecular engine. Accounts of Chemical Research , 2014, 47(6), 1663-1672. PMID: 24617966

Kamiya Y, Takagi T, Ooi H, Ito H, Liang X, Asanuma H. Synthetic Gene Involving Azobenzene-Tethered T7 Promoter for the Photocontrol of Gene Expression by Visible Light. ACS Synth Biol., 2014 Aug 27. PMID: 25144622

Kawanishi K, Nitta K, Yamato M, Okano T. Therapeutic Applications of Mesothelial Cell Sheets. Ther Apher Dial, 2014 Sep 4. PMID: 25195614

Kizaki S, Suzuki Y, Takenaka T, Endo M, Sugiyama H. AFM analysis of changes in nucleosome wrapping induced by DNA epigenetic modification. Biomaterials Science.  2, 1399-1403, 2014.  DOI:10.1039/c4bm00113c.

Kobayashi J, Hayashi M, Ohno T, Nishi M, Arisaka Y, Matsubara Y, Kakidachi H, Akiyama Y, Yamato M, Horii A, Okano T. Surface design of antibody-immobilized thermoresponsive cell culture dishes for recovering intact cells by low-temperature treatment. J Biomed Mater Res A., 2014 Nov;102(11):3883-93. PMID: 24339415

Koirala D, Shrestha P, Emura T, Hidaka K, Mandal S, Endo M, Sugiyama H, Mao H. Single-molecule mechanochemical sensing using DNA origami nanostructures. Angew Chem Int Ed Engl., 2014 Jul 28;53(31):8137-41. DOI:10.1002/anie.201404043. PMID: 24931175

Kondo M, Yamato M, Takagi R, Murakami D, Namiki H, Okano T. Significantly different proliferative potential of oral mucosal epithelial cells between six animal species. J Biomed Mater Res A., 2014 Jun;102(6):1829-37. PMID: 23818153

Kuzuya A, Ohya Y. Nanomechanical molecular devices made of DNA origami. Acc Chem Res., 2014 Jun 17;47(6):1742-9. PMID: 24772996

Kuzuya A, Watanabe R, Yamanaka Y, Tamaki T, Kaino M, Ohya Y. Nanomechanical DNA origami pH sensors. Sensors (Basel) . 2014 Oct 16;14(10):19329-35. DOI:10.3390/s141019329  PMID: 25325338

Matsumine H, Sasaki R, Yamato M, Okano T, Sakurai H. A polylactic acid non-woven nerve conduit for facial nerve regeneration in rats. J Tissue Eng Regen Med., 2014 Jun;8(6):454-62. PMID: 22689468

Matsumine H, Sasaki R, Tabata Y, Matsui M, Yamato M, Okano T, Sakurai H. Facial nerve regeneration using basic fibroblast growth factor-impregnated gelatin microspheres in a rat model. J Tissue Eng Regen Med., 2014 Apr 16. PMID: 24737684

Matsumine H, Sasaki R, Takeuchi Y, Miyata M, Yamato M, Okano T, Sakurai H. Vascularized versus nonvascularized island median nerve grafts in the facial nerve regeneration and functional recovery of rats for facial nerve reconstruction study. J Reconstr Microsurg., 2014 Feb;30(2):127-36. PMID: 24163227

Matsumine H, Takeuchi Y, Sasaki R, Kazama T, Kano K, Matsumoto T,Sakurai H, Miyata M, Yamato M. Adipocyte-derived and dedifferentiated fat cells promoting facial nerve regeneration in a rat model. Plast Reconstr Surg., 2014 Oct;134(4):686-97. PMID: 25357029

Mitani G, Sato M, Yamato M, Kokubo M, Takagaki T, Ebihara G, Okano T, Mochida J. Potential utility of cell sheets derived from the anterior cruciate ligament and synovium fabricated in temperature-responsive culture dishes. J Biomed Mater Res A., 2014 Sep;102(9):2927-33. PMID: 24089357

Miyamoto N. Shimasaki K, Yamamoto K, Shintate M, Kamachi Y. Bastakoti BP, Suzuki N, Motokawa R, Yamauchi Y. Three-Dimensional Mesoporous Silica as a Topologically Crosslinking Filler for Poly(N-Isopropylacrylamide) Hydrogel. Chem. Eur. J., 20, 14955-14958, 2014. DOI:10.1002/chem.201403762.

Morimoto N, Sasaki Y, Mitsunushi K, Korchagina E, Wazawa T, Qiu XP, Nomura SM, Suzuki M, Winnik FM. Temperature-responsive telechelic dipalmitoylglyceryl poly(N-isopropylacryla- mides) vesicles : real-time morphology observation in aqueous suspension and in the presence of giant liposomes. Chem. Commun ., 50, 8350-8352. 2014.  DOI:10.1039/C4CC03199G PMID: 24942471

Morita M, Onoe H, Yanagisawa M, Fujiwara K, Saito H, Takinoue M. The rapid synthesis of cell-sized liposomes by centrifuge-based microfluidic device.   Proceedings of The 18th International Conference on Miniaturized Systems for Chemistry and Life Sciences (microTAS2014), 336-338, 2014.

Nakamura S, Fujimoto K. Rapid potopolymerization of oligonucleotides by 3-cyanovinylcarbazole mediated DNA photocrosslinking. Journal of Photopolymer Sciecne and Technology, 2014, 27, 4, 485 – 490.,  DOI: 10.2494/photopolymer.27.485

Nakamura S, Fujimoto K. Creation of DNA Array Structure Equipped with heat resistance by Ultrafast Photocrosslinking. Journal of Chemical Technology & Biotechnology , 2014, 89, 1086 – 1090.,  DOI: 10.1002/jctb.4205

Ohsedo Y, Oono M, Saruhashi K, Watanabe H, Miyamoto N. A New Composite Thixotropic Hydrogel Composed of a Low-Molecular-Weight Hydrogelator and a Nanosheet. RSC Advances, 4, 44837-840, 2014.  DOI:10.1039/C4RA08542F

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

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. 2014 Aug 26;8(8):8130-40.  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., 2014. Jul;9(7):904-14. 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. 2014 Apr 7;9(4):e93853. 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., 2014 Jun;94(6):663-73. 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)., 2014 Aug 14;50(63):8743-6.  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., 2014 Apr 14;53(16):4107-12. PMID: 24623581

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., 2014 Jan 22;114(2):1493-520. 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., 2014 Sep 17;9(9):e106853. DOI:10.1371/journal.pone.0106853 PMID: 25229561

Sakai M, Suzuki Y. Evolution of Chemical Signals in ecological system evoked by the “cry-wolf” plants.  Artificial Life 14, 983-986, 2014.  DOI: 

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, 2014, 2, 9, 1154 – 1157., 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., 2014;25(5):431-43. 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., 2014 Feb;102(2):358-65. 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., 2014 Nov;134(5):970-8. 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., 2014 Oct;30(8):585-8. PMID: 24683132

Sato M, Yamato M, Hamahashi K, Okano T, Mochida J. Articular cartilage regeneration using cell sheet technology. Anat Rec (Hoboken) . 2014, Jan;297(1):36-43. 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., 2014 Dec;105(12):1631-7. PMID: 25311092

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, 2014: 25-36.

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., 2014 Aug;22(8):1544-55. 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, 2014, 310-313. 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., 2014 Sep;34(9):4747-54. 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., 2014 Jun;42(11):7421-8. 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., 2014 Jan 8;136(1):211-8. 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., 2014 Feb 5;136(5):1714-7. PMID: 24428846

Takagi R, Yamato M, Okano T. Regenerative medicine by cell sheet technology: the regeneration for stratified epithelial tissues. Arerugi., 2014 Nov;63(9):1223-8. 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, 2014 Nov 10;20(46):14951-4. 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

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., 2014;63(11):1085-98. PMID: 25341502

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

van Roekel HW, Meijer LH, Masroor S, Félix Garza ZC, Estévez-Torres A, Rondelez Y, Zagaris A, Peletier MA, Hilbers PA, de Greef TF. Automated Design of Programmable Enzyme-Driven DNA Circuits. ACS Synth Biol., 2014, Nov 10. PMID: 25365785

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., 2014 Jan-Feb;29(1):e117-21. 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 ., 2014 May 14;14(5):2286-92. 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., 2014 Jul 1;135(1):214-23. 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., 2014 Oct 22. pii: S1389-1723(14)00354-5. PMID: 25454697

Yamauchi Y, Yamashita M. Randomized Pattern Formation Algorithm for Asynchronous Oblivious Mobile Robots. Proceedings of the 28th International Symposium on Distributed Computing (DISC2014). 2014. LNCS8784. 137-151. 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, 2014 Aug 7;6(15):9122-6. DOI:10.1039/C4NR01598C PMID: 24974892

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)., 2014 Apr 25;50(32):4211-3. PMID: 24626780

Yasunaga M, Matsumura Y. Role of SLC6A6 in promoting the survival and multidrug resistance of colorectal cancer. Sci Rep. 2014 Apr 30;4:4852. 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.

Yokomori T, Okubo F. The computational capability of chemical reaction automata. Proc. of 20th International Conference on DNA Computing and Molecular Programming, Kyoto, Japan, (Lecture Notes in Computer Science 8727, Springer) pp.53-66, 2014.

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. 2014 Mar;10 Suppl 1:46-50; discussion 50. PMID: 24141478


Abe H, Hara Y, Maeda S, Hashimoto S. Surface modification method for adhesion of gels. Chemistry Letters, 43(2), 243-245, 2014. DOI:10.1246/cl.130905

Alina-MS, 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. 2013. DOI: 10.1016/j.crci.2012.11.022

Ataee-Esfahani H, Liu J, Hu M, Miyamoto N, Tominaka S, Wu KC, Yamauchi Y. Mesoporous Metallic Cells: Design of Uniformly Sized Hollow Mesoporous Pt-Ru Particles with Tunable Shell Thicknesses, Small, 1047-1051, 2013. DOI: 10.1002/smll.201202539  PMID: 23281242

Aubert N, Quang HD, Hagiya M, Fujii T, Iba H, Bredeche N, Rondelez Y. Evolution of Cheating DNA-based Agents Playing the Game of Rock-Paper-Scissors. ECAL、 1143-1150, 2013. DOI: 10.7551/978-0-262-31719-2-ch174

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 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

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, 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

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

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

Hara T, Saito H, Inoue T. Directed evolution of a synthetic RNA-protein module to create a new translational switch, Chemical Communications (Camb) , 49(37), 3833-3835, 2013.  DOI: 10.1039/c3cc38688k  PMID: 23381780

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

Inoue D, Kabir AMR, Mayama H, Gong JP, Sada K, Kakugo A. Growth of Ring Shaped Microtubule Assemblies through Stepwise Active Self-Organisation. Soft matter, 9, 7061-7068, 2013. DOI:10.1039/C3SM50704A

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, 2013. DOI:10.1038/pj.2013.89

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

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

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

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

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

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

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

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

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, 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

Tanaka-Takiguchi Y, Itoh T, Tsujita K, Yamada S, Yanagisawa MFujiwara K, Yamamoto A, Ichikawa M, Takiguchi KPhysicochemical 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

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, 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, 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, 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, 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

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

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

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

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