Taniguchi, H., Fujimoto, A., Kono, H., Furuta, M., and Nakagawa, H., (2018) Loss-of-function mutations in Zn-finger DNA-binding domain of HNF4A cause aberrant transcriptional regulation in liver cancer. Oncotarget. 9: 26144-26156

Luo, D., Kato, D., Nogami, J., Ohkawa, Y., Kurumizaka, H., and Kono, H., (2018) MNase, as a probe to study the sequence-dependent site exposures in the +1 nucleosomes of yeast. Nucleic Acids Research. 46: 7124-7137

Kono, H., Sakuraba, S., and Ishida, H., (2018) Free Energy Profiles for Unwrapping the Outer Superhelical Turn of Nucleosomal DNA. PLoS Comp. Biol. 14: e1006024

池部仁善, 櫻庭俊, and 河野秀俊, (2017) ヌクレオソーム中におけるヒストンテールの特性とアセチル化の影響 (H3 Histone Tail Structure within the Nucleosome and the Impact of the Acetylation). 日本生物物理学会誌. 57: 095-097

Tencer, A.H., Cox, K.L., Di, L., Bridgers, J.B., Lyu, J., Wang, X., Sims, J.K., Tyler, Allen, H.F., Zhang, Y., Gatchalian, J., Li, W., Ikebe, J., Wade, P.A., Hayes, J.J., Strahl, B.D., Kono, H., Poirier, M.G., Musselman, C.A., and Kutateladze, T.G., (2017) Covalent modifications of histone H3K9 promote binding of CHD3. Cell Reports. 21: 455-466

Sunami, T., Chatake, T., and Kono, H., (2017) DNA conformational transitions inferred from reevaluation of m|Fo|-D|Fc| electron density maps. Acta Crystal. D. D73: 600-608

Matsumoto, A., Miyazaki, N., Takagi, J., and Iwasaki, K., (2017) 2D hybrid analysis: Approach for building three-dimensional atomic model by electron microscopy image matching. Scientific Reports. 7: 377

Kato, D., Osakabe, A., Mizukami, Y., Adachi, F., Arimura, Y., Saikusa, K., Akashi, S., Nishimura, Y., Park, S.-Y., Matsumoto, A., Kono, H., Inoue, R., Sugiyama, M., and Kurumizaka, H., (2017) Crystal structure of the overlapping dinucleosome composed of hexasome and octasome. Science. 356: 205-208

Ishida, H. and Kono, H., (2017) H4 tails potentially produce the diversity in the orientation of two nucleosomes. Biophysical J. 113: 978-990

Gatchalian, J., Wang, X., Ikebe, J., Luo, D., Gibsono, M., Zhang, Y., Cox, K., Musselman, C.A., Poirior, M.G., Kono, H., Haynes, J.J., and Kutateladze, T.G., (2017) Accessibility of the histone H3 tail in the nucleosome for binding of paired readers. Nat. Comm. 8: 1489

Andrabi, M., Hutchins, A.P., Miranda-Saavedra, D., Kono, H., Nussinov, R., Mizuguchi, K., and Ahmad, S., (2017) Predicting conformational ensembles and genome-wide transcription factor binding sites from DNA sequences. Sci Rep. 7: 4071

Sakuraba, S. and Kono, H., (2016) Spotting the difference in molecular dynamics simulations of biomolecules. J. Chem. Phys. 145: 074116

Li, Z. and Kono, H., (2016) Distinct Roles of Histone H3 and H2A Tails in Nucleosome Stability. Scientific Reports. 6: 31437

Ishida, H. and Matsumoto, A., (2016) Mechanism for verification of mismatched and homoduplex DNAs by nucleotides-bound MutS analyzed by molecular dynamics simulations. Proteins. 84: 1287-1303

Ikebe, J., Sakuraba, S., and Kono, H., (2016) H3 Histone Tail Conformation within the Nucleosome and the Impact of K14 Acetylation Studied Using Enhanced Sampling Simulation. PLoS Comput Biol. 12: e1004788

Kono, H., Shirayama, K., Arimura, Y., Tachiwana, H., and Kurumizaka, H., (2015) Two Arginine Residues Suppress the Flexibility of Nucleosomal DNA in the Canonical Nucleosome Core. PLoS ONE. 10: e0120635

Ikebe, J., Umezawa, K., and Higo, J., (2015) Enhanced sampling simulations to construct free-energy landscape of protein?partner substrate interaction. Biophysical Reviews: 1-18

櫻庭俊, (2014) 相関から眺める生体分子運動の解析. 統計数理. 62: 171-184

Yang, L., kitano, A., Huang, B., and Go, N., (2014) Ligand-induced protein responses and mechanical signal propagation described by linear response theories. Biophysical Journal 107: 1415-25

Tsukasaki, Y., Miyazaki, N., Matsumoto, A., Nagae, S., Yonemura, S., Tanoue, T., Iwasaki, K., and Takeichi, M., (2014) Giant cadherins Fat and Dachsous self-bend to organize properly spaced intercellular junctions. Proc Natl Acad Sci U S A. 111: 16011-6 [pii]

Sakuraba, S. and Matsubayashi, N., (2014) ERmod: Fast and Versatile Computation Software for Solvation Free Energy with Approximate Theory of Solutions. J. Comp. Chem. 35: 1592-608

Nakagawa, H., Yonetani, Y., Nakajima, K., Ohira-kawamura, S., Kikuchi, T., Inamura, Y., Kataoka, M., and Kono, H., (2014) Local Dynamics Coupled to Hydration Water Determines DNA-sequence Dependent Deformability. Physical Reviews E. 90: 022723-11

Li, H., Sakuraba, S., Chandrasekaran, A., and Yang, L., (2014) Molecular binding sites are located near the interface of intrinsic dynamics domains (IDDs). Journal of Chemical Information and Modeling. 54: 2275-2285

Kai, T., Tokuhisa, A., Moribayashi, K., Fukuda, Y., Kono, H., and Go, N., (2014) Intensity of diffracted X-rays from biomolecules with radiation damage caused by strong X-ray pulses. Journal of the Physical Society of Japan. 83: 094301

Ishida, H. and Matsumoto, A., (2014) Free-energy landscape of reverse tRNA translocation through ribosome analyzed by electron microscopy density maps molecular dynamics simulations. PLoS ONE. 9: e101951

Ishida, H., (2014) Essential function of the N-termini tails of the proteasome for the gating mechanism revealed by molecular dynamics simulations. Proteins: Structure, Function, and Bioinformatics. 82: 1985-1999

Ikebe, J., Sakuraba, S., and Kono, H., (2014) Adaptive lambda square dynamics simulation: an efficient conformational sampling method for biomolecules. Journal of Computational Chemistry. 35: 39-50

池田思朗 and 河野秀俊, (2013) X線自由電子レーザーによる分子の電子密度推定. 統計数理. 61: 135-146

河野秀俊, (2013) 弱い回折パターンからの位相回復:単粒子構造解析に向けて. 日本放射光学会誌「放射光」. 1月号: 38-43

Yonetani, Y. and Kono, H., (2013) Dissociation Free-Energy Profiles of Specific and Nonspecific DNA-Protein Complexes. J Phys Chem B. 117: 7535-45

Tokuhisa, A., Arai, J., Joti, Y., Ohno, Y., Kameyama, T., Yamamoto, K., Hatanaka, M., Gerofi, B., Shimada, A., Kurokawa, M., Shoji, F., Okada, K., Sugimoto, T., Yamaga, M., Tanaka, R., Yokokawa, M., Hori.A., Ishikawa, Y., Hatsui, T., and Go, N., (2013) High-speed classification of coherent X-ray diffraction patterns on the K computer for high-resolution single bio-molecule imaging. Journal of Synchrotron Radiation: 1-16

Murakawa, T., Hayashi, H., Sunami, T., Kurihara, K., Tamada, T., Kuroki, R., Suzuki, M., Tanizawa, K., and Okajima, T., (2013) High Resolution Crystal Structure of Copper Amine Oxidase from Arthrobacter globiformis:Identification of Bound O2-like Diatomic Molecules. Acta Crystallographica Section D,

Kai, T., Tokuhisa, A., and Kono, H., (2013) Calculation of Molecular-Structure-Based Damage Caused by Short-Pulse High-Intensity X-ray Lasers. Journal of the Physical Society of Japan: 114301-1~5 35)

Chatake, T. and Sunami, T., (2013) Direct interactions between Z-DNA and alkaline earth cations, discovered in the presence of high concentrations of MgCl2 and CaCl2. Journal of Inorganic Biochemistry. 124: 15-25 Chatake, T., and Sunami, T. (2013) Direct interactions between Z-DNA and alkaline earth cations, discovered in the presence of high concentrations of MgCl2 and CaCl2, Journal of Inorganic Biochemistry 124, 15-25.

Sunami, T. and Kono, H. (2013) Local Conformational Changes in the DNA Interfaces of Proteins. PLoS ONE (Internet), 8, e56080.

Yamasaki, S., Terada, T., Kono, H., Shimizu, K. and Sarai, A. (2012) A New Method for Evaluating the Specificity of Indirect Readout in Protein-DNA Recognition. Nucleic Acids Res., 40, e129.

Adan-Kubo, J., Yoshii, S., Kono, H. and Miyata, M. (2012) Molecular Structure of Isolated MvspI, A Variable Surface Protein of Fish Pathogen Mycoplasma Mobile. J. Bacterio, 194, 3050-3057.

Adan-Kubo, J., Yoshii, S., Kono, H. and Miyata, M. (2012) Molecular Structure of Isolated MvspI, A Variable Surface Protein of Fish Pathogen Mycoplasma Mobile. J. Bacterio, 194, 3050-3057.

Tokuhisa, A., Taka, J., Kono, H. and Go, N. (2012) Classifying and Assembling 2D X-ray Laser Diffraction Patterns of a Single Particle to Reconstruct 3D Diffraction Intensity Function: Resolution Limit Due to The Quantum Noise. Acta Cryst. Sec. A, 68, 366-381.

Yonetani, Y. and Kono, H. (2012) What determines water-bridge lifetimes at the surface of DNA? Insight from systematic molecular dynamics analysis of water kinetics for various DNA sequences. Biophysical Chemistry, 160, 54-61.

Kono, H., Imanishi, M. et al. (2012) Rational Design of DNA Sequence-Specific Zinc Fingers. FEBS Letters 586: 918-923.

Ikeda, S. and Kono, H. (2012) Phase retrieval from single biomolecule diffraction pattern.Optics Express, 20, 3375-3387.

Ikeda, S. and Kono, H. (2011) Sparse phase retrieval. Proceedings of the Workshop: Signal Processing with Adaptive Sparse Structured Representations (SPARS2011): 106.

Ishida, H. (2011) Molecular Dynamics Simulation System for structural analysis of biomolecules by high performance computing. Progress in Nuclear Science and Technology, 2, 470-476.

Matsumoto, A. (2011) A new approach for building an atomic model from a three-dimensional electron microscopy data. Progress in Nuclear Science and Technology, 2, 486-490.

Higuchi, M., Fujii, J., Yonetani, Y., Kitao, A and Go, N., (2011) Enhanced resolution of molecular recognition to distinguish structurally similar molecules by different conformational responses of a protein upon ligand binding. J. Struct. Biol., 173, 20-28.

Ishida, H. (2010) Branch Migration of Holliday Junction in RuvA Tetramer Complex Studied by Umbrella Sampling Simulation Using a Path-search Algorithm. J. Comput. Chem., 31, 2317-2329.

Oikawa, M. and Yonetani, Y. (2010) Molecular Dynamics Free Energy Calculations to Assess the Possibility of Water Existence in Protein Nonpolar Cavities. Biophys. J., 98, 2974-2983.

Matsumoto, A. and Ishida, H. (2009) Global Conformational Changes of Ribosome Observed by Normal Mode Fitting for 3D Cryo-EM Structures. Structure, 17, 1605-1613.

Horie, A., Tomita, T., Saiki, A., Kono, H., Taka, H., Mineki, R., Fujimura, T., Nishiyama, C., Kuzuyama, T. and Nishiyama, M. (2009) Discovery of Proteinaceous N-modification in Lysine Biosynthesis of Thermus Thermophilus. Nat. Chem. Biol., 5, 673-679.

Yoshida, A., Tomita, T., Fushinobu, S., Kono, H., Kuzuyama, T. and Makoto, N. (2009) Crystal Structures of the Regulatory Subunit of Thr-sensitive Aspartate Kinase from Themus Thermophilus. FEBS J., 276, 3124-3136.

Yonetani, Y. and Kono, H. (2009) Sequence Dependencies of DNA Deformability and Hydration in the Minor Groove. Biophysical Journal, 97, 1138-1147.

Poornam, G.P., Matsumoto, A., Ishida, H. and Hayward, S. (2009) A Method for the Analysis of Domain Movements in Large Biomolecular Complexes. Proteins, 76, 201-212.

Srinivasan, A.R., Sauers, R.R., Fenley, M.O., Boschitsch, A.H., Matsumoto, A., Colasanti, A.V., and Olson, W. K. (2009) Properties of the nucleic-acid bases in free and Watson-Crick hydrogen-bonded states: computational insights into the sequence-dependent features of double-helical DNA. Biophys. Rev., 1 (1), 13-20.

Ishida, H. and Hayward, S. (2008) Path of Nascent Polypeptide in Exit Tunnel Revealed by Molecular Dynamics Simulation of Ribosome. Biophys. J., 95, 5962-5973.

Matsumoto, A., Kamata, T., Takagi, J., Iwasaki, K., and Yura, K. (2008) Key interactions in ectodomain of integrin responsible for global conformational change detected by elastic network normal mode analysis. Biophys. J., 95 (6), 2895-2908.

Miyazawa, Y., Nishioka, H., Yura, K., and Yamato, T. (2008) Discrimination of class I cyclobutane pyrimidine dimer photolyase from blue light photoreceptors by single methionine residue. Biophys. J., 94 (6), 2194-2203.

Yonetani, Y., Maruyama, Y., Hirata, F. and Kono, H. (2008) Comparison of DNA Hydration Patterns Obtained Using Two Distinct Computational Methods, Molecular Dynamics Simulation and Three-dimensional Reference Interaction Site Model Theory. J.Chem. Phys., 128, 185102.

Genome Information Integration Project and H-Invitational 2 consortium (2008) The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res., 36 D793-D799.

Kono, H., Yuasa, T., Nishiue, S. and Yura, K. (2008) coliSNP Database Server Mapping nsSNPs on Protein Structures. Nucleic Acids Res, 36, D409-D413.

Fujii, S., Kono, H., Takenaka, S., Go, N. and Sarai, A. (2007) Sequence-dependent DNA Deformability Studied using Molecular Dynamics Simulations. Nucleic Acids Res., 35, 6063-6074.

Shiina, J., Oikawa, M., Nakamura, K., Obata, R., and Nishiyama, S. (2007) Synthesis of pingusane-type sesquiterpenoids, acutifolone A and pinguisenol along with bisacutifolones through the Diels-Alder dimerization reaction. Eur. J. Org. Chem., 31 5190-5197.

Yonetani, Y., Kono, H., Fujii, S., Sarai, A. and Go, N. (2007) DNA Deformability and Hydration Studied by Molecular Dynamics Simulation. Mol. Simul., 33, 103-107.

Ishida, H., Kano, T., Yura, K. and Matsumoto, A. (2007) Analysis of Function of a Large-scale Supra-biomolecule System by Molecular Dynamics Simulation System, SCUBA (Simulation Codes for hUge Biomolecular Assembly). Annual Report of the Earth Simulator Center, 257-263.

Tokuhisa, A., Joti, Y., Nakagawa, H., Kitao, A. and Kataoka, M. (2007) Non-Gaussian Behavior of Elastic Inchoherent Neutron Scattering Profile of Protein Studied by Molecular Dynamics Simulation. Physi. Rev. E, 75, 041912.

Gong, X., Nakamura, K., Yu, H., Yura, K., Go, N. (2007) BAAQ: An infrastructure for application integration and knowledge discovery in bioinformatics. IEEE Transactions on Information Technology in Biomedicine, 11 (4), 428-434.

Kawabata, T. and Go, N. (2007) Detection of Pockets on Protein Surfaces Using Small and Large Probe Spheres to Find Putative Ligand Binding Sites. Proteins, 68, 516-529.

Ishida, H., Matsumoto, A., Tsutsumi, Y. and Yura, K. (2006) Conformational Analysis of the Structure of Ribosome Fit into Electron Microscopy Density Maps with Normal Mode Analyses and Molecula Dynamics Simulations. Proceedings of the16th International Microscopy Congress, Proceedings, 242.

Ahmad, S., Kono, H., Arauzo-Bravo, M.J. and Sarai, A. (2006) ReadOut: Structure-based Calculation of Direct and Indirect Readout Energies and Specificities for Protein-DNA Recognition. Nucleic Acids Res., 34, w124-127.

Ishida, H., Higuchi, M., Yonetani, Y., Kano, T., Joti, Y., Kitao, A and Go, N (2006) Analysis of Function of a Large-scale Supra-biomolecule System by Molecular Dynamics Simulation System, SCUBA (Simulation Codes for hUge Biomolecular Assembly). Annual Report of the Earth Simulator Center, 237-240.

Nakagawa, H., Tokuhisa, A., Kamikubo, H., Joti, Y., Kitao, A. and Kataoka, M. (2006) Dynamical Heterogeneity of Protein Dynamics Studied by Elastic Inchoherent Neutron Scattering and Molecular Simulations. Mater. Sci. Eng. A, 422, 356-360.

Nakagawa, H., Kataoka, M., Joti, Y., Kitao, A., Shibata, K., Tokuhisa, A., Tsukushi, I. and Go, N. (2006) Hydration-coupled Protein Boson Peak Measured by Incoherent Neutron Scattering. Physica B-Condensed Matter, 385-86, 871-873.

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Mizutani, M.Y., Takamatsu, Y., Ichinose, T., Nakamura, K. and Itai, A., (2006) Effective handling of induced-fit motion in flexible docking. Proteins: Struct. Funct. Bioinf., 63 (4), 878-891.(Google Scholar Cited by ...)

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Gromiha, M.M., Siebers, J.G., Selvaraj, S., Kono, H. and Sarai, A. (2005) Role of Inter and Intramolecular Interactions in Protein-DNA Recognition. Gene, 364, 108-113.

Nanda, V., Rosenblatt, M.M., Osyczka, A., Kono, H., Getahun, Z., Dutton, P.L., Saven, J.G. and DeGrado, W.F. (2005) De Novo Design of a Redox Active Minimal Rubredoxin Mimic. J. Am. Chem. Soc., 127, 5804 -5805.

Ohgiya, T., Nakamura, K., and Nishiyama, S., (2005)Total Synthesis of (+)-Tanikolide, Using Regioselective Elimination of a Vicinal Dibromoalkane. Bulletin of the Chemical Society of Japan.78, 1549-1554.

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Metsugi, S., Uenoyama, A., Adan, J., Miyata, M., Yura, K., Kono, H. and Go, N. (2005) Sequence Analysis of the Gliding Protein Gli349 in Mycoplasma Mobile. BIOPHYSICS, 1, 33-43.

Metsugi, S. (2005) Influence of Multidimensionality on Convergence of Sampling in Protein Simulation. J. Phys. Soc. Jpn., 74 (6), 1865-1870.

Sarai, A. and Kono, H. (2005) Protein-DNA Recognition Patterns and Predictions. Annu Rev Biophys Biomol Struct., 34, 379-398.

Sarai, A., Siebers, J., Selvaraj, S., Gromiha, M.M. and Kono, H. (2005) Integration of Bioinformatics and Computational Biology to Understand Protein-DNA Recognition Mechanism. J. Bioinform. Comput. Biol., 3, 1-15.

Park, S., Kono, H., Wang, W., Boder, E.T. and Saven, J.G. (2005) Progress in the Development and Application of Computational Methods for Probabilistic Protein Design. Comp. Chem. Eng., 29, 407-421.

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Joti, Y., Kitao, A. and Go, N. (2005) Protein Boson Peak Originated from Hydration-related Multiple Minima Energy Landscape. J Am Chem Soc, 127, 8705-8709.

Kang, A., Kim, S. K., Nakamura, K., Park, J. H., Yoon, Y. J., Lee, K. D., and Yoon, J. (2005) A new cavitand ionophore bearing two rigid crown ether groups. Tetrahedron Lett. 46 (2), 245-248.(Google Scholar Cited by ...)

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Slovic, A.M., Kono, H., Lear, J.D., Saven, J.G. and DeGrado, W.F. (2004) Computational Design of WSK, a Water-Soluble Analogue of the Potassium Channel K sA. Proc. Natl. Acad. Sci. USA, 101, 1828-1833.

Sarai, A., Selvaraj, S., Gromiha, M.M. and Kono, H. (2004) Structure-Function Relationship in DNA Sequence Recognition by Transcription Factors. Aust. Compt. Sci. Comm., 26, 233-238.

Kim, O.T., Yura, K., Go, N. and Harumoto, T. (2004) Highly Divergent Actins from Karyorelictean, Heterotrich, and Litostome Ciliates. J. Eukaryot. Microbiol., 51, 227-233.

Uehara, K., Kawabata, T. and Go, N. (2004) Filtering Remote Homologues Using Predicted Structural Information. Protein Eng., Des. Sel., 17, 565-570.

Basu, G., Sivanesan, D., Kawabata, T. and Go, N. (2004) Electrostatic Potential of Nucleotide-free Protein is Sufficient for Discrimination between Adenine and Guanine-specific Binding Sites. J. Mol. Biol., 342, 1053-1066.

Joti, Y., Kitao, A. and Go, N., (2004) Slow Protein Dynamics to be Detected in Inelastic Neutron Scattering Spectra Studied by Molecular Simulation, AIP Conference series, Proceedings of 3rd International Symposium on Slow Dynamics in Complex system, 358-359.

Joti, Y., Kitao, A. and Go, N., (2004) Molecular Simulation Study to Examine the Possibility of Detecting Collective Motion in Protein by Inelastic Neutron Scattering, Physica B, 350, e627-e630 Proceedings of 3rd European Conference on Neutron Scattering,

Nakamura, K., Kawabata, T., Yura, K., and Go, N. (2003) Novel Types of Two-domain Multi-copper Oxidases: Possible Missing Links in the Evolution. FEBS Letters, 553: 239-244.

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Oobatake, M., Kono, H., Wang, Y. and Sarai, A. (2003) A natomy of Specific Interactions between Lambda Repressor and Operator DNA. Proteins: Struct. Funct. Genet., 53: 33-43.

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河野秀俊、弱い回折パターンからの位相回復:単粒子構造解析に向けて.日本放射光学会誌「放射光」1月号, pp.38-43.

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由良敬 (2003) バイオインフォマティクスが追い求めるもの. 名古屋大学情報連携基盤センターニュース. 2 136-143.

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由良敬. (2002) ゲノム配列にもとづくタンパク質機能予測 「プロテオミクスの最新技術」(深見泰夫監修)シーエムシー出版 pp.93-101.

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