研究業績

査読つき論文(1996-)

  1. Atsushi Yamagata, Kaori Ito, Takehiro Suzuki, Naoshi Dohmae, Tohru Terada, and Mikako Shirouzu: Structural basis for antiepileptic drugs and botulinum neurotoxin recognition of SV2A, Nature Communications, 15, 3027 (2024).
  2. Fan Zhao, Yoshitaka Moriwaki, Tomohiro Noguchi, Kentaro Shimizu, Tomohisa Kuzuyama, and Tohru Terada: QM/MM Study of the Catalytic Mechanism and Substrate Specificity of the Aromatic Substrate C-Methyltransferase Fur6, Biochemistry, 63, 806–814 (2024).
  3. Tina Lusiany, Tohru Terada, Jun-ichi Kishikawa, Mika Hirose, David Virya Chen, Fuminori Sugihara, Hendra Saputra Ismanto, Floris J. van Eerden, Songling Li, Takayuki Kato, Hisashi Arase, Matsuura Yoshiharu, Masato Okada, Daron M. Standley: Enhancement of SARS-CoV-2 Infection via Crosslinking of Adjacent Spike Proteins by N-Terminal Domain-Targeting Antibodies, Viruses, 15, 2421 (2023).
  4. Kazue Terasawa, Tatsuro Seike, Kensaku Sakamoto, Kazumasa Ohtake, Tohru Terada, Takanori Iwata, Tetsuro Watabe, Shigeyuki Yokoyama, Miki Hara-Yokoyama: Site-specific photo-crosslinking/cleavage for protein–protein interface identification reveals oligomeric assembly of lysosomal-associated membrane protein type 2A in mammalian cells, Protein Science, 32,e4823 (2023).
  5. Tomoki Sawa, Yoshitaka Moriwaki, Hanting Jiang, Kohji Murase, Seiji Takayama, Kentaro Shimizu, Tohru Terada: Comprehensive computational analysis of the SRK–SP11 molecular interaction underlying self-incompatibility in Brassicaceae using improved structure prediction for cysteine-rich proteins, Computational and Structural Biotechnology Journal, 21, 5228-5239 (2023).
  6. Tatsuki Negami, Tohru Terada: Calculations of the binding free energies of the Comprehensive in vitro Proarrhythmia Assay (CiPA) reference drugs to cardiac ion channels, Biophysics and Physicobiology, 20, e200016 (2023).
  7. Wenchao Zhu, Shiori Takeuchi, Shosei Imai, Tohru Terada, Takumi Ueda, Yusuke Nasu, Takuya Terai & Robert E. Campbell: Chemigenetic indicators based on synthetic chelators and green fluorescent protein, Nature Chemical Biology, 19, 38–44 (2023).
  8. Shohei Nosaki, Nobutaka Mitsuda, Shingo Sakamoto, Kazuki Kusubayashi, Ayumi Yamagami, Yuqun Xu, Thi Bao Chau Bui, Tohru Terada, Kenji Miura, Takeshi Nakano, Masaru Tanokura & Takuya Miyakawa: Brassinosteroid-induced gene repression requires specific and tight promoter binding of BIL1/BZR1 via DNA shape readout, Nature Plants, 8, 1440–1452 (2022).
  9. Atsushi Yamagata, Yoshiko Murata, Kosuke Namba, Tohru Terada, Shuya Fukai & Mikako Shirouzu: Uptake mechanism of iron-phytosiderophore from the soil based on the structure of yellow stripe transporter, Nature Communications, 13, 7180 (2022).
  10. Kano Hasegawa, Yoshitaka Moriwaki, Tohru Terada, Cao Wei and Kentaro Shimizu: Feedback-AVPGAN: Feedback-guided generative adversarial network for generating antiviral peptides, Journal of Bioinformatics and Computational Biology, 20, 2250026 (2022).
  11. Shohei Yamaguchi, Haruka Nakashima, Yoshitaka Moriwaki, Tohru Terada, Kentaro Shimizu: Prediction of protein mononucleotide binding sites using AlphaFold2 and machine learning, Computational Biology and Chemistry, 100, 107744 (2022).
  12. Pi-Cheng Tsai, Joydeep Chakraborty, Chiho Suzuki-Minakuchi, Tohru Terada, Tatsurou Kotake, Jun Matsuzawa, Kazunori Okada, Hideaki Nojiri: The α- and β-Subunit Boundary at the Stem of the Mushroom-Like α3β3-Type Oxygenase Component of Rieske Non-Heme Iron Oxygenases Is the Rieske-Type Ferredoxin-Binding Site, Applied and Environmental Microbiology, 88, e00835-22 (2022).
  13. Miho Watanabe-Takahashi, Miki Senda, Ryunosuke Yoshino, Masahiro Hibino, Shinichiro Hama, Tohru Terada, Kentaro Shimizu, Toshiya Senda & Kiyotaka Nishikawa: A unique peptide-based pharmacophore identifies an inhibitory compound against the A-subunit of Shiga toxin, Scientific Reports, 12, 11443 (2022).
  14. Xiaoyu Yang, Natsuko I Kobayashi, Yoshiki Hayashi, Koichi Ito, Yoshitaka Moriwaki, Tohru Terada, Kentaro Shimizu, Motoyuki Hattori, Ren Iwata, Hisashi Suzuki, Tomoko M Nakanishi, Keitaro Tanoi: Mutagenesis analysis of GMN motif in Arabidopsis thaliana Mg2+ transporter MRS2-1, Bioscience, Biotechnology & Biochemistry, 86, 870–874 (2022).
  15. Peng Cao, Laura Bracun, Atsushi Yamagata, Bern M. Christianson, Tatsuki Negami, Baohua Zou, Tohru Terada, Daniel P. Canniffe, Mikako Shirouzu, Mei Li & Lu-Ning Liu: Structural basis for the assembly and quinone transport mechanisms of the dimeric photosynthetic RC-LH1 supercomplex, Nature Communications, 13, 1977 (2022).
  16. Tomohiro Noguchi, Shota Isogai, Tohru Terada, Makoto Nishiyama, and Tomohisa Kuzuyama: Cryptic Oxidative Transamination of Hydroxynaphthoquinone in Natural Product Biosynthesis, Journal of the American Chemical Society, 144, 5435–5440 (2022).
  17. Maki Kuzuya, Hidemi Hirano, Kenichi Hayashida, Masakatsu Watanabe, Kazumi Kobayashi, Tohru Terada, Md. Iqbal Mahmood, Florence Tama, Kazutoshi Tani, Yoshinori Fujiyoshi, and Atsunori Oshima: Structures of human pannexin-1 in nanodiscs reveal gating mediated by dynamic movement of the N terminus and phospholipids, Science Signaling, 15, eabg6941 (2022).
  18. Hayama Tsutsumi, Yoshitaka Moriwaki, Tohru Terada, Kentaro Shimizu, Kazuo Shin-ya, Yohei Katsuyama, Yasuo Ohnishi: Structural and Molecular Basis of the Catalytic Mechanism of Geranyl Pyrophosphate C6-Methyltransferase: Creation of an Unprecedented Farnesyl Pyrophosphate C6-Methyltransferase, Angewandte Chemie International Edition, 61, e202111217 (2022).
  19. Evgeniia Borisova, Ken Nishimura, Yuri An, Miho Takami, Jingyue Li, Dan Song, Mami Matsuo-Takasaki, Dorian Luijkx, Shiho Aizawa, Akihiro Kuno, Eiji Sugihara, Taka-aki Sato, Fumiaki Yumoto, Tohru Terada, Koji Hisatake, Yohei Hayashi: Structurally-discovered KLF4 variants accelerate and stabilize reprogramming to pluripotency, iScience, 25, 103525 (2022).
  20. Toma Kashima, Kouki Okumura, Akihiro Ishiwata, Machika Kaieda, Tohru Terada, Takatoshi Arakawa, Chihaya Yamada, Kentaro Shimizu, Katsunori Tanaka, Motomitsu Kitaoka, Yukishige Ito, Kiyotaka Fujita, Shinya Fushinobu: Identification of difructose dianhydride I synthase/hydrolase from an oral bacterium establishes a novel glycoside hydrolase family, Journal of Biological Chemistry, 297, 101324 (2021).
  21. Ryosuke Miyata, Yoshitaka Moriwaki, Tohru Terada, Kentaro Shimizu: Prediction and analysis of antifreeze proteins, Heliyon, 7, e07953 (2021).
  22. Tetsuhiro Ogawa, Kazutoshi Takahashi, Wataru Ishida, Toshihiro Aono, Makoto Hidaka, Tohru Terada, Haruhiko Masaki: Substrate recognition mechanism of tRNA-targeting ribonuclease, colicin D, and an insight into tRNA cleavage-mediated translation impairment, RNA Biology, 18, 1193–1205 (2021).
  23. Laura Bracun, Atsushi Yamagata, Bern M. Christianson, Tohru Terada, Daniel P. Canniffe, Mikako Shirouzu and Lu-Ning Liu: Cryo-EM structure of the photosynthetic RC-LH1-PufX supercomplex at 2.8-Å resolution, Science Advances, 7, eabf8864 (2021).
  24. Keisuke Yanagisawa, Yoshitaka Moriwaki, Tohru Terada, Kentaro Shimizu: EXPRORER: Rational Cosolvent Set Construction Method for Cosolvent Molecular Dynamics Using Large-Scale Computation, Journal of Chemical Information and Modeling, 61, 2744–2753 (2021).
  25. Mimin Zhang, Peng Lu, Tohru Terada, Miaomiao Sui, Haruka Furuta, Kilico Iida, Yukie Katayama, Yi Lu, Ken Okamoto, Michio Suzuki, Tomiko Asakura, Kentaro Shimizu, Fumihiko Hakuno, Shin-Ichiro Takahashi, Norimoto Shimada, Jinwei Yang, Tsutomu Ishikawa, Jin Tatsuzaki & Koji Nagata: Quercetin 3,5,7,3′,4′-pentamethyl ether from Kaempferia parviflora directly and effectively activates human SIRT1,  Communications Biology, 4, 209(2021).
  26. Shohei Nosaki, Tohru Terada, Akira Nakamura, Kei Hirabayashi, Yuqun Xu, Thi Bao Chau Bui, Takeshi Nakano, Masaru Tanokura & Takuya Miyakawa:  Highlighting the potential utility of MBP crystallization chaperone for Arabidopsis BIL1/BZR1 transcription factor-DNA complex, Scientific Reports, 11, 3879 (2021).
  27. Yuichi Yokoyama, Tohru Terada, Kentaro Shimizu, Kouki Nishikawa, Daisuke Kozai, Atsuhiro Shimada, Akira Mizoguchi, Yoshinori Fujiyoshi, Kazutoshi Tani: Development of a deep-learning-based method to identify “good” regions of a cryo-electron microscopy grid, Biophysics Reviews, 12, 349-354 (2020).
  28. Takashi Yasukawa, Aya Tsutsui, Chieri Tomomori-Sato, Shigeo Sato, Anita Saraf, Michael P. Washburn, Laurence Florens, Tohru Terada, Kentaro Shimizu, Ronald C. Conaway, Joan W. Conaway, Teijiro Aso: NRBP1-Containing CRL2/CRL4A Regulates Amyloid β Production by Targeting BRI2 and BRI3 for Degradation, Cell Reports, 30, 3478-3491 (2020).
  29. Tatsuki Negami, Kentaro Shimizu, Tohru Terada: Coarse-grained molecular dynamics simulation of protein conformational change coupled to ligand binding, Chemical Physics Letters, 742, 137144 (2020).
  30. Takatoshi Arakawa, Yuta Sato, Masayuki Yamada, Jumpei Takabe, Yoshitaka Moriwaki, Noriya Masamura, Masahiro Kato, Morihiro Aoyagi, Takahiro Kamoi, Tohru Terada, Kentaro Shimizu, Nobuaki Tsuge, Shinsuke Imai, Shinya Fushinobu: Dissecting the Stereocontrolled Conversion of Short-Lived Sulfenic Acid by Lachrymatory Factor Synthase, ACS Catalysis, 10, 9-19 (2020).
  31. Kohji Murase, Yoshitaka Moriwaki, Tomoyuki Mori, Xiao Liu, Chiho Masaka, Yoshinobu Takada, Ryoko Maesaki, Masaki Mishima, Sota Fujii, Yoshinori Hirano, Zen Kawabe, Koji Nagata, Tohru Terada, Go Suzuki, Masao Watanabe, Kentaro Shimizu, Toshio Hakoshima & Seiji Takayama . Mechanism of self/nonself-discrimination in Brassica self-incompatibility, Nature Communications, 11, 4916(2020).
  32. Tetsuhiro Ogawa, Kazutoshi Takahashi, Wataru Ishida, Toshihiro Aono, Makoto Hidaka, Tohru Terada, Haruhiko Masaki. Substrate recognition mechanism of tRNA-targeting ribonuclease, colicin D, and an insight into tRNA cleavage-mediated translation impairment, RNA Biology, in press (2020).
  33. Batuujin Burendei, Ruriko Shinozaki, Masakatsu Watanabe, Tohru Terada, Kazutoshi Tani, Yoshinori Fujiyoshi and Atsunori Oshima . Cryo-EM structures of undocked innexin-6 hemichannels in phospholipids, Science Advances, 6, eaax3157 (2020).
  34. Yoshitaka Moriwaki, Mirai Yato, Tohru Terada, Seiji Saito, Noriyuki Nukui, Takumi Iwasaki, Tatsunari Nishi, Yuko Kawaguchi, Ken Okamoto, Takatoshi Arakawa, Chihaya Yamada, Shinya Fushinobu, Kentaro Shimizu: Understanding the Molecular Mechanism Underlying the High Catalytic Activity of p-Hydroxybenzoate Hydroxylase Mutants for Producing Gallic Acid, Biochemistry, 58, 4543-4558 (2019).
  35. Peng Lu, Yoshitaka Moriwaki, Mimin Zhang, Yukie Katayama, Yi Lu, Ken Okamoto, Tohru Terada, Kentaro Shimizu, Mengyao Wang, Takehiro Kamiya, Toru Fujiwara, Tomiko Asakura, Michio Suzuki, Etsuro Yoshimura and Koji Nagata: Functional characterisation of two ferric-ion coordination modes of TtFbpA, the periplasmic subunit of an ABC-type iron transporter from Thermus thermophilus HB8, Metallomics, 11, 2078-2088 (2019).
  36. Zihan Tian, Cao Wei, Yoshitaka Moriwaki, Tohru Terada, Shugo Nakamura, Kazuya Sumikoshi, Fang Chun, and Kentaro Shimizu: Prediction of protein-metal ion-binding sites using sequence homology and machine-learning methods Advanced, Bioinformatics and Chemistry, 1, 025-036 (2019).
  37. Takayuki Osabe, Kentaro Shimizu, and Koji Kadota: Accurate classification of differential expression patterns in a Bayesian framework with robust normalization for multi-group RNA-seq count data, Bioinformatics and Biology Insights, 13 (2019).
  38. Chun Fang, Yoshitaka Moriwaki, Caihong Li and Kentaro Shimizu: Prediction of Antifungal Peptides by Deep Learning with Character Embedding, IPSJ Transactions on Bioinformatics, 12, 21-29 (2019).
  39. Chun Fang, Yoshitaka Moriwaki, Caihong Li, and Kentaro Shimizu: Prediction of MoRFs Based on n-gram Convolutional Neural Network,Proceedings of 11th International Conferenceon Bioinformatics and Computational Biology, 60, 113–119 (2019).
  40. Kenta Sato, Koki Tsuyuzaki, Kentaro Shimizu, and Itoshi Nikaido: CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA-sequencing, Genome Biology, 20, 31 (2019).
  41. Wei Su, Jianqiang Sun, Kentaro Shimizu, Koji Kadota, TCC-GUI: a Shiny-based application for differential expression analysis of RNA-Seq count data, BMC Research Notes, 12, 133 (2019).
  42. Kazunori Hirayama, Yuuki Fujiwara, Tohru Terada, Kentaro Shimizu, Keiji Wada, and Tomohiro Kabuta,: Virtual screening identification of novel chemical inhibitors for aberrant interactions between pathogenic mutant SOD1 and tubulin, Neurochemistry International, 126, 19-26(2019).
  43. Tatsuki Negami, Mitsugu Araki, Yasushi Okuno, and Tohru Terada. Calculation of absolute binding free energies between the hERG channel and structurally diverse drugs, Scientific Reports, 9, 16586 (2019).
  44. Nobukiyo Tanaka, Masahiro Nakajima, Megumi Narukawa-Nara, Hiroki Matsunaga, Shinji Kamisuki, Hiroki Aramasa, Yuta Takahashi, Naohisa Sugimoto, Koichi Abe, Tohru Terada, Akimasa Miyanaga, Tetsuro Yamashita, Fumio Sugawara, Takashi Kamakura, Shiro Komba, Hiroyuki Nakai and Hayao Taguchi. Identification, characterization, and structural analyses of a fungal endo-β-1,2-glucanase reveal a new glycoside hydrolase family, Journal of Biological Chemistry, 294, 7942–7965(2019).
  45. Kentaro Shimizu, Wei Cao, Gull Saad, Michiru Shoji, and Tohru Terada: Comparative analysis of membrane protein structure databases, BBA – Biomembranes, 1860, 1077-1091 (2018). (K.S. and W.C. are equal contribution.)
  46. Chun Fang, Yoshitaka Moriwaki, Aikui Tian, Caihong Li, and Kentaro Shimizu: Identifying short disorder-to-order binding regions in disordered proteins with a deep convolutional neural network method, Journal of Bioinformatics and Computational Biology, 10, 1142 (2018).
  47. Shitao Zhao, Jianqiang Sun, Kentaro Shimizu, and Koji Kadota: Silhouette scores for arbitrary defined groups in gene expression data and insights into differential expression results, Biological Procedures Online, 20, 5 (2018).
  48. Xi Fu, Jianqiang Sun, Engkong Tan, Kentaro Shimizu, Md Shaheed Reza, Shugo Watabe, and Shuichi Asakawa: High-throughput sequencing of the expressed torafugu (Takifugu rubripes) antibody sequences distinguishes IgM and IgT repertoires and reveals evidence of convergent evolution, Frontiers in Immunology, 9, 251 (2018).
  49. Chun Fang, Yoshitaka Moriwaki, Daming Zhu, and K. Shimizu: Identifying MoRFs in Disordered Protein Using Enlarged Conserved Features, 2018 6th International Conference on Bioinformatics and Computational Biology, 50-54 (2018).
  50. Kumar Nagarathinam, Yoshiko Nakada-Nakura, Christoph Parthier, Tohru Terada, Narinobu Juge, Frank Jaenecke, Kehong Liu, Yunhon Hotta, Takaaki Miyaji, Hiroshi Omote, So Iwata, Norimichi Nomura, Milton T. Stubbs, Mikio Tanabe. Outward open conformation of a Major Facilitator Superfamily multidrug/H+ antiporter provides insights into switching mechanism, Nature Communications, 9, 4005 (2018).
  51. Yifan Tang, Cao Wei, Kazuya Sumikoshi, Shugo Nakamura, Tohru Terada, Koji Kadota, and Kentaro Shimizu: Predicting protein-protein interactions using sequence homology and machine-learning methods, Research Journal of Life Sciences, Bioinformatics, Pharmaceutical, and Chemical Sciences, 3, 1–26 (2017).
  52. Atsushi Yamagata, Sakurako Goto-Ito, Yusuke Sato, Tomoko Shiroshima, Asami Maeda, Masahiko Watanabe, Takashi Saitoh, Katsumi Maenaka, Tohru Terada, Tomoyuki Yoshida, Takeshi Uemura, Shuya Fukai. Structural insights into modulation and selectivity of transsynaptic neurexin–LRRTM interaction, Nature Communications, 9, 3964 (2018).
  53. Koichi Abe, Naoki Sunagawa, Tohru Terada, Yuta Takahashi, Takatoshi Arakawa, Kiyohiko Igarashi, Masahiro Samejima, Hiroyuki Nakai, Hayao Taguchi, Masahiro Nakajima and Shinya Fushinobu. Structural and thermodynamic insights into β-1,2-glucooligosaccharide capture by a solute-binding protein in Listeria innocua, Journal of Biological Chemistry, 293, 8812–8828 (2018).
  54. Kei Moritsugu, Tohru Terada, Hironori Kokubo, Satoshi Endo, Toshimasa Tanaka, and Akinori Kidera. Multiscale enhanced sampling of glucokinase: Regulation of the enzymatic reaction via a large scale domain motion, Journal of Chemical Physics, 149, 072314 (2018).
  55. Yasuhiro Matsunaga, Tsutomu Yamane, Tohru Terada, Kei Moritsugu, Hiroshi Fujisaki, Satoshi Murakami, Mitsunori Ikeguchi, Akinori Kidera. Energetics and conformational pathways of functional rotation in the multidrug transporter AcrB, eLife, 7, e31715 (2018).
  56. Yifan Tang, Cao Wei, Kazuya Sumikoshi, Shugo Nakamura, Tohru Terada, Koji Kadota, and Kentaro Shimizu: Predicting protein-protein interactions using sequence homology and machine-learning methods, Research Journal of Life Sciences, Bioinformatics, Pharmaceutical, and Chemical Sciences, 3, 1–26 (2017).
  57. Masaki Banno, Yusuke Komiyama, Wei Cao, Yuya Oku, Kokoro Ueki, Kazuya Sumikoshi, Shugo Nakamura, Tohru Terada, and Kentaro Shimizu: Development of a sugar-binding residue prediction system from protein sequences using support vector machine, Journal of Computational Biology and Chemistry, 66, 36-43 (2017).
  58. Kei Moritsugu, Tohru Terada, and Akinori Kidera. Free-Energy Landscape of Protein–Ligand Interactions Coupled with Protein Structural Changes, Journal of Physical Chemistry B, 121, 731–740 (2017).
  59. Marie Kubota, Kaoru Takeuchi, Shumpei Watanabe, Shinji Ohno, Rei Matsuoka, Daisuke Kohda, Shin-ichi Nakakita, Hiroaki Hiramatsu, Yasuo Suzuki, Tetsuo Nakayama, Tohru Terada, Kentaro Shimizu, Nobutaka Shimizu, Mitsunori Shiroishi, Yusuke Yanagi, and Takao Hashiguchi: Trisaccharide containing α2,3-linked sialic acid is a receptor for mumps virus, Proceedings of the National Academy of Sciences, 113, 41, 11579-11584 (2016).
  60. Wayne Dawson, Ryota Jono, Tohru Terada, and Kentaro Shimizu: Electron transport in a dioxygenase-ferredoxin complex: long range charge coupling between the Rieske and non-heme iron center, PLoS ONE, 11, e0162031, 1-41 (2016).
  61. Shunsuke Shigemitsu, Wei Cao, Tohru Terada and Kentaro Shimizu: Development of a prediction system for tail-anchored proteins, BMC Bioinformatics, 18, 378, 1-11 (2016).
  62. Hiroto Tsujikawa, Kenta Sato, Cao Wei, Gul Saad, Kazuya Sumikoshi, Shugo Nakamura, Tohru Terada, and Kentaro Shimizu: Development of a protein–ligand-binding site prediction method based on interaction energy and sequence conservation, Journal of Structural and Functional Genomics, 17, 39-49 (2016).
  63. Kokoro Ueki, Shugo Nakamura, Tohru Terada, Kazuya Sumikoshi, and Kentaro Shimizu: Development of a computational method for lipid-binding protein prediction,Research Journal of Life Sciences, Bioinformatics, Pharmaceutical, and Chemical Sciences, 1, 223–236 (2016).
  64. Chiho Suzuki-Minakuchi, Kohei Kawazuma, Jun Matsuzawa, Delyana Vasileva, Zui Fujimoto, Tohru Terada, Kazunori Okada, Hideaki Nojiri. Structural similarities and differences in H-NS family proteins revealed by the N-terminal structure of TurB in Pseudomonas putida KT2440, FEBS Letters, 590, 3583–3594 (2016).
  65. Kei Moritsugu, Tohru Terada, Akinori Kidera. Multiscale enhanced sampling for protein systems: An extension via adiabatic separation, Chemical Physics Letters, 661, 279–283 (2016).
  66. Yoshitaka Moriwaki, Tohru Terada, Kouhei Tsumoto and Kentaro Shimizu: Rapid heme transfer reactions between NEAr transporter domains of Staphylococcus aureus: a theoretical study using QM/MM and MD simulations, PLoS ONE, 10, e0145125, 1-15 (2015).
  67. Yusuke Komiyama, Masaki Banno, Kokoro Ueki, Gul Saad, and Kentaro Shimizu: Automatic generation of bioinformatics tools for predicting protein-ligand binding sites, Bioinformatics, 31, 23, 901-907 (2015).
  68. Min Tang, Jianqiang SUN, Kentaro Shimizu, and Koji Kadota: Evaluation of methods for differential expression analysis on multi-group RNA-seq count data, BMC Bioinformatics, 16, 361, 1-14 (2015).
  69. Masayuki Yarimizu, Cao Wei, Yusuke Komiyama, Kokoro Ueki, Shugo Nakamura, Kazuya Sumikoshi, Tohru Terada, and Kentaro Shimizu: Tyrosine Kinase Ligand-Receptor Pair Prediction by Using Support Vector Machine, Advances in Bioinformatics, 528097, 1-5 (2015).
  70. Masanori Komatsu, Yoichi Sato, Tatsuki Negami, Tohru Terada, Osamu Sasaki, Jumpei Yasuda, Aisaku Arakawa, Chikara Yoshida, Hideaki Takahashi, Aduli E. O. Malau-Aduli, Keiichi Suzuki and Kentaro Shimizu: Overdominance effect of the bovine ghrelin receptor (GHSR1a)-DelR242 locus on growth in Japanese Shorthorn weaner bulls: Heterozygote advantage in bull selection and molecular mechanisms, G3: Genes, Genomes, Genetics, 5, 2, 271-279 (2015).
  71. Zuoqi Gai, Asuka Matsuno, Koji Kato, Sanae Kato, Md Rafiqul Islam Khan, Takeshi Shimizu, Takeya Yoshioka, Yuki Kato, Hideki Kishimura, Gaku Kanno, Yoshikatsu Miyabe, Tohru Terada, Yoshikazu Tanaka, Min Yao. Crystal Structure of the 3.8-MDa Respiratory Supermolecule Hemocyanin at 3.0 Å Resolution, Structure, 23, 2204–2212 (2015).
  72. Kayako Ogi, Haruyuki Yamashita, Tohru Terada, Ryousuke Homma, Akiko Shimizu-Ibuka, Etsuro Yoshimura, Yoshiro Ishimaru, Keiko Abe, and Tomiko Asakura. Long-Chain Fatty Acids Elicit a Bitterness-Masking Effect on Quinine and Other Nitrogenous Bitter Substances by Formation of Insoluble Binary Complexes, Journal of Agricultural and Food Chemistry, 63, 8493–8500 (2015).
  73. Taichi Koizumi, Tohru Terada, Ken-ichiro Nakajima, Masaki Kojima, Seizo Koshiba, Yoshitaka Matsumura, Kohei Kaneda, Tomiko Asakura, Akiko Shimizu-Ibuka, Keiko Abe, and Takumi Misaka. Identification of key neoculin residues responsible for the binding and activation of the sweet taste receptor, Scientific Reports, 5, 12947 (11 pages) (2015).
  74. Tatsuki Negami, Kentaro Shimizu, and Tohru Terada: Coarse-Grained Molecular Dynamics Simulations of Protein-Ligand Binding, Journal of Computational Chemistry, 35, 25, 1835-1845 (2014).
  75. Kengo Inoue, Yusuke Usami, Yuji Ashikawa, Haruko Noguchi, Takashi Umeda, Aiko Yamagami-Ashikawa, Tadafumi Horisaki, Hiromasa Uchimura, Tohru Terada, Shugo Nakamura, Kentaro Shimizu, Hiroshi Habe, Hisakazu Yamane, Zui Fujimoto and Hideaki Nojiri: Structural Basis of the Divergent Oxygenation Reactions Catalyzed by the Rieske Nonheme Iron Oxygenase Carbazole 1,9a-Dioxygenase Appl. Environ. Microbiol, 80, 9, 2821-2832 (2014).
  76. 込山悠介, 番野雅城, 鑓水優行, 加藤文彦, 大向一輝, 武田英明, 清水謙多郞: 生命科学の複数LODの統合による目的別タンパク質分子間相互作用Linked Open Dataの構築, 人工知能学会論文誌, 29, 4, 356-363 (2014).
  77. Fumiaki Ito, Masayuki Miyake, Shinya Fushinobu, Shugo Nakamura, Kentaro Shimizu, and Takayoshi Wakagi: Engineering the allosteric properties of archaeal non-phosphorylating glyceraldehyde-3-phosphate dehydrogenases. BBA – Proteins and Proteomics, 1844, 4, 759-766 (2014).
  78. Wayne Dawson, Toshikuni Takai, Nobuharu Ito, Kentaro Shimizu, and Gota Kawai: A new entropy model for RNA: part III, Is the folding free energy landscape of RNA funnel shaped? Journal of Nucleic Acids Investigation, 5, 1, 1-15 (2014).
  79. Kei Moritsugu, Tohru Terada, Akinori Kidera. Multiscale enhanced sampling driven by multiple coarse-grained models, Chemical Physics Letters, 616–617, 20–24 (2014).
  80. Kei Moritsugu, Tohru Terada, Akinori Kidera. Energy Landscape of All-Atom Protein-Protein Interactions Revealed by Multiscale Enhanced Sampling, PLoS Computational Biology, 10, e1003901 (2014).
  81. Chiho Suzuki, Kohei Kawazuma, Shoichiro Horita, Tohru Terada, Masaru Tanokura, Kazunori Okada, Hisakazu Yamane, Hideaki Nojiri. Oligomerization Mechanisms of an H-NS Family Protein, Pmr, Encoded on the Plasmid pCAR1 Provide a Molecular Basis for Functions of H-NS Family Members, PLoS ONE, 9, e105656 (2014).
  82. Yoshitaka Moriwaki, Tohru Terada, Jose M. M. Caaveiro, Yousuke Takaoka, Itaru Hamachi, Kouhei Tsumoto, and Kentaro Shimizu: Heme-binding mechanism of structurally similar Isd NEAT domains of Staphylococcus aureus exhibiting different affinities for heme. Biochemistry, 52, 49, 8866-8877 (2013).
  83. Nhuan T Vu, Yoshitaka Moriwaki, Jose M. M. Caaveiro, Tohru Terada, H. Tsutsumi, Hiroshi Tsutsumi, Kentaro Shimizu, and Kouhei Tsumoto: Selective binding of antimicrobial porphyrins to the heme-receptor IsdH-NEAT3 of Staphylococcus aureus. Protein Science, 22, 7, 942-953 (2013).
  84. Jianqiang Sun, Tomoaki Nishiyama, Kentaro Shimizu, and Koji Kadota: TCC: an R package for comparing tag count data with robust normalization strategies, BMC Bioinformatics, 14, 219, 1-13 (2013).
  85. Wayne K Dawson, Kenji Yamamoto, Kentaro Shimizu and Gota Kawai: A new entropy model for RNA: part II, Persistence-related entropic contributions to RNA secondary structure free energy calculation. Journal of Nucleic Acids Investigation, 4, 4, 4-18 (2013).
  86. Satoshi Yamasaki, Tohru Terada, Hidetoshi Kono, Kentaro Shimizu, and Akinori Sarai: A new method for evaluating the specificity of indirect readout in protein-DNA recognition, Nucleic Acids Res., 40, 17 (2012).
  87. Mizuki Morita, Masanori Kakuta, Kentaro Shimizu, and Shugo Nakamura: Blind prediction of quaternary structures of homo-oligomeric proteins from amino acid sequences based on templates, Journal of Proteome Science and Computational Biology, 1 (2012).
  88. Koji Kadota, Tomoaki Nishiyama and Kentaro Shimizu: A normalization strategy for comparing tag count data, Algorithms for Molecular Biology, 7, 5 (2012).
  89. Tohru Terada, Akinori Kidera. Comparative Molecular Dynamics Simulation Study of Crystal Environment Effect on Protein Structure, Journal of Physical Chemistry B, 116, 6810–6818 (2012).
  90. Yasuhiro Matsunaga, Hiroshi Fujisaki, Tohru Terada, Tadaomi Furuta, Kei Moritsugu, Akinori Kidera. Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase, PLoS Computational Biology, 8, e1002555 (2012).
  91. Kei Moritsugu, Tohru Terada, Akinori Kidera. Disorder-to-Order Transition of an Intrinsically Disordered Region of Sortase Revealed by Multiscale Enhanced Sampling, Journal of the American Chemical Society, 134, 7094–7101 (2012).
  92. Yoko Chiba, Tohru Terada, Masafumi Kameya, Kentaro Shimizu, Hiroyuki Arai, Masaharu Ishii, and Yasuo Igarashi: Mechanism for folate-independent aldolase reaction catalyzed by serine hydroxymethyltransferase, FEBS Journal, 279, 3, 504-514 (2011).
  93. Shinpei Kawaoka, Koji Kadota, Yuji Arai, Yutaka Suzuki, Tsuguru Fujii, Hiroaki Abe, Yuji Yasukochi, Kezuei Mita, Sumio Sugano, Kentaro Shimizu, Yukihide Tomari, Toru Shimada, and Susumu Katsuma: The silkworm W chromosome is a source 1 of female-enriched piRNAs 2, RNA, 17, 12, 2144-2151 (2011).
  94. Koji Kadota, and Kentaro Shimizu: Evaluating methods for ranking differentially expressed genes applied to microArray quality control data, BMC Bioinformatics, 12, 227 (2011).
  95. Shinpei Kawaoka, Yuji Arai, Koji Kadota, Yutaka Suzuki, Kahori Hara, Sumio Sugano, Kentaro Shimizu, Yukihide Tomari, Toru Shimada, and Susumu Katsuma: Zygotic amplification of secondary piRNAs during silkworm embryogenesis, RNA, 17, 7, 1401-1407 (2011).
  96. Mizuki Morita, Tohru Terada, Shugo Nakamura, and Kentaro Shimizu: BUDDY-system: A web service for constructing a dataset of protein pairs between ligand-bound and unbound states, BMC Research Notes, 4, 143 (2011).
  97. Wei Cao, Kazuya Sumikoshi, Shugo Nakamura, Tohru Terada, and Kentaro Shimizu: Prediction of N-myristoylation Modification of Proteins by SVM, Bioinformation, 6, 5 (2011).
  98. Kazuya Sumikoshi, Tohro Terada, Shogo Nakamura, and Kentaro Shimizu: Protein-Protein Docking Using Multi-layered Spherical Basis Functions, Proceedings of the 2011 International Conference on Bioscience, Biochemistry and Bioinformatics, 342-347 (2011).
  99. Ayako Koizumi, Asami Tsuchiya, Ken-ichiro Nakajima, Keisuke Ito, Tohru Terada, Akiko Shimizu-Ibuka, Loïc Briand, Tomiko Asakura, Takumi Misaka, and Keiko Abe. Human sweet taste receptor mediates acid-induced sweetness of miraculin, Proceedings of the National Academy of Sciences of the United States of America, 108, 16819–16824 (2011).
  100. Ken-ichiro Nakajima, Kanako Yokoyama, Taichi Koizumi, Ayako Koizumi, Tomiko Asakura, Tohru Terada, Katsuyoshi Masuda, Keisuke Ito, Akiko Shimizu-Ibuka, Takumi Misaka, Keiko Abe. Identification and Modulation of the Key Amino Acid Residue Responsible for the pH Sensitivity of Neoculin, a Taste-Modifying Protein, PLoS ONE, 6, e19448 (2011).
  101. Takashi Hagiwara, Seiji Saito, Yoshifumi Ujiie, Kensaku Imai, Masanori Kakuta, Koji Kadota, Tohru Terada, Kazuya Sumikoshi, Kentaro Shimizu, and Tatsunari Nishi: HPLC Retention time prediction for metabolome analysis, Bioinformation, 5, 6, 255-258 (2010).
  102. Seizi Someya, Masanori Kakuta, Mizuki Morita, Kazuya Sumikoshi, Wwi Cao, Zhenyi Ge, Osamu Hirose, Shugo Nakamura, Tohro Terada, and Kentaro Shimizu: Prediction of carbohydrate-binding proteins from sequences using support vector machines, Advances in Bioinformatics, 289301 (2010).
  103. Kei Urano, Takaaki Daimon, Yutaka Banno, Kazuei Mita, Tohru Terada, Kentaro Shimizu, Susumu Katsuma, and Toru Shimada: Molecular defect of isovaleryl-CoA dehydrogenase in the skunk mutant of silkworm, Bombyx mori. FEBS Journal, 277, 4452-4463 (2010).
  104. Osamu Hirose, and Kentaro Shimizu: A self-organizing state space approach to infer time-varying causalities between regulatory proteins, Proceedings of International Conference on Information Technology in Bio- and Medcial Informatics, 6266, 158-171 (2010).
  105. Ryota Jono, Yuusuke Watanabe, Kentaro Shimizu, and Tohru Terada: Multicanonical ab inito QM/MM Molecular Dynamics Simulation of a Peptide in an Aqueous Environment, J. Comput. Chem., 31, 6, 1168-1175 (2009).
  106. Satoshi Yamasaki, Tohru Terada, Kentaro Shimizu, Hidetoshi Kono, and Akinori Sarai: A Generalized Conformational Energy Function of DNA Derived from Molecular Dynamics Simulations, Nucleic Acids Res., 37, e135 (2009).
  107. Shugo Nakamura, K. Shimizu: Comprehensive analysis of sequence-structure relationships in the loop regions of proteins, GIW 2009, 23,
    106-116 (2009).
  108. Koji Kadota, Yuji Nakai, and Kentaro Shimizu: Ranking differentially expressed genes from Affymetrix gene expression data: methods with reproducibility,
    sensitivity, and specificity, Algorithms for Molecular Biology, 4, 7 (2009).
  109. Wei Cao, Junichi Maruyama, Katsuhiko Kitamoto, Kazuya Sumikoshi, Tohru Terada, Shugo Nakamura, and Kentaro Shimizu: Using a new GPI-anchored-protein identification system to mine the protein databases of Aspergillus fumigatus, Aspergillus nidulans, and Aspergillus oryzae, The Journal of General and Applied Microbiology, 55, 5, 381-393 (2009).
  110. Tadaomi Furuta, Kentaro Shimizu, and Tohru Terada: Accurate prediction of native tertiary structure of protein using molecular dynamics simulation with the aid of the knowledge of secondary structures, Chemical Physics Letters, 472, 134-139 (2009).
  111. W. Cao, K. Sumikoshi, T. Terada, S. Nakamura, K. Kitamoto, K. Shimizu: Computational Protocol for Screening GPI-anchored Proteins, Proceedings of the First International Conference on Bioinformatics and Computational Biology (BICoB), Springer Lecture Notes in Bioinformatics Series, 5462, 164-175 (2009).
  112. J. Inaba, S. Nakamura, K. Shimizu, T. Asami, Y. Suzuki: Anti-metatype
    peptides, a new molecular tool to monitor small ligands at high sensitivity
    and specificity. Analytical
    Biochemistry, 388, 63-70 (2009).
  113. Bhowmick, B.K., W. Dawson, P. Majumder and K. Shimizu: A consensus approach for intrinsic disorder analysis for heat shock protein family, Biotechnology, 8, 306-315 (2009).
  114. Yuji Morita, Ken-ichiro Nakajima, Kisho Iizuka, Tohru Terada, Akiko Shimizu-Ibuka, Keisuke Ito, Ayako Koizumi, Tomiko Asakura, Takumi Misaka, and Keiko Abe. pH-dependent structural change of neoculin in special reference to its taste-modifying activity, Bioscience, Biotechnology, and Biochemistry, 73, 2552–2555 (2009).
  115. Tokiha Masuda, Yutaka Ito, Tohru Terada, Takehiko Shibata, and Tsutomu Mikawa. A non-canonical DNA structure enables homologous recombination in various genetic systems, Journal of Biological Chemistry, 284, 30230–30239 (2009).
  116. Kengo Inoue, Yuji Ashikawa, Takashi Umeda, Mitsuru Abo, Junichi Katsuki, Yusuke Usami, Haruko Noguchi, Zui Fujimoto, Tohru Terada, Hisakazu Yamane, and Hideaki Nojiri. Specific interactions between the ferredoxin and terminal oxygenase components of a class IIB Rieske nonheme iron oxygenase, carbazole 1,9a-dioxygenase, Journal of Molecular Biology, 329, 436–451 (2009).
  117. Bhowmick, B.K., A.B.M.R. Islam, K. Shimizu and R.K. Paul: Study of horizontal gene transfer in Corynebacteria diphtheriae and its effects by using SOM algorithm, Mol. Genet. Microbiol. Virol., 23, 132-141 (2008).
  118. R. Ishitani, T. Terada, K. Shimizu: Refinement of comparative models of protein structure by using multicanonical molecular dynamics simulations. Molecular Simulation, 34, 327-336 (2008).
  119. K.Kadota, Y. Nakai, K. Shimizu: A weighted average difference method for detecting differentially expressed genes from microarray data. Algorithms Mol Biol,. 3, 8 (2008).
  120. T. Terada, K. Shimizu: A comparison of generalized Born methods in folding simulations. Chemical Physics Letters, 460, 295-299(2008).
  121. T. Terada, D. Satoh, T. Mikawa, Y. Ito, K. Shimizu: Understanding the roles of amino acid residues in tertiary structure formation of chignolin by using molecular dynamics simulation PROTEINS: Structure, Function, and Bioinformatics, 73, 3, 621-631 (2008).
  122. M. Morita, S. Nakamura, K. Shimizu: Highly accurate method for ligand-binding site prediction in unbound state (apo) protein structures PROTEINS: Structure, Function, and Bioinformatics, 73, 2, 468-479 (2008).
  123. Y. Nakai, H. Hashida, K. Kadota, M. Minami, K. Shimizu, I. Matsumoto, H. Kato, K. Abe: Genes Related to the Ubiquitin-Proteasome System Are Up-regulated in the Brown Adipose Tissue of 24 h-Fasted Rats, Bioscience, Biotechnology, and Biochemistry, 72, 1, 139-148 (2008).
  124. M. Kakuta, S. Nakamura, K. Shimizu: Prediction of protein-protein interaction sites using only sequence information and using both sequence and structural information, IPSJ Transactions on Bioinformatics, 49, 25-35 (2008).
  125. M. Kakuta, S. Nakamura, K. Shimizu: Prediction of protein-protein interaction sites using only sequence information and using both sequence and structural information, IPSJ Transactions on Bioinformatics, 49, 25-35 (2008).
  126. Akiko Shimizu-Ibuka, Yuji Nakai, Keisuke Nakamori, Yuji Morita, Ken-ichiro Nakajima, Koji Kadota, Hirohito Watanabe, Satoshi Okubo, Tohru Terada, Tomiko Asakura, Takumi Misaka, and Keiko Abe. Biochemical and Genomic Analysis of Neoculin Compared to Monocot Mannose-Binding Lectins, Journal of Agricultural and Food Chemistry, 56, 5338–5344 (2008).
  127. Ken-ichiro Nakajima, Yuji Morita, Ayako Koizumi, Tomiko Asakura, Tohru Terada, Keisuke Ito, Akiko Shimizu-Ibuka, Jun-ichi Maruyama, Katsuhiko Kitamoto, Takumi Misaka, and Keiko Abe. Acid-induced sweetness of neoculin is ascribed to its pH-dependent agonistic-antagonistic interaction with human sweet taste receptor, The FASEB Journal, 22, 2323–2330 (2008).
  128. K. Kadota, T. Konishi, K. Shimizu: Evaluation of two outlier-detection-based methods for detecting tissue-selective genes from microarray data, Gene Regulation and Systems Biology, 1, 9-15
    (2007).
  129. M. Hirano, R. S. Davis, W. D. Fine, S. Nakamura, K. Shimizu, H. Yagi, K. Kato, R. P. Stephan, M. D. Cooper: IgEb immune complexes activate macrophages through Fc-gamma RIV binding, Nature Immu., 8, 7, 762-771(2007).
  130. S. Yamasaki, S. Nakamura, T. Terada, K. Shimizu: Mechanism of the difference in the binding affinity of E.coli tRNAGln to glutaminyl-tRNA synthetase caused by non-interface nucleotides in variable loop, Biophysical Journal, 92, 192-200 (2007).
  131. Keisuke Ito, Tomiko Asakura, Yuji Morita, Ken-ichiro Nakajima, Ayako Koizumi, Akiko Shimizu-Ibuka, Katsuyoshi Masuda, Masaji Ishiguro, Tohru Terada, Jun-ichi Maruyama, Katsuhiko Kitamoto, Takumi Misaka, and Keiko Abe. Microbial production of sensory-active miraculin, Biochemical and Biophysical Research Communications, 360, 407–411 (2007).
  132. R. Jono, T. Terada, K. Shimizu: A multicanonical ab initio molecular dynamics method: application to conformation sampling of alanine tripeptide, Chemical Physics Letters, 432, 306-312 (2006).
  133. K. Kadota, J. Ye, Y. Nakai, T. Terada, K. Shimizu: ROKU: A novel method for identification of tissue-specific genes, BMC Bioinformatics, 7, 294 (2006).
  134. J. Doi, K. Shimizu, W. Sato, S. Morishita: High-precision Geometric Modeling of 3D Artifacts for Virtual Restoration,IEEE International Conference on Virtual Environments, Human-Computer Interfaces, and Measurement Systems, 136-141 (2006).
  135. T. Ishida, S. Nakamura, K. Shimizu: Potential for Assessing Quality of Protein Structure based on Contact Number Prediction, PROTEINS: Structure, Function, and Bioinformatics, 64, 4, 940-947 (2006).
  136. W. Cao, K. Sumikoshi, T. Terada, S. Nakamura, K. Shimizu: Insight of the Signal Motif of GPI-(like)-anchored Proteins by Using SVM Proceedings of the 2006 International Conference on Bioinformatics and Computational Biology(BIOCOMP’06), 541-546 (2006).
  137. D. Satoh, K. Shimizu, S. Nakamura, T. Terada: Folding free-energy landscape of a 10-residue mini-protein, chignolin, FEBS Letters, 580, 3422-3426 (2006).
  138. R. Ishitani, K. Shimizu, T. Terada: Evaluation of efficiency of reference potential spatial warping algorithm in conformational sampling of peptides, Journal of Chemical Physics, 124, 214902 (2006).
  139. W. Cao, K. Shimizu: Identification of GPI-(like)-anchored Proteins by using SVM, Proceedings of the First International Multi-symposiums of Computer Science and Computational Sciences (IMSCCS’06), 711-715(2006).
  140. Akiko Shimizu-Ibuka, Yuji Morita, Tohru Terada, Tomiko Asakura, Ken-ichiro Nakajima, So Iwata, Takumi Misaka, Hiroyuki Sorimachi, Soichi Arai, and Keiko Abe. Crystal Structure of Neoculin: Insights into its Sweetness and Taste-modifying Activity, Journal of Molecular Biology, 359, 148–158 (2006).
  141. K. Sumikoshi, T. Terada, S. Nakamura, K. Shimizu: A fast protein-protein docking algorithm using series expansion in terms of spherical basis functions, Genome Informatics, 16, 161-173 (2005).
  142. T. Murata, H. Hemmi, S. Nakamura, K. Shimizu, Y. Suzuki, I. Yamaguchi: Structure, epitope mapping, and docking simulation of a gibberellin mimic peptide as a peptidyl mimotope for a hydrophobic ligand, FEBS Journal, 272, 4938-4948 (2005).
  143. H. Nojiri, Y. Ashikawa, H. Noguchi, J.-W. Nam, M. Urata, Z. Fujimoto, H. Uchimura, T. Terada, S. Nakamura, K. Shimizu, T. Yoshida, H. Habe, T. Omori: Structure of the terminal oxygenase component of angular dioxygenase, carbazole 1,9a-dioxygenase, Journal of Molecular Biology, 351,355-370 (2005).
  144. X. Dong, S. Fushinobu, E. Fukuda, T. Terada, S. Nakamura, K. Shimizu, H. Nojiri, T. Omori, H. Shoun, T. Wakagi: Crystal structure of the terminal cumene dioxygenase component of Pseudomonas fluorescens IP01, Journal of Bacteriology, 187, 2483-2490 (2005).
  145. Hideaki Nojiri, Yuji Ashikawa, Haruko Noguchi, Jeong-Won Nam, Masaaki Urata, Zui Fujimoto, Hiromasa Uchimura, Tohru Terada, Shugo Nakamura, Kentaro Shimizu, Takako Yoshida, Hiroshi Habe, and Toshio Omori. Structure of the Terminal Oxygenase Component of Angular Dioxygenase, Carbazole 1,9a-Dioxygenase, Journal of Molecular Biology, 351, 355–370 (2005).
  146. Kazuhiko Arima, Kazuo Sato, Go Tanaka, Sachiko Kanaji, Tohru Terada, Eijiro Honjo, Ryota Kuroki, Yo Matsuo, and Kenji Izuhara. Characterization of the Interaction between Interleukin-13 and Interleukin-13 Receptors, Journal of Biological Chemistry, 280, 24915–24922 (2005).
  147. T. Ishizuka, T. Terada, S. Nakamura, K. Shimizu: Improvement of accuracy of free-energy landscapes of peptides calculated with generalized Born model by using numerical solutions of Poisson’s equation, Chemical Physics Letters, 393, 546-551 (2004).
  148. A. Nomoto, Y. Watanabe, W. Kaneko, S. Nakamura, K. Shimizu: Distributed shared arrays: Portable shared-memory programming interface for multiple computer systems, Cluster Computing, The Journal of Networks, Software Tools and Applications,7, 1, 65-72 (2004).
  149. A. Nomoto, W. Kaneko, T. Terada, S. Nakamura, K. Shimizu: Distributed shared arrays: Portable shared-memory programming interface for multiple computer systems, Proceedings of the 2004 Symposium on Applications & the Internet, 630-635 (2004).
  150. T. Ishida, T. Nishimura, M. Nozaki, T. Inoue, T. Terada, S. Nakamura, K. Shimizu: Development of an ab initio protein structure prediction system ABLE, Genome Informatics, 14, 228-237 (2003).
  151. W. Kaneko, A. Nomoto, Y. Watanabe, K. Shimizu and S. Nakamura: Design and implementation of a parallel programming environment based on distributed shared arrays, Proceedings of the fifth International Symposium on High Performance Computing, Lecture Notes in Computer Science, LNCS 2858, 402-411, Springer (2003).
  152. I. Matsumoto, Y. Emori, S. Nakamura, K. Shimizu, S. Arai and K. Abe: DNA microarray cluster analysis reveals tissue similarity and potential neuron-specific genes expressed in cranial sensory ganglia, Journal of Neuroscience Research, 74, 6, 818-828 (2003).
  153. 河野健二, 金子済, 清水謙多郎: 資源濫用攻撃に耐性のある資源管理方式, 情報処理学会ACS論文誌, 44, SIG11,191-200 (2003).
  154. K. Tsukamoto, S. Nakamura, and K. Shimizu: SAM1 semiempirical calculations on the catalytic cycle of nitric oxide reductase from Fusarium oxysporum, Journal of Molecular Structure: THEOCHEM, 624, 309-322 (2003).
  155. S. Nakamura, M. Ikeguchi and K. Shimizu: Dynamical analysis of tRNAGln-GlnRS complex using normal mode calculation, Chemical Physics Letters, 372, 423-431 (2003).
  156. A. Nomoto, Y. Watanabe, W. Kaneko, S. Nakamura and K. Shimizu: Distributed shared arrays: Portable shared-memory programming interface for multiple computer systems, Cluster computing The Journal of Networks, Software tools and applications, 7, 1, 65-72 (2003).
  157. W. Kaneko, K. Kono, and K. Shimizu: Preemptive resource management: Defending against resource monopolizing DoS, Proceedings of IASTED International Conference on Parallel and Distributed Computing and Networks, 378-327 (2003).
  158. K. Iwata, H. Nojiri, K. Shimizu, T. Yoshida, H. Habe, and T. Omori: Expression, purification, and characterization of 2′-aminobiphenyl-2,3-diol 1,2-dioxygenase from carbazole-degrader pseudomonas resinovorans strain CA10, Bioscince Biotechnology Biochemistry, 67, 300-307 (2003).
  159. H. Nojiri, H. Taira, K. Iwata, K. Morii, J.-W. Nam, T. Yoshida, H. Habe, S. Nakamura, K. Shimizu, H. Yamane, and T. Omori: Meta cleavage compound hydrolase involved in the degradation of carbazole by pseudomonas resinovorans strain CA10, Bioscience Biotechnology Biochemistry, 67, 36-45(2003).
  160. Tohru Terada, Yo Matsuo, and Akinori Kidera. A method for evaluating multicanonical potential function without iterative refinement: Application to conformational sampling of a globular protein in water, Journal of Chemical Physics, 118, 4306–4311 (2003).
  161. Takafumi Uchida, Mari Takamiya, Morito Takahashi, Hitoshi Miyashita, Hisafumi Ikeda, Tohru Terada, Yo Matsuo, Mikako Shirouzu, Shigeyuki Yokoyama, Fumihiro Fujimori, and Tony Hunter. Pin1 and Par14 Peptidyl Prolyl Isomerase Inhibitors Block Cell Proliferation, Chemistry & Biology, 10, 15–24 (2003).
  162. (Group1) Y. Ichikawa, T. Ishikawa, S. Takahashi, Y. Hamaguchi, T. Morita, I. Nishizuka, S. Yamaguchi, I. Endo, H. Ike, S. Togo, S. Oki, H. Shimada, (Group2) K. Kadota, S. Nakamura, H. Goto , H. Nitanda, S. Satomi, T. Sakai, I. Narita, F. Gejyo, Y. Tomaru, K. Shimizu, Y. Hayashizaki and Y. Okazaki: Identification of genes regulating colorectal carcinogenesis by using the ADMS (Algorithm for Diagnosing Malignant State) method, Biochemical and Biophysical Research Communications, 296, 497-506 (2002).
  163. M. Sekijima, S. Takasaki, S. Nakamura and K. Shimizu: Automatic improvement of scheduling policies in parsley parallel programming environment, Proceedings of the Parallel and Distributed Computing and
    Systems 2002    , 380-385 (2002).
  164. Y. Watanabe, S. Nakamura and K. Shimizu: Parallel programming environment based on distributed shared arrays: Design and applications to molecular biology, Proceedings of the Third International Conference on Parallel and Distributed Computing, Applications and Technologies, 44-51 (2002).
  165. S. Nakamura, D. Kyono, M. Ikeguchi and K. Shimizu: New method for parallel computation of hessian matrix of conformational energy function in internal coordinates, Journal of Computational Chemistry, 23, 4, 463-469(2002).
  166. Tohru Terada and Akinori Kidera. Generalized form of the conserved quantity in constant-temperature molecular dynamics, Journal of Chemical Physics, 116, 33–41 (2002).
  167. 繁田聡一, 清水謙多郎, 曽和将容: キー/ロック方式の拡張によるアクセスルートコントロール, 情報処理学会論文誌, 42, 6, 1545-1556 (2001).
  168. S. Shigeta, K. Shimizu and S. Sowa: Access route control by extended key/lock scheme, International Journal of Computer Systems, Science and Engineering, 16, 5, 319-325 (2001).
  169. M. Ikeguchi, S. Nakamura and K. Shimizu: Molecular dynamics study on hydrophobic effects in aqueous urea solutions, Journal of the American Chemical Society, 123, 4, 677-682 (2001).
  170. K. Kadota, R. Miki, H. Bono, Y. Hayashizaki and K. Shimizu: Preprocessing implementation for microarray (PRIM): An efficient method for processing cDNA microarray data, Physiological Genomics, 4, 3, 183-188 (2001).
  171. Tohru Terada, Mikako Shirouzu, Yasuhiro Fukumori, Fumihiro Fujimori, Yutaka Ito, Takanori Kigawa, Shigeyuki Yokoyama, and Takafumi Uchida. Solution Structure of the Human Parvulin-like Peptidyl Prolyl cis/trans Isomerase, hPar14, Journal of Molecular Biology, 305, 917–926 (2001).
  172. S. Takasaki, M. Sekijima, S. Nakamura, M. Ikeguchi and K. Shimizu: Scheduling policy and mechanism of parsley parallel programming environment, Proceedings of the IASTED 11th International Conference on Parallel and Distributed Computing and Systems, 605-610 (2000).
  173. M. Sekijima, S. Takasaki, S. Nakamura, M. Ikeguchi and K. Shimizu: A parallel programming environment with dependence-driven task scheduling in distributed-memory multiprocessor systems, Proceedings of the International Conference on Parallel and Distributed Computing Systems, 348-354 (2000).
  174. 関嶋政和, 高崎慎也, 中村周吾, 池口満徳, 清水謙多郎: サブタスク間の依存関係に基づくスケジューリング機構を備えた並列プログラミング環境の開発, 情報処理学会論文誌プログラミング, 41, SIG 2(PRO 6), 65-77 (2000).
  175. M. Zhu and K. Shimizu: A nonblocking group membership protocol for large-scale distributed systems, IEICE Transactions on Information and Systems, E83-D, 2, 177-189 (2000).
  176. Y. Kuhara, K. Shimizu and J. Doi: Neural network estimation of enzyme active site, Proceedings of the 5th International Conference on Engineering Applications of Neural Networks, 51-56 (1999).
  177. M. Sekijima, S. Takasaki, S. Nakamura, M. Ikeguchi and K. Shimizu: Parsley: A scalable framework for dependence-driven task scheduling in distributed-memory multiprocessor systems, Proceedings of the 11th IASTED International Conference on Parallel and Distributed Computing and Systems, 800-805 (1999).
  178. S. Nakamura, H. Hirose, M. Ikeguchi and K. Shimizu: Structural modeling of DNA mini-hairpin molecules with various loop sequences, Chemical Physics Letters, 308, 267-273 (1999).
  179. S. Shigeta, S. Okamoto, K. Shimizu, and M. Sowa: A flexible access control mechanism based on the key/lock scheme, Proceedings of International Technical Conference on Circuits/Systems, Computers and Communications,1385-1388 (1999).
  180. S. Shimizu and K. Shimizu: Alcohol denaturation: Thermodynamic theory of peptide unit solvation, Journal of the American Chemical Society, 121, 11, 2387-2394 (1999).
  181. S. Shimizu, M. Ikeguchi, S. Nakamura, and K. Shimizu: Size dependence of transfer free energies: a hard-sphere-chain-based formalism, Journal of Chemical Physics, 110, 2971-2982 (1999).
  182. Tohru Terada, Yutaka Ito, Mikako Shirouzu, Masaru Tateno, Kyoko Hashimoto, Takanori Kigawa, Toshikazu Ebisuzaki, Koji Takio, Takehiko Shibata, Shigeyuki Yokoyama, Brian O. Smith, Ernest D. Laue, and Jonathan A. Cooper. Nuclear Magnetic Resonance and Molecular Dynamics Studies on the Interactions of the Ras-binding Domain of Raf-1 with Wild-type and Mutant Ras Proteins, Journal of Molecular Biology, 286, 219–232 (1999).
  183. T. Murata, M. Sekijima, H. Masaki, S. Nakamura, M. Ikeguchi and K. Shimizu: Parallel programming environment with dependence-driven subtask scheduling: Design and application to molecular dynamics simulation,Proceedings of the 2nd International Conference on Parallel and Distributed Computing and Networks, 650-653 (1998).
  184. M. Ikeguchi, S. Shimizu, S. Nakamura, and K. Shimizu: Roles of hydrogen bonding and the hard core of water on hydrophobic hydration, Journal of Physical Chemistry, 102, 5891-5898 (1998).
  185. H. Kinoshita and K. Shimizu: Prediction of the GTPase activities by using the semiempirical molecular orbital theory, Bioorganic & Medicinal Chemistry Letters, 8, 1083-1088 (1998).
  186. J.-I. Sagara, S. Shimizu, T. Kawabata, S. Nakamura, M. Ikeguchi and K. Shimizu: The use of sequence comparison to detect identities in tRNA genes, Nucleic Acid Research, 26, 1974-1979 (1998).
  187. 吉川裕, 池口満徳, 中村周吾, 清水謙多郎, 土井淳多: 隠れマルコフモデルによるタンパク質構造クラスの解析, 電子情報通信学会論文誌, J81-D-II, 7, 1656-1665 (1998).
  188. Y. Kuhara, K. Shimizu, and J. Doi: Time-of-reduction-recovery prediction in neural networks of variable topology to improve enzyme classification, Proceedings of the International ISCS/IFAC Symposium on Neural
    Computation    , 23-25 (1998).
  189. S. Nakamura, M. Ikeguchi, and K. Shimizu: Parallel algorithm for efficient calculation of second derivatives of conformational energy function in internal coordinates, Journal of Computational Chemistry, 19, 1716-1723(1998).
  190. M. Ikeguchi, S. Shimizu, K. Tazaki, S. Nakamura, and K. Shimizu: Calculation of temperature dependence of free energy caused by potential function changes, Chemical Physics Letters, 288, 333-337 (1998).
  191. S. Shimizu, M. Ikeguchi, S. Nakamura, and K. Shimizu: Molecular volume, surface area, and curvature dependence of the configurational entropy change upon solvation: Effects of molecular bonding, Chemical Physics Letters, 284, 235-246 (1998).
  192. K. Tazaki and K. Shimizu: Molecular dynamics simulation in ionic aqueous solution: Application to free energy calculation of oligopeptides, Journal of Physical Chemistry B, 102, 33, 6419-6424 (1998).
  193. S. Shimizu, M. Ikeguchi and K. Shimizu: An off-lattice theory of solvation: Extension of the Flory χ parameter into continuum space, Chemical Physics Letters, 282, 79-90 (1998).
  194. Takashi Yabuki, Takanori Kigawa, Naoshi Dohmae, Koji Takio, Tohru Terada, Yutaka Ito, Ernest D. Laue, Jonathan A. Cooper, Masatsune Kainosho, Shigeyuki Yokoyama. Dual amino acid-selective and site-directed stable-isotope labeling of the human c-Ha-Ras protein by cell-free synthesis, Journal of Biolomecular NMR, 11, 295–306 (1998).
  195. H. Masaki, T. Miyata, K. Shimizu and H. Ashihara: Performance evaluation of global page placement policies in massively-parallel systems, Proceedings of the International Conference on Parallel and Distributed
    Computing and Networks    , 31-36 (1997).
  196. 芦原評, 清水謙多郎: 消費資源を含むシステムにおけるデッドロック検出, 情報処理学会論文誌, 38, 7, 1-10 (1997).
  197. 五明則人, 清水謙多郎, 芦原評, 張勇兵: 大規模並列システムにおける動的負荷分散のシミュレーションによる性能評価, 日本シミュレーション学会誌, 16, 9, 209-217 (1997).
  198. Y. Kuhara, K. Shimizu and J. Doi: Enzyme function prediction using neural networks of variable topology, Proceedings of International Conference on Engineering Applications of Neural Networks, 127-130 (1997).
  199. S. Shimizu, M. Ikeguchi and K. Shimizu: Extracting contact free energy from solubility: Excluded volume effects of polymers in continuum space, Chemical Physics Letters, 268, 93-100 (1997).
  200. K. Shimizu, A. Oishi, H. Ashihara, M. Ikeguchi and S. Nakamura: Design and Implementation of parallel programming environment with dynamic resource management services, Proceedings of the 12th ISCA International Conference on Computers and Their Applications, 226-231 (1997).
  201. Y. Kuhara, K. Shimizu and J. Doi: Chymotrypsin active site estimation using neural networks, Proceedings of the 13th Symposium on Artificial Intelligence and Computer Vision, 57-60 (1997).
  202. 芦原評, 清水謙多郎: 分散システムにおける読み書き問題に対するコテリーの構成とその応用, 情報処理学会論文誌, 38, 2, 167-179 (1997).
  203. T. Kudo, K. Shimizu and H. Ashihara: Parallel algorithms for mining association rules in large databases, Proceedings of the 6th ISCA International Conference on Intelligent Systems,125-129 (1997).
  204. Hideki Aihara, Yutaka Ito, Hitoshi Kurumizaka, Tohru Terada, Shigeyuki Yokoyama, and Takehiko Shibata. An Interaction between a Specific Surface of the C-terminal Domain of RecA Protein and Double-stranded DNA for Homologous Pairing, Journal of Molecular Biology, 274, 213–221 (1997).
  205. Yutaka Ito, Kazuhiko Yamasaki, Junji Iwahara, Tohru Terada, Akihide Kamiya, Mikako Shirouzu, Yutaka Muto, Gota Kawai, Shigeyuki Yokoyama, Ernest D. Laue, Markus Waelchli, Takehiko Shibata, Susumu Nishimura, and Tatsuo Miyazawa. Regional Polysterism in the GTP-Bound Form of the Human c-Ha-Ras Protein, Biochemistry, 36, 9109–9119 (1997).
  206. Satoko Akashi, Mikako Shirouzu, Tohru Terada, Yutaka Ito, Shigeyuki Yokoyama, and Koji Takio. Characterization of the Structural Difference between Active and Inactive Forms of the Ras Protein by Chemical Modification Followed by Mass Spectrometric Peptide mapping, Analytical Biochemistry, 248, 15–25 (1997).
  207. S. Shigeta, T. Tanimori, K. Shimizu and H. Ashihara: A fine-grained protection mechanism for object-based operating systems, Proceedings of International Workshop on Object-Oriented Operating Systems,156-160(1996).
  208. X. Jia, K. Shimizu and M. Maekawa: Atomic accesses to replicated files in reliable distributed file systems, International Journal of Computer Systems, Science and Engineering, 11, 3, 145-152 (1996).
  209. 岡坂史紀, 清水謙多郎: Act8オペレーティングシステムにおけるサーバ 開発の枠組み,電子情報通信学会論文誌, J79-B-I, 5, 286-292 (1996).
  210. S. Okasaka and K. Shimizu: A concurrent server model for service developments in the Act8 operating system, Proceedings of Multimedia JAPAN 96, 134-139 (1996).
  211. Brian O. Smith, Yutaka Ito, Andrew Raine, Sarah Teichmann, Liat Ben-Tovim, Daniel Nietlispach, R. William Broadhurst, Tohru Terada, Mark Kelly, Hartmut Oschkinat, Takehiko Shibata, Shigeyuki Yokoyama, and Ernest D. Laue. An approach to global fold determination using limited NMR data from larger proteins selectively protonated at specific residue types, Journal of Biomolecular NMR, 8, 360–368 (1996).