査読つき論文(1996-)

  1. 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 Mg2+ Transporter AtMRS2-1,Bioscience, Biotechnology, and Biochemistry, (2022)
  2. 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, Angew Chem Int Ed Engl, 61, e202111217 (2022)
  3. 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, J Biol Chem, 297, 101324 (2021)
  4. Takayuki Osabe, Kentaro Shimizu, Koji Kadota: Differential expression analysis using a model-based gene clustering algorithm for RNA-seq data, BMC Bioinformatics, 22, 10.1186 (2021)
  5. Ryosuke Miyata, Yoshitaka Moriwaki, Tohru Terada, Kentaro Shimizu: Prediction and analysis of antifreeze proteins, Heliyon, 7, e07953 (2021)
  6. Keisuke Yanagisawa, Yoshitaka Moriwaki, Tohru Terada, Kentaro Shimizu: EXPRORER: Rational Cosolvent Set Construction Method for Cosolvent Molecular Dynamics Using Large-Scale Computation, J Chem Inf Model, 61, 2744-2753 (2021)
  7. 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, Commun Biol, 4, 209 (2021)
  8. Jianqiang Sun 1, Rie Shimizu-Inatsugi 2, Hugo Hofhuis 3, Kentaro Shimizu 4, Angela Hay 3, Kentaro K Shimizu 2 5, Jun Sese: A Recently Formed Triploid Cardamine insueta Inherits Leaf Vivipary and Submergence Tolerance Traits of Parents, Front Genet, 3389, 10.3389 (2020)
  9. Koji Kadota, Kentaro Shimizu: Commentary: A Systematic Evaluation of Single Cell RNA-Seq Analysis Pipelines, Front Genet, 3389, 10.3389 (2020)
  10. 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, Nat Commun, 11, 4916 (2020)
  11. Miho Chikazawa, Yoshitaka Moriwaki, Mari Uramoto, Yoshio Yamauchi, Makoto Shimizu, Kentaro Shimizu, Ryuichiro Sato: Functional effect of nobiletin as a food-derived allosteric modulator of mouse CRFR2β in skeletal muscle, Biochem Biophys Res Commun, 529, 328-334 (2020)
  12. Masayuki Miyake, Tohru Terada, Michiko Shimokawa, Naohisa Sugimoto, Takatoshi Arakawa, Kentaro Shimizu, Kiyohiko Igarashi, Kiyotaka Fujita, Shinya Fushinobu: Structural analysis of β-L-arabinobiose-binding protein in the metabolic pathway of hydroxyproline-rich glycoproteins in Bifidobacterium longum, FEBS J, 287, 5114-5129 (2020)
  13. 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 Review, 12, 349-354 (2020)
  14. 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).
  15. 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).
  16. 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).
  17. 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).
  18. 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).
  19. 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).
  20. 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).
  21. 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).
  22. 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).
  23. 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).
  24. 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).
  25. 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) .
  26. 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.)
  27. 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).
  28. 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).
  29. 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).
  30. 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).
  31. 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).
  32. 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).
  33. 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).
  34. 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).
  35. 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).
  36. 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).
  37. 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).
  38. 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).
  39. 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).
  40. 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).
  41. 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).
  42. 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).
  43. 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).
  44. 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).
  45. 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).
  46. 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).
  47. 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).
  48. 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).
  49. 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).
  50. 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).
  51. 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).
  52. 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).
  53. 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).
  54. Koji Kadota, Tomoaki Nishiyama and Kentaro Shimizu: A normalization strategy for comparing tag count data, Algorithms for Molecular Biology, 7, 5 (2012).
  55. 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).
  56. 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).
  57. Koji Kadota, and Kentaro Shimizu: Evaluating methods for ranking differentially expressed genes applied to microArray quality control data, BMC Bioinformatics, 12, 227 (2011).
  58. 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).
  59. 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).
  60. Wei Cao, Kazuya Sumikoshi, Shugo Nakamura, Tohru Terada, and Kentaro Shimizu: Prediction of N-myristoylation Modification of Proteins by SVM, Bioinformation, 6, 5 (2011).
  61. 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).
  62. 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).
  63. 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).
  64. 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).
  65. 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).
  66. 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).
  67. 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).
  68. Shugo Nakamura, K. Shimizu: Comprehensive analysis of sequence-structure relationships in the loop regions of proteins, GIW 2009, 23, 106-116 (2009).
  69. 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).
  70. 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).
  71. 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).
  72. 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).
  73. 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).
  74. 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).
  75. 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).
  76. 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).
  77. 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).
  78. T. Terada, K. Shimizu: A comparison of generalized Born methods in folding simulations. Chemical Physics Letters, 460, 295-299 (2008).
  79. 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).
  80. 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).
  81. 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).
  82. 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).
  83. 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).
  84. 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).
  85. 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).
  86. 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).
  87. 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).
  88. 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).
  89. 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).
  90. 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).
  91. 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).
  92. 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).
  93. 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).
  94. 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).
  95. 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).
  96. 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).
  97. 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).
  98. 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).
  99. 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).
  100. 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).
  101. 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).
  102. 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).
  103. 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).
  104. 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).
  105. 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).
  106. S. Nakamura, M. Ikeguchi and K. Shimizu: Dynamical analysis of tRNAGln-GlnRS complex using normal mode calculation, Chemical Physics Letters, 372, 423-431 (2003).
  107. 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).
  108. 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).
  109. 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).
  110. 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).
  111. (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).
  112. 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).
  113. 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).
  114. 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).
  115. 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).
  116. 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).
  117. 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).
  118. 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).
  119. 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).
  120. 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).
  121. 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).
  122. 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).
  123. 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).
  124. 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).
  125. 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).
  126. 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).
  127. S. Shimizu and K. Shimizu: Alcohol denaturation: Thermodynamic theory of peptide unit solvation, Journal of the American Chemical Society, 121, 11, 2387-2394 (1999).
  128. 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).
  129. 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).
  130. 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).
  131. 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).
  132. 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).
  133. 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).
  134. 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).
  135. 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).
  136. 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).
  137. 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).
  138. 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).
  139. 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).
  140. 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).
  141. 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).
  142. 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).
  143. 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).
  144. 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).
  145. 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).
  146. 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).
  147. 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).
  148. 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).
  149. 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).
  150. 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).
  151. 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).
  152. 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).

その他(2009-)

  1. 孫建強、湯敏、西岡輔、清水謙多郞、門田幸二：次世代シーケンサーデータの解析手法第2回GUI 環境からコマンドライン環境へ, Japanese Journal of Lactic Acid Bacteria (2014).
  2. 門田幸二、孫建強、湯敏、西岡輔、清水謙多郞：次世代シーケンサーデータの解析手法第1回イントロダクション, Japanese Journal of Lactic Acid Bacteria (2014).
  3. 石畑清, 大岩元, 角田博保、清水謙多郎、玉井哲雄、長崎等、中里秀則、中谷多哉子、疋田輝雄、三浦孝夫、箕原辰夫、和田耕一、渡辺治（情報処理学会コンピュータ科学教育委 員会）: 理工系情報学科の授業内容分布のシラバスによる調査（中間報告）, 情報処理学会コンピュータと教育研究会情報教育シンポジウム (2010).
  4. 清水謙多郎: タンパク質の構造予測手法の開発, 科学技術振興機構中国科学技術月報 (2010).
  5. 清水謙多郎: アグリバイオインフォマティクス 教育研究プログラムの活動について, 第9回糸状菌分子生物学コンファレンスシンポジウム, 東京 (2009).
  6. W. Dawson, T. Terada, K. Shimizu: The role of H-doping in the electronic structure, spin localization and electron transfer of iron-sulfur [2Fe-2S] proteins, The 47th Annual Meeting of the Biophysical Society of Japan Symposia, Tokushima (2009).
  7. 中村周吾, 清水謙多郎: タンパク質のab initio構造予測, 遺伝子医学 (2009).

著書

  1. 土居範久 他(監訳), 10-11章担当: Operating System Concepts, 共立出版, 2010.
  2. 清水謙多郎, 中村周吾(監訳): バイオインフォマティクスコンピューティング, オーム社, 2004.
  3. 坂村健, 清水謙多郎, 越塚登: 高校教科書「情報A」, 「情報B」, 「情報C」, 数研出版, 2003-2010.
  4. 坂村健, 清水謙多郎, 越塚登: 大人のための「情報」教科書, 数研出版, 2003.
  5. 有澤博 他(編): エンサイクロペディア情報処理2000-2001, 情報処理学会編, オーム社, 2000, 同2002-2003, 2002.
  6. 清水謙多郎(監修): 詳細OSハンドブック, ソフトリサーチセンター, 1994.
  7. 清水謙多郎: オペレーティングシステム, 岩波書店, 1992.
  8. 前川守, 所真理雄, 清水謙多郎(編著): 分散オペレーティングシステム, 共立出版, 1991.
  9. 清水謙多郎: 分散オペレーティングシステムの実現技術, トリケップス, 1991.
  10. 前川守, 清水謙多郎(編): 高機能ワークステーション, 共立出版, 1989.
  11. 長谷部紀元, 清水謙多郎(訳): UNIX原典, パーソナルメディア, 1986.
その他、バイオインフォマティクス辞典, 物理学辞典, 情報処理ハンドブック、共立アルゴリズム辞典、情報ネットワークハンドブックなど、分担執筆・訳30以上.
shimizu@bi.a.u-tokyo.ac.jp