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  • 誌上発表・査読有り：2008年

論　文（誌上発表・査読有り：2008年）

  • Wijaya, E., Harada, H., Horton, P.: "Modeling Marginal Distribution of Gene Expression with Mixture Models", Proceedings of Bio-Science and Bio-Technology, 3, pp.84-89(2008). ■Abstract on the Journal Website.
  • 本野 千恵, 広川 貴次: "タンパク質立体構造予測モデルの評価関数の検討 (Validation of statistical functions for evaluating protein structural models)", 生物物理, 48(6), pp.335-337(2008).
  • Horton, P., Kielbasa, S.M., Frith, M.C.: "DisLex: a Transformation for Discontiguous Suffix Array Construction", Proceedings KLLBI-08, pp.1-11(2008).
  • 諏訪 牧子: "GPCR研究の新展開：新しい立体構造間の比較から見えてきたこと", 生物物理, 48(6), pp.335-337(2008). ■ジャーナルサイトのFull Text Paper
  • Nowozin, S., Tsuda, K.: "Frequent Subgraph Retrieval in Geometric Graph Databases", Proceedings of the 8th IEEE International Conference on Data Mining (ICDM 2008), pp.953-958(2008). ■PDF
  • Saigo, H., Tsuda, K.: "Iterative Subgraph Mining for Principal Component Analysis", Proceedings of the IEEE International Conference on Data Mining (ICDM 2008), pp.1007-1012(2008). ■Abstract on the Journal Website.
  • Imai, K., M. Gromiha, MM., Horton, P.: "Mitochondrial β-Barrel Proteins, an Exclusive Club?", Cell, 135(7), pp.158-159(2008). ■ScienceDirect
  • Ura, S., Honda, M., Yamashita, T., Ueda, T., Takatori, H., Nishino, R., Sunakozaka, H., Sakai, Y., Horimoto, K., Kaneko, S.: "Differential miRNA expression between hepatitis B and hepatitis C leading disease progression to HCC.", Hepatology, 49(4), pp.1098-112(2008). ■PubMed
  • 後藤 修, 中戸 隆一郎, 岩田 浩明: "ゲノム配列間ならびにゲノム配列と遺伝子転写産物配列間の比較法とその応用", 動物遺伝育種研究, 36(2), pp.177-183(2008).
  • Horton Paul, Szymon Kielbasa, Frith Martin: "DisLex: a Transformation for Discontiguous Suffix Array Construction", Journal of Bioinformatics and Computational Biology , pp.1-11(2008). ■PDF
  • Xia Q., Mita, K., Suwa, M.: "The genome of a lepidopteran model insect, the silkworm Bombyx mori.", Insect Biochemistry and Molecular Biology, 38(12), pp.1036-1045(2008). ■PubMed
  • Tsukamoto, K., Yoshikawa, T., Hourai, Y., Fukui, K., Akiyama, Y.: "Development of an affinity evaluation and prediction system by using the shape complementarity characteristic between proteins", Journal of Bioinformatics and Computational Biology, 6(6), pp.1133-1156(2008). ■PubMed
  • Morioka, R., Arita, M., Sakamoto, K., Kawaguchi, S., Tei, H., Horimoto, K.: "Phase Shifts of Circadian Transcripts in Rat Suprachiasmatic Nucleus.", Proceedings of the Second International Symposium on Optimization and Systems Biology (OSB’08), pp.109-114(2008). ■Full Text Paper(PDF) on the Journal Website.
  • Saigo, H., Nowozin, S., Kadowaki, T., Kudo, T., Tsuda, K.: "gBoost: A mathematical programming approach to graph classification and regression", Machine Learning, 75, pp.69-89(2008). ■Abstract on the Journal Website.
  • Gotoh, O.: "Direct Mapping and Alignment of Protein Sequences onto Genomic Sequence", Bioinformatics, 24(21), pp.2438-2444(2008). ■ジャーナルサイトのFull Text Paper(PDF)
  • Suzuki, H., Yamagaki, T., Tachibana, T., Fukui, K.: "Fragmentation of Lewis-Type Trisaccharides in the Gas Phase: Experimental and Theoretical Studies", INTERNATIONAL JOURNAL OF MASS SPECTROMETRY, 278, pp.1-9 (2008).
  • Gromiha, M.M, Huang, L.T., Lai, L.F.: "Sequence based Prediction of Protein Mutant Stability and Discrimination of Thermophilic Proteins", Lecture Notes in Bioinformatics, 5265, pp.1-12(2008).
  • Hamada S, Satoh K, Hirota M, Fujibuchi W, Kanno A, Umino J, Ito H, Satoh A, Kikuta K, Kume K, Masamune A, Shimosegawa T.: "Expression of the calcium-binding protein S100P is regulated by bone morphogenetic protein in pancreatic duct epithelial cell lines." CANCER SCIENCE, 100(1), pp.103-110(2008). ■ジャーナルサイトのFull Text Paper(PDF)
  • Frith MC, Park Y, Sheetlin SL, Spouge JL.: "The whole alignment and nothing but the alignment: the problem of spurious alignment flanks", NUCLEIC ACIDS RESEARCH, 36(10), pp.5863-5871(2008). ■ジャーナルサイトのFull Text Paper
  • Taguchi, Y., Gromiha, MM.: "Discrimination of GO term Annotated Proteins based on Amino Acid Occurrence and Composition", Proc. PRIB2008, pp.13-24(2008).
  • Tominaga, D., Tokumoto, Y., Nakatsui, M., Sun, F., Miyake, J., Horimoto, K.: "Analysis of network dynamics including hidden variables by symbolic-numeric approach", Proceedings of the Second International Symposium on Optimization and Systems Biology (OSB’08), pp.242-248(2008). ■PDF
  • Morioka, R., Arita, M., Sakamoto, K., Kawaguchi, S., Tei, H., Horimoto, K.: "Phase Shifts of Circadian Transcripts in Rat Suprachiasmatic Nucleus", Proceedings of the Second International Symposium on Optimization and Systems Biology (OSB’08), pp.109-114(2008). ■PDF
  • Nakatsui, M., Yoshida, H., Horimoto, K.: "An Algebraic-Numeric Algorithm for the Model Selection in Network Motifs in Escherichia coli", Proceedings of the Second International Symposium on Optimization and Systems Biology (OSB’08), pp.257-264(2008). ■PDF
  • Saito, S., Aburatani, S., Horimoto, K.: "Network evaluation from the consistency of the graph structure with the measured data.", BMC Systems Biology, 2(84), pp.1-14(2008). ■PubMed
  • Wu, Z.K., Zhang, Z.Y., Zhang, L.W., Horimoto, K.: "Revealing Disease Related Interactions by Correlation Analysis.", Proceedings of the Second International Symposium on Optimization and Systems Biology (OSB’08), 9, pp.341-349(2008). ■PDF
  • Zhang, Z.Y., Horimoto, K., Liu, Z.: "Time Series Segmentation for Gene Regulatory Process with Time-Window-Extension Technique.", Proceedings of the Second International Symposium on Optimization and Systems Biology (OSB’08), 9, pp.198-203(2008). ■PDF
  • Hayashida, M., Sun, F., Aburatani, S., Horimoto, K., Akutsu, T.: "Integer Programming-based Approach to Allocation of Reporter Genes for Cell Array Analysis.", Int. J. Bioinformatics Research and Applications", 4(4), pp.385-399(2008). ■PubMed
  • Saigo, H., Kramer, N., Tsuda, K.: "Partial Least Squares Regression for Graph Mining", Proceedings of the 14th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD2008), pp.578-586(2008). ■PDF
  • Tominaga, D., Horimoto, K.: "Judgment algorithm for periodicity of time series data based on Bayesian information criterion.", Journal of Bioinformatics and Conputational Biology, 6(4), pp.747-757(2008). ■PubMed
  • Ikeda, K., Hirokawa, T., Higo, J., Tomii, K.: "Protein-segment universe exhibiting transitions at intermediate segment length in conformational subspaces", BMC STRUCTURAL BIOLOGY, 8, pp.37 (2008). ■PubMed
  • Yoshikawa, T., Tsukamoto, K., Hourai, Y., Fukui, K.: "Parameter tuning and evaluation of an affinity prediction using protein-protein docking", Proceedings of the 10th WSEAS International Conference on Mathematical Methods and Computational Techniques i,(2008). ■Abstract
  • Tsukamoto, K., Fukui, K.: "Bio-scale Engine: Reaction Mechanism of Nitric Oxide Reductase Cytochrome P450nor from Fusarium oxysporum", Proceedings of The 12th WSEAS International Conference on Computers, PTS 1-3 - New Aspects of Computers, pp.452-457(2008).
  • Huang, LT., Gromiha, MM.: "Analysis and prediction of protein folding rates using quadratic response surface models", JOURNAL OF COMPUTATIONAL CHEMISTRY, 29(10), pp.1675-1683(2008). ■PubMed
  • Sato K, Mituyama T, Asai K, Sakakibara Y.: "Directed acyclic graph kernels for structural RNA analysis", BMC BIOINFORMATICS, 9, pp.318(2008). ■ジャーナルサイトのFull Text Paper
  • Tomii, K.: "Correlation between amino acid preferences and patterns of residue packing in globular proteins", Protein Science, 17(1), pp.146-147 (2008).
  • Ikeda, J., Ohno, K., Akioka, S., Orita, M., Muraoka, M., Noguchi, T., Sekijima, M.: "Large Scale Computing for Protein - Protein Binding Free Energy Calculation", Proceedings of The 2008 International Conference on Parallel and Distributed Processing Techniques and Applications, pp.771-775(2008).
  • Tokunaga, S., Ikeda, K., Honda, S., Sawada, Y., Muraoka, Y., Noguchi, T., Sekijima, M.: "Development of state transition probability analysis system based on largescale molecular dynamics simulation", Proceedings of The 17th IASTED International Conference on Applied Simulation and Modelling, pp.164-169 (2008).
  • Ou YY, Gromiha MM, Chen SA, Suwa M.: "TMBETADISC-RBF: Discrimination of beta-barrel membrane proteins using RBF networks and PSSM profiles.", COMPUTATIONAL BIOLOGY AND CHEMISTRY, 32, pp.227-231 (2008).■PubMed
  • Gromiha,MM, Yabuki, Y.: "Function based discrimination of membrane proteins using machine learning algorithms", BMC BIOINFORMATICS, 9, pp.135 (2008). ■ジャーナルサイトのFull Text Paper(PDF)/閲覧にはオンラインジャーナルの契約等が必要です。
  • Taguchi, Y.-h., Gromiha, M.M.: "Gene Ontology term prediction based upon amino acid　occurrence", Proc. WCCI 2008, pp.616-621 (2008).
  • Gromiha, M.M., Ahmad, S., Suwa, M.: "Neural Network based Prediction of Protein Structure and Function: Comparison with Other Machine Learning Methods", Proc. IEEE World congress on computational intelligence, pp.1740-1745 (2008).
  • Katada, S., Hirokawa, T., Touhara, K.: "Exploring the Odorant Binding Site of a G-Protein-Coupled Olfactory Receptor", CURRENT COMPUTER-AIDED DRUG DESIGN, 4(2), pp.123-131(2008).
  • Ou YY, Gromiha MM, Chen SA, Suwa M.: "TMBETADISC-RBF: Discrimination of beta barrel memebrane proteins using RBF networks and PSSM profiles", COMPUTATIONAL BIOLOGY AND CHEMISTRY, Issue 3, pp.227-231(2008). ■PubMed
  • Azuma-Mukai, A., Oguri, H., Mituyama, T., Qian, ZR., Asai, K., Siomi, H., Siomi, MC.: "Characterization of endogenous human Argonautes and their miRNA partners in RNA silencing", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105(23), pp.7964-7969 (2008). ■PubMed
  • Frith MC, Saunders NF, Kobe B, Bailey TL.: "Discovering Sequence Motifs with Arbitrary Insertions and Deletions", PLoS Computational Biology, 4(5), e1000071 (2008). ■PubMed
  • Kawamura, Y., Saito, K., Kin, T., Ono, Y., Asai, K., Sunohara, T., Okada, TN., Siomi, MC., Siomi, H.: "Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells", NATURE, 453, pp.793-796 (2008). ■ジャーナルサイトのFull Text Paper(PDF)/閲覧にはオンラインジャーナルの契約等が必要です。
  • Mori, Y., Hirokawa, T., Aoki, K., Satomi, H., Takeda, S., Aburada, M., Miyamoto, K.: "Structure activity relationships of quinoxalin-2-one derivatives as Platelet-Derived Growth Factor-beta Receptor (PDGF-beta R) inhibitors, derived from molecular modeling", CHEMICAL & PHARMACEUTICAL BULLETIN, 56(5), pp.682-687 (2008). ■ジャーナルサイトのFull Text Paper(PDF)
  • Yoshida, H., Horimoto, K., Anai, K.: "Inference of Probabilities over a Stochastic IL-System by Quantifier Elimination.", Mathematics in Computer Science, 1, pp.473-485(2008). ■Abstract on the Journal Website
  • Nishino, R., Honda, M., Yamashita, T., Takatori, H., Minato, H., Zen, Y., Sasaki, M., Takamura, H., Horimoto, K., Ohta, T., Nakanuma, Y., Kaneko, S.: "Identification of novel candidate tumour marker genes for intrahepatic cholangiocarcinoma.", Journal of Hepatology, 49, pp.207-216(2008). ■PubMed
  • Yoshikawa, T., Tsukamoto, K., Hourai, Y., Fukui, K.: "Parameter tuning and evaluation of an affinity prediction using protein-protein docking", Proceedings of the 10th WSEAS International Conference on Mathematical Methods and Computational Techniques in Electrical Engineering, pp.312-317(2008). ■Abstract on the Journal Website
  • Okada K, Asai K.: "Expansion of signaling genes for adaptive immune system evolution in early vertebrates", BMC GENOMICS, 9(218), (2008). ■PubMed
  • Gromiha, M.M., Selvaraj, S.: "Bioinformatics approaches for understanding and predicting protein folding rates", CURRENT BIOINFORMATICS, 3, pp.1-8 (2008).
  • Horton Paul: "アミノ酸配列に基づくタンパク質の細胞内局在予測", バイオインフォマティクスツールの開発と生命研究への応用の最前線, 26(7), pp.140-146 (2008).
  • Kumar M, Gromiha MM, Raghava GP.: "Prediction of RNA binding sites in a protein using SVM and PSSM profile.", PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 71, pp.189-194 (2008). ■PubMed
  • Horton Paul: "ヌクレオソーム位置とその配列解析", ファルマシア, 44(4), pp.352-353 (2008).
  • Asai, K.., Kiryu, H., Hamada, M., Tabei, Y., Sato, K., Matsui, H., Sakakibara, Y., Terai, G., Mituyama, T.: "Software.ncrna.org: web servers for analyses of RNA sequences", Nucleic Acids Research, 36(Web), pp.W75-W78 (2008). ■PubMed
  • Tsuda, K., Kurihara, K.: "Graph mining with variational Dirichlet process mixture models", Proceedings of 2008 SIAM Data Mining Conference, pp.432-442(2008). ■Full Text Paper on the Journal Website.
  • Gromiha MM, Suresh MX.: "Discrimination of mesophilic and thermophilic proteins using machine learning algorithms.", PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 70, pp.1274-1279 (2008). ■PubMed
  • Sasaki, H., Miura, K., Horii, A., Kaneko, N., Fujibuchi, W., Kiseleva, L., Gu, Z., Murat,a Y., Karasawa, H., Mizoi, T., Kobayashi, T., Kinouchi, M., Ohnuma, S., Yazaki, N., Unno, M., Sasaki, I.: "Orthotopic implantation mouse model and cDNA microarray analysis indicates several genes potentially involved in lymph node metastasis of colorectal cancer", CANCER SCIENCE, 99(4), pp.711-719 (2008). ■PubMed
  • Shin, H., Tsuda, K., B. Scholkopf.: "Protein Functional Class Prediction With a Combined Graph", Expert Systems with Applications, 36(2), pp.3284-3292(2008). ■PDF
  • Gotoh O.: "A space-efficient and accurate method for mapping and aligning cDNA sequences onto", NUCLEIC ACIDS RESEARCH, 36(8), pp.2630-2638 (2008). ■ジャーナルサイトのFull Text Paper(PDF)
  • Martis, R.L., Singh, S.K., Gromiha, M.M., Santhosh, C.: "Role of cation-pi interactions in single chain 'all-alpha' proteins.", JOURNAL OF THEORETICAL BIOLOGY, 250, pp.655-662(2008). ■ScienceDirect 1
  • Fukuda, K.: "INOH pathway database: Curation, Annotation, Integration", InterOntology08, 1(1), pp.47-50 (2008).
  • Kiryu, H., Kin, T., Asai, K.: "Rfold: An algorithm for computing local base pairing probabilities.", BIOINFORMATICS, 24(3), pp.367-373 (2008). ■ジャーナルサイトのFull Text Paper(PDF)
  • Gromiha, M.M.: "Influence of neighboring and contacting residues for understanding protein folding and stability", Proc. Intl. conf. Macromolecular Structure and Function, (2008).
  • Tabei Y, Kiryu H, Kin T, Asai K.: "A fast structural multiple alignment method for long RNA sequences", BMC BIOINFORMATICS, 9(33), ■PubMed
  • Okada K, Asai K.: "Retention of genes involved in the adenohypophysis-mediated endocrine system in early vertebrates", GENE, 412（1-2）, pp.71-83(2008).
  • Gromiha, MM., Yabuki, Y.: "Functional discrimination of membrane proteins using machine learning techniques.", BMC BIOINFORMATICS, 9(135), (2008). ■ジャーナルサイトのFull Text Paper(PDF)/閲覧にはオンラインジャーナルの契約等が必要です。
  • Istomin, AY., Gromiha, MM., Vorov, OK., Jacobs, DJ., Livesay, DR.: "New insight into long-range nonadditivity within protein double-mutant cycles", PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 70(3), pp.915-924 (2008).■PubMed
  • Kaneiwa, K., Iwazume, M., Fukuda, K.: "An Upper Ontology for Event Classifications and Relations", Proc. of AI2007, Lecture Notes in Computer Science, pp.394-404 (2008). ■PDF(118KB)
  • Motono, C., Gromiha, MM., Kumar, S.: "Thermodynamic and kinetic determinants of Thermotoga maritima cold shock protein stability: A structural and dynamic analysis", Proteins: Sturcture, Function, and Bioinformatics, 71(2), pp.655-669 (2008). ■PubMed
  • Sato, K., Hamada, S., Kimura, K., Kanno, A., Hirota, M., Fujibuchi, W., Tanaka, N., Miura, K., Masamune, A., Vonderhaar, B.K. and Shimosegawa, T.: "Up-regulation of MSX2 enhances the malignant phenotype and associates with Twist 1 expression in human pancreatic cancer cells", AMERICAN JOURNAL OF PATHOLOGY,172(4), pp.926-939(2008). ■Abstract on the journal website
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