Papers¡Ê2008¡Ë

  • 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.
  • Horton, P., Kielbasa, S.M., Frith, M.C.:"DisLex: a Transformation for Discontiguous Suffix Array Construction", Proceedings KLLBI-08, pp.1-11(2008).
  • Yoshikawa, T.,¡¡Tsukamoto, K., Hourai, Y., Fukui, K.:"Affinity Evaluation and Prediction for Protein-Protein Docking", Proceedings of the CBI Society Annual Meeting 2008, p.108(2008).
  • Imai, K., M. Gromiha, MM., Horton, P.:"Mitochondrial ¦Â-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
  • 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
  • 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.
  • 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¡Ç08), 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).
    ¢£Full Text Paper(PDF) on the Journal Website.
  • 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).
    ¢£Full Text Paper(PDF) on the Journal Website.
  • 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).
    ¢£Full Text Paper(PDF) on the Journal Website.
  • 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¡Ç08), 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¡Ç08), 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¡Ç08), 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¡Ç08), 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¡Ç08), 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
  • 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
  • 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
  • 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
  • Tomii, K.:"Correlation between amino acid preferences and patterns of residue packing in globular proteins", Protein Science, 17(1), pp.146-147 (2008).
  • 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).
    ¢£Full Text Paper(PDF) on the Journal Website.
  • 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).
  • 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
  • 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).
    ¢£Abstract on the Journal Website. You need the license for the electrical journal.
  • 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).
  • 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).
    ¢£Full Text Paper on the Journal Website. You need the license for the electrical journal.
  • 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).
    ¢£Free Full Text Paper on Journal website(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).
  • 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
  • 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
  • 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
  • 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.
  • 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).
    ¢£Full Text Paper on Journal site(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).
    ¢£Full Text Paper on Journal website(PDF) You need the license for the electrical journal.
  • 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¡Ê1-2¡Ë, pp.71-83(2008).
    ¢£ScienceDirect
    ¢£PDF(2036KB)
  • Gromiha, MM., Yabuki, Y.:"Functional discrimination of membrane proteins using machine learning techniques.", BMC BIOINFORMATICS, 9(135), (2008).
    ¢£Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal.
  • 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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