Papers¡Ê2009¡Ë

  • Gromiha, M.M., Yokota, K., Fukui, K.: "Energy Based Approach for Understanding the Recognition Mechanism in Protein-Protein Complexes", MOLECULAR BIOSYSTEMS, 5, pp.1779-1786(2009).
    ¢£PubMed
  • Wijaya, E., Frith, M.C., Suzuki, Y., Horton, P.: "Recount: Expectation Maximization Based Error Correction Tool for Next Generation Sequencing Data", GENOME INFORMATICS, 23, pp.189-201(2009).
    ¢£Software Home Page
    ¢£Full Text Paper(PDF) on GIW2009 Home Page.
  • Kawahara, Y., Nagano, K., Tsuda, K., Bilmes, J.A.: "Submodularity Cuts and Applications", Advances in Neural Information Processing Systems, pp.916-924(2009).
  • Tagami, U., Shimba, N., Nakamura, M., Yokoyama, K., Suzuki, E., Hirokawa, T.: "Substrate specificity of microbial transglutaminase as revealed by three-dimensional docking simulation and mutagenesis", PROTEIN ENGINEERING DESIGN & SELECTION, 22(12), pp.747-752(2009).
    ¢£Abstract on the Journal Website.
  • Hamada, M., Sato, K., Kiryu, H., Mituyama, T. Asai, K.: "CentroidAlign: Fast and Accurate Aligner for Structured RNAs by Maximizing Expected Sum-of-pairs Score", BIOINFORMATICS, 25(24), pp.3236-3243(2009).
    ¢£Abstract on the Journal Website.
  • Sakashita, Y., Ito, J., Asai, K., Tomii, K.: "Classification and Identification of Indiscernible Metal Binding Sites of Proteins", The 20th International Conference on Genome Informatics, pp.P035-1-P035-2(2009).
    ¢£Full Text Paper(PDF) on GIW2009 Home Page.
  • "Ito, J., Junichi Higo, Tomii, K.: "Classification of Protein Fragments with a Spectral Graph Technique", The 20th International Conference on Genome Informatics, pp.P034-1-P034-2(2009).
    ¢£Full Text Paper(PDF) on GIW2009 Home Page.
  • Wang, X., Gotoh, O.: "Cancer Classification Using Single Genes", GENOME INFORMATICS, 23, pp.179-188(2009).
    ¢£PubMed
  • Wan, R., Kielbasa, S.M., Horton, P., Frith, M.C.: "The Effect Read Length has on the Performance of Adaptive Seeds for Sequence Alignment", The 20th International Conference on Genome Informatics, Posters and Software Demonstrations, (2009).
    ¢£Full Text Paper(PDF)
  • Frith, M.C., Hamada, M., Horton, P.: "How (not) to align Genomes", The 20th International Conference on Genome Informatics, Posters and Software Demonstrations, (2009).
    ¢£Full Text Paper(PDF) on GIW2009 Home Page.
  • Nishida, K.M., Okada, T.N., Kawamura, T., Mituyama, T., Kawamura, Y., Inagaki, S., Huang, H., Chen, D., Kodama, T., Siomi, H. Siomi, M.C.: "Functional involvement of Tudor and dPRMT5 in the piRNA processing pathway in Drosophila germlines", EMBO JOURNAL, 28, pp.3820-3831(2009).
    ¢£Abstract on the Journal Website.
  • Terai, G., Yoshizawa, A., Okida, H., Asai, K., Mituyama, T.: "Discovery of short pseudogenes derived from messenger RNAs.", NUCLEIC ACIDS RESEARCH, 38(4), pp.1163-1171(2009).
    ¢£Abstract on the Journal Website.
  • Tsuda, K., Georgii, E.: "Dense Module Enumeration in Biological Networks", Journal of Physics: Conference Series, 197, pp.12012(2009).
    ¢£Full Text Paper(PDF)
  • Wan, R., Kielbasa, S.M., Horton, P., Frith, M.:"The Effect Read Length has on the Performance of Adaptive Seeds for Sequence Alignment.", The 20th International Conference on Genome Informatics, Posters and Software Demonstrations, (2009). ¢£Abstract
  • Kayano, M., Takigawa, I., Shiga, M., Tsuda, K., Mamitsuka, H.: "Efficiently Finding Genome-wide Three-way Gene Interactions from Transcript- and Genotype-Data", BIOINFORMATICS, 25(21), pp.2735-2743(2009).
    ¢£Full Text Paper(PDF) on the Journal Website.
  • Kashima, H., Yamanishi, Y., Kato, T., Sugiyama, M., Tsuda, K.: "Simultaneous Inference of Biological Networks of Multiple Species from Genome-wide Data and Evolutionary Information: A Semi-supervised Approach", BIOINFORMATICS, 25(22), pp.2962-2968(2009).
    ¢£Full Text Paper(PDF) on the Journal Website.
  • Nemoto, W., Fukui, K., Toh, H.: "GRIP: A server for predicting interfaces for GPCR oligomerization", JOURNAL OF RECEPTORS AND SIGNAL TRANSDUCTION, 29(6), pp.312-317(2009).
    ¢£PubMed
  • Hamada, M., Sato, K., Kiryu, H., Mituyama, T., Asai, K.: "Predictions of RNA secondary structure by combining homologous sequence information", BIOINFORMATICS, 25(12),pp.330-338(2009)., pp.330-338(2009).
    ¢£Full Text Paper(PDF) on the Journal Website.
  • Wan, R. , Kiseleva, L., Harada, H., Mamitsuka, H. Horton, P.: "HAMSTER: visualizing microarray experiments as a set of minimum spanning trees", SOURCE CODE FOR BIOLOGY AND MEDICINE, 4(8), (2009).
    ¢£PubMed
  • Gromiha, M.M.: "Intrinsic Relationship of Amino Acid Composition/Occurrence with Topological Parameters and Protein Folding Rates", Open Structural Biology, 3, pp.126-132(2009).
    ¢£Full Text Paper(PDF) on the Journal Website.
  • Wang, X., Gotoh, O.: "Accurate molecular classification of cancer using simple rules", BMC MEDICAL GENETICS, 2, pp.64(2009).
    ¢£Full Text Paper(PDF) on the Journal Website.
  • Wan Raymond: "Efficient Probabilistic Latent Semantic Analysis Through Parallelization", Proc. 5th Asia Information Retrieval Symposium, doi:10.1007/978-3-642-04769-5_38, (2009).
    ¢£Abstract on the Journal Website.
  • Shimizu, K., Toh, H.: "Interaction between intrinsically disordered proteins frequently occurs in a human protein-protein interaction network", Journal of Molecular Biology, 392(5), pp.1253-1265(2009).
    ¢£PubMed
  • Motono, C., Hirokawa, T.:"Virtual screening to separate active ligands from decoys using MD simulation and concavity shape comparing.", À¸ÊªÊªÍý, 49(Áý´©), pp.S 99-(2009).
  • Sato, K., Hamada, M., Mituyama, T., Asai, K., Sakakibara, Y.: "A non-parametric Bayesian approach for predicting RNA secondary structures", Lecture Notes in Bioinformatics, 5724, pp.286-297(2009).
    ¢£Abstract on the Journal Website.
  • Saito, K., Inagaki, S., Mitsuyama, T., Kawamura, Y., Ono, K., Sakota, E., Kotani, H., Asai, K., Shiomi, H., Shiomi, M.: "A regulatory circuit for piwi by the large Maf gene traffic jam in Drosophila", Nature, doi:10.1083/nature08501,(2009).
    ¢£Full Text Paper(PDF) on the Journal Website.
  • Koga, N., Kameda, T., Okazaki, K., Takada, S.: "Paddling mechanism for the substrate translocation by AAA+ motor revealed by multiscale molecular simulations", Proceedings of the National Academy of Sciences of the United States of America, (2009).
    ¢£Abstract on the Journal Website.
  • Fujibuchi, W., Chiba, H., Akiyama, H., Shiku, H.: "Designing Pyro-Primer Sequences Using a Simulated Annealing Algorithm, to Critically Target mRNAs in Quantitative Cell Analysis", Progress on Post-genome Technologies -Proceedings of the 6'th International Forum on Post-genome Technologies, pp.253-257(2009).
  • Nakatsui, M., Horimoto, K.: "Parameter Optimization in the network dynamics including unmeasured variables by the symbolic-numeric approach.", Proceedings of the Third International Symposium on Optimization and Systems Biology (OSB'09), pp.245-253(2009).
    ¢£Full Text Paper(PDF)
  • Gromiha, M.M., Yokota, K., Fukui, K.: "Identification and analysis of binding site residues in protein-protein complexes", Proc. World Academy of Sciene and Technology, 57, pp.127-132(2009).
  • Horton, P.: "A Tiling Bound for Pairwise Global Sequence Alignment", Communications in Computer and Information Science 30, pp.93-98(2009).
    ¢£Abstract on the Journal Website.
    ¢£Full Text Paper(PDF)
  • Nemoto, W., Fukui, K., Toh, H.:"Web services to promote GPCRs peptide mimetics.", ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 232, pp.U100-U101(2009).
  • Fukui, K.:"The development of an affinity evaluation and prediction system by using protein-protein docking simulations and parameter tuning.", ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY , 232, pp.U200-U201(2009).
  • Fukui, K.:"Computationally and experimentally derived general rules for fragmentation of various glycosyl bonds in sodium adduct oligosaccharides.", ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY , 232, pp.U250-U251(2009).
  • Fujibuchi, W., Kim, H., Okada, Y., Taniguchi, T., Sone, H.: "High-Performance Gene Expression Module Analysis Tool and Its Application to Chemical Toxicity Data.", Methods in Molecular Biology, 577, pp.55-65(2009).
    ¢£PubMed
  • Koshimizu, H., Kiyosue, K., Hara, T., Hazama, S., Suzuki, S., Uegaki, K., Nagappan, G., Zaitsev, E., Hirokawa, T., Tatsu, Y., Ogura, A., Lu, B., Kojima, M.: "Multiple functions of precursor BDNF to CNS neurons: negative regulation of neurite growth, spine formation and cell survival", Molecular Brain, ISSN1756-6606(2009).
    ¢£PubMed
  • Huang, LT., Gromiha, M.M..: "Reliable Prediction of Protein Thermostability Change upon Double Mutation from Amino Acid Sequence", Bioinformatics, 25(17), pp.2181-2187(2009).
    ¢£PubMed
  • Kawajiri, K., Kobayashi, Y., Ohtake, F., Ikuta, T., Matsushima, Y., Mimura, J., Pettersson. S., Pollenz, RS., Sakaki, T., Hirokawa, T., Akiyama, T., Kurosumi, M., Poellinger, L., Kato, S., Fujii-Kuriyama, Y.: "Aryl hydrocarbon receptor suppresses intestinal carcinogenesis in ApcMin/+ mice with natural ligands", Proceedings of the National Academy of Sciences of the United States of America, 106(32), pp.13481-13486(2009).
    ¢£Abstract on the Journal Website.
  • Yoshida T, Kadota Y, Hitaoka S, Kori E, Horikawa Y, Taguchi M, Tsuji D, Hirokawa T, Chuman H, Itoh K.: "Expression and molecular dynamics studies on effect of amino acid substitutions at Arg344 in human cathepsin A on the protein local conformation.", Biochimica et Biophysica Acta - Proteins and Proteomics, 1794(11), pp.1693-1699(2009).¢£PubMed
  • Tashiro, T., Nakagawa, R., Hirokawa, T., Inoue, S., Watarai, H., Taniguchi, M., Mor,i K.: "RCAI-37, 56, 59, 60, 92, 101, and 102, cyclitol and carbasugar analogs of KRN7000: their synthesis and bioactivity for mouse lymphocytes to produce Th1-biased cytokines.", Bioorganic & Medicinal Chemistry Letters, 17, pp.6360-6373(2009).
    ¢£PubMed
  • Elisabeth Georgii, Tsuda, K., Bernhard Scholkopf: "Multi-Way Set Enumeration in Real-Valued Tensors", Proceedings of the KDD 2009 Workshop on Data Mining using Matrices and Tensors, pp.32-41(2009).
    ¢£Abstract on the Journal Website.
  • Tokumoto, Y., Horimoto, K., Miyake, J.: "TRAIL inhibited the cyclic AMP responsible element mediated gene expression.", Biochem. Biophys. Res. Commun, 381, pp.533-536(2009).
    ¢£PubMed
  • Michael Gromiha: "Revisiting "reverse hydrophobic effect": Applicable only to coil mutations at the surface.", BIOPOLYMERS, 91(7), pp.591-599(2009).
    ¢£PubMed¢£Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal.
  • Wang, X., Gotoh, O.: "Microarray-Based Cancer Prediction Using Soft Computing Approach", CANCER INFORMATICS, 7, pp.123-139(2009).
    ¢£Abstract on the Journal Website.
  • Tanaka, K., Uda,Y., Ono, Y., Nakagawa, T., Suwa, M., Yamaoka, R., Touhara, K.: "Highly Selective Tuning of a Silkworm Olfactory Receptor to a Key Mulberry Leaf Volatile", Current Biology, 19, pp.1-10(2009).
    ¢£PubMed
  • Bailey TL., Boden M., Buske FA., Frith M., Grant CE., Clementi L., Ren J., Li WW., Noble WS.: "MEME Suite: tools for motif discovery and searching", Nucleic Acids Research, 37, W202-W208(2009).
    ¢£PubMed
  • Chiappa, S., Saigo, H., Tsuda, K.: "A Bayesian Approach to Graph Regression with Relevant Subgraph Selection", Proceedings of 2009 SIAM International Conference on Data Mining (SDM09), pp.295-304(2009).
    ¢£PDF
  • Kashima, H., Kato, T., Yamanishi, Y., Sugiyama, M., Tsuda, K.: "Link Propagation: A Fast Semi-supervised Learning Algorithm for Link Prediction Proceedings of 2009 SIAM International Conference on Data Mining", pp.1099-1110(2009).
    ¢£PDF
  • Sato K., Hamada M., Asai K., Mituyama T.: "CentroidFold: a web server for RNA secondary structure prediction", Nucleic Acids Research, 1(37(Web Server issue), pp.277-280(2009).
    ¢£Abstract on the Journal Website.
  • Tomii, K., Itoh, J.: "Universal partitioning of the hierarchical fold network of 50-residue segments in proteins", BMC Structural Biology 9(34), (2009).
    ¢£PubMed¢£Full Text Paper(PDF) on the Journal Website.
  • Ura, S., Honda, M., Yamashita, T., Ueda, T., Takatori, H., Nishino, R., Sunakozaka, H., Sakai, Y., Horimoto, K., Kaneko, S.: "Differential microRNA expression between hepatitis B and hepatitis C leading disease progression to hepatocellular carcinoma.", HEPATOLOGY, 49, pp.1098-1112(2009).
    ¢£PubMed
  • Wijaya, E., Harada, H., Horton, P.: "Characterizing Genes By Marginal Expression Distribution", Lecture Notes Computer Science - CCIS, 28, pp.164-175(2009).
    ¢£Abstract on the Journal Website.
  • Gromiha, M.M.: "Multiple Contact Network is a Key Determinant to Protein Folding Rates", Journal of Chemical Information and Modeling, 49(4), pp.1130-1135(2009).
    ¢£PubMed
  • Tabei, Y., Asai, K.: "A local multiple alignment method for detection of non-coding RNA sequences", Bioinformatics, 25(12), pp.1498-1505(2009).
    ¢£Full Text Paper(PDF) on the Journal Website.
  • Kashima H., Koyama S., Yamanishi Y., Tsuda K.: "On Pairwise Kernels: An Efficient Alternative and Generalization Analysis", Proceedings of the 13th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD), pp.1030-1037(2009).
    ¢£PDF
  • Georgii E., Dietmann S., Uno T., Pagel P., Tsuda K.: "Enumeration of condition-dependent dense modules in protein interaction networks", Bioinformatics, 25(7), pp.933-940(2009).
    ¢£PubMed¢£Full Text Paper(PDF) on the Journal Website.
  • Gromiha Michael: "Computer algorithms for discriminating protein folds and predicting protein folding rates based on contact information", Proc. IACSIT conference, pp.569-573(2009).
  • Hamada, M., Kin, T., Asai, K.: "Large Scale Similarity Search for Locally Stable Secondary Structures among RNA Sequences", IPSJ Transactions on Bioinformatics, 2, pp.36-46(2009).
    ¢£Full Text Paper(PDF)
  • Gromiha, M.M.: "Bioinformatics Approaches for Understanding the Structure and Function of Membrane Proteins", Proc. OSCADD2009, pp.15(2009).
  • Karasawa, H., Miura, K., Fujibuchi, W., K., Kaneko, N., Kinouchi, M., Okabe, M., Ando, T., Murata, y., Sasaki, H., Takami, K., Yamamura, A., Shibata, C., Sasaki, I.: "Downregulation of cIAP2 enhances 5-FU sensitivity through the apoptotic pathway in human colon cancer cells", Cancer Science 100(5) pp.903-913(2009).
    ¢£PubMed
  • Yoshikawa T, Tsukamoto K, Hourai Y, Fukui K.: "Improving the Accuracy of an Affinity Prediction Method by Using Statistics on Shape Complementarity between Proteins.", Journal of Chemical Information and Modeling, 49, pp.693-703(2009).
    ¢£PubMed
  • Nishida, K., Frith MC, Nakai, K.: "Pseudocounts for transcription factor binding sites", Nucleic Acid Research, 37(3), pp.939-944(2009).
    ¢£PubMed
  • Hamada M, Kiryu H, Sato K, Mituyama T, Asai K.: "Prediction of RNA secondary structure using generalized centroid estimators.", Bioinformatics, 25(4), pp.465-473(2009).
    ¢£Abstract on the Journal Website.¡¡
  • Sasaki, YT., Ideue, T., Sano, M., Mituyama, T., Hirose T.: "MENepsilon/beta noncoding RNAs are essential for structural integrity of nuclear paraspeckles", Proceedings of The National Academy of Sciences of The United States of America, 106(8), pp.2525-30(2009).¢£PubMed
  • Fukui, K.: "The development of an affinity evaluation and prediction system by using protein-protein docking simulations and parameter tuning", The abstract of the american chemical society, (2009).
  • Dietmann, S., Georgii, E., Antonov, A., Tsuda, K., Mewes, HW.: "The DICS repository: module-assisted analysis of disease-related gene lists", Bioinformatics, 25(6), pp.830-831(2009).
    ¢£Abstract on the Journal Website.
  • Tsuda, K.: "Machine Learning with Quantum Relative Entropy", Journal of Physics Conference Series, 143, 12021(9p), (2009).
    ¢£Abstract on the Journal Website.
  • Morita, K., Saito, Y., Sato, K., Oka, K., Hotta, K., Sakakibara, Y.: "Genome-wide searching with base-pairing kernel functions for non-coding RNAs: computational and expression analysis f snoRNA families in Caenorhabditis elegans", Nucleic Acids Research, 37(3), pp.999-1009(2009).
    ¢£Abstract on the Journal Website.¢£Full Text Paper on the Journal Website.
  • Mituyama T, Yamada K, Hattori E, Okida H, Ono Y, Terai G, Yoshizawa A, Komori T, Asai K.: "The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs.", Nucleic Acid Research, 37(Database issue), D89-92(2009).
    ¢£Full Text Paper(PDF) on the Journal Website.¡¡
  • Suzuki, H., Kameyama, A., Tachibana, K., Narimatsu, H., Fukui, K.: "Computationally and Experimentally Derived General Rules for Fragmentation of Various Glycosyl Bonds in Sodium Adduct Oligosaccharides", ANALYTICAL CHEMISTRY, 81(3), pp.1108-1120(2009).
    ¢£PubMed
  • Ohnuma S, Miura K, Horii A, Fujibuchi W, Kaneko N, Gotoh O, Nagasaki H, Mizoi T, Tsukamoto N, Kobayashi T, Kinouchi M, Okabe M, Sasaki H, Shiiba K, Miyagawa K, Sasaki I.: "Cancer-associated splicing variants of the CDCA1 and MSMB genes expressed in cancer cell lines and surgically resected gastric cancer tissues", SURGERY, 145(1), pp.57-68(2009).
    ¢£PubMed
  • Tsukamoto K, Yoshikawa T, Yokota K, Hourai Y. Fukui K.: "The development of an affinity evaluation and prediction system by using protein-protein docking simulations and parameter tuning.", Computational Biology and Chemistry: Advances and Applications, 2, pp.1-15(2009).
    ¢£Abstract on the Journal Website
  • Gromiha, MM., Yabuki, Y., Suresh, MX., Thangakani, AM., Suwa, M., Fukui, K.: "TMFunction: database for functional residues in membrane proteins", Nucleic Acids Research, 37(Database issue), pp.D201-204(2009).
    ¢£Abstract on the Journal Website.
  • Gromiha, MM.,. Yabuki, Y., Imai, K., Horton, P., Fukui, K.: "Database development and discrimination algorithms for membrane protein functions", Proc. World Academy of Science, Engineering and Technology, 37, pp.358-362(2009).
    ¢£PDF on the Journal Website
  • Gromiha, M.M., Selvaraj, S.: "Proteins: Computational Analysis of Structure, Function and Stability", Wiley Encyclopedia of Chemical Biology, 4, pp.174-182(2009).
    ¢£Abstract on the Journal Website.
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