Papers¡Ê2007¡Ë

  • Yoshikawa, T., Tsukamoto, K., Hourai, Y., Fukui, K.,:"Development of Affinity Prediction System Using Protein-Protein Docking", The Proceedings of the 2007 Annual Conference of the Japanese Society for Bioinformatics, pp.1-2(2007).
  • Shimizu, K., Noguchi, T.:"Analysis of intrinsic protein disorder in human genome", The proceedings of the 2007 annual conference of the japanese society for bioinformatics, (2007).
  • Yoshikawa, T.,¡¡Tsukamoto, K., Hourai, Y., Fukui, K.:"Development of Affinity Prediction System Using Protein-Protein Docking", The Proceedings of the 2007 Annual Conference of the Japanese Society for Bioinformatics, pp.1-2(2007).
  • Motono, C., Gromiha, MM., Kumar, S.:"A Structural and Dynamic Analysis of Hyperthermophilic Cold Shock Protein Stability", The proceedings of the 2007 annual conference of the Japanese society for bioinformatics, pp.P091-2 (2007).
  • Gromiha MM, Suwa M.:"Computational analysis on beta-barrel Membrane Protein Sequences and Structures: Genome-wide Applications", Proc. Annual Meeting of CBRC, pp.12-15 (2007).
  • Frith MC, Carninci P, Kai C, Kawai J, Bailey TL, Hayashizaki Y, Mattick JS.:"Splicing bypasses 3' end formation signals to allow complex gene architectures.", GENE, 403(1-2), pp.188-193 (2007).¢£PubMed
  • Steinke, F., Seeger, M., Tsuda, K.:"Experimental design for efficient identification of gene regulatory networks using sparse Bayesian models", BMC Systems Biology, 1(51), pp.1-15(2009).
    ¢£PubMed
    ¢£Full Text Paper(PDF) on the Journal Website.
  • Nowozin, S., Bakir, G., Tsuda, K.:""Discriminative Subsequence Mining for Action Classification". Proceedings of the 2007 IEEE Computer Society Conference on Computer Vision and Pattern Recognition, (2007).
    ¢£PDF
  • Okada, Y., Ohkubo, K., Horton, P., Fujibuchi, W.:"Exhaustive Search Method of Gene Expression Modules and Its Application to Human Tissue Data, IAENG International Journal of Computer Science, 34(1) , pp.119-126(2007).
  • Saigo, H., Uno, T., Tsuda, K.:"Mining complex genotypic features for predicting HIV-1 drug resistance", Bioinformatics, 23, Issue 18, pp.2455-2462(2007).
    ¢£Full Text Paper on the Journal Website.
  • Kiryu, H., Tabei, Y., Kin, T., Asai, K.:"Murlet: a practical multiple alignment tool for structural RNA sequences.", BIOINFORMATICS, 23(13), pp.1588-1598(2007).
    ¢£PubMed
  • Tominaga, D., Horimoto, K.:"Judgment algorithm for detection of periodicity and its application", Proceedings of the 3rd Moscow Conference on Computational Molecular Biology, pp.p.296(2007).
  • Nowozin, S., Tsuda, K., Uno, T., Kudo, T., Bakir, G.:"Weighted Substructure Mining for Image Analysis", Proceedings of the 2007 IEEE Computer Society Conference on Computer Vision and Pattern Recognition. (2007).
    ¢£Abstract on the Journal Website.
    ¢£PDF
  • Tsuda, K.:"Entire Regularization Paths for Graph Data", Proceedings of the 24th International Conference on Machine Learning, pp.919-926(2007).
    ¢£Full Text Paper on The International Machine Learning Society Website.
  • Horton, P., Park, K. J., Obayashi, T., Fujita, N., Harada, H., Adams-Collier CJ, Nakai, K.:"WoLF PSORT: Protein Localization Predictor", Nucleic Acids Research, 35, pp.585-587(2007).¢£PubMed
    ¢£Full Text Paper on the Journal Website.
  • Ide, T., Tsuda, K.:"Change-Point Detection using Krylov Subspace Learning", Proceedings of the SIAM International Conference on Data Mining, pp.515-520, (2007).
    ¢£Full Text Paper(PDF) on the Conference Website.
  • Seeger, M., Steinke, F., Tsuda, K.:"Bayesian Inference and Optimal Design in the Sparse Linear Model", Proceedings of the 11th International Conference on Artificial Intelligence and Statistics, pp.444-451(2007).
    ¢£Full Text Paper(PDF) on the Journal Website.
  • Kin, T., Yamada, K., Terai, G., Okida, H., Yoshinari, Y., Ono, Y., Kojima, A., Kimura, Y., Komori, T., Asai, K.:"fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences" NUCLEIC ACIDS RESEARCH, 35¡ÊDatabase Issue ¡Ë, pp.D145-148(2007).
    ¢£PubMed
  • Okada, Y., Horton, P., Fujibuchi, W.:"SAMURAI: a tool for gene expression module mining", The Proc. of the 2007 Annual Conference of the Japanese Society for Bioinformatics, (2007).
  • Gromiha, M.M.:"Prediction of protein stability upon point mutation", Proc. 2007 Annual Conf. JSBi, 35(6), pp.1569-73(2007).
  • Gromiha, M.M., Motono. C., Kumar, S.:"A structural and dynamic analysis of hyperthermophilic cold shock protein stability", Proc. Annual conference on JSBi, (2007).
  • Hourai, Y.:"Upgrade of 3D-Convolution Library CONV3D for Faster Docking", JSBi2007, (2007).
  • Nukada, A., Hourai, Y., Nishida, A., Akiyama, A.:"High Performance 3D Convolution for Protein Docking on IBM Blue Gene", Lecture Notes in Computer Science, 4742, pp.958-969(2007).
    ¢£Full Text Paper(PDF) on the Journal Website.
  • Nakazawa, M., Takada, M., Yokota, K., Sekijima, M., Noguchi, M., Joe, K.:"Development of SVM based Prediction System for Metalbinding Sites in Protein", Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA 2007) , CSREA Press, 135, pp.157-164(2007).
  • Nagano, N., Nakagawa, Y., Arita, M., Ttsukamoto, H., Noguchi, N.:"EzCatDB", Nucleic Acids Research, 613, (2007).
    ¢£Nucleic Acids Research
  • Gromiha, M.M., Yabuki, Y., Suwa,:"TMB finding pipeline: novel approach for detecting beta-barrel membrane proteins in genomic sequences", Journal of Chemical Information and Modeling, 47, pp.2456-2461 (2007).¢£PubMed
  • Gromiha, M.M., Kumar, M., Raghava, PG.:"Identification of DNA-binding proteins using support vector machines and evolutionary profiles", BMC BIOINFORMATICS, 8(463), pp.1-10 (2007).¢£Full Text Paper on Journal Website(PDF)
  • Gromiha, M.M., Taguchi, Y.:"Protein Fold Recongnition based upon the Amino Acid Occurrence", Lecture notes in Bioinformatics, 4774, pp.120-131 (2007).
  • Usui, T., Ban, HS., Kawada, J., Hirokawa, T., Nakamura, H.:"Discovery of indenopyrazoles as EGFR and VEGFR-2 tyrosine kinase inhibitors by in silico high-throughput screening.", BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 18, pp.285-288 (2007).¢£PubMed
  • Tominaga, D., Iguchi, F., Akiyama, Y., Horimoto, K.:"Development of automated image processing procedure for cell-arrays", The 11th World Multi-Conference on Systemics, Cybernetics and Informatics Proceedings, 4, pp.19-24 (2007).
  • Tominaga, D., Horimoto, K.:"Symbolic approach for dynamical analysis of biological network modules", The 11th World Multi-Conference on Systemics, Cybernetics and Informatics Proceedings, 4, pp.25-29 (2007).
  • Tominaga, D., Iguchi, F., Akiyama, Y., Horimoto, K.:"High-throughput Automated Image Processing System for Cell Array Observations", IPSJ Transactions on Bioinformatics, 48(17-3), pp.1-7 (2007).
  • Gromiha, MM.,Suwa, M.:"Current developments on beta-barrel membrane proteins: sequence and structure analysis, discrimination and prediction", CURRENT PROTEIN & PEPTIDE SCIENCE, 8(6), pp.580-599 (2007).
  • Gromiha, M.M.:""Prediction of protein stability upon point mutations", BIOCHEMICAL SOCIETY TRANSACTIONS, 35(6), pp.1569-1573 (2007).¢£PubMed
  • Okada, Y., Okubo, K., Horton, P., Fujibuchi, W.:"Exhaustive Search Method of Gene Expression Modules and Its Application to Human Tissue Data", IAENG International Journal of Computer Science, 34(1), pp.119-126 (2007).¢£Full Text Paper(PDF)
  • Terai, G., Komori, T., Asai, K., Kin, T.:"miRRim: a novel system to find conserved miRNAs with high sensitivity and specificity.", RNA-A PUBLICATION OF THE RNA SOCIETY, 13(12), pp.2081-2090 (2007).¢£Full Text Paper on Journal Website(PDF)
  • Horton, P., Park, KJ., Obayashi, T., Nakai, K.:"Protein Subcellular Localization Prediction with WoLF PSORT", Proceedings Asian Pacific Bioinformatics Conference APBC06, pp.39-48 (2007).¢£Full text paper(PDF)
  • Shimizu, K., Hirose, S., Noguchi, T.:"POODLE-S: web application for predicting protein disorder by using physicochemical features and reduced amino acid set of a position-specific scoring matrix.", Bioinformatics, 23(17), pp.2337-2338 (2007).¢£PubMed
  • Fujibuchi, W., Kiseleva, L., Taniguchi, T., Harada, H., Horton, P.:"CellMontage: similar expression profile search server.", BIOINFORMATICS, 23(22), pp.3103-3104 (2007).¢£Full Text Paper on Journal Website(PDF)
  • Kin, T., Ono, Y.:"Idiographica: a general-purpose web application to build idio-grams on-demand for human, mouse and rat ", Bioinformatics, 23(21), pp.2945-2946 (2007).¢£Full Text Paper on Journal Website(PDF)
  • Gromiha, MM.:"Bioinformatics on beta-barrel Membrane Proteins: Sequence and Structural Analysis, Discrimination and Prediction", LECTURE NOTES IN COMPUTER SCIENCE, 4774, pp.148-157 (2007).
  • Huang, LT., Gromiha, MM., Ho, SY.:"Sequence analysis and rule development of predicting protein stability change upon mutation using decision tree model.", JOURNAL OF MOLECULAR MODELING, 13(8), pp.879-890 (2007).
  • Parthiban, V., Gromiha, MM., Abhinandan M, Schomburg D.:"Computational modeling of protein mutant stability: analysis and optimization of statistical potentials and structural features reveal insights into prediction model development.", BMC STRUCTURAL BIOLOGY, 7(54), pp.54 (2007).¢£Full Text Paper on Journal Website(PDF)
  • Taguchi, YH., Gromiha, MM.:"Application of amino acid occurrence for discriminating different folding types of globular proteins", BMC BIOINFORMATICS, 8(1), pp.404 (2007).¢£Full Text Paper on Journal Site(PDF)
  • Sakakibara, Y., Popendorf, K., Ogawa, N., Asai, K., Sato, K.:"Stem kernels for RNA sequence analyses.", JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 5(5), pp.1103-1122 (2007).¢£PubMed
  • Osato, N., Suzuki, Y., Ikeo, K., Gojobori, T.:"Transcriptional interferences in cis natural antisense transcripts of humans and mice", The Proceedings of the 2007 Annual Conference of the Japanese Society for Bioinformatics, 176(2), pp.1299-1306 (2007).¢£PubMed
  • Fujibuchi, W., Okada, Y., Horton, P.:"Global and Local Similarity Searches of Gene Expression Data", The Proceedings of the 2007 Annual Conference of the Japanese Society for Bioinformatics, pp.33-34 (2007).
  • Okada, Y., Fujibuchi, W.:"Mining a Large-scale Microarray Database for Similar Gene Expression Modules to Find Distant Relationships between Down Syndrome and Huntington's Disease", Critical Assessment of Microarray Analysis Conference, Valencia, Proceedings, (2007).
  • Sekijima, M., Doi, A., Honda, S., Nogudhi, T., Shimizu, K., Akiyama, Y.:"Development of Free Energy Landscape Analysis System based on Parallel Molecular Dynamics Simulation", IPSJ Transactions on Bioinformatics, 48(17), pp.30-39 (2007).
  • Okada, Y., fujibuchi, W., Horton, P.:"A Biclustering Method for Gene Expression Module Discovery Using a Closed Itemset Enumeration Algorithm". IPSJ Transactions on Bioinformatics, 48(SIG5), pp.183-192 (2007).¢£Full Text Paper on Journal Website(PDF)
  • Mukai, Y., Hirokawa, T., Tomii, K., Asai, K., Akiyama, Y., Suwa, M.:"Identification of glycosyltransferases focusing on Golgi transmembrane region", Trends In Glycoscience And Glycotechnology, 19(105), pp.41-47 (2007).
  • Hirokawa, T.:"Receptor-ligand docking simulation for membrane proteins", Yakugaku Zasshi-Journal Of The Pharmaceutical Society Of Japan, 127(1), pp.123-131 (2007). ¢£PubMed
  • Kimura, S., Sekijima, M., Takada, M., Noguchi, M., Joe, K.:"Development of Molecular Dynamics Simulation based Flexible Docking System", Proceedings of the 2007 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA 2007), pp.732-745 (2007).
  • Sasaki, M., Sekijima, M., Takada, M., Joe, K.:"Optimization of Molecular Dynamics Simulation on Cell Processor", Proceedings of the 2007 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA 2007), pp.780-783 (2007).
  • Sakakibara, Y., Asai, K., Sato, K.:"Stem Kernels for RNA Sequence Analyses", Lecture Notes in Bioinformatics, 4414, pp.278-291 (2007).
  • Okada, Y., Fujibuchi, W., Horton, P.:"Exhaustive search of maximal biclusters in gene expression data", Proceedings of IAENG International Conference on Computer Science (ICCS'07), Lecture Notes in Engineering and Computer Science, 2(1), pp.307-312(2007).
    ¢£Full Text Paper on Journal Website(PDF)
  • Doi, J., Shimizu, K., Sekijima, M.:"High-Density Surface Reconstruction of Fine Arts and Documents for Complete Reproduction and Counterfeit Detection", Proceedings of the 2007 IEEE International Conference on Networking, Sensing and Control (ICNSC2007), pp.392-397 (2007). ¢£Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal.
  • Huang, LT., Gromiha, MM, Ho, SY.:"iPTREE-STAB: interpretable decision tree based method for predicting protein stability changes upon mutations", Bioinformatics, 23(10), pp.1292-1293 (2007).
    ¢£Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal.
  • Tashiro, T., Nakagawa, R., Hirokawa, T., Inoue, H., Watarai, H., Taniguchi, M., Mori, K.:"RCAI-56, a carbocyclic analogue of KRN7000: its synthesis and potent activity for natural killer (NK) T cells to preferentially produce interferon-¦Ã", Tetrahedron Letters, 48(19), pp.3343-3347 (2007).¢£Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal.
  • Shimizu, K., Muraoka, Y., Hirose, S., Tomii, K., Noguchi, T.:"Predicting mostly disordered proteins by using structure-unknown protein data Predicting mostly", BMC Bioinformatics, 8(78), (2007). ¢£Free Full Text Paper(PDF) on the Journal Website. ¢£PubMed
  • Kin, T., Yamada, K., Terai, G., Okida, H., Yoshinari, Y., Ono, Y., Kojima, A., Kimura, Y., Komori, T., Asai, K.:"fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences", Nucleic Acids Res, 35(Database issue), pp.D145-D148 (2007). ¢£Free Full Text Paper(PDF) on the Journal Website. ¢£PubMed
  • Iwaya, N., Goda, N., Unzai, S., Fujiwara, K., Tanaka, T., Tomii, K., Tochio, H., Shirakawa, M., Hiroaki, H.:"Fine-tuning of protein domain boundary by minimizing potential coiled coil regions", Journal of Biomolecular NMR, 37(1), pp.53-63 (2007). ¢£Free Full Text Paper(PDF) on the Journal Website. ¢£PubMed
  • Sekijima, M., Doi, J., Noguchi, T., Akiyama, Y., Shimizu, S.:"Optimization and Evaluation of Parallel Molecular Dynamics Simulation on Blue Gene/L", Proceedings of the 25th IASTED International Conference on Parallel and Distributed Computing and Networks, pp257-262 (2007).
  • Gromiha, M.M., Yabuki, Y., Kundu, S., Suharnan, S., Suwa, M.:"TMBETA-GENOME: database for annotated beta-barrel membrane proteins in genomic sequences", Nucleic Acids Research, 35(Database issue), pp.D314-D316 (2007). ¢£Free Full Text Paper(PDF) on the Journal Website. ¢£PubMed
  • Huang, L.T., Saraboji, K., Ho, S.Y., Hwang, S.F., Ponnuswamy, M.N., Gromiha, M.M.:"Prediction of protein mutant stability using classification and regression tool", Biophysical Chemistry, 125(2-3), pp.462-470 (2007). ¢£Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ¢£PubMed
  • Parthiban, V., Gromiha, M.M., Hoppe, C., Schomburg, D.:"Structural analysis and prediction of protein mutant stability using distance and torsion potentials: role of secondary structure and solvent accessibility", Proteins: Structure, Function, and Bioinformatics, 66(1), pp.41-52 (2007). ¢£Free Full Text Paper(PDF) on the Journal Website. ¢£PubMed
  • Nagano, N., Noguchi, N., Akiyama, Y.:"Systematic Comparison of Catalytic Mechanisms of Hydrolysis and Transfer Reactions Classified in the EzCatDB Database", PROTEINS: Structure, Function, and Bioinformatics, 66(1), pp.147-159 (2007). ¢£Free Full Text Paper(PDF) on the Journal Website. ¢£PubMed
  • Fukuda, K., Yamamoto, S., Sakai, N., Nakanishi, Y., Nakamura, H., Takagi, T.:"Graphical Syntax and Query for Pathway Database", The 10th World Multi-Conference on Systemics, Cybernetics and Infrmatics, pp7-10 (2006).
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