Papers（2010）

  • Saito Y, Sato K, Sakakibara Y. "Robust and accurate prediction of noncoding RNAs from aligned sequences.", BMC BIOINFORMATICS, 11(7) pp.S3 (2010). headAbstract (PubMed) headJournal Site
  • Kato, T., Suwa, K., Nagano, N.: "Parametric Templates: A New Enzyme Active-Site Prediction Algorithm.", 2010IEEE International Conference on Data Mining Workshops, ) pp.711-718 (2010). headJournal Site
  • Kato, T., Suwa, K., Nagano, N.:"Parametric Templates: A New Enzyme Active-Site Prediction Algorithm.", 2010 IEEE International Conference on Data Mining Workshops, pp.711-718(2010). headAbstract headFull Text
  • Miura, K., Fujibuchi, W., Sasaki, I.:"Alternative pre-mRNA splicing in digestive tract malignancy.", CANCER SCIENCE, 102(2), pp.309-316(2010). headAbstract headFull Text
  • Horton, P., Wijaya, E., Pessiot, K.J-F., Frith, M., Fujibuchi, W., Asai, K.:"In Search of True Reads: A Classification Approach to Next Generation Sequencing Data Selection.", International Conference on Bioinformatics and Biomedicine Workshops, 37pp.561-566(2010).
  • Wan, R., Asai, K.:"Sorting Next Generation Sequencing Data Improves Compression Effectiveness.", Proc. 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) - Workshops and Posters, pp.567-572(2010). headAbstract
  • Iizuka, Y., Okuno, T., Saeki, K., Uozaki, H., Okada, S., Misaka, T., Sato, T., Toh, H., Fukayama, M., Kita, Y., Shimizu, T., Nakamura, M., Yokomizo, T.:"Protective roles of second leukotriene B4 receptor BLT2 in murine model of inflammatory colitis.", FASEB JOURNAL, 24(12), pp.4678-4690(2010). headPubMed
  • Nagao, A., Mituyama, T., Huang, H., Chen, D., Siomi, M.C., Siomi, H.: "Biogenesis pathways of piRNAs loaded onto AGO3 in the Drosophila testis", RNA-A PUBLICATION OF THE RNA SOCIETY, 16, pp.2503-2515(2010).
    headFull Text Paper(PDF) on the Journal Website.
  • Gromiha, M.M., Yokota, K., Fukui, K.:"Understanding the Recognition Mechanism of Protein-RNA Complexes using Energy Based Approach .", CURRENT PROTEIN & PEPTIDE SCIENCE, 11(7), pp.629-638(2010). headAbstract
  • Terakawa, T., Kameda, T., Takada, S.:"On easy implementation of a variant of the replica exchange with solute tempering in GROMACS.", JOURNAL OF COMPUTATIONAL CHEMISTRY, (2010). headAbstract headFull Text
  • Tominaga, D.:"Periodicity detection method for small-sample time series datasets.", Bioinformatics and Biology Insights, 4(pp.127-136(2010). headAbstract headFull Text
  • Hamada, M., Sato, K., Asai, K.:"Prediction of RNA secondary structure by maximizing pseudo-expected accuracy.", BMC BIOINFORMATICS, 11(586), (2010). headAbstract headFull Text
  • Imai, K., Nakai, K.:"Prediction of subcellular locations of proteins: where to proceed?.", PROTEOMICS, 10(22), pp.3970-3983(2010). headAbstract headFull Text
  • Tabei, Y., Uno, T., Sugiyama, M., Tsuda, K.:"Single versus multiple sorting in all pairs similarity search.", Proceedings of the 2nd Asian Conference on Machine Learning, pp.155-170(2010). headAbstract
  • Aburatani, S.: "Development of network inference among LexA/RecA-dependent manner genes in SOS response.", Journal of Nucleic Acids Investigation, 1(1) pp.71-75 (2010). headJournal Site
  • Kato, T., Nagano, N.:"Metric Learning for Enzyme Active-Site Search", BIOINFORMATICS, 26(21), pp.2698-2704(2010).
    headPubMed
  • Hirano, A., Kameda, T., Arakawa, T., Shiraki, K.:"Arginine-Assisted Solubilization System for Drug Substances: Solubility Experiment and Simulation", JOURNAL OF PHYSICAL CHEMISTRY B, 114(42), pp.13455-13462(2010).
    headAbstract on the Journal Website.
  • Johansson, F., Toh, H.:"RELATIVE VON NEUMANN ENTROPY FOR EVALUATING AMINO ACID CONSERVATION.", JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 8(5), pp.809-823(2010). headAbstract headFull Text
  • Kashima, H., Oyama, S., Yamanishi, Y., Tsuda, K.:"Cartesian Kernel: An Efficient Alternative to the Pairwise Kernel.", IEICE TRANSACTIONS ON INFORMATION AND SYSTEMS, E93D(10), pp.2672-2679(2010). headAbstract
  • Huang, L-T., Gromiha, M.M.:"First insight into the prediction of protein folding rate change upon point mutation", BIOINFORMATICS, 26(17), pp.2121-2127(2010).
    headAbstract on the Journal Website.
  • Li, W., Yoshii, H., Hori, N., Kameda, T., Takada, S.:"Multiscale methods for protein folding simulations", METHODS, 52, pp.106-114(2010).
  • Miura, K., Kinouchi, M., Ishida, K., Fujibuchi, W., Naitoh, T., Ogawa, H., o, T., Yazaki, N., Watanabe, K., Haneda, S., Shibata, C., Sasaki, I.:"5-FU Metabolism in Cancer, and Orally-Administrable 5-FU Drugs", CANCERS, 2(3), pp.1717-1730(2010).
    headFull Text Paper(PDF) on the Journal Website.
  • Takahashi, H., Morioka, R., Ito, R., Oshima, T., Altaf-Ul-Amin, M., Ogasawara, N., Kanaya, S.:"Dynamics of Time-Lagged Gene-to-Metabolite Networks of Escherichia coli Elucidated by Integrative Omics Approach.", OMICS: A Journal of Integrative Biology, 15(1-2)pp.15-23(2010). headAbstract headFull Text
  • Kato, Y., Sato, K., Hamada, M., Watanabe, Y., Asai, K., Akutsu, T.:"RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming.", BIOINFORMATICS, 26(18), pp.i460-i466(2010). headAbstract headFull Text
  • Hamada, M., Sato, K., Asai, K.:"Improving the accuracy of predicting secondary structure for aligned RNA sequences .", NUCLEIC ACIDS RESEARCH, 39(2), pp.393-402(2010). headAbstract headFull Text
  • Oda, Y., Yoshimura, Y., Ohnishi, H., Tadokoro, M., Katsube, Y., Sasao, M., Kubo, Y., Hattori, K., Saito, S., Horimoto, K., Yuba, S., Ohgushi, H.:"Induction of pluripotent stem cells from human third molar mesenchymal stromal cells..", JOURNAL OF BIOLOGICAL CHEMISTRY, 285pp.29270-29278(2010). headAbstract headFull Text
  • Nakatsui, M., Horimoto, K., Okamoto, M., Tokumoto, Y., Miyake J.:"Parameter Optimization by Using Differential Elimination: a General Approach for Introducing Constraints into Objective Functions..", BMC SYSTEMS BIOLOGY, 4(2), pp.9-(2010). headAbstract headFull Text
  • Pessiot, J.F., Chiba, H., Hyakkoku, H., Taniguchi, T., Fujibuchi, W.:"PeakRegressor identifies composite sequence motifs responsible for STAT1 binding sites and their potential rSNPs", PLOS ONE, 5(8), pp.e11881(2010).
    headFull Text Paper(PDF) on the Journal Website.
  • Nagao, C., Nagano, N., Mizuguchi, K.:"Relationships between functional subclasses and information contained in active-site and ligand-binding residues in diverse superfamilies", PROTEINS, 78(10), pp.2369-2384(2010).
    headPubMed
  • Huang, L-T., Lai, L-F., Wu, C-C. Gromiha, M.M.:"Development of knowledge based system for predicting the stability of proteins upon point mutations", NEUROCOMPUTING, 73, pp.2293-2299(2010).
    headAbstract on the Journal Website.
  • Katoh, K., Toh, H.:"Parallelization of the MAFFT multiple sequence alignment program", BIOINFORMATICS, 26(15), pp.1899-1900(2010).
    headFull Text Paper(PDF) on the Journal Website.
  • Gromiha, M.M., Selvaraj, S., Jayaram, B. Fukui, K.:"Identification and analysis of binding site residues in protein complexes: energy based approach", LECTURE NOTES IN COMPUTER SCIENCE, 6215, pp.626-633(2010).
    headAbstract on SpringerLink website.
  • Chen, S-A., Ou, Y-Y., Gromiha, M.M.:"Topology Prediction of alpha-helical and beta-barrel Transmembrane Proteins using RBF Networks", LECTURE NOTES IN COMPUTER SCIENCE, 6215, pp.642-649(2010).
    headAbstract on SpringerLink website.
  • Park, M.R., Yun, K.Y., Mohanty, B., Herath, V., Xu, F., Wijaya, E., Bajic, V.B., Yun, S.J. de los Reyes, B.G.:"Supra-optimal expression of the cold-regulated OsMyb4 transcription factor in transgenic rice changes the complexity of transcriptional network with major effects on stress tolerance and panicle development", PLANT CELL AND ENVIRONMENT, 33, pp.2209-2230(2010).
    headPubMed
  • Honda, M., Sakai, A., Yamashita, T., Nakamoto, Y., Mizukoshi, E., Sakai, Y., Yamashita, T., Nakamura, M., Shirasaki, T., Horimoto, K., Tanaka, Y., Tokunaga, K., Mizokami, M., Kaneko, S.:"Hepatic ISG Expression Is Associated With Genetic Variation in Interleukin 28B and the Outcome of IFN Therapy for Chronic Hepatitis C.", GASTROENTEROLOGY, 139(2), pp.499-509(2010). headAbstract headFull Text
  • Katoh, K., Toh, H.: "Parallelization of the MAFFT multiple sequence alignment program.", BIOINFORMATICS, 26(15) pp.1899-1900 (2010). headAbstract (PubMed)
  • Itsuki,A., Aburatani,S., Kanazawa,S.: "Soil ecology of laurel-leaved and Cryptomeria japonica forests assessed by dilution plate count and direct microscopic count methods.", the 19th World Congress of Soil Science, pp.187-190 (2010).
  • Hirose, S., Yokota, K., Kuroda, Y., Wako, H., Endo, S., Kanai, S., Noguchi, T.: "Prediction of protein motions from amino acid sequence and its application to protein-protein interaction.", BMC STRUCTURAL BIOLOGY, 10(20) (2010). headAbstract (PubMed) headJournal Site
  • Tochigi, Y., Sato, N., Sahara, T., Wu, C., Saito, S., Irie, T., Fujibuchi, W., Goda, T., Yamaji, R., Ogawa, M., Ohmiya, Y., Ohgiya, S.:"Sensitive and convenient yeast reporter assay for high-throughput analysis by using a secretory luciferase from Cypridina noctiluca.", ANALYTICAL CHEMISTRY, 82(13), pp.5768-5776(2010).
    headAbstract on the Journal Website.
    headPubMed
  • Gromiha, M.M., Yokota, K., Samuel, S., Fukui, K.:"Comparative analysis of binding site residues and recognition mechanisms of protein-protein and protein-RNA complexes using energy based approach", Proc. ISMB2010, 10, pp.54(2010).
    headAbstract on ISMB2010 website.
  • Johansson, F., Toh, H.:"A comparative study of conservation and variation scores.", BMC BIOINFORMATICS, 11pp.388-(2010). headAbstract headFull Text
  • Ootsuji, H., Honda, M., Kaneko, S., Usui, S., Okajima, M., Okada, H., Sakai, Y., Takamura, T., Horimoto, K., Takamura, M.:"Altered Hepatic Gene Expression Profiles Associated with Myocardial Ischemia.", CIRCULATION-CARDIOVASCULAR GENETICS, 3pp.68-77(2010). headAbstract headFull Text
  • Kayano, M., Takigawa, I., Shiga, M., Tsuda, K., Mamitsuka, H.:"ON THE PERFORMANCE OF METHODS FOR FINDING A SWITCHING MECHANISM IN GENE EXPRESSION.", GENOME INFORMATICS SERIES, 24pp.69-83(2010). headAbstract
  • Suwa, M., Ono, Y.:"A bioinformatics strategy to produce a cyclically developing project structure (Comprehensive functional analysis of the drug design target genes: Translation from Synthesiology, Vol.2 No.4, pp.299-309.).", Synthesiology English edition, 3(1), pp.1-12(2010). headFull Text
  • Gromiha, M., Yokota, K., Fukui, K.:"Energy based approach for comparative analysis of binding site residues in protein-protein and protein-RNA complexes .", Proc. Protein Science Society of Japan, S10, pp.128-(2010).
  • Uchikoga, N., Hirokawa, T.:"Analysis of protein-protein docking decoys using interaction fingerprints: application to the reconstruction of CaM-ligand complexes", BMC BIOINFORMATICS, 11, pp.236(2010).
    headPubMed
  • Watanabe, M., Hirokawa, T., Kobayashi, T., Yoshida, A., Ito, Y., Yamada, S., Orimoto, N., Yamasaki, Y., Arisawa, M., Shuto, S.:"Investigation of the bioactive conformation of histamine H3 receptor antagonists by the cyclopropylic strain-based conformational restriction strategy", JOURNAL OF MEDICINAL CHEMISTRY, 53(9), pp.3585-3593(2010).
    headPubMed
  • Iida, K., Tera, M., Hirokawa, T., Shin-ya, K., Nagasawa, K.:"Synthesis of macrocyclic hexaoxazole (6OTD) dimers, containing guanidine and amine functionalized side chains, and an evaluation of their telomeric G4 stabilizing properties", JOURNAL OF NUCLEIC ACIDS, 2010(Article ID 217627), pp.9(2010).
    headFull Text Paper(PDF) on the Journal Website.
  • Sato, K., Whitington, T., Bailey, T.L., Horton, P.:"Improved Prediction of Transcription Binding Sites from Chromatin Modification Data.", Proceedings IEEE CIBCB 2010, pp.1-7(2010).
  • Saigo, H., Tsuda, K.:"Graph Mining in Chemoinformatics.", Chemoinformatics and Advanced Machine Learning Perspectives: Complex Computational Methods and Collaborative Techniques, pp.95-128(2010). headAbstract on IGI Gobal website
  • Kashima, H., Saigo., H, Hattori, M., Tsuda, K.:"Graph Kernels for Chemoinformatics.", Chemoinformatics and Advanced Machine Learning Perspectives: Complex Computational Methods and Collaborative Techniques, pp.1-15(2010). headAbstract on IGI Gobal website
  • Ou, Y-Y., Chen, S-A., Gromiha, M.M.:"Classification of transporters using efficient radial basis function net-works with position-specific scoring matrices and biochemical properties", PROTEINS, 78(7), pp.1789-1797(2010).
    headPubMed
  • Huang, L-T., Lai, L-F., Gromiha, M.M.:"Human-readable Rule Generator for Integrating Amino Acid Sequence Information and Stability of Mutant Proteins", IEEE-ACM Transactions on Computational Biology and Bioinformatics, 7(4), pp.681-687(2010).
    headPubMed
  • Kumar, S., Singh, S.K., Gromiha, M.M.:"Temperature Dependent Molecular Adaptations in Microbial Proteins: Lessons for Structure Based Biotherapeutics Design and Development", Encyclopedia of Industrial Biotechnology: Bioprocess, Bioseparation, and Cell Technology., pp.1-22(2010).
    headAbstract on Wiley Online Library
  • Hirose, S., Shimizu, K., Noguchi, T.:"POODLE-I: Disordered region prediction by integrating POODLE series and structural information predictors based on a workflow approach", IN SILICO BIOLOGY, 10, pp.15(2010).
    headAbstract on the Journal Website.
  • Izumikawa, M., Hashimoto, J., Hirokawa, T., Sugimoto, S., Kato, T., Takagi, M., Shin-Ya, K.:"JBIR-22, an inhibitor for protein-protein interaction of the homodimer of proteasome assembly factor 3.", J Nat Prod.,73(4), pp.628-631(2010).
    headAbstract on the Journal Website.
  • Nakato, R., Gotoh, O.:"Cgaln: fast and space-efficient whole-genome alignment", BMC BIOINFORMATICS, 11, pp.224(2010).
    headFull Text Paper(PDF) on the Journal Website.
  • Sato, K., Hamada, M., Mituyama, T., Asai, K., Sakaikibara, Y.:"A non-parametric Bayesian approach for predicting RNA.", JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 8(4), pp.727-742(2010). headAbstract on WorldSciNet website headFull Text on WorldSciNet website
  • Wang, X., Gotoh, O.:"Inference of Cancer-specific Gene Regulatory Networks Using Soft Computing Rules", Gene Regulation and Systems Biology, 4, pp.19-34(2010).
    headFull Text Paper(PDF) on PubMed Website.
  • Standley, D., Toh, H., Nakamura, H.:"SeSAW: balancing sequence and structural information in protein functional mapping..", BIOINFORMATICS, 26(9), pp.1258-1259(2010). headPubMed
  • Tsuda, K., Saigo, H.:"Graph Classification.", Managing and Mining Graph Data, pp.337-(2010). headSpringerLink
  • Frith, M.C., Hamada, M., Horton, P.:"Parameters for accurate genome alignment", BMC BIOINFORMATICS, 11(1), pp.80(2010).
    headFull Text Paper(PDF) on the Journal Website.
  • Gromiha, M.M., Yokota, K., Fukui, K.:"Sequence and structural analysis of binding site residues in protein-protein complexes", INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES, 46, pp.187-192(2010).
    headPubMed
  • Sone, H., Okura, M., Zaha, H., Fujibuchi, W., Taniguchi, T., Akanuma, H., Nagano, R., Ohsako, S., Yonemoto, J.:"Profiles of Chemical Effects on Cells (pCEC): a toxicogenomics database with a toxicoinformatics system for risk evaluation and toxicity prediction of environmental chemicals", JOURNAL OF TOXICOLOGICAL SCIENCES, 35(1), pp.115-123(2010).
    headPubMed
    headFull Text Paper(PDF) on the Journal Website.
  • Wang, X., Gotoh, O.:"A Robust Gene Selection Method for Microarray-based Cancer Classification", CANCER INFORMATICS, 9, pp.15-30(2010).
  • Ou, Y-Y., Chen, S-A., Gromiha, M.M.:"Prediction of membrane spanning segments and topology in beta-barrel membrane proteins at better accuracy.", JOURNAL OF COMPUTATIONAL CHEMISTRY, 31, pp.217-223(2010).
    headFull Text Paperon PubMed Website.
  • Gromiha, M.M., Sarai, A.:"Thermodynamic Database for Proteins: Features and Applications", METHODS IN MOLECULAR BIOLOGY, 609, pp.97-112(2010).
    headPubMed
  • Saigo, H., Hattori, M. , Kashima, H., Tsuda, K.:"Reaction Graph Kernels Predict EC Numbers of Unknown Enzymatic Reactions in Plant Secondary Metabolism", BMC BIOINFORMATICS, 11(Suppl. 1), pp.S1-(2010).
    headFull Text Paper(PDF) on the Journal Website.
  • Yagi-Utsumi, M., Kameda, T., Yamaguchi, Y., Kato, K.:"NMR characterization of the interactions between lyso-GM1 aqueous micelles and amyloid β", FEBS LETTERS, 584(4), pp.831-836(2010).
    headFull Text Paper on the Journal Website.
  • Frith, M.C., Wan, R., Horton, P.:"Incorporating sequence quality data into alignment improves DNA read mapping", NUCLEIC ACIDS RESEARCH, pp.1-9(2010).
    headFull Text Paper(PDF) on the Journal Website.
  • Yun, K-Y., Park, M-R., Mohanty, B., Herath, V., Xu, F., Mauleon, R., Wijaya, E., Bajic, V.B., Bruskiewich, R., de los Reyes, B.G.:"Transcriptional regulatory network triggered by oxidative signals configures the early response mechanisms of japonica rice to chilling stress", BMC PLANT BIOLOGY, 10, pp.16(2010).
    headFull Text Paper on the Journal Website.
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