Computational Biology Research Center[CBRC]

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2006

Papers（2006）

Polouliakh, N., Natsume, T., Harada, H., Fujibuchi, W., Horton, P.,: "Comparative genomic analysis of transcription regulation elements involved in the human MAP-kinase G-protein coupling pathway", JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 4(2), pp.469-482(2006).
■PubMed
Gromiha, M.M., Suwa, M., Ahmad, S.: "Structural Analysis, Discrimination Of & β-Barrel Membrane Proteins And Prediction Of Their Membrane Spnning Segments", Proc. 4th Asia Pacific Bioinformatics Conference, pp.44(2006).
Gromiha, M.M., Suwa, M., Suresh, X.: "Analysis and understanding of membrane protein-ligand interactions using novel statistical parameters", Proc. 20th IUBMB Congress, pp.4P-B-086(2006).
Gromiha, M.M., Suwa, M.: "Sequence and Structural Analysis of b-barrel Membrane Proteins: Applications to Discrimination", Proc. 20th IUBMB Congress, pp.4P-B-087(2006).
Kameda, S., Takada, S.: "Secondary structure provides a template for the folding of nearby polypeptides", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103(47), pp.17765-17770(2006).
Saigo, H., Kadowaki, T., Tsuda, K.: "A Linear Programming Approach for Molecular QSAR analysis", Proceedings of the International Workshop on Mining and Learning with Graphs 2006, pp.85-96(2006).
■Full Text Paper(PDF) on the Journal Website.
Tsuda, K., Kudo, T.: "Clustering graphs by weighted substructure mining", Proceedings of the 23rd International Conference on Machine Learning, pp.953-960(2006).
■Abstract on web the Journal site
Ren, F., Tsubota, A., Hirokawa, T., Kumada, H., Yang, Z., Tanaka, H.: "A unique amino acid substitution, T126I, in human genotype C of hepatitis B virus S gene and its possible influence on antigenic structural change". GENE, 15(383), pp.43-51 (2006).
Oka, Y., Katada, S., Omura, M., Suwa, M., Yoshihara, Y., Touhara, K.: "Odorant receptor map in the mouse olfactory bulb: in vivo sensitivity and specificity of receptor-defined glomeruli". NEURON, 52(5), pp.857-869 (2006).
Aburatani, S.: "Serial Network Inference in Cell Cycle regulation on Yeast". Proceedings of the 10th World Multiconference on Systemics, Cybernetics and Informatics, 4, pp.1-6 (2006).■PDF(206MB)
Kiryu H., Kin T., Asai K.: "Robust prediction of consensus secondary structures using averaged base pairing probability matrices". BIOINFORMATICS, 23(4), pp.434-441 (2006).
Horton, P., Kiseleva, L., Fujibuchi, W.: "RaPiDS: An Algorithm for Rapid Expression Profile Database Search", Genome Informatics, 17(2), pp.67-76 (2006). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Tominaga, D., Horton, P.: "Inference of Scale-free Networks From Gene Expression Time Series", Journal of Bioinformatics and Computational Biology, 4(2), pp.503-514 (2006). ■PubMed
Yamada, S., Gotoh, O., Yamana, H.: "Improvement in accuracy of multiple sequence alignment using novel group-to-group sequence alignment algorithm with piecewise linear gap cost", BMC Bioinformatics, 7, 524 (2006). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Gromiha, M.M., Thangakani, A.M., Selvara,j S.: "FOLD-RATE: prediction of protein folding rates from amino acid sequence", Nucleic Acids Research, 34(Web Server issue), pp.W70-W74 (2006). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Gromiha, M.M., Suwa, M.: "Influence of amino acid properties for discriminating outer membrane proteins at better accuracy", Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics, 1764(9), pp.1493-1497 (2006). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Shimizu, K., Adachi, J., Muraoka, Y.: "ANGLE: a sequencing errors resistant program for predicting protein coding regions in unfinished cDNA", Journal of Bioinformatics and Computational Biology, 4(3), pp.649-664 (2006). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Hamada, M., Tsuda, K., Kudo, T., Kin, T., Asai, K.: "Mining frequent stem patterns from unaligned RNA sequences", Bioinformatics, 22(20), pp.2480-2487 (2006). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Prabakaran, P., Siebers, J.G., Ahmad, S., Gromiha, M.M., Singarayan, M.G., Sarai, A.: "Classification of Protein-DNA Complexes Based on Structural Descriptors", Structure, 14(9) pp.1355-1367 (2006). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Fukui, K., Akiyama, Y.: "Fragmentation Studies of Peptide and Oligosaccharide using a Mid-IR Free Electron Laser", The Journal of Japan Society for Laser Surgery and Medicine, 27(6), pp.92-97 (2006).
Fukui, K., Takada, Y., Sumiyoshi, T., Imai, T., Takahashi, K.: "Infrared Multiphoton Dissociation Spectroscopic Analysis of Peptides and Oligosaccharides by Using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry with a Midinfrared Free-Electron Laser", Journal of Physical Chemistry B, 110(32), pp.16111-16116 (2006). ■Free Full Text Paper(PDF) on the Journal Website.
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Kato, T., Fujibuchi, W., Asai, K.: "Learning Kernels from Distance Constraints ", IPSJ, 47(SIG10)(CVIM15), pp.1-11 (2006).
Tabei, Y., Tsuda, K., Kin, T., Asai, K.: "SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments", Bioinformatics, 22(14), pp.1723-1729 (2006). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Chakkaravarthi, S., Babu, M.M., Gromiha, M.M., Jayaraman, G., Sethumadhavan, R.: "Exploring the environmental preference of weak interactions in (a/b)8 barrel proteins", Proteins: Structure, Function, and Bioinformatics, pp.75-86 (2006). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Gromiha, M.M., Selvaraj, S., Thangakani A.M.: "A statistical method for predicting protein unfolding rates from amino acid sequence", Journal of Chemical Information and Modeling, 46 (3), pp.1503 - 1508 (2006). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Parthiban, V., Gromiha, M.M., Schomburg, D.: "CUPSAT: prediction of protein stability upon point mutations", Nucleic Acids Research, 34(Web Server issue), pp. W239-W24 (2006). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Gromiha, M.M., Thangakani, A.M., Selvaraj, S.: "FOLD-RATE: prediction of protein folding rates from amino acid sequence", Nucleic Acids Research, 34(Web Server issue), pp.W70-74 (2006). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Polouliakh, N., Natsume, T., Harada, H., Fujibuchi, W., Horton, P.: "Comparative genomic analysis of transcription regulation elements involved in the human MAP-kinase G-protein coupling pathway", Journal of Bioinformatics and Computational Biology, 4(2), pp.469-482 (2006). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Nagasaki, H., Arita, M., Nishizawa, T., Suwa, M., Gotoh, O.: "Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns", Bioinformatics, 22(10), pp.1211-1216 (2006). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Gromiha, M.M., Suwa, M.: "Discrimination of outer membrane proteins using machine learning algorithms", Proteins-Structure Function and Bioinformatics, 63(4), pp.1031-1037 (2006). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Saraboji, K., Gromiha, M.M., Ponnuswamy, M.N.: "Average assignment method for predicting the stability of protein mutants", Biopolymers, 82(1), pp.80-92 (2006). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Tomii, K.: "Protein Structure Prediction Using a Profile-Profile Comparison Method: FORTE", SEIBUTSU BUTSURI, 46(2), pp.106-110 (2006). (In Japanese) ■Free Full Text Paper(PDF) on the Journal Website.
Tominaga, D., Horton, P.:"Optimization of S-system models for quantitative time-developing gene networks", Journal of Bioinformatics and Computational Biology, 4(2), pp.503-514 (2006).
Fukui, K., Kameyama, A., Mukai, Y., Takahashi, K., Ikeda, N., Akiyama, Y., Narimatsu, H.: "A computational study of structure-reactivity relationships in Na-adduct oligosaccharides in collision-induced dissociation reactions", Carbohydrate Research, 341(5), pp.624-633 (2006). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Muramatsu, T., Suwa, M.: "Statistical analysis and prediction of functional residues effective for GPCR-G-protein coupling selectivity", PROTEIN ENGINEERING DESIGN & SELECTION, 19(6), pp.277-283 (2006). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Suenaga, A., Okimoto, N., Futatsugi, N., Hirano, Y., Narumi, T., Ohno, Y., Yanai, R., Hirokawa, T., Ebisuzaki, T., Konagaya, A., Taiji, M.: "Structure and dynamics of RNA polymerase II elongation complex", Biochemical and Biophysical Research Communications, 343(1), pp.90-98 (2006). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
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Tomii, K., Toh, H.: "Current Progress in Molecular Biology Databases : Development of Similarity Search for Sequence Database", IPSJ, 47(3), pp.227-232 (2006). (In Japanese)
Fukuda, K., Goto, S.: "Current Progress in Molecular Biology Databases : Formation and Representation of Biological Knowledge", IPSJ, 47(3), pp.233-240 (2006). (In Japanese)
Kato, T., Murata, Y., Miura, K., Asai, K., Horton, P.B., Tsuda, K., Fujibuchi, W.: "Network-based de-noising improves prediction from microarray data", BioMed Central Bioinformatics, 7(Suppl 1), pp.S1-4 (2006). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Chakkaravarthi, S., Gromiha, M.M.: "Analysis of cation-π interactions to the structural stability of RNA binding proteins", 47(2), pp. 709-721 (2006). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal.
Yamagaki, T., Fukui, K., Tachibana, K.: "Analysis of glycosyl bond cleavage and related isotope effects in collision-induced dissociation quadrupole-time-of-flight mass spectrometry of isomeric trehaloses", Analytical chemistry, 78(4), pp.1015-1022 (2006). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Kushida, T., Takagi, T., Fukuda, K.: "Event Ontology: A Pathway-Centric Ontology for Biological Processes", Pacific Symposium on Biocomputing, 11, pp.152-163 (2006). ■Free Full Text Paper(PDF) on the Journal Website.
Kumar, M.D., Gromiha, M.M.: "PINT: Protein-protein Interactions Thermodynamic Database", Nucleic Acids Research, 34(Database issue), pp.D195-D198 (2006). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Kumar, M.D., Bava, K.A., Gromiha, M.M., Prabakaran, P., Kitajima, K., Uedaira, H., Sarai, A.: "ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions", Nucleic Acids Research, 34(Database issue), pp.D204-D206 (2006). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Singh, Y.H., Gromiha, M.M., Sarai, A., Ahmad, S.: "Atom-wise statistics and prediction of solvent accessibility in proteins", Biophysical Chemistry, 124(2), pp.145-154(2006). ■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。 ■PubMed

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