Computational Biology Research Center[CBRC]

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2004

Papers（2004）

Kin, T., Kato, T., Tsuda, K.:"Protein Classification via Kernel Matrix Completion", Kernel Methods in Computational Biology, pp.261-274(2004). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal.
Ahmad, S., Gromiha, M.M., Sarai, A.: "Predictive annotation of DNA binding residues and proteins based on sequence and structure information", SEIBUTSU BUTSURI, 44(SUPPLEMENT_1), pp.S138 (2004).
Gromiha, M.M., Ahmad, S., Suwa, M.: "Sequence and Structural Analysis of Outer Membrane Proteins: Applications to Discrimination and Prediction", Genome Informatics, 15(2), pp.P151-1 - P151-2 (2004).
Tsuda, K., Raetsch, G., Warmuth, M.: "Matrix Exponential Updates for On-line Learning and Bregman Projection", Advances in Neural Information Proecssing Systems, 17, pp.1425-1432 (2004). ■Free Full Text Paper(PDF) on the Journal Website.
Fukui, K., Naito, Y., Akiyama, Y., Takahashi, K.: "Fragmentation study of peptides using Fourier transform ion cyclotron resonance with infrared multiphoton dissociation: experiment and simulation European", Journal of Mass Spectrometry, 10, pp.639-648 (2004). ■PubMed
Shiozawa, K., Maita, N., Tomii, K., Seto, A., Goda, N., Akiyama, Y., Shimizu, T., Shirakawa, M., Hiroaki, H.: "Crystallographic characterization of the N-terminal domain of PEX1", Biological Crystallography, 60(Pt 11), pp.2098-2099 (2004). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Shiozawa, K., Maita, N., Tomii, K., Seto, A., Goda, N., Akiyama, Y., Shimizu, T., Shirakawa, M., Hiroaki, H.: "Structure of the N-terminal domain of PEX1 AAA-ATPase. Characterization of a putative adaptor-binding domain", Journal of Biological Chemistry, 279(48), pp.50060-50068 (2004). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
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Sakamoto, K., Kadota, K., Oishi, K.: "Light-induced phase-shifting of the peripheral circadian oscillator in the hearts of food-deprived mice", Experimental Animals, 53(5), pp.471-474 (2004). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Gromiha, M.M., Siebers, J., Selvaraj, S., Kono, H., Sarai, A.: "Role of Inter and intramolecular interactions in protein-DNA recognition", Proceeding of 14th International workshop on Beyond the Indentification of Transcribed Sequences, pp.64 (2004).
Gromiha, M.M., Parry, D.A.: "Characteristic features of amino acid residues in coiled-coil protein structures", Biophysical Chemistry, 111(2), pp.95-103 (2004). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Wang, J.Y., Ahmad, S., Gromiha, M.M., Sarai, A.: "Look-up tables for protein solvent accessibility prediction and nearest neighbor effect analysis", Biopolymers, 75(3), pp.209-216 (2004). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Gromiha, M.M., Selvaraj, S.: "Inter-residue interactions in protein folding and stability", Progress in Biophysics and Molecular Biology, 86(2), pp.235-277 (2004). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Kumondai, K., Toyoda, M., Iwamoto, K., Ishihara, M., Katakuse, I.: "Ion/Molecule Reactions of Silver Cluster Cations with Crown Ethers in a Cylindrical Ion Trap", Japanese Journal of Applied Physics, 43(10), pp.7282-7286 (2004). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal.
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Gokhan, H., Bakir, A.Z., Tsuda, K.: "Learning to Find Graph Pre-images", Lecture Notes in Computer Science (Pattern Recognition: 26th DAGM Symposium, Tubingen, Germany, August 30 - September 1, 2004. Proceedings), 3175, pp.253-261 (2004). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal.
Aita, T., Morinaga, S., Husimi, Y.: "Thermodynamical interpretation of evolutionary dynamics on a fitness landscape in a evolution reactor, I", Bulletin of Mathematical Biology, 66(5), pp.1371-1403 (2004). ■Abstract ■PubMed
Fukui, K., Akiyama, Y., Takahashi, K.: "Theoretical and experimental studies for isomers of oligosaccharides using CID-MS/MS quadropole/time-of-flight mass spectrometry", Abstracts of paper of the American Chemical Society, 228, pp.U230 (2004).
Kato, T., Tsuda, K., Tomii, K., Asai, K.: "A New Variational Framework for Rigid-Body Alignment", Lecture Notes in Computer Science (Structural, Syntactic, and Statistical Pattern Recognition: Joint IAPR International Workshops, SSPR 2004 and SPR 2004, Lisbon, Portugal, August 18-20, 2004. Proceedings), 3138, pp.171-179 (2004). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal.
Tsuda, K., Noble, W.S.: "Learning kernels from biological networks by maximizing entropy", Bioinformatics, 20(Suppl 1) pp.I326-I333 (2004). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Sarai, K., Gromiha, M.M., Ahmad, S., Kono, H.: "Developing Genome-Scale Prediction System for Transcription Factors and Their Targets", Proceeding of 12th ISMB and 3rd ECCB, pp.195(2004).
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Gromiha, M.M., Pujadas, G., Magyar, C., Selvaraj, S., Simon, I.: "Identifying the Stabilizing Residues in (a/b)8 Barrel Proteins Based on Hydrophobicity, Long-range Interactions and Sequence Conservation", Proceeding of 12th ISMB and 3rd ECCB, pp.195 (2004).
Arai, M., Mitsuke, H., Ikeda, M., Xia, J.X., Kikuchi, T., Satake, M., Shimizu, T.: "ConPred II: a consensus prediction method for obtaining transmembrane topology models with high reliability", Nucleic Acids Research, 32(Web Server issue), pp.W390-W393 (2004). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Yokota Hirai, M., Yano, M., Goodenowe, D.B., Kanaya, S., Kimura, T., Awazuhara, M., Arita, M., Fujiwara, T., Saito, K.: "Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana", PNAS, 101(27), pp.10205-10210 (2004). ■Free Full Text Paper(PDF) on the Journal Website.
Uedaira, H., Gromiha, M.M., Sarai, A.: "Thermodynamic database for biomolecules: Proteins and mutants", Comprehensive Handbook of Calorimetry and Thermal Analysis, pp.276-279 (2004).
Sarai, A., Gromiha, M.M., Ahmad, S., Kono, H.: "Genome scale prediction of transcription factors and their targets", Proceeding of 4th International conference on bioinformatics of genome regulation and structure (2004).
Gromiha, M.M., Pujadas, G., Magyar, C., Selvaraj, S., Simon, I.: "A Consensus Approach for Identifying the Stabilizing Residues in (alpha/beta)8 Barrel Proteins", Proceeding of CBI meeting 2004, pp.89 (2004).
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Selvaraj, S., Gromiha, M.M.: "Importance of hydrophobic cluster formation through long-range contacts in the folding transition state of two-state proteins", Proteins: Structure, Function, and Bioinformatics, 55(4), pp.1023-1035 (2004). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Gromiha, M.M., Santhosh, C., Ahmad, S.: "Structural analysis of cation?π interactions in DNA binding proteins", International Journal of Biological Macromolecules, 34(3), pp.203-211 (2004). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal.
Tsuda, K., Raetsch, G.: "Image Reconstruction by Linear Programming", Advances in Neural Information Processing Systems, 16, pp.57-64 (2004). ■Free Full Text Paper(PDF) on the Journal Website.
Imanishi, T., et al.(incl. Nagasaki, H., Suwa, M. from CBRC): "Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones", PLoS Biology, 2(6), pp.e162 (2004). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Sogawa, K., Numayama-Tsuruta, K., Takahashi, T., Matsushita, N., Miura, C., Nikawa, J., Gotoh, O., Kikuchi, Y., Fujii-Kuriyama, Y.: "A novel induction mechanism of the rat CYP1A2 gene mediated by Ah receptor-Arnt heterodimer", Biochemical and Biophysical Research Communications, 318(3), pp.746-755 (2004). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Fukui, K., Naito, Y., Akiyama, Y., Takahashi, K.: "Charge-state selective fragmentation analysis for protonated peptides in infrared multiphoton dissociation", International Journal of Mass Spectrometry, 235(1), pp.25-32 (2004). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal.
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Fukuda, K., Yamagata, Y., Takagi, T.: "Pathway Database : Higher Order Knowledge in Biology", IPSJ(Tranzaction), 45(SIG 7(TOD 22)), pp.77-84 (2004). (In Japanese) ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal.
Ahmad, S., Gromiha, M.M., Fawareh, H., Sarai, A.: "ASAView: database and tool for solvent accessibility representation in proteins", BMC Bioinformatics, 5, pp.51 (2004). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Gromiha, M.M., Pujadas, G., Magyar, C., Selvaraj, S., Simon, I.: "Locating the stabilizing residues in (alpha/beta)8 barrel proteins based on hydrophobicity, long-range interactions, and sequence conservation", Proteins, 55(2), pp.316-329 (2004). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Polouliakh, N., Konno, M., Horton, P., Nakai, K.: "Parameter Landscape Analysis for Common Motif Discovery Programs", Lecture Notes in Computer Science (Regulatory Genomics: RECOMB 2004 International Workshop, RRG 2004, San Diego, Ca, USA, March 26-27, 2004, Revised Selected Papers), 3318, pp.79-87 (2004). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal.
Igarashi, S., Hirokawa, T., Sode, K.: "Engineering PQQ glucose dehydrogenase with improved substrate specificity. Site-directed mutagenesis studies on the active center of PQQ glucose dehydrogenase", Biomolecular Engineering, 21(2), pp.81-89 (2004). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Arita, M.: "Computational resources for metabolomics", Briefings in Functional Genomics and Proteomics, 3(1), pp.84-93 (2004). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
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Asai, R., Nishimura, S., Aita, T., Takahashi, K.: "In Vitro Selection of DNA Aptamers on Chips Using a Method for Generating Point Mutations", Analytical Letters, 37(4), pp.645-656 (2004). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal.
Gromiha, M.M., Ahmad, S., Suwa, M.: "Neural network-based prediction of transmembrane beta-strand segments in outer membrane proteins", Journal of Computational Chemistry, 25(5), pp.762-767 (2004). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Hourai, Y., Akutsu, T., Akiyama, Y.: "Optimizing substitution matrices by separating score distributions", Bioinromatics, 20(6), pp.863-873 (2004). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Gromiha, M.M., Siebers, J.G., Selvaraj, S., Kono, H., Sarai, A.: "Intermolecular and Intramolecular Readout Mechanisms in Protein-DNA Recognition", Journal of Molecular Biology, 337(2), pp.285-294 (2004). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Ahmad, S., Gromiha, M.M., Sarai, A.: "Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information", Bioinformatics, 20(4), pp.477-486 (2004). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Yabuki, Y., Mukai, Y., Swindells, M.B., Suwa, M.: "GENIUS II: a high-throughput database system for linking ORFs in complete genomes to known protein three-dimensional structures", Bioinformatics, 20(4), pp.596-598 (2004). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
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Tomii, K., Akiyama, Y.: "FORTE: a profile-profile comparison tool for protein fold recognition", Bioinformatics, 20(4), pp.594-595 (2004). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Sarai, A., Selvaraj, S., Gromiha, M.M., Kono, H.: "Structure-function relationship in DNA sequence recognition by transcription factors", Proceedings of the second conference on Asia-Pacific bioinformatics, 26, pp.233-238 (2004). ■Free Full Text Paper(PDF) on the Journal Website.
Gromiha, M.M., Saraboji, K., Ahmad, S., Ponnuswamy, M.N., Suwa, M.: "Role of non-covalent interactions for determining the folding rate of two-state proteins", Biophysical Chemistry, 107(3), pp.263-272 (2004). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Gromiha, M.M., Selvaraj, S.: "Folding mechanism of all-beta globular proteins", Preparative Biochemistry & Biotechnology, 34(1), pp.13-23 (2004). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Shimoji, T., Kanda, H., Kitagawa, T., Kadota, K., Asai, R., Takahashi, K., Kawaguchi, N., Matsumoto, S., Hayashizaki, Y., Okazaki, Y., Shinomiya, K.: "Clinico-molecular study of dedifferentiation in well-differentiated liposarcoma", Biochemical and Biophysical Research Communications, 314(4), pp.1133-1140 (2004). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Arita, M.: "The metabolic world of Escherichia coli is not small", PNAS, 101(6), pp.1543-1547 (2004). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal.
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Tsuda, K., Uda, S., Kin, T., Asai, K.: "Minimizing the Cross Validation Error to Mix Kernel Matrices of Heterogeneous Biological Data", Neural Processing Letters, 19(1), pp.63-72 (2004). ■Free Full Text Paper(PDF) on the Journal Website.You need the license for the electrical journal.
Bava, K.A., Gromiha, M.M., Uedaira, H., Kitajima, K., Sarai, A.: "ProTherm, version 4.0: Thermodynamic Database for Proteins and Mutants", Nucleic Acids Research, 32(Database issue), pp.D120-D121 (2004). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Gromiha, M.M., Santhosh, C., Suwa, M.: "Influence of cation-π interactions in protein-DNA complexes", Polymer, 45(2), pp.633-639 (2004). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal.
Yamazaki, Y., Kitajima, M., Arita, M., Takayama, H., Sudo, H., Yamazaki, M., Aimi, N., Saito, K.: "Biosynthesis of camptothecin. In silico and in vivo tracer study from [1-13C]glucose", Plant Physiology, 134(1), pp.161-170 (2004). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Fukuda, K., Takagi, T.: "A Pathway Editor for Literature-based Knowledge Curation", Proceedings of the second conference on Asia-Pacific bioinformatics, 29 pp.339-344(2004). ■Free Full Text Paper(PDF) on the Journal Website.
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Tsuda, K., Akaho, S., Kawanabe, M., Muller, K.R.: "Asymptotic properties of the Fisher kernel", Neural Computation, 16(1), pp.115-137 (2004). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Ota, T., et al. (incl. Yada, T. from CBRC): "Complete sequencing and characterization of 21,243 full-length human cDNAs", Nature Genetics, 36(1), pp.40-45 (2004). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed

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