Computational Biology Research Center[CBRC]

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2003

Papers（2003）

Ueno, Y., Arita, M., Kumagai, T., Asai, K.: "Processing sequence annotation data using the Lua programming language", Genome informatics, 14, pp.154-163 (2003). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Fukuda, K., Yamagata, Y., Takagi, T.: "FREX: A query interface for biological processes with hierarchical and recursive structures", In Silico BIOLOGY, 4(0007) (2003). ■Free Full Text Paper(PDF) on the Journal Website.
Kadota, K., Tominaga, D., Asai, R., Takahashi, K.: "Correlation Analysis of mRNA and Protein Abundances in Human Tissues", Genome Letters, 2(4), pp.139-148 (2003). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal.
Ikeda, K., Higo, J.: "FREE-energy landscape of a chameleon sequence in explicit water and its inherent alpha/beta bifacial property", Protein Science, 12(11), pp.2542-2548 (2003). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Nakamura, T., Motoyama, T., Hirokawa, T., Hirono, S., Yamaguchi, I.: "Computer-aided modeling of pentachlorophenol 4-monooxygenase and site-directed mutagenesis of its active site", Chemical & pharmaceutical bulletin, 51(11), pp.1293-1298 (2003). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Imashimizu, M., et al. (incl. Hirokawa, T. from CBRC): "Thymine at -5 is crucial for cpc promoter activity of Synechocystis sp. strain PCC 6714", Journal of Bacteriology, 185(21), pp.6477-6480 (2003). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
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Aita, T., Husimi, Y.: "Thermodynamical interpretation of an adaptive walk on a Mt. Fuji-type fitness landscape: Einstein relation-like formula holds in a stochastic evolution", Journal of Theoretical Biology, 225(2), pp.215-228 (2003). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Arita, M.: "In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism", Genome Research, 13, pp.2455-2466 (2003). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Kato, T.,, Tsuda, K., Tomii, K., Asai, K.: "(In Japanese)", IBIS2003, pp.189-194 (2003). (In Japanese)
Oishi, K., et al. (incl. Kadota, K. from CBRC): "Genome-wide expression analysis of mouse liver reveals CLOCK-regulated circadian output genes", The Journal of biological chemistry, 278(42), pp.41519-41527 (2003). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Ohshima, K., Hattori, M., Yada, T., Gojobori, T., Sakaki, Y., Okada, N.: "Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates", Genome Biology, 4(11), pp.R74 (2003). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Tominaga, D., Takahashi, K., Akiyama, Y.: "Distributed Genetic Algorithm for Inference of Biological Scale-FREE Network Structure", Lecture Notes in Computer Science, 2858, pp.214-221 (2003). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal.
Sekijima, M., Motono, C., Yamasaki, S., Kaneko, K., Akiyama, Y.: "Molecular Dynamics Simulation of Prion Protein by Large Scale　Cluster Computing", Lecture Notes in Computer Science, 2858, pp.476-485 (2003). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal.
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Asai, R., et al.: "PCR-based ribosomal DNA detection technique for microalga (Heterosigma carterae) causing red tide and its application to a biosensor using labeled probe", Marine Biotechnology, 5(5), pp.417-423 (2003). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Gromiha, M,M., Suwa, M.: "Variation of amino acid properties in all-beta globular and outer membrane protein structures International", Journal of Biological Macromolecules, 32(3-5), pp.93-98 (2003). ■Free Full Text Paper(PDF) on the Journal Website.
Ahmad, S., Gromiha, M.M., Sarai, A.; "RVP-net: online prediction of real valued accessible surface area of proteins from single sequences", Bioinformatics, 19(14), pp.1849-1851 (2003). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Park, K.J., Kanehisa, M.: "Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino acid pairs", Bioinformatics, 19(13), pp.1656-1663 (2003). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Kashima, H., Tsuda, K., Inoguchi, A.: "Marginalized Kernels Between Labeled Graphs", Proceedings of 20th International Conference on Machine Learning, pp.321-328 (2003).
Gromiha, M.M.: "Importance of native-state topology for determining the folding rate of two-state proteins", Journal of chemical information and computer science, 43(5), pp.1481-1485 (2003). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
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Ahmad, S., Gromiha, M.M.: "Design and training of a neural network for predicting the solvent accessibility of prote", Journal of Computational Chemistry, 24(11), pp.1313-1320 (2003). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Sekijima, M., Motono, C., Yamasaki, S., Kaneko, K., Akiyama, Y.: "Molecular dynamics simulation of dimeric and monomeric forms of human prion protein: insight into dynamics and properties", Biophysical Journal, 85, pp.1176-1185 (2003). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Tsuda, K., Kawanabe, M., Mueller, K.-R.: "Clustering with the Fisher Score", Advances in Neural Information Processing Systems, 15, pp.729-736 (2003). ■Free Full Text Paper(PDF) on the Journal Website.
Gromiha, M.M.: "Factors influencing the thermal stability of buried protein mutants", Polymer, 44(14), pp.4061-4066 (2003). ■Free Full Text Paper(PDF) on the Journal Website.
Kobayashi, S., Kondo, T., Arita, M.: "On Template Method for DNA Sequence Design", DNA Computing : 8th International Workshop on DNA-Based Computers, DNA8 Sapporo, Japan, June 10-13, 2002. Revised Papers, 2568, pp.205-214 (2003). ｱ@Abstract on SpringerLink Website
Asai, R., Nakamura, C., Ikebukuro, K., Karube, I., Miyake, J.: "A Bioassay to Detect Contaminant-Induced Messenger RNA Using a Transcriptomic Approach: Detection of RT-PCR-Amplified Single-Stranded DNA Based on the SPR Sensor in Cyanobacteria", Analytical Letters, 36(8), pp.1475-1491 (2003). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal.
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Asai, R., Nakanishi, K., Nakamura, C., Ikebukuro, K., Miyake, J., Karube, I.: "A polymerase chain reaction-based ribosomal DNA detection technique using a surface plasmon resonance detector for a red tide causing microalga, Alexandrium affine", Phycologycal Research, 51(2), pp.118-125 (2003). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal.
Aita, T., Ota, M., Husimi, Y.: "An in silico exploration of the neutral network in protein sequence space", Journal of Theoretical Biology, 221(5), pp.599-613 (2003). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Nishikawa, K., et al. (incl. Hirokawa, T. from CBRC): "Alterations of structure and hydrolase activity of parkinsonism-associated human ubiquitin carboxyl-terminal hydrolase L1 variants", Biochemical and Biophysical Research Communications, 304(1), pp.176-183 (2003). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Kawana, K., Ikuta, T., Kobayashi, Y., Gotoh, O., Takeda, K., Kawajiri, K.: "Molecular mechanism of nuclear translocation of an orphan nuclear receptor SXR", Molecular Pharmacology, 63(3), pp.524-531 (2003). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Gromiha, M.M.: "Influence of Inter-residue Interactions in Protein Structures", BIOPHYSICS, 43(2), pp.87-92 (2003).
Ahmad, S., Gromiha, M.M., Sarai, A.: "Real value prediction of solvent accessibility from amino acid sequence", Proteins: Structure, Function, and Genetics, 50(4), pp.629-635 (2003). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
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Gromiha, M.M.: "Influence of cation-pi interactions in different folding types of membrane proteins", Biophysical Chemistry, 103(3), pp.251-258 (2003). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Selvaraj, S., Gromiha, M.M.: "Role of hydrophobic clusters and long-range contact networks in the folding of (alpha/beta)8 barrel proteins", Biophysical Journal, 84(3), pp.1919-1925 (2003). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Kikuchi, S., Tominaga, D., Arita, M., Takahashi, K., Tomita, M.: "Dynamic modeling of genetic networks using genetic algorithm and S-system", Bioinformatics, 19(5), pp.643-650 (2003). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Kadota, K., Nishimura, S., Bono, H., Nakamura, S., Hayashizaki, Y., Okazaki, Y., Takahashi, K.: "Detection of genes with tissue-specific expression patterns using Akaike's information criterion procedure", Physiological Genomics, 12(3), pp.251-259 (2003). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Kadota, K., Tominaga, D., Akiyama, Y., Takahashi, K.: "Detecting outlying samples in microarray data: A critical assessment of the effect of outliers on sample classification", Chem-Bio Informatics Journal, 3(1), pp.30-45 (2003). ■Free Full Text Paper(PDF) on the Journal Website.
Moriyama, M., et al. (incl. Nishimura, S. from CBRC): "Relevance network between chemosensitivity and transcriptome in human hepatoma cells", Molecular Cancer Therapeutics, 2(2), pp.199-205 (2003). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
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Tominaga, D., Takahashi, K.: "(In Japanese)", MPS Symposium, 2003(2), pp.185-188 (2003). (In Japanese)
Ida-Hosonuma, M., Sasaki, Y., Toyoda, H., Nomoto, A., Gotoh, O., Yonekawa, H., Koike, S.: "Host range of poliovirus is restricted to simians because of a rapid sequence change of the poliovirus receptor gene during evolution Archives of Virology", ARCHIVES OF VIROLOGY, 148(1), pp.29-44 (2003). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Suwa, M., Sato, T., Okouchi, I., Arita, M., Matsumoto, S., Tsutsumi, S., Aburatani, H., Asai, K., Akiyama. Y.: "SEVENS", Nucleic Acids Research, Database Summary Paper 373 (2003). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal.
Aita, T., Husimi, Y.: "Statistical formulae of the energy distribution among a globular protein structure ensemble", Journal of Theoretical Biology, 220(1), pp.107-121 (2003). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Noguchi, T., Akiyama, Y.: "PDB-REPRDB", Nucleic Acids Research, Database Summary Paper 277 (2003). ■Summary Paper
Noguchi, T., Akiyama, Y.: "PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003", Nucleic Acids Research, 31(1), pp.492-493 (2003). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed

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