2006 (Last Updated: 18th Oct., 2006)

Year: 2007 / 2006 / 2005 / 2004 / 2003 / 2002 / 2001

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• 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).
   


• 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).
   


• Chakkaravarthi, S., Babu, M.M., Gromiha, M.M., Jayaraman, G., Sethumadhavan, R.: "Exploring the environmental preference of weak interactions in (alpha/beta)8 barrel proteins", Proteins: Structure, Function, and Bioinformatics, 65(1), pp.75-86 (2006).
  


• 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).
  


• 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).
   


• 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).
   


• 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).
  


• 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).
  


• 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).
   


• 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).
   


• 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).
   


• 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).
   


• 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).
   


• 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).
   
• 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).
   


• 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).
   


• 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).
   


• Tomii, K.: "Protein Structure Prediction Using a Profile-Profile Comparison Method: FORTE", SEIBUTSU BUTSURI, 46(2), pp.106-110 (2006). (In Japanese)
  


• 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).
   


• 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).
   


• 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).
   


• 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).
   


• Chakkaravarthi, S., Gromiha, M.M.: "Analysis of cation-p interactions to the structural stability of RNA binding proteins", 47(2), pp. 709-721 (2006).
   


• 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).
   


• Kushida, T., Takagi, T., Fukuda, K.: "Event Ontology: A Pathway-Centric Ontology for Biological Processes", Pacific Symposium on Biocomputing, 11, pp.152-163 (2006).
  


• Kumar, M.D., Gromiha, M.M.: "PINT: Protein-protein Interactions Thermodynamic Database", Nucleic Acids Research, 34(Database issue), pp.D195-D198 (2006).
   


• 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).
   

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