Kihara, Daisuke - Purdue University - Department of Biological Sciences

个人简介

Ph.D., Kyoto University (Japan) BS., The University of Tokyo (Japan)

近期论文

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Yang, Y. D., Park, C., Kihara, D. 2008. Threading without optimizing weighting factors for scoring function. Proteins. in press. Hawkins, T., Chitale, M., Luban, S., Kihara, D. 2008. PFP: Automated prediction of gene ontology functional annotations with confidence scores using protein sequence data. Proteins. in press. view article Chen, H., Kihara, D. 2008. Estimating quality of template-based protein models by alignment stability. Proteins. 71: 1255-1274. Li, B., S. Turuvekere, M. Agrawal, D. La, K. Ramani, and D. Kihara. 2008. Characterization of local geometry of protein surfaces with the visibility criterion. Proteins. 71: 670-683. Hawkins, T., M. Chitale, and D. Kihara. 2008. New paradigm in protein function prediction for large scale omics analysis. Mol Biosyst. 4: 223-231. Hu, J. C., Aramayo, R., Bolser, D., Conway, T., Elsik, C. G., Gribskov, M., Kelder, T., Kihara, D., Knight, T. F., Pico, A. R., Siegele, D. A., Wanner, B. L., Welch, R. D. 2008. The emerging world of wikis. Science. 320: 1289-1290. Hawkins, T., Kihara, D. 2007. Function prediction of uncharacterized proteins. J Bioinform Comput Biol. 5: 1-30. Luban, S., Kihara, D. 2007. Comparative genomics of small RNAs in bacterial genomes. Omics-a Journal of Integrative Biology. 11: 58-73. Kihara, D., T. Hawkins, S. Luban, B. Li, K. Ramani, and M. Agrawal. 2007. Protein function prediction in proteomics era. Frontiers Comput Sci. 143-148. Hawkins, T., Luban, S., Kihara, D. 2006. Enhanced automated function prediction using distantly related sequences and contextual association by PFP. Protein Sci. 15: 1550-1556. Hu, J., Yang, Y. D., Kihara, D. 2006. EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences. BMC Bioinformatics. 7: 342. Kihara, D., Yang, Y. D., Hawkins, T. 2006. Bioinfornatics resources for cancer research with an emphasis in gene function and structure prediction tools. Cancer Informatics. 2: 25-35. Tan, Y. H., Huang, H., Kihara, D. 2006. Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences. Proteins. 64: 587-600. Hu, J., Li, B., Kihara, D. 2005. Limitations and potentials of current motif discovery algorithms. Nucleic Acids Res. 33: 4899-4913. Kihara, D. 2005. The effect of long-range interactions on the secondary structure formation of proteins. Protein Sci. 14: 1955-1963. Kihara, D., Skolnick, J. 2004. Microbial genomes have over 72% structure assignment by the threading algorithm PROSPECTOR_Q. Proteins. 55: 464-473. Skolnick, J., Kihara, D., Zhang, Y. 2004. Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm. Proteins. 56: 502-518. Turuvekere, S. S., Agrawal, M., Kihara, D., Ramani, K. 2004. Feature recognition based identification of potential binding sites on the molecular surfaces. Protein Science. 13: 68-68. Kihara, D., Skolnick, J. 2003. The PDB is a covering set of small protein structures. J Mol Biol. 334: 793-802. Li, W., Zhang, Y., Kihara, D., Huang, Y. J., Zheng, D., Montelione, G. T., Kolinski, A., Skolnick, J. 2003. TOUCHSTONEX: protein structure prediction with sparse NMR data. Proteins. 53: 290-306. Skolnick, J., Zhang, Y., Arakaki, A. K., Kolinski, A., Boniecki, M., Szilagyi, A., Kihara, D. 2003. TOUCHSTONE: a unified approach to protein structure prediction. Proteins. 53 Suppl 6: 469-479. Kihara, D., Zhang, Y., Lu, H., Kolinski, A., Skolnick, J. 2002. Ab initio protein structure prediction on a genomic scale: application to the Mycoplasma genitalium genome. Proc Natl Acad Sci U S A. 99: 5993-5998. Zhang, Y., Kihara, D., Skolnick, J. 2002. Local energy landscape flattening: parallel hyperbolic Monte Carlo sampling of protein folding. Proteins. 48: 192-201.