Research Topics
| Kengo SatoSummaryAffiliation: Keio University Country: Japan Publications
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Detail Information
Publications
RNA secondary structural alignment with conditional random fieldsKengo Sato
Department of Biosciences and Informatics, Keio University, Hiyoshi Kohoku ku, Yokohama, Japan
Bioinformatics 21:ii237-42. 2005..Several methods have been proposed to accomplish the structural alignment tasks for RNA sequences, and we found that one of the most important points is to estimate an accurate score matrix for calculating structural alignments...- Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structuresHiroshi Matsui
Keio University, Department of Biosciences and Informatics, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
Bioinformatics 21:2611-7. 2005..We believe that our implemented program based on PSTAGs is the first grammar-based and practically executable software for comparative analyses of RNA pseudoknot structures, and, further, non-coding RNAs... - Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structuresYutaka Saito
Department of Biosciences and Informatics, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Yokohama, Kanagawa 223 8522, Japan
BMC Bioinformatics 12:S48. 2011..Such heuristics degrade the quality of clustering results, especially when the similarity among family members is not detectable at the primary sequence level... - Stem kernels for RNA sequence analysesYasubumi Sakakibara
Department of Biosciences and Informatics, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Yokohama, Kanagawa 223 8522, Japan
J Bioinform Comput Biol 5:1103-22. 2007..This is because the string kernel is proven to work for the remote homology detection of protein sequences. These experimental results have convinced us to apply the stem kernel in order to find novel RNA families from genome sequences... - Robust and accurate prediction of noncoding RNAs from aligned sequencesYutaka Saito
Department of Biosciences and Informatics, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Yokohama, Kanagawa 223 8522, Japan
BMC Bioinformatics 11:S3. 2010..Therefore, the evaluation of the robustness against alignment errors is necessary as well as the development of accurate prediction methods... - Genome-wide searching with base-pairing kernel functions for noncoding RNAs: computational and expression analysis of snoRNA families in Caenorhabditis elegansKensuke Morita
Department of Biosciences and Informatics, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Yokohama, Kanagawa 223 8522, Japan
Nucleic Acids Res 37:999-1009. 2009..Finally, highly expressed six candidates were identified as the original target regions by DNA sequencing... - Improved measurements of RNA structure conservation with generalized centroid estimatorsYohei Okada
Department of Biosciences and Informatics, Keio University Yokohama, Japan
Front Genet 2:54. 2011..We conclude that our methods are more suitable for genome-wide alignments which are of low quality from the point of view on secondary structures than the original SCI and BPD... - Software.ncrna.org: web servers for analyses of RNA sequencesKiyoshi Asai
Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, 5 1 5 Kashiwa no ha, Chiba 277 8561, Japan
Nucleic Acids Res 36:W75-8. 2008..The servers are located at http://software.ncrna.org, along with the information for the evaluation and downloading. This website is freely available to all users and there is no login requirement... - PSSMTS: position specific scoring matrices on tree structuresKengo Sato
Japan Biological Informatics Consortium, 2 45 Aomi, Koto ku, Tokyo 135 8073, Japan
J Math Biol 56:201-14. 2008..Experimental results show that PSSMs enable us to find individual RNA families efficiently, especially if we have biological knowledge such as sequence motifs... - Directed acyclic graph kernels for structural RNA analysisKengo Sato
Japan Biological Informatics Consortium JBIC, 2 45 Aomi, Koto ku, Tokyo 135 8073, Japan
BMC Bioinformatics 9:318. 2008..However, applying stem kernels directly to large data sets of ncRNAs is impractical due to their computational complexity...