Research Topics
| Yasubumi SakakibaraSummaryAffiliation: Keio University Country: Japan Publications
| Collaborators
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Detail Information
Publications
Grammatical inference in bioinformaticsYasubumi Sakakibara
Department of Biosciences and Informatics, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Yokohama, 223 8522, Japan
IEEE Trans Pattern Anal Mach Intell 27:1051-62. 2005....- COPICAT: a software system for predicting interactions between proteins and chemical compoundsYasubumi Sakakibara
Biosciences and Informatics, Keio University, 3 14 1 Hiyoshi, Yokohama 223 8522, Japan
Bioinformatics 28:745-6. 2012..dna.bio.keio.ac.jp. All functions, including the prediction function are freely available via anonymous login without registration. Registered users, however, can use the system more intensively... - Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read dataYukari Nishito
Department of Biosciences and Informatics, Keio University, Hiyoshi, Kohoku Ku, Yokohama, Japan
BMC Genomics 11:243. 2010..subtilis natto, from very short read data is more challenging, particularly with our aim to assemble one fully connected scaffold from short reads around 35 bp in length... - 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... - Pair hidden Markov models on tree structuresYasubumi Sakakibara
Department of Biosciences and Informatics, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Yokohama, 223 8522, Japan
Bioinformatics 19:i232-40. 2003..We demonstrate some computational experiments to show the effectiveness of our method for structural alignments, and discuss a complexity issue of PHMMTSs... - 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... - [Development of a large-scale comparative genome system and its application to the analysis of mycobacteria genomes]Yasubumi Sakakibara
Department of Biosciences and Informatics, Keio University, Japan
Nihon Hansenbyo Gakkai Zasshi 76:251-6. 2007..g. three mammal chromosomes) in a matter of minutes. We also demonstrate an application of Murasaki to the comparative analysis of multiple mycobacteria genomes... - Integrating statistical predictions and experimental verifications for enhancing protein-chemical interaction predictions in virtual screeningNobuyoshi Nagamine
Department of Biosciences and Informatics, Keio University, Yokohama, Japan
PLoS Comput Biol 5:e1000397. 2009.... - 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... - 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... - 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... - 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... - Accurate identification of orthologous segments among multiple genomesTsuyoshi Hachiya
Department of Biosciences and Informatics, Keio University, Seikei University, Japan
Bioinformatics 25:853-60. 2009..Although a number of algorithms for detecting orthologous segments have been proposed, none of them contain a framework for optimizing their parameter values... - 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... - Murasaki: a fast, parallelizable algorithm to find anchors from multiple genomesKris Popendorf
Department of Biosciences and Informatics, Keio University, Yokohama, Japan
PLoS ONE 5:e12651. 2010.... - Statistical prediction of protein chemical interactions based on chemical structure and mass spectrometry dataNobuyoshi Nagamine
Department of Biosciences and Informatics, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Yokohama, Japan
Bioinformatics 23:2004-12. 2007..In this field, 3D structure-based methods such as docking analysis have been developed. However, the genomewide application of these methods is not really feasible as 3D structural information is limited in availability... - Identifying cooperative transcriptional regulations using protein-protein interactionsNobuyoshi Nagamine
Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
Nucleic Acids Res 33:4828-37. 2005..However, since a typical problem using protein-protein interaction data is that many false-positive data are contained, we propose a method combining various biological data to increase the prediction accuracy... - Construction of a genetic AND gate under a new standard for assembly of genetic partsShotaro Ayukawa
Department of Computational Intelligence and Systems Science, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, Midori ku, Yokohama, Kanagawa, Japan
BMC Genomics 11:S16. 2010..Thus, a standardized method for integrating operator sequences to the regulatory region of a plasmid is required... - 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... - SAMSCOPE: an OpenGL-based real-time interactive scale-free SAM viewerKris Popendorf
Biosciences and Informatics, Keio University, 3 14 1 Hiyoshi, Yokohama, 223 8522, Japan
Bioinformatics 28:1276-7. 2012..Availability and implementation: The SAMSCOPE software, implemented in C++ for Linux, with source code, binary packages and documentation are freely available from http://samscope.dna.bio.keio.ac.jp. CONTACT: yasu@bio.keio.ac.jp... - The Dugesia ryukyuensis database as a molecular resource for studying switching of the reproductive systemHideyuki Ishizuka
Department of Biological Sciences and Informatics, Keio University, Hiyoshi, Yokohama, Japan
Zoolog Sci 24:31-7. 2007..bio.keio.ac.jp/planaria/) is an open-access, online resource providing access to sequence, classification, clustering, and annotation data. This database should constitute a powerful tool for analyzing sexualization in planarians... - 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...