Yasubumi Sakakibara

Summary

Affiliation: Keio University
Country: Japan

Publications

  1. ncbi request reprint Grammatical inference in bioinformatics
    Yasubumi 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
  2. pmc Comprehensive predictions of target proteins based on protein-chemical interaction using virtual screening and experimental verifications
    Hiroki Kobayashi
    Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Yokohama, 223 8522, Japan
    BMC Chem Biol 12:2. 2012
  3. pmc Improved measurements of RNA structure conservation with generalized centroid estimators
    Yohei Okada
    Department of Biosciences and Informatics, Keio University Yokohama, Japan
    Front Genet 2:54. 2011
  4. pmc Identifying cooperative transcriptional regulations using protein-protein interactions
    Nobuyoshi 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
  5. doi request reprint COPICAT: a software system for predicting interactions between proteins and chemical compounds
    Yasubumi Sakakibara
    Biosciences and Informatics, Keio University, 3 14 1 Hiyoshi, Yokohama 223 8522, Japan
    Bioinformatics 28:745-6. 2012
  6. pmc Directed acyclic graph kernels for structural RNA analysis
    Kengo Sato
    Japan Biological Informatics Consortium JBIC, 2 45 Aomi, Koto ku, Tokyo 135 8073, Japan
    BMC Bioinformatics 9:318. 2008
  7. ncbi request reprint Pair hidden Markov models on tree structures
    Yasubumi Sakakibara
    Department of Biosciences and Informatics, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Yokohama, 223 8522, Japan
    Bioinformatics 19:i232-40. 2003
  8. ncbi request reprint Stem kernels for RNA sequence analyses
    Yasubumi 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
  9. ncbi request reprint [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
  10. pmc Integrating statistical predictions and experimental verifications for enhancing protein-chemical interaction predictions in virtual screening
    Nobuyoshi Nagamine
    Department of Biosciences and Informatics, Keio University, Yokohama, Japan
    PLoS Comput Biol 5:e1000397. 2009

Collaborators

Detail Information

Publications36

  1. ncbi request reprint Grammatical inference in bioinformatics
    Yasubumi 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
    ....
  2. pmc Comprehensive predictions of target proteins based on protein-chemical interaction using virtual screening and experimental verifications
    Hiroki Kobayashi
    Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Yokohama, 223 8522, Japan
    BMC Chem Biol 12:2. 2012
    ....
  3. pmc Improved measurements of RNA structure conservation with generalized centroid estimators
    Yohei 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...
  4. pmc Identifying cooperative transcriptional regulations using protein-protein interactions
    Nobuyoshi 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...
  5. doi request reprint COPICAT: a software system for predicting interactions between proteins and chemical compounds
    Yasubumi Sakakibara
    Biosciences and Informatics, Keio University, 3 14 1 Hiyoshi, Yokohama 223 8522, Japan
    Bioinformatics 28:745-6. 2012
    ....
  6. pmc Directed acyclic graph kernels for structural RNA analysis
    Kengo 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...
  7. ncbi request reprint Pair hidden Markov models on tree structures
    Yasubumi Sakakibara
    Department of Biosciences and Informatics, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Yokohama, 223 8522, Japan
    Bioinformatics 19:i232-40. 2003
    ..Especially, the concept of Pair HMMs (PHMMs) have been examined extensively as mathematical models for alignments and gene finding...
  8. ncbi request reprint Stem kernels for RNA sequence analyses
    Yasubumi 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...
  9. ncbi request reprint [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...
  10. pmc Integrating statistical predictions and experimental verifications for enhancing protein-chemical interaction predictions in virtual screening
    Nobuyoshi Nagamine
    Department of Biosciences and Informatics, Keio University, Yokohama, Japan
    PLoS Comput Biol 5:e1000397. 2009
    ....
  11. ncbi request reprint Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures
    Hiroshi 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...
  12. ncbi request reprint RNA secondary structural alignment with conditional random fields
    Kengo 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...
  13. doi request reprint Accurate identification of orthologous segments among multiple genomes
    Tsuyoshi 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...
  14. pmc Genome-wide searching with base-pairing kernel functions for noncoding RNAs: computational and expression analysis of snoRNA families in Caenorhabditis elegans
    Kensuke 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...
  15. pmc Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures
    Yutaka 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...
  16. ncbi request reprint Statistical prediction of protein chemical interactions based on chemical structure and mass spectrometry data
    Nobuyoshi 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...
  17. pmc An efficient algorithm for de novo predictions of biochemical pathways between chemical compounds
    Masaomi Nakamura
    Biosciences and Informatics, Keio University, 3 14 1 Hiyoshi, Yokohama 223 8522, Japan
    BMC Bioinformatics 13:S8. 2012
    ....
  18. doi request reprint DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition
    Kengo Sato
    Department of Biosciences and Informatics, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Yokohama 223 8522, Japan
    Bioinformatics 28:3218-24. 2012
    ..To tackle this dilemma, we require a fast and accurate aligner that takes structural information into consideration to yield reliable structural alignments, which are suitable for common secondary structure prediction...
  19. pmc Robust and accurate prediction of noncoding RNAs from aligned sequences
    Yutaka 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...
  20. pmc Murasaki: a fast, parallelizable algorithm to find anchors from multiple genomes
    Kris Popendorf
    Department of Biosciences and Informatics, Keio University, Yokohama, Japan
    PLoS ONE 5:e12651. 2010
    ....
  21. doi request reprint SAMSCOPE: an OpenGL-based real-time interactive scale-free SAM viewer
    Kris Popendorf
    Biosciences and Informatics, Keio University, 3 14 1 Hiyoshi, Yokohama, Japan
    Bioinformatics 28:1276-7. 2012
    ..The extensive pre-processing and fast OpenGL interface of SAMSCOPE provides instantaneous and intuitive browsing of complex data at all levels of detail across multiple experiments...
  22. pmc MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads
    Toshiaki Namiki
    Department of Biosciences and Informatics, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Yokohama 223 8522, Japan
    Nucleic Acids Res 40:e155. 2012
    ..MetaVelvet also reconstructed relatively low-coverage genome sequences as scaffolds. On real datasets of human gut microbial read data, MetaVelvet produced longer scaffolds and increased the number of predicted genes...
  23. pmc Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data
    Yukari 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...
  24. pmc Resequencing of the common marmoset genome improves genome assemblies and gene-coding sequence analysis
    Kengo Sato
    Department of Biosciences and Informatics, Keio University, Japan
    Sci Rep 5:16894. 2015
    ....
  25. pmc Whole-Genome Sequencing and Comparative Genome Analysis of Bacillus subtilis Strains Isolated from Non-Salted Fermented Soybean Foods
    Mayumi Kamada
    Department of Biosciences and Informatics, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Yokohama 223 8522, Japan
    PLoS ONE 10:e0141369. 2015
    ....
  26. pmc Whole genome complete resequencing of Bacillus subtilis natto by combining long reads with high-quality short reads
    Mayumi Kamada
    Department of Biosciences and Informatics, Keio University, Kohoku Ku, Yokohama, Japan
    PLoS ONE 9:e109999. 2014
    ....
  27. pmc Construction of a genetic AND gate under a new standard for assembly of genetic parts
    Shotaro 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...
  28. ncbi request reprint Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures
    Hiroshi Matsui
    Department of Biosciences and Informatics, Keio University, Kohoku Ku, Yokohama, Japan
    Proc IEEE Comput Syst Bioinform Conf . 2004
    ..On the other hand, tree adjoining grammars (TAGs) is a subclass of context-sensitive grammar, which is suitable for modeling pseudoknots. Our goal is to extend PHMMTSs by incorporating TAGs to be able to handle pseudoknots...
  29. ncbi request reprint Improvement of structure conservation index with centroid estimators
    Yohei Okada
    Department of Biosciences and Informatics, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Yokohama, Kanagawa 223 8522, Japan
    Pac Symp Biocomput . 2010
    ..Furthermore, the accuracy of the C-SCI on CLUSTAL W alignments is comparable with that of the original SCI on structural alignments generated with RAF for which 4.7-fold expensive computational time is required on average...
  30. pmc SHARAKU: an algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing
    Mariko Tsuchiya
    Department of Biosciences and Informatics, Keio University, Yokohama 161 0031, Japan
    Bioinformatics 32:i369-i377. 2016
    ..Recent next-generation sequencing studies have revealed not only the typical maturation process of miRNAs but also the various processing mechanisms of small RNAs derived from tRNAs and snoRNAs...
  31. ncbi request reprint Discriminative discovery of transcription factor binding sites from location data
    Yuji Kawada
    Department of Biosciences and Informatics, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Yokohama, 223 8522, Japan
    Proc IEEE Comput Syst Bioinform Conf . 2005
    ..The availability of genome-wide location analyses based on chromatin immunoprecipitation (ChIP) data gives a new insight for in silico analysis of transcriptional regulations...
  32. pmc MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning
    - Afiahayati
    Department of Biosciences and Informatics, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Yokohama 223 8522, Japan
    DNA Res 22:69-77. 2015
    ....
  33. ncbi request reprint The Dugesia ryukyuensis database as a molecular resource for studying switching of the reproductive system
    Hideyuki 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...
  34. ncbi request reprint PSSMTS: position specific scoring matrices on tree structures
    Kengo 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...
  35. pmc Software.ncrna.org: web servers for analyses of RNA sequences
    Kiyoshi 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...