論文

• Jiyuan Yang, Kengo Sato, Martin Loza, Sung-Joon Park, Kenta Nakai. RNA secondary structure prediction by conducting multi-class classifications, Computational and Structural Biotechnology Journal, 2025.  公式リンク  
  
• Manato Akiyama, Yasubumi Sakakibara, Kengo Sato. Direct Inference of Base-Pairing Probabilities with Neural Networks Improves Prediction of RNA Secondary Structures with Pseudoknots, Genes, Nov. 2022.  公式リンク  
  
• Shunya Kashiwagi, Kengo Sato, Yasubumi Sakakibara. A Max-Margin Model for Predicting Residue—Base Contacts in Protein–RNA Interactions, Life, Oct. 2021.  公式リンク  
  
• Akito Taneda, Kengo Sato. A Web Server for Designing Molecular Switches Composed of Two Interacting RNAs, International Journal of Molecular Sciences, Vol. 22, No. 5, pp. 2720, Mar. 2021.  公式リンク  
  
• Kengo Sato, Manato Akiyama, Yasubumi Sakakibara. RNA secondary structure prediction using deep learning with thermodynamic integration, Nature Communications, Feb. 2021.  公式リンク  
  
• Kengo Sato. An accessibility-incorporated method for accurate prediction of RNA--RNA interactions from sequence data, Bioinformatics, pp. btw603, 2016.
• Kengo Sato. Generation of a nonhuman primate model of severe combined immunodeficiency using highly efficient genome editing, Cell Stem Cell, Vol. 19, No. 1, pp. 127-138, 2016.
• Inatsuki, T., Sato, K., Sakakibara, Y., Kengo Sato. Prediction of gene structures from RNA-seq data using dual decomposition, IPSJ Transactions on Bioinformatics, Vol. 9, pp. 1-6, 2016.  公式リンク  
  
• Kengo Sato. Rtools: a web server for various secondary structural analyses on single RNA sequences, Nucleic acids research, pp. gkw337, 2016.
• Tsuchiya, M., Amano, K., Abe, M., Seki, M., Hase, S., Sato, K., Sakakibara, Y., Kengo Sato. SHARAKU: An algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing, Bioinformatics, Vol. 32, No. 12, pp. i369-i377, 2016.  公式リンク  
  
• Kumozaki, S., Sato, K., Sakakibara, Y., Kengo Sato. A Machine Learning Based Approach to de novo Sequencing of Glycans from Tandem Mass Spectrometry Spectrum, IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 12, No. 6, pp. 1267-1274, 2015.  公式リンク  
  
• Afiahayati, Sato, K., Sakakibara, Y., Kengo Sato. MetaVelvet-SL: An extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning, DNA Research, Vol. 22, No. 1, pp. 69-77, 2015.  公式リンク  
  
• Sato, K., Kuroki, Y., Kumita, W., Fujiyama, A., Toyoda, A., Kawai, J., Iriki, A., Sasaki, E., Okano, H., Sakakibara, Y., Kengo Sato. Resequencing of the common marmoset genome improves genome assemblies and gene-coding sequence analysis, Scientific Reports, Vol. 5, 2015.  公式リンク  
  
• Kamada, M., Hase, S., Fujii, K., Miyake, M., Sato, K., Kimura, K., Sakakibara, Y., Kengo Sato. Whole-genome sequencing and comparative genome analysis of bacillus subtilis strains isolated from non-salted fermented soybean foods, PLoS ONE, Vol. 10, No. 10, 2015.  公式リンク  
  
• Kamada, M., Hase, S., Sato, K., Toyoda, A., Fujiyama, A., Sakakibara, Y., Kengo Sato. Whole genome complete resequencing of Bacillus subtilis natto by combining long reads with high-quality short reads, PLoS ONE, Vol. 9, No. 10, 2014.  公式リンク  
  
• Afiahayati, Sato, K., Sakakibara, Y., Kengo Sato. An extended genovo metagenomic assembler by incorporating paired-end information, PeerJ, Vol. 2013, No. 1, 2013.  公式リンク  
  
• Nakamura, M., Hachiya, T., Saito, Y., Sato, K., Sakakibara, Y., Kengo Sato. An efficient algorithm for de novo predictions of biochemical pathways between chemical compounds., BMC bioinformatics, Vol. 13 Suppl 17, 2012.  公式リンク  
  
• Sakakibara, Y., Hachiya, T., Uchida, M., Nagamine, N., Sugawara, Y., Yokota, M., Nakamura, M., Popendorf, K., Komori, T., Sato, K., Kengo Sato. COPICAT: A software system for predicting interactions between proteins and chemical compounds, Bioinformatics, Vol. 28, No. 5, pp. 745-746, 2012.  公式リンク  
  
• Sato, K., Kato, Y., Akutsu, T., Asai, K., Sakakibara, Y., Kengo Sato. DAFS: Simultaneous aligning and folding of RNA sequences via dual decomposition, Bioinformatics, Vol. 28, No. 24, pp. 3218-3224, 2012.  公式リンク  
  
• Kato, Y., Sato, K., Asai, K., Akutsu, T., Kengo Sato. Rtips: Fast and accurate tools for RNA 2D structure prediction using integer programming, Nucleic Acids Research, Vol. 40, No. W1, 2012.  公式リンク  
  
• Kiełbasa, S.M., Wan, R., Sato, K., Horton, P., Frith, M.C., Kengo Sato. Adaptive seeds tame genomic sequence comparison, Genome Research, Vol. 21, No. 3, pp. 487-493, 2011.  公式リンク  
  
• Hamada, M., Yamada, K., Sato, K., Frith, M.C., Asai, K., Kengo Sato. CentroidHomfold-LAST: Accurate prediction of RNA secondary structure using automatically collected homologous sequences, Nucleic Acids Research, Vol. 39, No. SUPPL. 2, 2011.  公式リンク  
  
• Saito, Y., Sato, K., Sakakibara, Y., Kengo Sato. Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures, BMC Bioinformatics, Vol. 12, No. SUPPL. 1, 2011.  公式リンク  
  
• Sato, K., Kato, Y., Hamada, M., Akutsu, T., Asai, K., Kengo Sato. IPknot: Fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming, Bioinformatics, Vol. 27, No. 13, 2011.  公式リンク  
  
• Okada, Y., Saito, Y., Sato, K., Sakakibara, Y., Kengo Sato. Improved measurements of RNA structure conservation with generalized centroid estimators, Frontiers in Genetics, Vol. 2, No. AUG, 2011.  公式リンク  
  
• Hamada, M., Sato, K., Asai, K., Kengo Sato. Improving the accuracy of predicting secondary structure for aligned RNA sequences, Nucleic Acids Research, Vol. 39, No. 2, pp. 393-402, 2011.  公式リンク  
  
• Kato, Y., Sato, K., Hamada, M., Watanabe, Y., Asai, K., Akutsu, T., Kengo Sato. RactIP: Fast and accurate prediction of RNA-RNA interaction using integer programming, Bioinformatics, Vol. 27, No. 13, pp. i460-i466, 2011.  公式リンク  
  
• Poolsap, U., Kato, Y., Sato, K., Akutsu, T., Kengo Sato. Using binding profiles to predict binding sites of target RNA<inf>s</inf>, Journal of Bioinformatics and Computational Biology, Vol. 9, No. 6, pp. 697-713, 2011.  公式リンク  
  
• Sato, K., Hamada, M., Mituyama, T., Asai, K., Sakakibara, Y., Kengo Sato. A non-parametric bayesian approach for predicting rna secondary structures, Journal of Bioinformatics and Computational Biology, Vol. 8, No. 4, pp. 727-742, 2010.  公式リンク  
  
• Hamada, M., Sato, K., Asai, K., Kengo Sato. Prediction of RNA secondary structure by maximizing pseudo-expected accuracy, BMC Bioinformatics, Vol. 11, 2010.  公式リンク  
  
• Saito, Y., Sato, K., Sakakibara, Y., Kengo Sato. Robust and accurate prediction of noncoding RNAs from aligned sequences, BMC Bioinformatics, Vol. 11, No. SUPPL. 7, 2010.  公式リンク  
  
• Hamada, M., Sato, K., Kiryu, H., Mituyama, T., Asai, K., Kengo Sato. CentroidAlign: Fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score, Bioinformatics, Vol. 25, No. 24, pp. 3236-3243, 2009.  公式リンク  
  
• Sato, K., Hamada, M., Asai, K., Mituyama, T., Kengo Sato. CentroidFold: A web server for RNA secondary structure prediction, Nucleic Acids Research, Vol. 37, No. SUPPL. 2, 2009.  公式リンク  
  
• Morita, K., Saito, Y., Sato, K., Oka, K., Hotta, K., Sakakibara, Y., Kengo Sato. Genome-wide searching with base-pairing kernel functions for noncoding RNAs: Computational and expression analysis of snoRNA families in Caenorhabditis elegans, Nucleic Acids Research, Vol. 37, No. 3, pp. 999-1009, 2009.  公式リンク  
  
• Sato, K., Saito, Y., Sakakibara, Y., Kengo Sato. Gradient-based optimization of hyperparameters for base-pairing profile local alignment kernels., Genome informatics. International Conference on Genome Informatics, Vol. 23, No. 1, pp. 128-138, 2009.  公式リンク  
  
• Hamada, M., Kiryu, H., Sato, K., Mituyama, T., Asai, K., Kengo Sato. Prediction of RNA secondary structure using generalized centroid estimators, Bioinformatics, Vol. 25, No. 4, pp. 465-473, 2009.  公式リンク  
  
• Hamada, M., Sato, K., Kiryu, H., Mituyama, T., Asai, K., Kengo Sato. Predictions of RNA secondary structure by combining homologous sequence information, Bioinformatics, Vol. 25, No. 12, 2009.  公式リンク  
  
• Sato, K., Mituyama, T., Asai, K., Sakakibara, Y., Kengo Sato. Directed acyclic graph kernels for structural RNA analysis, BMC Bioinformatics, Vol. 9, 2008.  公式リンク  
  
• Sato, K., Morita, K., Sakakibara, Y., Kengo Sato. PSSMTS: Position specific scoring matrices on tree structures, Journal of Mathematical Biology, Vol. 56, No. 1-2, pp. 201-214, 2008.  公式リンク  
  
• Asai, K., Kiryu, H., Hamada, M., Tabei, Y., Sato, K., Matsui, H., Sakakibara, Y., Terai, G., Mituyama, T., Kengo Sato. Software.ncrna.org: web servers for analyses of RNA sequences., Nucleic acids research, Vol. 36, No. Web Server issue, 2008.  公式リンク  
  
• Sakakibara, Y., Popendorf, K., Ogawa, N., Asai, K., Sato, K., Kengo Sato. Stem kernels for RNA sequence analyses, Journal of Bioinformatics and Computational Biology, Vol. 5, No. 5, pp. 1103-1122, 2007.  公式リンク  
  
• Matsui, H., Sato, K., Sakakibara, Y., Kengo Sato. Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures, Bioinformatics, Vol. 21, No. 11, pp. 2611-2617, 2005.  公式リンク  
  
• Sato, K., Sakakibara, Y., Kengo Sato. RNA secondary structural alignment with conditional random fields, Bioinformatics, Vol. 21, No. SUPPL. 2, 2005.  公式リンク  
  
• Matsui, H., Sato, K., Sakakibara, Y., Kengo Sato. Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures., Proceedings / IEEE Computational Systems Bioinformatics Conference, CSB. IEEE Computational Systems Bioinformatics Conference., pp. 290-299, 2004.  公式リンク  
  

著書

• Sato, K., Hamada, M., Mituyama, T., Asai, K., Sakakibara, Y., Kengo Sato. A non-parametric bayesian approach for predicting RNA secondary structures, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Vol. 5724 LNBI, pp. 286-297, 2009.  公式リンク  
• Sakakibara, Y., Kobayashi, S., Sato, K., Nishino, T., Tomita, E., Kengo Sato. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Vol. 4201 LNAI, 2006.  公式リンク  

国際会議発表 (査読有り)

• Sato, K., Whitington, T., Bailey, T.L., Horton, P., Kengo Sato. Improved prediction of transcription binding sites from chromatin modification data, 2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2010, pp. 220-226, 2010.  公式リンク  
  
• Okada, Y., Sato, K., Sakakibara, Y., Kengo Sato. Improvement of structure conservation index with centroid estimators, Pacific Symposium on Biocomputing 2010, PSB 2010, pp. 88-97, 2010.  公式リンク  
  
• Sakakibara, Y., Asai, K., Sato, K., Kengo Sato. Stem kernels for RNA sequence analyses, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Vol. 4414 LNBI, pp. 278-291, 2007.  公式リンク  
  

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