@book{CTT100937988,
  author = {Sato, K. and Hamada, M. and Mituyama, T. and Asai, K. and Sakakibara, Y. and Kengo Sato},
  title = {A non-parametric bayesian approach for predicting RNA secondary structures},
  publisher = {},
  year = 2009,
}

@book{CTT100938000,
  author = {Sakakibara, Y. and Kobayashi, S. and Sato, K. and Nishino, T. and Tomita, E. and Kengo Sato},
  title = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface},
  publisher = {},
  year = 2006,
}

@article{CTT100937955,
  author = {Jiyuan Yang and Kengo Sato and Martin Loza and Sung-Joon Park and Kenta Nakai},
  title = {RNA secondary structure prediction by conducting multi-class classifications},
  journal = {Computational and Structural Biotechnology Journal},
  year = 2025,
}

@article{CTT100937956,
  author = {Manato Akiyama and Yasubumi Sakakibara and Kengo Sato},
  title = {Direct Inference of Base-Pairing Probabilities with Neural Networks Improves Prediction of RNA Secondary Structures with Pseudoknots},
  journal = {Genes},
  year = 2022,
}

@article{CTT100937957,
  author = {Shunya Kashiwagi and Kengo Sato and Yasubumi Sakakibara},
  title = {A Max-Margin Model for Predicting Residue—Base Contacts in Protein–RNA Interactions},
  journal = {Life},
  year = 2021,
}

@article{CTT100937958,
  author = {Akito Taneda and Kengo Sato},
  title = {A Web Server for Designing Molecular Switches Composed of Two Interacting RNAs},
  journal = {International Journal of Molecular Sciences},
  year = 2021,
}

@article{CTT100937959,
  author = {Kengo Sato and Manato Akiyama and Yasubumi Sakakibara},
  title = {RNA secondary structure prediction using deep learning with thermodynamic integration},
  journal = {Nature Communications},
  year = 2021,
}

@article{CTT100937960,
  author = {Kengo Sato},
  title = {An accessibility-incorporated method for accurate prediction of RNA--RNA interactions from sequence data},
  journal = {Bioinformatics},
  year = 2016,
}

@article{CTT100937961,
  author = {Kengo Sato},
  title = {Generation of a nonhuman primate model of severe combined immunodeficiency using highly efficient genome editing},
  journal = {Cell Stem Cell},
  year = 2016,
}

@article{CTT100937962,
  author = {Inatsuki, T. and Sato, K. and Sakakibara, Y. and Kengo Sato},
  title = {Prediction of gene structures from RNA-seq data using dual decomposition},
  journal = {IPSJ Transactions on Bioinformatics},
  year = 2016,
}

@article{CTT100937963,
  author = {Kengo Sato},
  title = {Rtools: a web server for various secondary structural analyses on single RNA sequences},
  journal = {Nucleic acids research},
  year = 2016,
}

@article{CTT100937964,
  author = {Tsuchiya, M. and Amano, K. and Abe, M. and Seki, M. and Hase, S. and Sato, K. and Sakakibara, Y. and Kengo Sato},
  title = {SHARAKU: An algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing},
  journal = {Bioinformatics},
  year = 2016,
}

@article{CTT100937965,
  author = {Kumozaki, S. and Sato, K. and Sakakibara, Y. and Kengo Sato},
  title = {A Machine Learning Based Approach to de novo Sequencing of Glycans from Tandem Mass Spectrometry Spectrum},
  journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics},
  year = 2015,
}

@article{CTT100937966,
  author = {Afiahayati and Sato, K. and Sakakibara, Y. and Kengo Sato},
  title = {MetaVelvet-SL: An extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning},
  journal = {DNA Research},
  year = 2015,
}

@article{CTT100937967,
  author = {Sato, K. and Kuroki, Y. and Kumita, W. and Fujiyama, A. and Toyoda, A. and Kawai, J. and Iriki, A. and Sasaki, E. and Okano, H. and Sakakibara, Y. and Kengo Sato},
  title = {Resequencing of the common marmoset genome improves genome assemblies and gene-coding sequence analysis},
  journal = {Scientific Reports},
  year = 2015,
}

@article{CTT100937968,
  author = {Kamada, M. and Hase, S. and Fujii, K. and Miyake, M. and Sato, K. and Kimura, K. and Sakakibara, Y. and Kengo Sato},
  title = {Whole-genome sequencing and comparative genome analysis of bacillus subtilis strains isolated from non-salted fermented soybean foods},
  journal = {PLoS ONE},
  year = 2015,
}

@article{CTT100937969,
  author = {Kamada, M. and Hase, S. and Sato, K. and Toyoda, A. and Fujiyama, A. and Sakakibara, Y. and Kengo Sato},
  title = {Whole genome complete resequencing of Bacillus subtilis natto by combining long reads with high-quality short reads},
  journal = {PLoS ONE},
  year = 2014,
}

@article{CTT100937970,
  author = {Afiahayati and Sato, K. and Sakakibara, Y. and Kengo Sato},
  title = {An extended genovo metagenomic assembler by incorporating paired-end information},
  journal = {PeerJ},
  year = 2013,
}

@article{CTT100937971,
  author = {Nakamura, M. and Hachiya, T. and Saito, Y. and Sato, K. and Sakakibara, Y. and Kengo Sato},
  title = {An efficient algorithm for de novo predictions of biochemical pathways between chemical compounds.},
  journal = {BMC bioinformatics},
  year = 2012,
}

@article{CTT100937972,
  author = {Sakakibara, Y. and Hachiya, T. and Uchida, M. and Nagamine, N. and Sugawara, Y. and Yokota, M. and Nakamura, M. and Popendorf, K. and Komori, T. and Sato, K. and Kengo Sato},
  title = {COPICAT: A software system for predicting interactions between proteins and chemical compounds},
  journal = {Bioinformatics},
  year = 2012,
}

@article{CTT100937973,
  author = {Sato, K. and Kato, Y. and Akutsu, T. and Asai, K. and Sakakibara, Y. and Kengo Sato},
  title = {DAFS: Simultaneous aligning and folding of RNA sequences via dual decomposition},
  journal = {Bioinformatics},
  year = 2012,
}

@article{CTT100937974,
  author = {Kato, Y. and Sato, K. and Asai, K. and Akutsu, T. and Kengo Sato},
  title = {Rtips: Fast and accurate tools for RNA 2D structure prediction using integer programming},
  journal = {Nucleic Acids Research},
  year = 2012,
}

@article{CTT100937975,
  author = {Kiełbasa, S.M. and Wan, R. and Sato, K. and Horton, P. and Frith, M.C. and Kengo Sato},
  title = {Adaptive seeds tame genomic sequence comparison},
  journal = {Genome Research},
  year = 2011,
}

@article{CTT100937976,
  author = {Hamada, M. and Yamada, K. and Sato, K. and Frith, M.C. and Asai, K. and Kengo Sato},
  title = {CentroidHomfold-LAST: Accurate prediction of RNA secondary structure using automatically collected homologous sequences},
  journal = {Nucleic Acids Research},
  year = 2011,
}

@article{CTT100937977,
  author = {Saito, Y. and Sato, K. and Sakakibara, Y. and Kengo Sato},
  title = {Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures},
  journal = {BMC Bioinformatics},
  year = 2011,
}

@article{CTT100937978,
  author = {Sato, K. and Kato, Y. and Hamada, M. and Akutsu, T. and Asai, K. and Kengo Sato},
  title = {IPknot: Fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming},
  journal = {Bioinformatics},
  year = 2011,
}

@article{CTT100937979,
  author = {Okada, Y. and Saito, Y. and Sato, K. and Sakakibara, Y. and Kengo Sato},
  title = {Improved measurements of RNA structure conservation with generalized centroid estimators},
  journal = {Frontiers in Genetics},
  year = 2011,
}

@article{CTT100937980,
  author = {Hamada, M. and Sato, K. and Asai, K. and Kengo Sato},
  title = {Improving the accuracy of predicting secondary structure for aligned RNA sequences},
  journal = {Nucleic Acids Research},
  year = 2011,
}

@article{CTT100937981,
  author = {Kato, Y. and Sato, K. and Hamada, M. and Watanabe, Y. and Asai, K. and Akutsu, T. and Kengo Sato},
  title = {RactIP: Fast and accurate prediction of RNA-RNA interaction using integer programming},
  journal = {Bioinformatics},
  year = 2011,
}

@article{CTT100937982,
  author = {Poolsap, U. and Kato, Y. and Sato, K. and Akutsu, T. and Kengo Sato},
  title = {Using binding profiles to predict binding sites of target RNA<inf>s</inf>},
  journal = {Journal of Bioinformatics and Computational Biology},
  year = 2011,
}

@article{CTT100937983,
  author = {Sato, K. and Hamada, M. and Mituyama, T. and Asai, K. and Sakakibara, Y. and Kengo Sato},
  title = {A non-parametric bayesian approach for predicting rna secondary structures},
  journal = {Journal of Bioinformatics and Computational Biology},
  year = 2010,
}

@article{CTT100937986,
  author = {Hamada, M. and Sato, K. and Asai, K. and Kengo Sato},
  title = {Prediction of RNA secondary structure by maximizing pseudo-expected accuracy},
  journal = {BMC Bioinformatics},
  year = 2010,
}

@article{CTT100937987,
  author = {Saito, Y. and Sato, K. and Sakakibara, Y. and Kengo Sato},
  title = {Robust and accurate prediction of noncoding RNAs from aligned sequences},
  journal = {BMC Bioinformatics},
  year = 2010,
}

@article{CTT100937989,
  author = {Hamada, M. and Sato, K. and Kiryu, H. and Mituyama, T. and Asai, K. and Kengo Sato},
  title = {CentroidAlign: Fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score},
  journal = {Bioinformatics},
  year = 2009,
}

@article{CTT100937990,
  author = {Sato, K. and Hamada, M. and Asai, K. and Mituyama, T. and Kengo Sato},
  title = {CentroidFold: A web server for RNA secondary structure prediction},
  journal = {Nucleic Acids Research},
  year = 2009,
}

@article{CTT100937991,
  author = {Morita, K. and Saito, Y. and Sato, K. and Oka, K. and Hotta, K. and Sakakibara, Y. and Kengo Sato},
  title = {Genome-wide searching with base-pairing kernel functions for noncoding RNAs: Computational and expression analysis of snoRNA families in Caenorhabditis elegans},
  journal = {Nucleic Acids Research},
  year = 2009,
}

@article{CTT100937992,
  author = {Sato, K. and Saito, Y. and Sakakibara, Y. and Kengo Sato},
  title = {Gradient-based optimization of hyperparameters for base-pairing profile local alignment kernels.},
  journal = {Genome informatics. International Conference on Genome Informatics},
  year = 2009,
}

@article{CTT100937993,
  author = {Hamada, M. and Kiryu, H. and Sato, K. and Mituyama, T. and Asai, K. and Kengo Sato},
  title = {Prediction of RNA secondary structure using generalized centroid estimators},
  journal = {Bioinformatics},
  year = 2009,
}

@article{CTT100937994,
  author = {Hamada, M. and Sato, K. and Kiryu, H. and Mituyama, T. and Asai, K. and Kengo Sato},
  title = {Predictions of RNA secondary structure by combining homologous sequence information},
  journal = {Bioinformatics},
  year = 2009,
}

@article{CTT100937995,
  author = {Sato, K. and Mituyama, T. and Asai, K. and Sakakibara, Y. and Kengo Sato},
  title = {Directed acyclic graph kernels for structural RNA analysis},
  journal = {BMC Bioinformatics},
  year = 2008,
}

@article{CTT100937996,
  author = {Sato, K. and Morita, K. and Sakakibara, Y. and Kengo Sato},
  title = {PSSMTS: Position specific scoring matrices on tree structures},
  journal = {Journal of Mathematical Biology},
  year = 2008,
}

@article{CTT100937997,
  author = {Asai, K. and Kiryu, H. and Hamada, M. and Tabei, Y. and Sato, K. and Matsui, H. and Sakakibara, Y. and Terai, G. and Mituyama, T. and Kengo Sato},
  title = {Software.ncrna.org: web servers for analyses of RNA sequences.},
  journal = {Nucleic acids research},
  year = 2008,
}

@article{CTT100937999,
  author = {Sakakibara, Y. and Popendorf, K. and Ogawa, N. and Asai, K. and Sato, K. and Kengo Sato},
  title = {Stem kernels for RNA sequence analyses},
  journal = {Journal of Bioinformatics and Computational Biology},
  year = 2007,
}

@article{CTT100938001,
  author = {Matsui, H. and Sato, K. and Sakakibara, Y. and Kengo Sato},
  title = {Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures},
  journal = {Bioinformatics},
  year = 2005,
}

@article{CTT100938002,
  author = {Sato, K. and Sakakibara, Y. and Kengo Sato},
  title = {RNA secondary structural alignment with conditional random fields},
  journal = {Bioinformatics},
  year = 2005,
}

@article{CTT100938003,
  author = {Matsui, H. and Sato, K. and Sakakibara, Y. and Kengo Sato},
  title = {Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures.},
  journal = {Proceedings / IEEE Computational Systems Bioinformatics Conference, CSB. IEEE Computational Systems Bioinformatics Conference.},
  year = 2004,
}

@inproceedings{CTT100937984,
  author = {Sato, K. and Whitington, T. and Bailey, T.L. and Horton, P. and Kengo Sato},
  title = {Improved prediction of transcription binding sites from chromatin modification data},
  booktitle = {2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2010},
  year = 2010,
}

@inproceedings{CTT100937985,
  author = {Okada, Y. and Sato, K. and Sakakibara, Y. and Kengo Sato},
  title = {Improvement of structure conservation index with centroid estimators},
  booktitle = {Pacific Symposium on Biocomputing 2010, PSB 2010},
  year = 2010,
}

@inproceedings{CTT100937998,
  author = {Sakakibara, Y. and Asai, K. and Sato, K. and Kengo Sato},
  title = {Stem kernels for RNA sequence analyses},
  booktitle = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
  year = 2007,
}