"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,
"Manato Akiyama,Yasubumi Sakakibara,Kengo Sato","Direct Inference of Base-Pairing Probabilities with Neural Networks Improves Prediction of RNA Secondary Structures with Pseudoknots",,"Genes",,,,,2022,Nov.
"Shunya Kashiwagi,Kengo Sato,Yasubumi Sakakibara","A Max-Margin Model for Predicting Residue?Base Contacts in Protein?RNA Interactions",,"Life",,,,,2021,Oct.
"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",2021,Mar.
"Kengo Sato,Manato Akiyama,Yasubumi Sakakibara","RNA secondary structure prediction using deep learning with thermodynamic integration",,"Nature Communications",,,,,2021,Feb.
"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,
"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,
"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,
"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,
"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,
"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,
"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,
"Afiahayati,Sato, K.,Sakakibara, Y.,Kengo Sato","An extended genovo metagenomic assembler by incorporating paired-end information",,"PeerJ",,"Vol. 2013","No. 1",,2013,
"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,
"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,
"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,
"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,
"Kie?basa, 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,
"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,
"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,
"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,
"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,
"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,
"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,
"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,
"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,
"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,
"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,
"Hamada, M.,Sato, K.,Asai, K.,Kengo Sato","Prediction of RNA secondary structure by maximizing pseudo-expected accuracy",,"BMC Bioinformatics",,"Vol. 11",,,2010,
"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,
"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,
"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,
"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,
"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,
"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,
"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,
"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,
"Sato, K.,Mituyama, T.,Asai, K.,Sakakibara, Y.,Kengo Sato","Directed acyclic graph kernels for structural RNA analysis",,"BMC Bioinformatics",,"Vol. 9",,,2008,
"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,
"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,
"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,
"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,
"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,
"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,
"Sato, K.,Sakakibara, Y.,Kengo Sato","RNA secondary structural alignment with conditional random fields",,"Bioinformatics",,"Vol. 21","No. SUPPL. 2",,2005,
"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,