Publications

Kengo Sato, Michiaki Hamada (2023). Recent trends in RNA informatics: a review of machine learning and deep learning for RNA secondary structure prediction and RNA drug discovery. Brief. Bioinform., bbad186.

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Manato Akiyama, Kengo Sato (2023). RNA Secondary Structure Prediction Based on Energy Models. RNA Structure Prediction (Methods in Molecular Biology, Springer), 89–105.

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Manato Akiyama, Yasubumi Sakakibara, Kengo Sato (2022). Direct inference of base-pairing probabilities with neural networks improves prediction of RNA secondary structures with pseudoknots. Genes, 13(11):2155.

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Soichiro Nishiyama, Kengo Sato, Ryutaro Tao (2022). Integer programming for selecting set of informative markers in paternity inference. BMC Bioinformatics, 23:265.

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Kengo Sato, Yuki Kato (2022). Prediction of RNA secondary structure including pseudoknots for long sequences. Brief. Bioinform., 23(1), bbab395.

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Shunya Kashiwagi, Kengo Sato, Yasubumi Sakakibara (2021). A max-margin model for predicting residue-base contacts in protein-RNA interactions. Life, 11(11):1135.

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Akito Taneda, Kengo Sato (2021). A web server for designing molecular switches composed of two interacting RNAs. Int. J. Mol. Sci., 22(5):2720.

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Kengo Sato, Manato Akiyama, Yasubumi Sakakibara (2021). RNA secondary structure prediction using deep learning with thermodynamic integration. Nat. Commun., 12:941.

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Vasanthan Jayakumar, Hiromi Ishii, Misato Seki, Wakako Kumita, Takashi Inoue, Sumitaka Hase, Kengo Sato, Hideyuki Okano, Erika Sasaki, Yasubumi Sakakibara (2020). An improved de novo genome assembly of the common marmoset genome yields improved contiguity and increased mapping rates of sequence data. BMC Genomics, 21:243.

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Wakako Kumita, Kenya Sato, Yasuhiro Suzuki, Yoko Kurotaki, Takeshi Harada, Yang Zhou, Noriyuki Kishi, Kengo Sato, Atsu Aiba, Yasubumi Sakakibara, Guoping Feng, Hideyuki Okano, Erika Sasaki (2019). Efficient generation of Knock-in/Knock-out marmoset embryo via CRISPR/Cas9 gene editing. Sci. Rep., 9:12719.

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Maya Hirohara, Yutaka Saito, Yuki Koda, Kengo Sato, Yasubumi Sakakibara (2018). Convolutional neural network based on SMILES representation of compounds for detecting chemical motif. BMC Bioinformatics, 19:526.

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Manato Akiyama, Kengo Sato, Yasubumi Sakakibara (2018). A max-margin training of RNA secondary structure prediction integrated with the thermodynamic model. J. Bioinform. Comput. Biol., 16(6):1840025.

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Yoshimasa Aoto, Tsuyoshi Hachiya, Kazuhiro Okumura, Sumitaka Hase, Kengo Sato, Yuichi Wakabayashi, Yasubumi Sakakibara (2017). DEclust: A statistical approach for obtaining differential expression profiles of multiple conditions. PLoS One, 12(11):e0188285.

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Yuki Kato, Tomoya Mori, Kengo Sato, Shingo Maegawa, Hiroshi Hosokawa, Tatsuya Akutsu (2017). An accessibility-incorporated method for accurate prediction of RNA-RNA interactions from sequence data. Bioinformatics, 33(2):202-209.

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Michiaki Hamada, Yukiteru Ono, Hisanori Kiryu, Kengo Sato, Yuki Kato, Tsukasa Fukunaga, Ryota Mori, Kiyoshi Asai (2016). Rtools: a web server for various secondary structural analyses on single RNA sequences. Nucleic Acids Res., 44(W1):W302–W307.

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Kenya Sato, Ryo Oiwa, Wakako Kumita, Rachel Henry, Tetsushi Sakuma, Ryoji Ito, Ryoko Nozu, Takashi Inoue, Ikumi Katano, Kengo Sato, Norio Okahara, Junko Okahara, Yoshihisa Shimizu, Masafumi Yamamoto, Kisaburo Hanazawa, Takao Kawakami, Yoshie Kametani, Ryuji Suzuki, Takeshi Takahashi, Edward J Weinstein, Takashi Yamamoto, Yasubumi Sakakibara, Sonoko Habu, Jun-Ichi Hata, Hideyuki Okano, Erika Sasaki (2016). Generation of a Nonhuman Primate Model of Severe Combined Immunodeficiency Using Highly Efficient Genome Editing. Cell Stem Cell, 19(1):127-138.

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Mariko Tsuchiya, Kojiro Amano, Masaya Abe, Misato Seki, Sumitaka Hase, Kengo Sato, Yasubumi Sakakibara (2016). SHARAKU: an algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing. Bioinformatics, 32(12):i369-i377.

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Tatsumu Inatsuki, Kengo Sato, Yasubumi Sakakibara (2016). Prediction of Gene Structures from RNA-seq Data Using Dual Decomposition. IPSJ Transactions on Bioinformatics, 9:1-6.

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Kengo Sato, Yoko Kuroki, Wakako Kumita, Asao Fujiyama, Atsushi Toyoda, Jun Kawai, Atsushi Iriki, Erika Sasaki, Hideyuki Okano, Yasubumi Sakakibara (2015). Resequencing of the common marmoset genome improves genome assemblies and gene-coding sequence analysis. Sci. Rep., 5:16894.

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Shotaro Kumozaki, Kengo Sato, Yasubumi Sakakibara (2015). A Machine Learning Based Approach to de novo Sequencing of Glycans from Tandem Mass Spectrometry Spectrum. IEEE/ACM Trans. Comput. Biol. Bioinform., 12(6):1267-1274.

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Mayumi Kamada, Sumitaka Hase, Kazushi Fujii, Masato Miyake, Kengo Sato, Keitarou Kimura, Yasubumi Sakakibara (2015). Whole-Genome Sequencing and Comparative Genome Analysis of Bacillus subtilis Strains Isolated from Non-Salted Fermented Soybean Foods. PLoS One, 10(10):e0141369.

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Afiahayati, Kengo Sato, Yasubumi Sakakibara (2015). MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning. DNA Res., 22(1):69-77.

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Mayumi Kamada, Sumitaka Hase, Kengo Sato, Atsushi Toyoda, Asao Fujiyama, Yasubumi Sakakibara (2014). Whole genome complete resequencing of Bacillus subtilis natto by combining long reads with high-quality short reads. PLoS One, 9(10):e109999.

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Afiahayati, Kengo Sato, Yasubumi Sakakibara (2013). An extended genovo metagenomic assembler by incorporating paired-end information. PeerJ, 1:e196.

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Kengo Sato, Yuki Kato, Tatsuya Akutsu, Kiyoshi Asai, Yasubumi Sakakibara (2012). DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition. Bioinformatics, 28(24):3218-3224.

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Masaomi Nakamura, Tsuyoshi Hachiya, Yutaka Saito, Kengo Sato, Yasubumi Sakakibara (2012). An efficient algorithm for de novo predictions of biochemical pathways between chemical compounds. BMC Bioinformatics, 13:S8.

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Yuki Kato, Kengo Sato, Kiyoshi Asai, Tatsuya Akutsu (2012). Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming. Nucleic Acids Res., 40(W1):W29-W34.

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Yasubumi Sakakibara, Tsuyoshi Hachiya, Miho Uchida, Nobuyoshi Nagamine, Yohei Sugawara, Masahiro Yokota, Masaomi Nakamura, Kris Popendorf, Takashi Komori, Kengo Sato (2012). COPICAT: a software system for predicting interactions between proteins and chemical compounds. Bioinformatics, 28(5):745-746.

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Unyanee Poolsap, Yuki Kato, Kengo Sato, Tatsuya Akutsu (2011). Using binding profiles to predict binding sites of target RNAs. J. Bioinform. Comput. Biol., 9(6):697-713.

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Yohei Okada, Yutaka Saito, Kengo Sato, Yasubumi Sakakibara (2011). Improved measurements of RNA structure conservation with generalized centroid estimators. Front. Genet., 2:54.

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Kengo Sato, Yuki Kato, Michiaki Hamada, Tatsuya Akutsu, Kiyoshi Asai (2011). IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. Bioinformatics, 27(13):i85-i93.

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Michiaki Hamada, Koichiro Yamada, Kengo Sato, Martin C Frith, Kiyoshi Asai (2011). CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences. Nucleic Acids Res., 39(suppl 2):W100-W106.

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Szymon M Kiełbasa, Raymond Wan, Kengo Sato, Paul Horton, Martin C Frith (2011). Adaptive seeds tame genomic sequence comparison. Genome Res., 21:487-493.

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Yutaka Saito, Kengo Sato, Yasubumi Sakakibara (2011). Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures. BMC Bioinformatics, 12:S48.

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Michiaki Hamada, Kengo Sato, Kiyoshi Asai (2011). Improving the accuracy of predicting secondary structure for aligned RNA sequences. Nucleic Acids Res., 39(2):393-402.

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Michiaki Hamada, Kengo Sato, Kiyoshi Asai (2010). Prediction of RNA secondary structure by maximizing pseudo-expected accuracy. BMC Bioinformatics, 11:586.

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Yutaka Saito, Kengo Sato, Yasubumi Sakakibara (2010). Robust and accurate prediction of noncoding RNAs from aligned sequences. BMC Bioinformatics, 11:S3.

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Yuki Kato, Kengo Sato, Michiaki Hamada, Yoshihide Watanabe, Kiyoshi Asai, Tatsuya Akutsu (2010). RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming. Bioinformatics, 26(18):i460-i466.

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Kengo Sato, Michiaki Hamada, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara (2010). A non-parametric Bayesian approach for predicting RNA secondary structures. J. Bioinform. Comput. Biol., 8(4):727-742.

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Yohei Okada, Kengo Sato, Yasubumi Sakakibara (2010). Improvement of structure conservation index with centroid estimators. Pac. Symp. Biocomput. 2010, p. 88-97.

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Kengo Sato, Tom Whitington, Timothy L. Bailey, Paul Horton (2010). Improved prediction of transcription binding sites from chromatin modification data. Proceedings of the 2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2010, Montreal, QC, Canada, May 2-5, 2010.

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Kengo Sato, Yutaka Saito, Yasubumi Sakakibara (2009). Gradient-based optimization of hyperparameters for base-pairing profile local alignment kernels. Genome Inform. 2009, 128-138.

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Kengo Sato, Michiaki Hamada, Kiyoshi Asai, Toutai Mituyama (2009). CENTROIDFOLD: a web server for RNA secondary structure prediction. Nucleic Acids Res., 37(Suppl 2):W277-W280.

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Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama, Kiyoshi Asai (2009). Predictions of RNA secondary structure by combining homologous sequence information. Bioinformatics, 25(12):i330-i338.

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Michiaki Hamada, Hisanori Kiryu, Kengo Sato, Toutai Mituyama, Kiyoshi Asai (2009). Prediction of RNA secondary structure using generalized centroid estimators. Bioinformatics, 25(4):465–473.

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Kensuke Morita, Yutaka Saito, Kengo Sato, Kotaro Oka, Kohji Hotta, Yasubumi Sakakibara (2009). Genome-wide searching with base-pairing kernel functions for noncoding RNAs: computational and expression analysis of snoRNA families in Caenorhabditis elegans. Nucleic Acids Res., 37(3):999-1009.

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Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama, Kiyoshi Asai (2009). CentoroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score. Bioinformatics, 25(24):3236-43.

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Kiyoshi Asai, Hisanori Kiryu, Michiaki Hamada, Yasuo Tabei, Kengo Sato, Hiroshi Matsui, Yasubumi Sakakibara, Goro Terai, Toutai Mituyama (2008). Software.ncrna.org: web servers for analyses of RNA sequences. Nucleic Acids Res., 36(Suppl 2):W75–W78.

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Kengo Sato, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara (2008). Directed acyclic graph kernels for structural RNA analysis. BMC Bioinformatics, 9:318.

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Kengo Sato, Kensuke Morita, Yasubumi Sakakibara (2008). PSSMTS: position specific scoring matrices on tree structures. J. Math. Biol., 56:201–214.

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Yasubumi Sakakibara, Kris Popendorf, Nana Ogawa, Kiyoshi Asai, Kengo Sato (2007). Stem kernels for RNA sequence analyses. J. Bioinform. Comput. Biol., 5(5):1103-1122.

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Yasubumi Sakakibara, Kiyoshi Asai, Kengo Sato (2007). Stem Kernels for RNA Sequence Analyses. Bioinformatics Research and Development, First International Conference, BIRD 2007, pp 278–291, Berlin, Germany, March 12-14.

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Kengo Sato, Yasubumi Sakakibara (2005). RNA secondary structural alignment with conditional random fields. Bioinformatics, 21(Suppl 2):ii237–ii242.

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Hiroshi Matsui, Kengo Sato, Yasubumi Sakakibara (2005). Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures. Bioinformatics, 21(11):2611-2617.

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Hiroyuki Okamoto, Kengo Sato, Hiroaki Saito (2003). Preferential Presentation of Japanese Near-synonyms using Definition Statements. Proceedings of the Second International Workshop on Paraphrasing, pp. 17–24, IWP@ACL 2003, Sapporo, Japan, July 11, 2003.

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Kengo Sato, Hiroaki Saito (2002). Extracting Word Sequence Correspondences with Support Vector Machines. 19th International Conference on Computational Linguistics, COLING 2002, pp. 870–876, Howard International House and Academia Sinica, Taipei, Taiwan, August 24 - September 1, 2002.

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Kengo Sato, Masakazu Nakanishi (1998). Maximum Entropy Model Learning of the Translation Rules. 36th Annual Meeting of the Association for Computational Linguistics and 17th International Conference on Computational Linguistics, COLING-ACL ‘98, Pages 1171–1175, August 10-14, 1998, Université de Montréal, Montréal, Quebec, Canada.

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Shiho Nobesawa, Junya Tsutsumi, Sun Da Jiang, Tomohisa Sano, Kengo Sato, Masakazu Nakanishi (1996). Segmenting Sentences into Linky Strings Using D-bigram Statistics. 16th International Conference on Computational Linguistics, Proceedings of the Conference, COLING 1996, pp. 586–591, Center for Sprogteknologi, Copenhagen, Denmark, August 5-9, 1996.

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