Publications

Refereed Journal Articles

  • Sato, K., Kuroki, Y., Kumita, W., Fujiyama, A., Toyoda, A., Kawai, J., Iriki, A., Sasaki, E., Okano, H., Sakakibara, Y.: Resequencing of the common marmoset genome improves genome assemblies and gene-coding sequence analysis, Scientific Reports, Vol.5, 16894 (Nov. 2015) [PubMed] [DOI]
  • Kamada, M., Hase, S., Fujii, K., Miyake, M., Sato, K.,  Kimura, K., Sakakibara, Y.: Whole-genome sequencing and comparative genome analysis of Bacillus subtilis strains isolated from non-salted fermented soybean foods, PLoS ONE, vol.10, no.10, e0141369 (Oct. 2015) [PubMed] [DOI]
  • Inatsuki, T, Sato, K., Sakakibara, Y.: Prediction of gene structures from RNA-seq data using dual decomposition, IPSJ Transactions on Bioinformatics, in press (2015)
  • Kumozaki, S.*, Sato, K.*, Sakakibara, Y.: A machine learning based approach to de novo sequencing of glycans from tandem mass spectrometry spectrum, IEEE/ACM Transactions on Computatinal Biology and Bioinformatics, vol.12, no.6, pp.1267-1274 (Dec. 2015) (*Joint First Authors) [DOI]
  • Afiahayati, Sato, K., Sakakibara, Y.: MetaVelvet-SL: An extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning, DNA Research, vol.29, no.1, pp.69-77 (Feb. 2015) [PubMed] [DOI]
  • Kamada, M., Hase, S., Sato, K., Toyoda, A., Fujiyama, A., Sakakibara, Y.: Whole genome complete resequencing of Bacillus subtilis natto by combining long reads with high-quality short reads, PLoS ONE, vol.9, no.10, e109999 (Oct. 2014) [PubMed] [DOI]
  • Afiahayati, Sato, K., Sakakibara, Y.: An extended genovo metagenomic assembler by incorporating paired-end information, PeerJ, 1:e196 (Oct. 2013) [PubMed] [DOI]
  • Sato, K., Kato, Y., Akutsu, T., Asai, K., Sakakibara, Y.: DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition, Bioinformatics, vol.28, no.24, pp.3218-3224 (Dec. 2012) [PubMed] [DOI]
  • Nakamura, M., Hachiya, T., Saito, Y., Sato, K., Sakakibara, Y.: An efficient algorithm for de novo predictions of biochemical pathways between chemical compounds, BMC Bioinformatics, 13(Suppl 17):S8 (Oct. 2012) [PubMed] [DOI]
  • Kato, Y., Sato, K., Asai, K., Akutsu, T.: Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming, Nucleic Acids Res., vol. 40, pp. W29-W34 (Jul. 2012) [PubMed] [DOI]
  • Sakakibara, Y., Hachiya, T., Uchida, M., Nagamine, N., Sugawara, Y., Yokota, M., Nakamura, M., Poperdorf, K., Komori, T., Sato, K.: COPICAT: A software system for predicting interactions between proteins and chemical compounds, Bioinformatics, vol.28, no.5, pp.745-756 (Mar. 2012) [PubMed] [DOI]
  • Okada, Y., Saito, Y., Sato, K., Sakakibara, Y.: Improved measurements of RNA structure conservation with generalized centroid estimators, Front. Genet., 2:54 (Aug. 2011) [PubMed] [DOI]
  • Poolsap, U., Kato, Y., Sato, K., Akutsu, T.: Using binding profiles to predict binding sites of target RNAs, J. Bioinform. Comput. Biol., vol.9, no.6, pp.697-713 (Dec. 2011) [PubMed] [DOI]
  • Hamada, M., Yamada, K., Sato, K., Frith, MC., Asai, K.: CentroidHomfold-LAST: Accurate prediction of RNA secondary structure using automatically collected homologous sequences, Nucleic Acids Res., vol.39, pp.W100-106 (Jun. 2011) [PubMed] [DOI]
  • Sato, K.*, Kato, Y.*, Hamada, M., Akutsu, T., Asai, K.: IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming, Bioinformatics, vol.27, no.13, pp.i85-i93 (Jul. 2011) (*Joint First Authors) [PubMed] [DOI]
  • Kielbasa, SM., Wan, R., Sato, K., Horton, P., Frith, MC.: Adaptive seeds tame genomic sequence comparison, Genome Res., vol.21, no.3., pp.487-493 (Mar. 2011) [PubMed] [DOI]
  • Saito, Y., Sato, K., Sakakibara, Y.: Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures, BMC Bioinformatics, 12(Suppl 1):S48 (Feb. 2011) [PubMed] [DOI]
  • Hamada, M., Sato, K., Asai, K.: Improving the accuracy of predicting secondary structure for aligned RNA sequences, Nucleic Acids Res., vol.39, no.2, pp.393-402 (Jan. 2011) [PubMed] [DOI]
  • Hamada, M., Sato, K., Asai, K.: Prediction of RNA secondary structure by maximizing pseudo-expected accuracy, BMC Bioinformatics, 11:586 (Nov. 2010) [PubMed] [DOI]
  • Saito, Y., Sato, K., Sakakibara, Y.: Robust and accurate prediction of noncoding RNAs from aligned sequences, BMC Bioinformatics, 11(Suppl 7):S3 (Oct. 2010) [PubMed] [DOI]
  • Kato, Y.*, Sato, K.*, Hamada, M., Watanabe, Y., Asai, K., Akutsu, T.: RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming, Bioinformatics, vol.26, no.18, pp.i460-i466 (Sep. 2010) (*Joint First Authors) [PubMed] [DOI]
  • Sato, K., Hamada, M., Mituyama, T., Asai, K., Sakakibara, Y.: A non-parametric Bayesian approach for predicting RNA secondary structures, J. Bioinform. Comput. Biol., vol.8, no.4, pp.727-742 (Aug. 2010) [DOI]
  • Hamada, M., Sato, K., Kiryu, H., Mituyama, T., Asai, K.: CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score, Bioinformatics, vol.25, pp.3236-3243 (Dec. 2009) [PubMed] [DOI]
  • Sato, K., Hamada, M., Asai, K., Mituyama, T.: CentroidFold: a web server for RNA secondary structure prediction, Nucleic Acids Res., vol.37, pp.W277-280 (Jul. 2009) [PubMed] [DOI]
  • Hamada, M., Sato, K., Kiryu, H., Mituyama, T., Asai, K.: Predictions of RNA secondary structure by combining homologous sequence information, Bioinformatics vol.25, no. 12, pp.i330-i338 (Jun. 2009) [PubMed] [DOI]
  • Morita, K.*, Saito, Y.*, Sato, K.*, Oka, K., Hotta, K., Sakakibara, Y.: Genome-wide searching with base-pairing kernel functions for non-coding RNAs: computational and expression analysis of snoRNA families in Caenorhabditis elegans, Nucleic Acids Res., vol.37, no.3, pp.999-1009 (Feb 2009) (* Joint First Authors) [PubMed] [DOI]
  • Hamada, M., Kiryu, H., Sato, K., Mituyama, T., Asai, K.: Predictions of RNA secondary structure using generalized centroid estimators, Bioinformatics, vol.25, pp.465-473 (Feb 2009) [PubMed] [DOI]
  • Sato, K., Mituyama, T., Asai, K., Sakakibara, Y.: Directed acyclic graph kernels for structural RNA analysis, BMC Bioinformatics, 9:318 (Jul. 2008) [PubMed] [DOI]
  • Asai, K., Kiryu, H., Hamada, M., Tabei, Y., Sato, K., Matsui, H., Sakakibara, Y., Terai, G., Mituyama, T.: Software.ncrna.org: web servers for analyses of RNA Sequences, Nucleic Acids Res., vol. 36, Web Server issue, pp. W75-W78 (Jul. 2008) [PubMed] [DOI]
  • Sato, K.*, Morita, K.*, Sakakibara, Y.: PSSMTS: position specific scoring matrices on tree structures, J. Math. Biol., vol. 56, no. 1-2, pp. 201-214 (Jan. 2008) (* Joint First Authors) [PubMed] [DOI]
  • Sakakibara, Y., Popendorf, K., Ogawa, N., Asai, K., Sato, K.: Stem kernels for RNA sequence analyses, J. Bioinform. Comput. Biol., vol. 5, no. 5, pp. 1103-1122 (Oct. 2007) [PubMed] [DOI]
  • Sakakibara, Y., Sato, K.: Sequence and structural analyses for functional non-coding RNAs (in Japanese), Journal of Japanese Society for Artificial Intelligence, vol. 22, no. 1, pp. 54-62 (Jan. 2007) [CiNii]
  • Sato, K., Sakakibara, Y.: RNA secondary structural alignment with conditional random fields, Bioinformatics, vol. 21, suppl. 2, pp. ii237-ii242 (Oct. 2005) [PubMed] [DOI]
  • Matsui, H., Sato, K., Sakakibara, Y.: Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA strucutres, Bioinformatics, vol. 21, no. 11, pp. 2611-2617 (Mar. 2005) [PubMed] [DOI]
  • Sato, K., Saito, H.: Extracting word sequence correspondences based on support vector machines (in Japanese), Journal of Natural Language Processing, vol. 10, no. 4, pp. 109-124 (Jul. 2003) [CiNii]
  • Nobesawa, S., Sato, K., Saito, H.: The use of domain-specific statistical data for Japanese morphological analysis (in Japanese), Journal of Natural Language Processing, vol. 9, no. 3, pp. 21-40 (Jul. 2002) [CiNii]
  • Sato, K., Saito, H.: Extracting bilingual word pairs with maximum entropy modeling (in Japanese), Journal of Natural Language Processing, vol. 9, no. 1, pp. 101-115 (Jan. 2002) [CiNii]

Refereed Conference Proceedings

  • Sato, K., Kashiwagi, S., Sakakibara, Y.: A max-margin model for predicting residue-base contacts in protein-RNA interactions, Proc. of GIW/InCoB 2015 (Sep. 2015) [preprint]
  • Kumozaki, S.*, Sato, K.*, Sakakibara, Y.: A machine learning based approach to de novo sequencing of glycans from tandem mass spectrometry spectrum, Proc. of the 13th Asia Pacific Bioinformatics Conference (APBC 2015), (Jan. 2015) (*Joint First Authors) (This paper will be also published in TCBB)
  • Afiahayati, Sato, K., Sakakibara, Y.: An extended genovo metagenomic assembler by incorporating paired-end information, Proc. of the 12th International Conference on Bioinformatics (InCoB 2013), (Sep. 2013) (This paper was also published in PeerJ)
  • Nakamura, M., Hachiya, T., Saito, Y., Sato, K., Sakakibara, Y.: An efficient algorithm for de novo predictions of biochemical pathways between chemical compounds, Proc. of the 11th International Conference on Bioinformatics (InCoB 2012), (Oct. 2012) (This paper was also published in BMC Bioinformatics)
  • Sato, K.*, Kato, Y.*, Hamada, M., Akutsu, T., Asai, K.: IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming, Proc. of ISMB/ECCB 2011, pp.i85-i93 (Jul. 2011) (*Joint First Authors) (This paper was also published in Bioinformatics vol.27, no.13) [PubMed] (acceptance rate: 48/258=18.6%)
  • Saito, Y., Sato, K., Sakakibara, Y.: Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures, Proc. of the 9th Asia Pacific Bioinformatics Conference (APBC 2011), 12(Suppl 1):S48, (Jan. 2011) (This paper was also published in BMC Bioinformatics.) [PubMed] (acceptance rate: 55/164=33.5%)
  • Saito, Y., Sato, K., Sakakibara, Y.: Robust and accurate prediction of noncoding RNAs from aligned sequences, Proc. of the International Conference on Bioinformatics (InCoB 2010), 11(Suppl 7):S3 (Sep. 2010) (This paper was also published in BMC Bioinformatics.) [PubMed] (acceptance rate: 47/108=43.5%)
  • Kato, Y.*, Sato, K.*, Hamada, M., Watanabe, Y., Asai, K., Akutsu, T.: RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming, Proc. of the 9th European Conference on Computational Biology (ECCB 2010), pp.i460-i466 (Sep. 2010) (*Joint First Authors) (This paper was also published in Bioinformatics vol.26, no.18) [PubMed] (acceptance rate: 36/215 = 16.7%)
  • Sato, K., Whitington, T., Bailey, T., Horton, P.: Improved prediction of transcription binding sites from chromatin modification data, Proc. of the 2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2010), pp.220-226 (May 2010) [DOI]
  • Okada, Y., Sato, K., Sakakibara, Y.: Improvement of structure conservation index with centroid estimators, Proc. of the 15th Pacific Symposium on Biocomputing (PSB 2010), pp.88-97 (Jan. 2010) [PubMed]
  • Sato, K., Saito, Y., Sakakibara, Y.: Gradient-based optimization of hyperparameters for base-pairing profile local alignment kernels, Proc. of the 20th International Conference on Genome Informatics (GIW 2009) , pp.128-138 (Dec. 2009) [PubMed]
  • Sato, K., Hamada, M., Mituyama, T., Asai, K., Sakakibara, Y.: A non-parametric Bayesian approach for predicting RNA secondary structures, Proc. of the 9th Workshop on Algorithms in Bioinformatics (WABI 2009), Lecture Notes in Bioinformatics (LNBI) 5724, pp.286-297 (Sep. 2009) [DOI] (acceptance rate: 34/90 = 37.8%)
  • Hamada, M., Sato, K., Kiryu, H., Mituyama, T., Asai, K.: Predictions of RNA secondary structure by combining homologous sequence information, Proc. of ISMB/ECCB 2009, pp.i330-i338 (Jun. 2009) (This paper was also published in Bioinformatics vol.25, no. 12) [PubMed] (acceptance rate: 46/238 = 19.3%)
  • Sakakibara, Y., Asai, K., Sato, K.: Stem kernels for RNA sequence analyses, Proc. of the 1st International Conference on Bioinformatics Research and Development (BIRD 2007), Lecture Notes in Bioinformatics (LNBI) 4414, pp. 278-291 (Mar. 2007) [DOI]
  • Sato, K., Sakakibara, Y.: RNA secondary structural alignment with conditional random fields, Proc. of the 4th European Conference on Computational Biology (ECCB 2005), pp. ii237-ii242 (Oct. 2005) (This paper is also published in Bioinformatics vol. 21, suppl. 2) [PubMed] (acceptance rate: 45/209 = 21.5%)
  • Saito, H., Ohara, K., Sato, K., Ito, K., Okamoto, H.: A new e-learning paradigm through annotating operations, Proc. of COLING 2004 eLearning for Computational Linguistics and Computational Linguistics for eLearning, pp. 86-89 (Aug. 2004)
  • Matsui, H., Sato, K., Sakakibara, Y., Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA strucutres, Proc. of 2004 IEEE Computational Systems Bioinformatics Conference (CSB 2004), pp. 290-299 (Aug. 2004) [PubMed]
  • Yamaguchi, F., Nobesawa, S., Sato, K.: Rongorongo character listing tool, Proc. of the 3rd IASTED International Conference on Visualization, Imaging and Image Processing (VIIP '03), vol. 1, pp. 158-162 (Sep. 2003)
  • Okamoto, H., Sato, K., Saito, H: Preferential presentation of Japanese near-synonyms using definition statements, Proc. of the 2nd International Workshop on Paraphrasing (IWP 2003), pp. 17-24 (Jul. 2003)[DOI]
  • Sato, K., Saito, H.: Extracting word sequence correspondences with support vector machines, Proc. of the 19th International Conference on Computational Linguistics (COLING 2002), pp. 870-876 (Aug. 2002) [DOI] (acceptance rate: 66/256=25.8%)
  • Sato, K., Saito, H.: Extracting bilingual word pairs with maximum entropy modeling, Proc. of the 6th World Multiconference on Sementics, Cybernetics and Informatics (SCI 2002), vol. 3, pp. 412-417 (Jul. 2002)
  • Kikuchi, H., Sato, K., Saito, H.: Extraction of Japanese web-wite top-pages for the directory of the web, Proc. of the 6th World Multiconference on Sementics, Cybernetics and Informatics (SCI 2002), vol. 3, pp. 400-405 (Jul. 2002)
  • Nobesawa, S., Sato, K., Saito, H.: Recognition of domain-specific terms with d-bigram model, Proc. of the 6th World Multiconference on Sementics, Cybernetics and Informatics (SCI 2002), vol. 3, pp. 406-411 (Jul. 2002)
  • Yoshida, A., Sato, K., Nobesawa, S., Saito, H.: Authorship identification based on support vector machine, Proc. of the 6th World Multiconference on Sementics, Cybernetics and Informatics (SCI 2002), vol. 3, pp. 423-428 (Jul. 2002)
  • Takaoka, E., Maeda, A., Sato, K., Yamaguchi, F., Nakanishi, M.: A visual system for education of machine language, Proc. of the International Conference on Information and Communication Technologies for Education, pp. 289-298 (Dec. 2000)
  • Sato, K., Nakanishi, M.: Maximum entropy model learning of the translation rules, Proc. of the 36th Annual Meeting of the Association for Computational Linguistics and the 17th International Conference on Computational Linguistics (COLING-ACL '98), pp. 1171-1175 (Aug. 1998) [DOI] (acceptance rate: 137/550=24.9%)
  • Nobesawa, S., Tsutsumi, J., Sun, D. J., Sano, T., Sato, K., Nakanishi, M.: Segmenting sentences into linky strings using d-bigram statistics, Proc. of the 16th International Conference on Computational Linguistics (COLING '96), pp. 586-591 (Aug. 1996) [DOI]

Books

  • Sakakibara, Y., Sato, K.: Sequence and structural analyses for functional non-coding RNAs, Algorithmic Bioprocesses, Springer, pp.63-79 (Aug. 2009) [Publisher's site]
  • Sato, K., Sakakibara, Y.: Sequence analysis of functional RNAs based on secondary structures (in Japanese), Experimental Medicine (Jikken Igaku), vol. 26, no. 7, pp. 121-126 (Apr. 2008) [Publisher's site]
  • Sakakibara, Y., Kobayashi, S., Sato, K., Nishino, T., Tomita, E. (Eds): Grammatical Inference: Algorithms and Applications, Lecture Notes in Artificial Intelligence (LNAI) 4201, Springer (Sep. 2006) [Publisher's site]