Publications

(2022). Integer programming for selecting set of informative markers in paternity inference. BMC Bioinformatics, 23:265.

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(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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(2019). Efficient generation of Knock-in/Knock-out marmoset embryo via CRISPR/Cas9 gene editing. Sci. Rep., 9:12719.

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(2018). Convolutional neural network based on SMILES representation of compounds for detecting chemical motif. BMC Bioinformatics, 19:526.

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(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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(2017). DEclust: A statistical approach for obtaining differential expression profiles of multiple conditions. PLoS One, 12(11):e0188285.

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(2017). An accessibility-incorporated method for accurate prediction of RNA-RNA interactions from sequence data. Bioinformatics, 33(2):202-209.

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

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(2015). Resequencing of the common marmoset genome improves genome assemblies and gene-coding sequence analysis. Sci. Rep., 5:16894.

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(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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(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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(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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(2012). DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition. Bioinformatics, 28(24):3218-3224.

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(2012). An efficient algorithm for de novo predictions of biochemical pathways between chemical compounds. BMC Bioinformatics, 13:S8.

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(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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(2012). COPICAT: a software system for predicting interactions between proteins and chemical compounds. Bioinformatics, 28(5):745-746.

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(2011). Using binding profiles to predict binding sites of target RNAs. J. Bioinform. Comput. Biol., 9(6):697-713.

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(2011). Improved measurements of RNA structure conservation with generalized centroid estimators. Front. Genet., 2:54.

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(2011). IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. Bioinformatics, 27(13):i85-i93.

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(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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(2011). Adaptive seeds tame genomic sequence comparison. Genome Res., 21:487-493.

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

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(2010). Prediction of RNA secondary structure by maximizing pseudo-expected accuracy. BMC Bioinformatics, 11:586.

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(2010). Robust and accurate prediction of noncoding RNAs from aligned sequences. BMC Bioinformatics, 11:S3.

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(2010). RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming. Bioinformatics, 26(18):i460-i466.

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(2010). A non-parametric Bayesian approach for predicting RNA secondary structures. J. Bioinform. Comput. Biol., 8(4):727-742.

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(2010). Improvement of structure conservation index with centroid estimators. Pac. Symp. Biocomput. 2010, p. 88-97.

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(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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(2009). CENTROIDFOLD: a web server for RNA secondary structure prediction. Nucleic Acids Res., 37(Suppl 2):W277-W280.

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(2009). Predictions of RNA secondary structure by combining homologous sequence information. Bioinformatics, 25(12):i330-i338.

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(2009). Prediction of RNA secondary structure using generalized centroid estimators. Bioinformatics, 25(4):465–473.

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(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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(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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(2008). Software.ncrna.org: web servers for analyses of RNA sequences. Nucleic Acids Res., 36(Suppl 2):W75–W78.

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(2008). Directed acyclic graph kernels for structural RNA analysis. BMC Bioinformatics, 9:318.

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(2008). PSSMTS: position specific scoring matrices on tree structures. J. Math. Biol., 56:201–214.

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(2007). Stem kernels for RNA sequence analyses. J. Bioinform. Comput. Biol., 5(5):1103-1122.

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

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

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(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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(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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(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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(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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