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Yasubumi Sakakibara

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1987 …2023

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  • 2012

    Poster: In silico microarray algorithm: Accurate and fast taxonomic profiling from short read sequences

    Tagami, T., Hachiya, T. & Sakakibara, Y., 2012 May 8, 2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012. 6182660. (2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • 2011

    MetaVelvet: AAAn extension of Velvet assembler to de novo metagenome assembly from short sequence reads

    Namiki, T., Hachiya, T., Tanaka, H. & Sakakibara, Y., 2011 Dec 1, 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011. p. 116-124 9 p. (2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    15 Citations (Scopus)
  • 2010

    Development of a bacteria computer: From in silico finite automata to in vitro and in vivo

    Sakakibara, Y., 2010 Jul 29, Programs, Proofs, Processes - 6th Conference on Computability in Europe, CiE 2010, Proceedings. p. 362-371 10 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 6158 LNCS).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Improvement of structure conservation index with centroid estimators

    Okada, Y., Sato, K. & Sakakibara, Y., 2010, Pacific Symposium on Biocomputing 2010, PSB 2010. p. 88-97 10 p. (Pacific Symposium on Biocomputing 2010, PSB 2010).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    3 Citations (Scopus)
  • 2009

    A non-parametric bayesian approach for predicting RNA secondary structures

    Sato, K., Hamada, M., Mituyama, T., Asai, K. & Sakakibara, Y., 2009, Algorithms in Bioinformatics - 9th International Workshop, WABI 2009, Proceedings. p. 286-297 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 5724 LNBI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    1 Citation (Scopus)

  • Operon structure optimization by random self-assembly

    Nakagawa, Y., Yugi, K., Tsuge, K., Itaya, M., Yanagawa, H. & Sakakibara, Y., 2009 Nov 27, DNA Computing - 14th International Meeting on DNA Computing, DNA14, Revised Selected Papers. p. 33-40 8 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 5347 LNCS).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • 2007

    Stem kernels for RNA sequence analyses

    Sakakibara, Y., Asai, K. & Sato, K., 2007, Bioinformatics Research and Development - First International Conference, BIRD 2007 Proceedings. Springer Verlag, p. 278-291 14 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4414 LNBI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    1 Citation (Scopus)
  • 2006

    Development of an in vivo computer based on Escherichia coli

    Nakagawa, H., Sakamoto, K. & Sakakibara, Y., 2006 Jul 13, DNA Computing - 11th International Workshop on DNA Computing, DNA11, Revised Selected Papers. p. 203-212 10 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 3892 LNCS).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    13 Citations (Scopus)

  • Discriminative detection of cis-acting regulatory variation from location data

    Kawada, Y. & Sakakibara, Y., 2006 Dec 1, Proceedings of the 4th Asia-Pacific Bioinformatics Conference, APBC 2006. p. 89-98 10 p. (Series on Advances in Bioinformatics and Computational Biology; vol. 3).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    1 Citation (Scopus)

  • Intensive in vitro experiments of implementing and executing finite automata in test tube

    Kuramochi, J. & Sakakibara, Y., 2006 Jul 13, DNA Computing - 11th International Workshop on DNA Computing, DNA11, Revised Selected Papers. p. 193-202 10 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 3892 LNCS).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    5 Citations (Scopus)
  • 2005

    Discriminative discovery of transcription factor binding sites from location data

    Kawada, Y. & Sakakibara, Y., 2005 Dec 1, Proceedings - 2005 IEEE Computational SystemsBioinformatics Conference, CSB 2005. p. 86-92 7 p. 1498010. (Proceedings - 2005 IEEE Computational Systems Bioinformatics Conference, CSB 2005; vol. 2005).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    1 Citation (Scopus)
  • 2004

    Grammatical inference: Algorithms and applications: 7th international colloquium, ICGI 2004 Athens, Greece, october 11-13, 2004 proceedings

    Paliouras, G. & Sakakibara, Y., 2004, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Springer Verlag, Vol. 3264. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 3264).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures

    Matsui, H., Sato, K. & Sakakibara, Y., 2004 Jan 1, Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004. IEEE Computer Society, p. 290-299 10 p. (Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    7 Citations (Scopus)
  • 2002

    Population computation and majority inference in test tube

    Sakakibara, Y., 2002, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Springer Verlag, Vol. 2340. p. 82-91 10 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 2340).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    1 Citation (Scopus)
  • 2001

    Solving computational learning problems of boolean formulae on DNA computers

    Sakakibara, Y., 2001, DNA Computing - 6th International Workshop on DNA-Based Computers, DNA 2000 Leiden, The Netherlands, June 13-17, 2000 Revised Papers. Rozenberg, G. & Condon, A. (eds.). Springer Verlag, p. 220-230 11 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 2054).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    4 Citations (Scopus)
  • 2000

    Learning context-free grammars from partially structured examples

    Sakakibara, Y. & Muramatsu, H., 2000, Grammatical Inference: Algorithms and Applications - 5th International Colloquium, ICGI 2000, Proceedings. Oliveira, A. L. (ed.). Springer Verlag, p. 229-240 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 1891).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    33 Citations (Scopus)
  • 1996

    Stochastic simple recurrent neural networks

    Golea, M., Matsuoka, M. & Sakakibara, Y., 1996, Grammatical Inference: Learning Syntax from Sentences - 3rd International Colloquium, ICGI-1996, Proceedings. de la Higuera, C. & Miclet, L. (eds.). Springer Verlag, p. 262-273 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 1147).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • 1995

    Grammatical inference: An old and new paradigm

    Sakakibara, Y., 1995, Algorithmic Learning Theory - 6th International Workshop, ALT 1995, Proceedings. Jantke, K. P., Shinohara, T. & Zeugmann, T. (eds.). Springer Verlag, p. 1-24 24 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 997).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    3 Citations (Scopus)

  • Stochastic context-free grammars for modeling RNA

    Sakakibara, Y., Brown, M., Underwood, R. C., Mian, I. S. & Haussler, D., 1995 Jan 1, Proceedings of the Hawaii International Conference on System Sciences. Nunamaker, J. F. & Sprague, R. H. J. (eds.). Publ by IEEE, p. 284-293 10 p. (Proceedings of the Hawaii International Conference on System Sciences; vol. 5).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    34 Citations (Scopus)
  • 1994

    Learning languages by collecting cases and tuning parameters

    Sakakibara, Y., Jantke, K. P. & Lange, S., 1994, Algorithmic Learning Theory - 4th International Workshop on Analogical and Inductive Inference, AII 1994 and 5th International Workshop on Algorithmic Learning Theory, ALT 1994, Proceedings. Arikawa, S. & Jantke, K. P. (eds.). Springer Verlag, p. 532-546 15 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 872 LNAI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    4 Citations (Scopus)

  • Recent methods for rna modeling using stochastic context-free grammars

    Sakakibara, Y., Brown, M., Hughey, R., Mian, S., Sjölander, K., Underwood, R. C. & Haussler, D., 1994, Combinatorial Pattern Matching - 5th Annual Symposium, CPM 1994, Proceedings. Crochemore, M. & Gusfield, D. (eds.). Springer Verlag, p. 290-306 17 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 807 LNCS).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    17 Citations (Scopus)
  • 1993

    Text classification and keyword extraction by learning decision trees

    Sakakibara, Y., Misue, K. & Koshiba, T., 1993, Proceedings of the Conference on Artificial Intelligence Applications. Publ by IEEE, p. 466 1 p. (Proceedings of the Conference on Artificial Intelligence Applications).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    12 Citations (Scopus)
  • 1992

    Noise model on learning sets of strings

    Sakakibara, Y. & Siromoney, R., 1992 Dec 1, Proceedings of the Fifth Annual ACM Workshop on Computational Learning Theory. Publ by ACM, p. 295-302 8 p. (Proceedings of the Fifth Annual ACM Workshop on Computational Learning Theory).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    15 Citations (Scopus)
  • 1987

    Programming in modal logic: An extension of PROLOG based on modal logic

    Sakakibara, Y., 1987, Logic Programming 1986 - Proceedings of the 5th Conference. Wada, E. (ed.). Springer Verlag, p. 81-91 11 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 264 LNCS).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    6 Citations (Scopus)