• 2508 Citations
  • 25 h-Index
1987 …2020

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Research Output

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A non-parametric bayesian approach for predicting RNA secondary structures

Sato, K., Hamada, M., Mituyama, T., Asai, K. & Sakakibara, Y., 2009 Nov 2, 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 proceedingConference contribution

1 Citation (Scopus)

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 proceedingConference contribution

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 proceedingConference contribution

12 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 proceedingConference contribution

1 Citation (Scopus)

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 proceedingConference contribution

1 Citation (Scopus)

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 proceedingConference contribution

Grammatical inference: An old and new paradigm

Sakakibara, Y., 1995 Jan 1, Algorithmic Learning Theory - 6th International Workshop, ALT 1995, Proceedings. Jantke, K. P., Zeugmann, T. & Shinohara, 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 proceedingConference contribution

2 Citations (Scopus)

Improvement of structure conservation index with centroid estimators

Okada, Y., Sato, K. & Sakakibara, Y., 2010 Dec 1, 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 proceedingConference contribution

3 Citations (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 proceedingConference contribution

5 Citations (Scopus)

Learning context-free grammars from partially structured examples

Sakakibara, Y. & Muramatsu, H., 2000, Grammatical Inference: Algorithms and Applications - 5th International Colloquium, ICGI 2000, Proceedings. Springer Verlag, Vol. 1891. 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 proceedingConference contribution

30 Citations (Scopus)

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 proceedingConference contribution

4 Citations (Scopus)

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 proceedingConference contribution

13 Citations (Scopus)

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 proceedingConference contribution

15 Citations (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 proceedingConference 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 proceedingConference contribution

5 Citations (Scopus)

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 proceedingConference contribution

1 Citation (Scopus)

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 proceedingConference contribution

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

Sakakibara, Y., 1987 Jan 1, 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 proceedingConference contribution

6 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 Jan 1, 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 proceedingConference contribution

16 Citations (Scopus)

Solving computational learning problems of boolean formulae on DNA computers

Sakakibara, Y., 2001 Jan 1, 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 proceedingConference contribution

4 Citations (Scopus)

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 proceedingConference contribution

1 Citation (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 proceedingConference contribution

32 Citations (Scopus)

Stochastic simple recurrent neural networks

Golea, M., Matsuoka, M. & Sakakibara, Y., 1996, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Springer Verlag, Vol. 1147. 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 proceedingConference contribution

Text classification and keyword extraction by learning decision trees

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

Research output: Chapter in Book/Report/Conference proceedingConference contribution

8 Citations (Scopus)