Research Output per year

## Research Output

## 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 proceeding › Conference contribution

## 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

## 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

## 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

## 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

## 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

## 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 proceeding › Conference contribution

## 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 proceeding › Conference contribution

## 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

## 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 proceeding › Conference contribution

## 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

## 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

## 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

## 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

## 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

## 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

## 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

## 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 proceeding › Conference contribution

## 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 proceeding › Conference contribution

## 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 proceeding › Conference contribution

## 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

## 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

## 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 proceeding › Conference 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 proceeding › Conference contribution