Tetsuo Shibuya's publications

Please feel free to contact me at tshibuya 'at-mark' hgc 'dot' jp to request copies of papers whose files are not provided.

Refereed Journal Papers

Tetsuo Shibuya, Searching Protein 3-D Structures in Faster Than Linear Time, Journal of Computational Biology, Vol. 17, No. 4, 2010, pp. 593-602. (preprint) (journal site)
Tetsuo Shibuya, Fast Hinge Detection Algorithms for Flexible Protein Structures, IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 7, no. 2, 2010, pp. 333-341. (preprint) (journal site)
Tetsuo Shibuya, Searching Protein 3-D Structures in Linear Time, Journal of Computational Biology, Vol. 17, No. 3, pp. 203-219, 2010. (Preliminary version has appeared in RECOMB '09) (journal site)
Tetsuo Shibuya, Geometric Suffix Tree: Indexing Protein 3-D Structures, Journal of the ACM, Vol. 57, No. 3, Article No.15 pp.:1-17, 2010.(ACM portal)
Tetsuo Shibuya, Jesper Jansson, and Kunihiko Sadakane, Linear-Time Protein 3-D Structure Searching with Insertions and Deletions, BMC Algorithms for Molecular Biology, Vol. 5:7, 2010. (journal site) (PDF file at the journal site)
Ben Hachimori and Tetsuo Shibuya, Lazy Suffix Array: the Data Structure for Online Construction and Pattern Searching, IEICE Transactions on Fundamentals, Vol. E92-A, No. 8, pp. 1750-1756, 2009. (J-Stage)
Tetsuo Shibuya, Efficient Substructure RMSD Query Algorithms, Journal of Computational Biology, Vol. 14, No. 9, pp. 1201-1207, 2007. (journal site) (preprint)
Tetsuo Shibuya, Generalization of a Suffix Tree for RNA Structural Pattern Matching, Algorithmica, Vol. 39, No. 1, pp. 1 - 19, 2004. (journal site) (preprint)
Tetsuo Shibuya, Hisashi Kashima, and Akihiko Konagaya, Efficient Filtering Methods for Clustering cDNAs with Spliced Sequence Alignment, Bioinformatics, Vol. 20, pp. 29-39, 2004. (journal site)
Eain Murphy, Isidore Rigoutsos, Tetsuo Shibuya, and Thomas Shenk, Re-evaluation of Human Cytomegalovirus Coding Potential, Proceedings of the National Academy of Sciences, Vol. 100, No. 23, pp. 13585-13590, November 11, 2003. (journal site)
Tien Huynh, Isidore Rigoutsos, Laxmi Parida, Daniel Platt, and Tetsuo Shibuya, The IBM Bioinformatics Group Web Server - Tools and Content, Nucleic Acids Research, Vol. 31, No. 13, pp. 3645-3650, 2003. (journal site)
Tetsuo Shibuya, Constructing the Suffix Tree of a Tree with a Large Alphabet, IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences, Vol. E86-A, No.5, pp. 1061-1066, May 2003. (journal site) (PDF file)
Tetsuo Shibuya and Isidore Rigoutsos, Dictionary-driven Prokaryotic Gene Finding, Nucleic Acids Research, Vol. 30, pp. 2710-2725, 2002. (journal site) (PDF file)
Hiroshi Kawazoe, Tetsuo Shibuya, and Takeshi Tokuyama, Optimal On-line Algorithms for an Electronic Commerce Money Distribution System, Algorithmica, Vol. 33, pp. 287-299, March 25, 2002. (journal site) (preprint)
Tetsuo Shibuya, Computing the n x m Shortest Paths Efficiently, the ACM Journal of Experimental Algorithmics, ISSN 1084-6654, Vol. 5, No. 9, 2000. (journal site) (PDF file)
Tetsuya Ueda, Hiroki Sasaki, Yoshitaka Kuwahara, Masahiko Nezu, Tetsuo Shibuya, Hiromi Sakamoto, Kazuyoshi Yanagihara, Kennichi Mafune, Masatoshi Makuuchi, and Masaaki Terada, Deletion of the Carboxyl-Terminal Exons of K-sam/FPGR2 by Short Homology-Mediated Recombination, Generating Preferential Expression of Specific mRNAs, Cancer Research, Vol. 59, No. 24, pp. 6080-6086, Dec 15, 1999. (journal site)
Tetsuo Shibuya, Hiroshi Imai, Shigeki Nishimura, Hiroshi Shimoura, and Kenji Tenmoku, Finding Useful Detours in Geographical Databases, IEICE Transactions on Information and Systems, Vol. E82-D, No. 1, pp. 282-290, January 1999. (journal site) (PDF file)
Tetsuo Shibuya and Hiroshi Imai, New Flexible Approaches for Multiple Sequence Alignment, Journal of Computational Biology, Vol. 4, No. 3, Mary Ann Liebert, Inc., pp. 385-413, 1997. (preprint)

Refereed Conference Papers

Tetsuo Shibuya, Jesper Jansson and Kunihiko Sadakane, Linear-Time Protein 3-D Structure Searching with Insertions and Deletions, 9th Workshop on Algorithms in Bioinformatics (WABI 2009), LNCS, vol. 5724, pp. 310-320, 2009. (PDF file)
Ritsuko Onuki, Tetsuo Shibuya and Minoru Kanehisa, New Kernel Methods for Phenotype Prediction from Genotype Data, Proc. 9th Annual Workshop on Bioinformatics and Systems Biology (IBSB), Genome Informatics, Vol. 22, pp. 132-141, 2009. (PDF file)
Tetsuo Shibuya, Searching Protein 3-D Structures in Linear Time, Proc. 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2009), LNCS 5817 (LNBI 5541), pp. 1-15, 2009. (PDF file) (Best Paper Award)
Tetsuo Shibuya, Prefix-Shuffled Geometric Suffix Tree, Proc. 14th String Processing and Information Retrieval Symposium (SPIRE 2007), LNCS 4726, pp. 300-309, 2007. (PDF file)
Ritsuko Onuki, Tetsuo Shibuya, and Minoru Kanehisa, Haplotype Inference Probability-based Genotype Clustering, Proc. 7th Annual Workshop on Bioinformatics and Systems Biology (IBSB), Genome Informatics, Vol. 18, pp. 26-27, 2007.
Tetsuo Shibuya, Geometric Suffix Tree: A New Index Structure for Protein 3-D Structures, Proc. Combinatorial Pattern Matching 2006 (CPM 2006), LNCS 4009, pp. 84-93, 2006. (PDF file)
Hiroki Sakai, Hiroo Murakami, Sachiyo Aburatani, Tetsuo Shibuya, Katsuhisa Horimoto, and Minoru Kanehisa, Bayesian Approach for Sequence Pattern Search in Tissue Specific Alternative Splicing, Proc. 9th World Multi-Conference on Systemics, Cybernetics and Informatics, Vol. 3, pp. 25-30, 2005.
Tetsuo Shibuya and Igor Kurochkin, Match Chaining Algorithms for cDNA Mapping. Proc. Algorithms in Bioinformatics (WABI'03), LNCS 2182, pp. 462-473, 2003. (PDF file)
Makoto Kano, Hisashi Kashima, Tetsuo Shibuya, Kaori Ide, Aiko Kashihara, Noriko Nakagawa, Seiki Kuramitsu, Mariko Hatakeyama, and Akihiko Konagaya, Method for Normalization of Gene Expression Data, Genome Informatics Vol. 14, p. 336-337, 2003.
Kunihiko Sadakane and Tetsuo Shibuya, Indexing Huge Genome Sequences for Solving Various Problems. Genome Informatics vol. 12, pp. 175-183, 2001. (PDF file)
Tetsuo Shibuya, Generalization of a Suffix Tree for RNA Structural Pattern Matching, Proc. 7th Scandinavian Workshop on Algorithm Theory (SWAT'00), LNCS 1851, pp. 393-406, 2000.
Tetsuo Shibuya, Constructing the Suffix Tree of a Tree with a Large Alphabet, Proc. 10th annual International Symposium on Algorithms and Computation (ISAAC'99), LNCS 1741, pp. 225-236, 1999.
Tetsuo Shibuya, Computing the n x m Shortest Paths Efficiently, Proc. 1st International Workshop on Algorithm Engineering and Experimentation (ALENEX'99), LNCS 1619, pp. 210-225, 1999.
Hiroshi Kawazoe, Tetsuo Shibuya, and Takeshi Tokuyama, Optimal On-line Algorithms for an Electronic Commerce Money Distribution System, Proc. 10th ACM-SIAM Symposium on Discrete Algorithms (SODA 99), pp. 527-536, 1999.
Tetsuo Shibuya and Hiroshi Imai, New Flexible Approaches for Multiple Sequence Alignment, Proc. 1st Annual International Conference on Computational Molecular Biology (RECOMB '97), pp. 267-276, 1997.
Tetsuo Shibuya and Hiroshi Imai, Enumerating Suboptimal Alignments of Multiple Biological Sequences Efficiently, Proc. Pacific Symposium on Biocomputing '97, pp. 409-420, 1997.
Tetsuo Shibuya and Hiroshi Imai, Parametric Alignment of Multiple Biological Sequences, Genome Informatics, Vol 7, pp. 41-50, 1996.
Tetsuo Shibuya, Hiroshi Imai, Shigeki Nishimura, Hiroshi Shimoura, and Kenji Tenmoku, Detour Queries in Geographical Databases for Navigation and Related Algorithm Animations, Proc. International Symposium on Cooperative Database Systems for Advanced Applications (CODAS'96), Vol. 2, pp. 333-340, 1996.
Tsuyoshi Ono, Yoshiaki Kyoda, Tomonari Masada, Kazuyoshi Hayase, Motoki Nakade, Kunihiko Sadakane, Tetsuo Shibuya, Mary Inaba, Hiroshi Imai, Keiko Imai, and David Avis, A Package for Traiangulations. Proc. 12th Annual ACM Symposium on Computational Geometry, pp. V17-V18, 1996.
Tetsuo Shibuya and Hiroshi Imai, Suboptimal Alignments of Multiple Biological Sequences. Intelligent Systems on Molecular Biology '96, Book of Abstracts, p. 76, June 1996.
Tetsuo Shibuya, Takahiro Ikeda, Hiroshi Imai, Shigeki Nishimura, Hiroshi Shimoura, and Kenji Tenmoku, Finding a Realistic Detour by AI Search Techniques, Proc. 2nd Intelligent Transportation Systems, Vol. 4, pp. 2037-2044, 1995.

Invited Journal/Magazine Articles

Tetsuo Shibuya, Current Bioinformatics and Its Future, Journal of the Institute of Electronics, Information and Communication Engineers, vol. 90, no. 2, 2007, pp. 145-147. (In Japanese, see my Japanese publication list)
Tetsuo Shibuya, BDGF Method, Bio Venture, 2(6), pp. 86-89, 2002. (In Japanese, see my Japanese publication list)

Books

Kengo Kinoshita, Tetsuo Shibuya, and Kenta Nakai, "Computational Biology", Gendai Suuri Kagaku Jiten, Heisuke Hiranaka eds., 2009, .pp. 342-354. (In Japanese. See my Japanese publication list)
Neil C.Jones and Pavel Pevzner, Introduction to Bioinformatics Algorithms, translated to Japanese by Tetsuo Shibuya and Hideo Bannai, 2007. (publisher's site) (Japanese Translation. See my Japanese publication list)
Kenta Nakai, et al. eds., Encyclopedia of Bioinformatics, Kyoritsu Shuppan, 2006. (In Japanese, as an editor and an author, , see my Japanese publication list). (publisher's site)
Tetsuo Shibuya, Basics of Datamining in Bioinformatics, Genome Kenkyuu Jikken Handbook, pp. 45-48, Yodosha, 2004. (In Japanese. See my Japanese publication list). (publisher's site)

Invited Talks

Tetsuo Shibuya, Next-Generation Cancer Genome Analysis Pipeline, 2nd NUS-UT Workshop on Computational Systems Biology, Plenary Lecture, Feburuary 2010.
Tetsuo Shibuya, A New Algorithm Design Framework for Searching Protein 3-D Structures, GCOE (Decipherring Biosphere from Genome Big Bang) Special Lecture, 2010. (In Japanese, see my Japanese publication list)
Tetsuo Shibuya, Combinatorial Pattern Matching for Protein 3-D Structures, SEQUOIA seminar, INRIA, 2008.
Tetsuo Shibuya, Protein Structures and Combinatorial Pattern Matching. SIG FPAI-68, 2008. (In Japanese, see my Japanese publication list)
Tetsuo Shibuya, Combinatorial Structural Pattern Matching, The Second Japan-Taiwan Bilateral Symposium on Bioinformatics, November 7-9, 2006.
Tetsuo Shibuya, Indexing Structures for Biomolecular Structures, The First Japan-Taiwan Bilateral Symposium on Bioinformatics, March 13-15, 2006.
Tetsuo Shibuya, Indexing Technologies and Its Application to Gene Finding, Seimei-Jouhou-Kagaku Special Seminar, CBRC, Advanced Industrial Science and Technology, November 20, 2002. (In Japanese, see my Japanese publication list)
Tetsuo Shibuya, Searching Techniques for Genome Informatics, RAMP Symposium, Proceedings of the 14th RAMP Symposium, pp. 47-60, September 24, 2002. (In Japanese, see my Japanese publication list)
Tetsuo Shibuya, Pattern Discovery and Mining in Large Databases, BioEXPO 2002. Senmon-Gijutsu Seminar, July 12, 2002. (In Japanese, see my Japanese publication list)
Tetsuo Shibuya, New Approaches to Flexible Alignment of Multiple Biological Sequences, Combinatorial Optimization Seminar: Theory and Applications (COSTA), 97-4, October 25, 1997. (In Japanese, see my Japanese publication list)

Invited Conference Panel Discussions

Antonia Kwan, Satoru Miyano, Yasushi Okazaki and Tetsuo Shibuya, What are the applications and limitations of microarray datamining for immunology? First International Immunoinformatics Symposium, Feburuary 26, 2004.

Non-refereed Technical Reports / Talks

Tetsuo Shibuya, Linear-Time Algorithm for Searching Protein 3-D Structures, IPSJ SIG Notes SIGAL 123-4, pp. 25-32, 2009.
Koichi Suematsu, Tetsuo Shibuya, Flexible Protein Alignment of 3D-Structures Allowing Dynamic Transformation, ISPSJ SIG Notes SIGBIO 12-12, pp. 87-94, 2008.
Tetsuo Shibuya, Efficient Substructure RMSD Query Algorithms, IPSJ SIG Notes SIGAL 114-8, pp. 57-64, 2007.
Tetsuo Shibuya, Fast and Accurate Algorithms for Protein Hinge Detection, IPSJ SIG Notes SIGBIO 10-4, pp. 25-32, 2007. (IPSJ Yamashita SIG Research Award, March 11, 2009)
Tetsuo Shibuya, Prefix-Shuffled Geometric Suffix Tree, IPSJ SIG Notes SIGAL 112-1, 2007, pp. 1-8.
Kohichi Suematsu, Michihiro Araki, and Tetsuo Shibuya, Graph tiling algorithm for molecular synthesis analysis, SIGAL 106-4, pp. 25-32, 2006.
Tetsuo Shibuya, Geometric Suffix Tree: A New Index Structure for Protein 3-D Structures, IPSJ SIG Notes SIGAL 105-3, pp. 17-24, 2006.
Tetsuo Shibuya, and Igor Kurochkin, Match Chaining Algorithms for cDNA Mapping. Technical Report of IEICE, Vol. 103, No. 326, COMP2003-37, pp. 1-8, 2003.
Tetsuo Shibuya, Christian Schoenbach, Hisashi Kashima and Akihiko Konagaya, Accurate cDNA Clustering Algorithm based on Spliced Sequence Alignment, Technical Report of IEICE, COMP2002-11, pp. 17-24, May 26, 2002.
Tien Huynh, Isidore Rigoutsos, Laxmi Parida, Daniel Platt and Tetsuo Shibuya, The IBM Bioinformatics Group Web Server - Tools and Content, IBM Technical Report RC22726, 2002
Tetsuo Shibuya and Isidore Rigoutsos, Motif Search Algorithm and Its Applications for Gene Finding, Technical Report of IEICE, Vol. 101, No. 376, COMP2001-48, pp. 85-92, 2001.
Tetsuo Shibuya and Isidore Rigoutsos, Dictionary-driven Microbial Gene Finding,
IBM Technical Report RC22051, 2001.
Tetsuo Shibuya, Generalization of a Suffix Tree for RNA Structural Pattern Matching,
IBM TRL Report RT0342, 2000.
Tetsuo Shibuya, New Approaches for Analyzing Recombinations of Biological Sequences, IBM TRL Report RT0343, 2000.
Tetsuo Shibuya, Constructing the Suffix Tree of a Tree with a Large Alphabet, IPSJ SIG Notes SIGAL 69-4, pp. 25-32, 1999.
Tetsuo Shibuya, New Approaches for Analyzing Recombinations of Biological Sequences, Technical Report of IEICE, Vol. 99, No. 30, COMP99-1, pp. 1-8, 1999.
Hiroshi Kawazoe, Tetsuo Shibuya, Takeshi Tokuyama, Optimal On-line Algorithms for an Electronic Commerce Money Distribution System, IBM TRL Report RT0317, 1999.
Tetsuo Shibuya, Constructing the Suffix Tree of a Tree with a Large Alphabet, IBM TRL Report RT0320, 1999.
Hiroshi Kawazoe, Tetsuo Shibuya, and Takeshi Tokuyama, Optimal On-line Algorithms for an Electronic Commerce Money Distribution System, Technical Report of IEICE, Vol. 98, No. 283, COMP98-32, pp. 17-24, 1998.
Tetsuo Shibuya, Computing the n x m Shortest Paths Efficiently By Using the A* Algorithm, IPSJ SIG Notes SIGAL 62-2, pp. 9-16, 1998.
Tetsuo Shibuya and Hiroshi Imai, New Approaches to Flexible Alignment of Multiple Biological Sequences, Cooperative Research Report, "Modeling and Algorithms 9", The Institute of Statical Mathematics, 1997.
Tetsuo Shibuya, Computing the n x m Shortest Paths Efficiently By Using the A* Algorithm, IBM TRL Report RT5133. 1997.
Tetsuo Shibuya and H. Imai, On Parametric Alignments of Multiple Biological Sequences, IPSJ SIG Notes SIGAL52-4, IPSJ, pp. 25-32, 1996, In Japanese.
Tetsuo Shibuya and Hiroshi Imai, Suboptimal Alignments of Multiple Biological Sequences, IPSJ SIG Notes SIGAL51-1, IPSJ, pp. 1-8, 1996.
Hiroshi Imai and Tetsuo Shibuya, K-opt Algorithm for Multiple Alignment, Cooperative Research Report, "Modeling and Algorithms 8", The Institute of Statical Mathematics, 1996.
Tetsuo Shibuya, Finding the k Shortest Paths by AI Search Techniques, Cooperative Research Report, "Modeling and Algorithms 7", The Institute of Statical Mathematics, Vol.77, pp. 212-222, 1995.

Non-refereed Poster Presentation

Akihiro Fujimoto, Hidwaki Nakagawa, Naoya Hosono, Kaoru Nakano, Tetsuo Abe, Masao Nagasaki, Rui Yamaguchi, Tetsuo Shibuya, Michiaki Kubo, Satoru Miyano, Usuke Nakamura and Tatsuhiko Tsunoda, Construction of analysis pipeline and accurate variant calls of a Japanese individual using massively parallel sequencing, The 2nd Biosupercomputing symposium, P-52, p. 146, 2010.
Tetsuo Shibuya, Faster Structural Pattern Matching Algorithms, The 9th International Workshop on Bioinformatics and Systems Bilogy, 2009.
Ritsuko Onuki, Tetsuo Shibuya, and Minoru Kanehisa, A New Method for Genotype Clustering based on Haplotype Inference, Biochemistry and Molecular Biology (BMB 2007), 1P-1071, 2007.
Ritsuko Onuki, Tetsuo Shibuya, and Minoru Kanehisa, Genotype Clustrering based on Haplotype Inference Probabilities, The 52nd Annual Meeting of the Japan Society of Human Genetics, 2007.
Yoshihiro Ohta and Tetsuo Shibuya, Extracting Causalities in Large Biological Data Sets, Japanese Society of Molecular Biology, 1998 Annual meeting, December 1999, Yokohama.

Theses

Tetsuo Shibuya, Research on Fast Algorithms for Comparison and Indexing of Biological Sequence Information, Ph. D Thesis, Department of Information Science, Faculty of Science, University of Tokyo, December 2002.
Tetsuo Shibuya, New Approaches to Flexible Alignment of Multiple Biological Sequences, Master Thesis, Deptartment of Infomation Science, Faculty of Science, University of Tokyo, February 1997.
Tetsuo Shibuya, Finding the k shortest paths by AI search techniques. Bachelor Thesis, Deptartment of Infomation Science, Faculty of Science, University of Tokyo, February 1995.

Others

Publications in Japanese
List of patents (In Japanese)
List of newspaper articles (In Japanese)