Genome Informatics Project 1996-2000
List of Publications

Genome Informatics Series (ISSN 0919-9454)

Akutsu, T., Asai, K., Hagiya, M., Kuhara, S., Miyano, S., and Nakai, K. (eds.); "Genome Informatics Workshop 1996", Universal Academy Press, Tokyo, 1996 (ISBN 4-946443-37-1).

Miyano, S. and Takagi, T. (eds.); "Genome Informatics 1997", Universal Academy Press, Tokyo, 1997 (ISBN 4-946443-47-9).

Miyano, S. and Takagi, T. (eds.); "Genome Informatics 1998", Universal Academy Press, Tokyo, 1998 (ISBN 4-946443-52-5).

Other Publications

Akutsu, T.; Protein structure alignment using dynamic programming and iterative improvement. IEICE Trans. Information and Systems E79-D, 1629-1636 (1996).

Akutsu, T. and Miyano, S.; On the approximation of protein threading. Proc. 1st Int. Conf. on Computational Molecular Biology, pp. 3-8 (1997).

Akutsu, T., Onizuka, K., and Ishikawa, M.; Rapid protein fragment search using hash functions based on the Fourier transform. CABIOS 13, 357-364 (1997).

Akutsu, T. and Tashimo, H.; Linear programming based approach to the derivation of a contact potential for protein threading. PSB 3, 413-424 (1998).

Akutsu, T., Kuhara, S., Maruyama, O., and Miyano, S.; Identification of gene regulatory networks by strategic gene disruptions and gene overexpressions. Proc. 9th Annual ACM-SIAM Symposium on Discrete Algorithms, 695-702 (1998).

Asai, K., Yada, T., and Itou, K.; Finding genes by hidden Markov models with a protein motif dictionary. Genome Informatics 7, 88-97 (1996).

Ueno, Y. and Asai, K.; A new plug-in software architecture applied for a portable molecular structure browser. ISMB 5, 329-332 (1997).

Asai, K., Itou, K., Ueno, Y., and Yada, T.; Recognition of human genes by stochastic parsing. PSB 3, 228-239 (1998).

Ueno, Y. and Asai, K.; A hight-throughput graphics library designed for portable molecular structure viewer. PSB 3, 201-212 (1998).

Yada, T., Totoki, Y., Ishikawa, M., Asai, K., and Nakai, K.; Automatic extraction of motifs represented in the hidden markov model from a number of DNA sequences. Bioinformatics 14, 317-325 (1998).

Kitamura, Y., Nakanishi, H., Nozaki, T., Miura, T., and Ishida, T.; MetaViewer and MetaCommander: applying WWW tools to genome informatics. Genome Informatics 7, 137-146 (1996).

Shibuya, T. and Imai, H.; Parametric alignment of multiple biological sequen ces. Genome Informatics 7, 41-50 (1996).

Shibuya, T. and Imai, H.; Enumerating suboptimal alignments of multiple biological sequences efficiently. PSB 2, 409-420 (1997)

Shibuya, T. and Imai, H.; New flexible approaches for multiple sequence alig nment. J. Comp. Biol. 4, 385-413 (1997).

Doi, K. and Imai, H.; Greedy algorithms for finding a small set of primers satisfying cover length resolution conditions in PCR experiments. Genome Informatics 1997, Universal Academic Press, 43-52 (1997).

Ogata, H., Bono, H., Fujibuchi, W., Goto, S., and Kanehisa, M.; Analysis of binary relations and hierarchies of enzymes in the metabolic pathways. Genome Informatics 7, 128-136 (1996).

Goto, S., Bono, H., Ogata, H., Fujibuchi, W., Nishioka, T., Sato, K., and Kanehisa, M.; Organizing and computing metabolic pathway data in terms of binary relations. PSB 2, 175-186 (1997).

Fujibuchi, W. and Kanehisa, M.; Prediction of gene expression specificity by promoter sequence patterns. DNA Res. 4, 81-90 (1997).

Kanehisa, M.; A database for post-genome analysis. Trends Genet. 13, 375-376 (1997).

Kanehisa, M.; Linking databases and organisms - GenomeNet resources in Japan. Trends Biochem. Sci. 22, 442-444 (1997).

Fujibuchi, W., Goto, S., Migimatsu, H., Uchiyama, I., Ogiwara, A., Akiyama, Y., and Kanehisa, M.; DBGET/LinkDB: an Integrated Database Retrieval System. PSB 3, 683-694 (1998).

Bono, H., Ogata, H., Goto, S., and Kanehisa, M.; Reconstruction of amino acid biosynthesis pathways from the complete genome sequence. Genome Res. 8, 203-210 (1998).

Ogata, H., Goto, S., Fujibuchi, W., and Kanehisa, M.; Computation with the KEGG pathway database. BioSystems 47, 119-128 (1998).

Goto, S., Nishioka, T., and Kanehisa, M.; LIGAND: Chemical database for enzyme reactions. Bioinformatics 14, 591-599 (1998).

Tomii, K. and Kanehisa, M.; A comparative analysis of ABC transporters in the complete microbial genomes. Genome Res. 8, 1048-1059 (1998).

Kanehisa, M.; Databases of Biological Information. Trends Guide to Bioinformatics, pp. 24-26 (1988).

Kihara, D., Shimizu, T., and Kanehisa, M.; Prediction of membrane proteins based on classification of transmembrane segments. Protein Eng., in press (1998).

Bono, H., Goto, S., Fujibuchi, W., Ogata, H., and Kanehisa, M.; Systematic prediction of orthologous units of genes in the complete genomes. Genome Informatics, in press (1998).

Tomii, K. and Kanehisa, M.; Systematic detection of protein structural motifs. In "Pattern Discovery in Molecular Biology" (Wang, J.T., Shapiro, B.A., and Shasha, D., eds.), in press, Oxford Univ. Press (1998).

Kanehisa, M.; KEGG - from genes to biochemical pathways. In "Molecular Biology Databases" (Letovsky, S., ed.), in press, Kluwer Academic Press (1998).

Miura, T. and Ishida, T.; Stochastic node caching for memory-bounded search. Proc. National Conference on Artificial Intelligence (AAAI-98), 450-456 (1998).

Tsukamoto, Y., Takiguchi, K., Satou, K., Furuichi, E., Takagi, T., and Kuhara, S.; Application of a deductive database system for topological and similar three dimensional structures in protein. CABIOS 13, 183-190 (1997).

Satou, K., Ono, T., Yamamura, Y., Furuichi, E., Kuhara, S., and Takagi, T.; Extraction of substructures of proteins essential to their biological functions by a data mining technology. ISMB, 5, 254-257 (1998).

Tho, H., Kamikawaji, N., Tana, T., Sasazuki, T., and Kuhara, S.; Molecular dynamics simulations of HLA-DR4(DRB*0405) complexed with analogoue peptide: Comformational changes in putative T-cell receptor binding regions. Protein Engneering, accepted.

Akutsu, T., Miyano, S., and Kuhara, S.; Identification of genetic networks from a small number of gene expression patterns under the boolean network mode. PSB99, accepted.

Furukawa, N., Matsumoto, S., Shinohara, A., Shoudai, T., and Miyano, S.; HAKKE: a multi-strategy prediction system for sequences, Genome Informatics 7, 98-107 (1996).

Kida, T., Takeda, M., and Shinohara, A.; Multiple pattern matching in LZW compressed text. Data Compression Conference, 103-112 (1998).

Hayashi, Y., Matsumoto, S., Shinohara, A., and Takeda, M.; Uniform characterizations of polynomial-query learnabilities. Proc. 1st Inter. Conf. on Discovery Science, to appear (1998).

Satou, K., Furuichi, E., Hashimoto, S., Tsukamoto, Y., Kuhara, S., Takagi, T., and Ushijima, K.; Development of a deductive database system for computing closures of similarity relationships among protein structures. J. Jap. Soc. Artificial Intelligence, 11, 440-450 (1996).

Satou, K., Shibayama, G., Ono, T., Yamamura, Y., Furuichi, E., Kuhara, S., and Takagi, T.; Finding association rules on heterogeneous genome data. PSB 2, 397-408 (1997).

Ohta, Y., Yamamoto, Y., Okazaki, T., Uhicyama, I., and Takagi, T.; Automatic construction of knowledge base from biological papers. ISMB 5, 218-225 (1997).

Satou, K., Ono, T., Yamamura, Y., Furuichi, E., Kuhara, S., and Takagi, T.; Extraction of substructures of proteins essential to their biological functions by data mining technique. ISMB 5, 254-257 (1997).

Murakami, K. and Takagi, T.; Gene recognition by combination of several gene- finding programs. Bioinformatics, in press (1998).

Tsunoda, T. and Takagi, T.; A new cut-off estimating algorithm for transcription factor bindability on DNA. BGRS'98, 199-202 (1998).

Nishida, K., Makino, T., Torisawa, K., Tateisi, Y., and Tsujii, J.; Extension of a feature structure abstract machine for partial unification. PACLING 97, 232-243 (1997).

Ninomiya, T., Torisawa, K., Taura, K., and Tsujii, J.; A parallel cky parsing algorithm on large-scale distributed-memory parallel machines. Proc. PACLING '97, 223-231 (1997).

Makino, T., Torisawa, K., and Tsujii, J.; LiLFeS---Practical unification-based programming system for typed feature structures. Proc. NLPRS 97, 239-244 (1997).

Tomita, M., Shimizu, N., and Brutlag, D. L.; Introns and reading frames: correlation between splicing sites and their condon positions. Molecular Biology and Evolution 13, 1229-1223 (1996).

Nakai, K.; Refinement of the prediction methods of signal peptides for the genome analyses of Saccharomyces cerecisiae and Bacillus subtilis. Genome Informatics 7, 72-81 (1996).

Horton, P. and Nakai, K.; Better prediction of protein cellular localization sites with the k nearest neighbor classifier. ISMB 5, 147-152 (1997).

Yada, T., Totoki, Y., Ishii, T., and Nakai, K.; Functional prediction of B. subtilis genes from their regulatory sequences. ISMB 5, 354-357 (1997).

Yada, T., Totoki, Y., Ishikawa, M., Asai, K., and Nakai, K.; Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences. Bioinformatics, 14, 317-325 (1998).

Sakamoto, K., Kiga, D., Komiya, K., Gouzu, H., Yokoyama, S., Ikeda, S., Sugiyama, H., and Hagiya, M.; State transitions by molecules. Preliminary Proceedings, Fourth International Meeting on DNA Based Computers, University of Pennsylvania, 87-99 (1998).

Hagiya, M.; Towards autonomous molecular computers. Genetic Programming 1998, 691-699 (1998).

Matsuda, H., Ishihara, T., and Hashimoto, A.; A clustering method for nolecular sequences based on pairwise similarity. Genome Informatics 7, 23-32 (1996).

Matsuda, H., Taniguchi, F., and Hashimoto, A.; An approach to detection of protein structural motifs using an encoding scheme of backbone conformations. PSB 2, 280-291 (1997).

Matsuda, H., Kawabata, T., and Kaneda Y.; Implementation of a parallel prolog system on a distributed memory parallel computer. IEICE Trans. Information and Systems E80-D, 504-509 (1997).

Imai, T., Matsuda, H., Sekihara, T., Nakanishi, M., and Hashimoto, A.; Implementing an integrated system for heterogeneous molecular biology databases with intelligent agents. Proc. IEEE Pacific Rim Conf. on Communications, Computers, and Signal Processing, pp. 807-810 (1997).

Matsuda, H., Ishihara, T., and Hashimoto, A.; Classifying molecular sequences using a linkage graph with their pairwise similarities. Theoretical Computer Science, 210, in press (1998).

Matsuda, H., Yamanaka , H., and Hashimoto, A.; An approximation algorithm for genome rearrangements with reversals and transpositions. IPSJ Transactions on Mathematical Modeling and Problem Solving, 1, in press (1998).

Fujio, F. and Matsumoto, Y.; Japanese dependency structure analysis based on lexicalized statistics. Proceedings of the 3rd Conference on Empirical Methods in Natural Language Processing, 88-96 (1998).

Nagamine, K., Peterson, P., Scott, H. S., Kudoh, J., Minoshima, S., Heino, M., Krohn, K. J. E., Lalioti, M. D., Mullis, P. E., Antonarakis, S. E., Kawasaki, K., Asakawa, S., Ito, F., and Shimizu, N.; Positional cloning of the APECED gene. Nature Genet, 17, 393-398 (1997).

Kitada, T., Asakawa, S., Hattori, N., Matsumine, H., Yamamura, Y., Minoshima, S., Yokochi, M., Mizuno, Y., and Shimizu, N.; Deletion mutation in a novel ubiquitin-like protein (PARKIN) gene causes autosomal recessive juvenile Parkinsonism (AR-JP). Nature, 392, 605-608 (1998).

Footz, T. K., Birren, B., Minoshima, S., Asakawa, S., Shimizu, N., Riazi, M. A., and McDermid, H. E.; The gene for death agonist BID2 maps to the region of human 22q11.2 duplicated in cat eye syndrome chromosomes and to mouse chromosome 6. Genomics, 51, 472-475 (1998).

Tateishi, E., Maruyama, O., and Miyano, S.; Extracting best consensus motifs from positive and negative examples. Lecture Notes in Computer Science 1046, 219-230 (1996).

Maruyama, O., Uchida, T., Shoudai, T., and Miyano, S.; Toward genomic hypothesis creator: View designer for discovery. Lecture Notes in Artificial Intelligence, in press, (1998).

Akutsu, T., Maruyama, O., Kuhara, S., and Miyano, S.; Identification of gene regulatory networks by strategic gene disruptions and gene overexpressions, Proc. 9th ACM-SIAM Symposium on Discrete Algorithms, 695-702 (1998).

Yamaguchi, A., Nakano, K., and Miyano, S.; An approximation algorithm for the minimum common supertree problem. Nordic J. Computing 4, 303-316 (1997).

Yamamoto, Y., et al.; Construction of a contiguous 874-kb sequence of the escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features. DNA RESEARCH 4, 91-113, 169-178, Supplement, (1998).

Watanabe, H., Mori, H., Itoh, T., and Gojobori, T.; Genome plasticity as a paradigm of eubacteria evolution. J. Mol. Evol. 44, 57-64 (1997).

Hirano, M., Mori, H., Onogi, T., Yamazoe, M., Niki, H., Ogura, T., and Hiraga, S.; Autoregulation of the partition of the mini-F plasmid and the intracellular localization of their products in escherichia coli. Mol. Gen. Genet. 257, 392-403 (1998).

Morishita, S.; On classification and regression. Lecture Notes in Computer Science, in press (1998).

Fukuda, T., Morimoto, Y., Morishita, S., and Tokuyama, T.; Mining optimized association rules for numeric attributes. Journal of Computer and System Sciences - Special issue on the 15th ACM SIGACT-SIGMOD-SIGART Symposium on Principles of Database Systems, in press (1998).

Morimoto, Y., Fukuda, T., Morishita, S., and Tokuyama, T.; Implementation and evaluation of decision trees with range and region splitting. Constraints, An Internat, in press (1998).

Kato, H. and Takahashi, Y.; Three-dimensional structural feature search of proteins. Bull.Chem.Soc.Jpn. 70, 1523-1529 (1997).

Kato, H. and Takahashi, Y.; SS3D-P2: A three-dimensional substructure search program for protein motifs based on secondary structure elements. CABIOS, in press (1997).

Nakaya, A., Yonezawa, A., and Yamamoto, K.; Classification of RNA decondary structures using the techniques of cluster analysis. J. Theor. Biol 183, 105-117 (1996).

Gu, Q.P., Peng, S., and Sudborough, H.; Approximation algorithms for genome rearrangements. Genome Informatics 7, 13-22 (1996).