Genome Informatics Project 1991-1995
List of Publications

Genome Informatics Series (ISSN 0919-9454)

Takagi, T., Imai, H., Miyano, S., Mitaku, S., and Kanehisa, M. (eds.); "Proceedings of Genome Informatics Workshop IV", Universal Academy Press, Tokyo, 1993 (ISBN 4-946443-20-7).

Miyano, S., Akutsu, T., Imai, H., Gotoh, O., and Takagi, T. (eds.); "Proceedings of Genome Informatics Workshop 1994", Universal Academy Press, Tokyo, 1994 (ISBN 4-946443-24-X).

Hagiya, M., Miyano, S., Nakai, K., Suyama, A., Yokomori, T., Takagi, T. (eds.); "Proceedings of Genome Informatics Workshop 1995", Universal Academy Press, Tokyo, 1995 (ISBN 4-946443-33-9).

Other Publications

Akutsu, T., Kobayashi, S., Hori, K., and Ohsuga, S.; Algorithms for finding the largest subtree whose copies cover all the leaves. IEICE Trans. Information and Systems E76-D, 707-710 (1993).

Akutsu, T.; A linear time pattern matching algorithm between a string and a tree. Proc. 4th Symposium on Combinatorial Pattern Matching, pp. 1-10 (1993).

Akutsu, T.; Efficient and robust three-dimensional pattern matching algorithms using hashing and dynamic programming techniques. Proc. 27th Hawaii International Conference on System Sciences, pp. 225-234 (1994).

Akutsu, T.; A linear time pattern matching algorithm between a string and a tree. IEICE Trans. Information and Systems E77-D, 281-287 (1994).

Akutsu, T.; Approximate string matching with don't care characters. Lecture Notes in Computer Science 807, 240-249 (1994).

Akutsu, T., Onizuka, K., and Ishikawa, M.; New hashing techniques and their application to a protein structure database system. Proc. 28th Hawaii International Conference on System Science 5, 197-206 (1995).

Akutsu, T.; Approximate string matching with don't care characters. Information Processing Letters 55, 235-239 (1995).

Akutsu, T. and Tashimo, H.; Protein structure comparison using representation by line segment sequences. Proc. Pacific Symposium on Biocomputing '96, pp. 25-40 (1996).

Mukouchi, Y. and Arikawa, S.; Towards a mathematical theory of machine discovery from facts. Thoret. Comput. Sci. 137, 53-84 (1995).

Ikemura, T.; Codon usage. In "Plant Molecular Biology LABFAX" (Brown, T.A., ed.), pp. 38-48, Blackwell Sci. Pub. (1993).

Sugaya, K., Fukagawa, T., Matsumoto, K., Mita, K., Takahashi, E., Ando, A., Inoko, H., and Ikemura, T.; Three genes in the human MHC class III region near the junction with the class II: gene for receptor of advanced glycosylation end products, PBX2 homeobox gene and a Notch homolog, human counterpart of mouse mammary tumor gene int-3. Genomics 23, 408-419 (1994). [7835890]

Fukagawa, T., Sugaya, K., Matsumoto, K., Okumura, K., Ando, A., Inoko, H., and Ikemura, T.; A boundary of long-range G+C% mosaic domains in the human MHC locus: pseudoautosomal boundary-like sequence exists near the boundary. Genomics 25, 184-191 (1995). [7774916]

Fukagawa, T., Nakamura, Y., Okumura, K., Ando, K., Inoko, H., Saitou, N., and Ikemura, T.; Human pseudoautosomal boundary-like sequences (PABLs): core and consensus sequence, expression, and involvement in formation of the present day pseudoautosomal boundary of short arm of human sex chromosomes. Hum. Mol. Genet. 5, 23-32 (1996). [8789436]

Kanaya, S., Kudo, Y., Nakamura, Y. and Ikemura, T.; Detection of genes in Escherichia coli sequences determined by genome projects and prediction of protein production levels, based on multivariate diversity in codan usage. Comput. Appl. Biosci., 12, 213-225 (1996). [8872390]

Ishikawa, M., Toya, T., Hoshida, M., Nitta, K., Ogiwara, A., and Kanehisa, M.; Multiple sequence alignment by parallel simulated annealing. Comput. Appl. Biosci. 9, 267-273 (1993). [8324627]

Hirosawa, M., Totoki, Y., Hoshida, M., and Ishikawa, M.; Comprehensive study on iterative algorithms of multiple sequence alignment. Comput. Appl. Biosci. 11, 13-18 (1995). [7796270]

Hakata, K. and Imai, H.; The longest common subsequence problem for small alphabet size between many strings. Lecture Notes in Computer Science 650, 469-478 (1992).[Imai.Lab]

Ogasawara, N., Nakai, S., and Yoshikawa, H.; Systematic sequencing of the 180 kilobase region of the Bacillus subtilis chromosome containing the replication origin. DNA Res. 1, 1-14 (1994). [7584024]

Yoshida, K., Sano, H., Miwa, Y., Ogasawara, N., and Fujita, Y.; Cloning an nucleotide sequence of a 15kb region of the Bacillus subtilis genome containing the iol operon. Microbiology 140, 2289-2298 (1994). [7952181]

Ogasawara, N., Fujita, Y., Kobayashi, Y., Sadaie, Y., Tanaka, T., Takahashi, H., Yamane, K., and Yoshikawa, H.; Systematic sequencing of the Bacillus subtilis genome: progress report of the Japanese group. Microbiology 141, 257-259 (1995). [7704252]

Akagawa, E., Kurita, K., Sugawara, T., Nakamura K., Kasahara, Y., Ogasawara, N., and Yamane K.; Determination of 17, 484 bp nucleotide sequence around the 39o region of the Bacillus subtilis chromosome and similarity analysis of the products of putative ORFs. Microbiology 141, 3241-3245 (1995). [8574415]

Ogiwara, A., Uchiyama, I., Seto, Y., and Kanehisa, M.; Construction of a dictionary of sequence motifs that characterize groups of related proteins. Protein Eng. 5, 479-488 (1992). [1438158]

Fujibuchi, W. and Kanehisa, M.; A method to extract functional motifs for transcriptional regulation in eukaryotic sequences. Bull. Inst. Chem. Res., Kyoto Univ. 71, 317-326 (1993).

Ohkubo, Z. and Kanehisa, M.; Characterization of spatially close peptide segments in proteins. Bull. Inst. Chem. Res., Kyoto Univ. 71, 327-337 (1993).

Uchiyama, I., Ogiwara, A., and Kanehisa, M.; A library of signature pentapeptides for the Protein Data Bank. In "Protein Structures by Distance Analysis" (Bohr, H. and Brunak, S., eds.), 237-246, IOS Press (1994).

Mizuno, M. and Kanehisa, M.; Distribution profiles of GC content around the translation initiation site in different species. FEBS Lett. 352, 7-10 (1994). [7925946]

Ogata, H., Akiyama, Y., and Kanehisa, M.; A genetic algorithm based molecular modeling technique for RNA stem-loop structures. Nucleic Acids Res. 23, 419-426 (1995). [7533901]

Tomii, K. and Kanehisa, M.; Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng. 9, 27-36 (1996). [9053899]

Ogata, H., Fujibuchi, W., and Kanehisa, M.; The size differences among mammalian introns are due to the accumulation of small deletions. FEBS Lett. 390, 99-103 (1996). [8706839]

Ogiwara, A., Uchiyama, I., Takagi, T., and Kanehisa, M.; Construction and analysis of a profile library characterizing groups of structurally known proteins. Prot. Sci. 5, 1991-1999 (1996). [8897599]

Kuhara, S., Kanehisa, M., and Yoshida, Y.; A gene mapping database HyperGenome System. Proc. International Symposium on Advanced Computing for Life-Science, pp. 250-252 (1992).

Satou, K., Furuichi, E., Takiguchi, K., Takagi, T., and Kuhara, S.; A deductive database system PACADE for analyzing 3-D and secondary structures of protein. Comput. Appl. Biosci. 9, 259-265 (1993). [8324626]

Satou, K., Furuichi, E., Takagi, T., Kuhara, S., and Ushijima, K.; Similar structure search in deductive database. Proc. International Symposium on Next Generation Database Systems and Their Applications, pp. 130-137 (1993).

Furuichi, E., Kamikawaji, N., Sasazuki, T., and Kuhara, S.; Estimation of the mechanism of peptide binding to HLA class III molecules. In "Modern Trends in Biothermokinetics" (Schuster, S. et al., eds.), Plenum, pp. 377-381 (1993).

Satou, K., Furuichi, E., Takiguchi, K., Kuhara, S., and Takagi, T.; Application of a deductive database system PACADE toward discovery of cluster of similar structures in proteins. Proc. 27th Hawaii International Conference on System Sciences, Vol. 5, pp. 160-169 (1994).

Nishikawa, A., Satou, E., Furuichi, E., Kuhara, S., and Takagi, T.; Equipments for statistical analysis in a deductive database system. Proc. International Symposium on Advanced Database Technologies and Their Integration, pp. 237-244 (1994).

Nishikawa, A., Satou, E., Furuichi, E., Kuhara, S., and Ushijima, K.; Data claasification component in a deductive database system and its application to protein structural analysis. IEICE Trans. Information and Systems E78-D, 1377-1386 (1995).

Gotoh, O.; Optimal alignment between groups of sequences and its application to multiple sequence alignment. Comput. Appl. Biosci. 9, 361-370 (1993). [8324637]

Gotoh, O.; Further improvement in methods of group-to-group sequence alignment with generalized profile operations. Comput. Appl. Biosci. 10, 379-387 (1994). [7804871]

Gotoh, O.; A weighting system and algorithm for aligning many phylogenetically related sequences. Comput. Appl. Biosci. 11, 543-551 (1995). [8590178]

Niwa-Kawakita, M., Miyoshi, H., Gotoh, O., Matsushima, Y., Nishimura, M., Shisa, H., and Ohki, M.; Cloning and gene mapping of the mouse homologue of the CBFA2T1 gene associated with human acute myeloid leukemia. Genomics 29, 755-759 (1995). [8575770]

Gotoh, O.; Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignment. J. Mol. Biol. 264, 823-838 (1996).[8980688]

Barnes, T.M., Kohara, Y., Coulson, A., and Hekimi, S.; Meiotic recombination, noncoding DNA and genomic organization in Caenorhabditis elegans. Genetics 141, 159-179 (1995). [8536965]

Takagi, T.; ODS: Overlapping Oligonucleotide Database with deductive engine for signal sequence search. Proc. 2nd International Conference on Bioinformatics, Supercomputing & Complex Genome Analysis, pp. 263-272 (1992).

Sakamoto, N., Takagi, T., and Sakaki, Y.; Development of Overlapping Oligonucleotide Database and its application to signal sequence search of the human genome. Comput. Appl. Biosci. 9, 427-434 (1993). [7691383]

Goto, S., Sakamoto, N., and Takagi, T.; Object-oriented database with rule-based query interface for genomic computation. Proc. 3rd International Symposium on Database Systems for Advanced Applications, pp. 65-72 (1993).

Goto, S., Sakamoto, N., Takagi, T., and Ushijima, K.; A deductive language in object-oriented database for genome analysis. Proc. International Symposium on Next Generation Database Systems and Their Applications, pp. 123-129 (1993).

Suzuki, T., Takagi, T., Kuhara, S., and Kanehisa, M.; Development of an integrated database for genome mapping and nucleotide sequences. Proc. 27th Hawaii International Conference on System Sciences, Vol. 5, pp. 68-76 (1994).

Sakamoto, N., Goto, S., and Takagi, T.; A deductive database system for analyzing human nucleotide sequence data. Int. J. Bio-Medical Computing, 171-179 (1994). [7960201]

Murakami, K., Tsukuni, S., Takagi, T., and Hattori, M.; Evaluation of exon prediction tools using a long DNA sequence data. Proc. Gene-Finding and Gene Structure Prediction Workshop (1995).

Takaoka, T.; Approximate pattern matching with samples. Lecture Notes in Computer Science 834, 234-242 (1994).

Kamimura, M., Takahashi, Y., and Sasaki, S.; Phi-psi conformational pattern clustering of protein amino acid residues using the potential function method. J. Protein. Chem. 11, 393-394 (1992).

Kamimura, M. and Takahashi, Y.; Phi-psi conformational pattern clustering of protein amino acid residues using the potential function method. Comput. Appl. Biosci. 10, 163-169 (1994). [8019864]

Nakai, K. and Sakamoto, H.; Construction of a novel database containing aberrant splicing mutations of mammalian genes. Gene 141, 171-177 (1994). [8163185]

Nakai, K., Tokimori, T., Ogiwara, A., Uchiyama, U., and Niiyama, T.; Gnome: an Internet-based sequence analysis tool. Comput. Appl. Biosci. 10, 547-550 (1994). [7828072]

Horton, P. and Nakai, K.; A probabilistic classification system for predicting the cellular location sites of proteins. ISMB 4, 109-115 (1996). [8877510]

Nakata, K.; Prediction of zinc finger DNA-binding protein. Comput. Appl. Biosci. 11, 125-131 (1994). [7620983]

Suyama, M., Ogiwara, A., Nishioka, T., and Oda, J.; Searching for amino acid sequence motifs among enzymes: the Enzyme-Reaction Database. Comput. Appl. Biosci. 9, 9-15 (1993). [8435774]

Suyama, M., Nishioka, T., and Oda, J.; Searching for common sequence patterns among distantly related proteins. Protein Eng. 8, 1075-1080 (1995). [8819973]

Hagiya, M.; A typed lambda-calculeus for proving-by-example and bottom-up generalization procedure, algorithmic learning theory. Lecture Notes in Artificial Intelligence 744, 73-86, (1993).

Hagiya, M. and Toda, Y.; On implicit arguments, logic, language and computation - Festschrift in honor of Satoru Takasu. Lecture Notes in Computer Science 792, 10-30 (1994).

Shimada, T., Hagiya, M., Arita, M., Nishizaki, S., and Tan, C.L.; Knowledge-based simulation of regulatory action in lambda phage. Int. J. Artificial Intelligence Tools, 4, 511-523 (1995).

Yoshikawa, H., Nagai, H., Matsubara, K., and Fujiyama, A.; Two-dimensional gel electrophoretograms of human chromosome specific restriction DNA fragments. Biochem. Biophys. Res. Com. 196, 1566-1572 (1993). [8250912]

Husimi, Y., Murata, G., Yoshino, K., et al; Continuous culture of virus as a model of evolving systems and its application to evolutionary molecular engineering. In "The Origin and Evolution of the Cell" (Hartman, , H. and Matsuno, K., eds.), pp.375-386, World Sci. (1992).

Husimi, Y., Mori, Y., Ushijima, S., and Aita, T.; Modes of population changeovers in continuous culture of bacterial and viral mutants spectrum. J. Theoret. Biol. 165, 577-591 (1993). [8114508]

Aita, T. and Husimi, Y.; Period-dependent selection in continuous culture of viruses in periodic environment. J. Theoret. Biol. 168, 281-289 (1994). [8072295]

Nemoto, N. and Husimi, Y.; A model of the virus-type strategy in the early stage of encoded molecular evolutions. J. Theoret. Biol. 176, 67-77 (1995). [7475108]

Aita, T. and Husimi, Y.; Fitness spectrum among random mutants on Mt.Fuji-type fitness landscape. J. Theoret. Biol., 182, 469-485 (1996). [8944894]

Kaneda, Y. and Matsuda, H.; A priority control system for OR-parallel Prolog and its performance evaluation. Lecture Notes in Computer Science 748, 42-53 (1993).

Matsuda, H. and Kaneda, Y.; An application of an OR-parallel prolog system to phylogenetic analysis. Lisp and Symbolic Computation 7, 211-229 (1994).

Matsuda, H.; Querying genomic database by using a parallel logic programming system on distributed computing environment. Proc. IEEE Pacific Rim Conference on Communications, Computers, and Signal Processing, pp. 333-336 (1995).

Matsuda, H.; Protein phylogenetic inference using maximum likelihood with a genetic algorithm. Proc. Pacific Symposium on Biocomputing '96, pp. 512-523 (1996).

Mitaku, S., Suwa, M., and Saito, N.; A computer system for predicting membrane protein structure. J. Protein Chem. 11, 390-391 (1992).

Suwa, M., Mitaku, S., Shimazaki, K., and Chuman, T.; Characterization of Transmembrane Helices by a Probe Helix of Molecular Energy Calculation. Jpn. J. Appl. Phys. 31, 951-956 (1992).

Suwa, M., Mitaku, S., and Kuroda, Y.; Theoretical analysis of amino acid sequence of human dystrophin. Biochem. Biophys. Res. Commun. 191, 782-789 (1993). [8466516]

Suwa, M., Hirokawa, T., and Mitaku, S.; A continuum theory for the prediction of lateral and rotational positioning of a-helices in membrane proteins: bacteriorhodopsin. Proteins 22, 363-377 (1995). [7479710]

Dohi, H., Ishizuka, M., Minoshima, S., and Shimizu, N.; GeneView: multi-language human gene mapping library with a graphical user interface. Comput. Appl. Biosci. 9, 459-464 (1993). [8402212]]

Arikawa, S., Kuhara, S., Miyano, S., Shinohara, A., and Shinohara, T.; A learning algorithm for elementary formal systems and its experiments on identification of transmembrane domains. Proc. 25th Hawaii International Conference on System Sciences, Vol. 1, pp. 675-684 (1992).

Arikawa, S., Kuhara, S., Miyano, S., Mukouchi, Y., Shinohara, A., and Shinohara, T.; A machine discovery from amino acid sequences by decision trees over regular patterns. New Generation Computing 11, 361-375 (1993).

Shimozono, S., Shinohara, A., Shinohara, T., Miyano, S., Kuhara, S., and Arikawa, S.; Finding alphabet indexing for decision trees over regular patterns: An approach to bioinformatical knowledge acquisition. Proc. 26th Hawaii International Conference on System Sciences, Vol. 1, pp. 763-772 (1993).

Miyano, S.; Learning theory toward genome informatics. Proc. 4th International Workshop on Algorithmic Learning Theory, pp. 19-36 (1993).

Shimozono, S., Shinohara, A., Shinohara, T., Miyano, S., Kuhara, S., and Arikawa, S.; Knowledge acquisition from amino acid sequences by machine learning system BONSAI. Trans. Information Processing Society of Japan 35, 2009-2018 (1994).

Shoudai, T., Lappe, M., Miyano, S., Shinohara, A., Okazaki, T., Arikawa, S., Uchida, T., Shimozono, S., Shinohara, T., and Kuhara, S.; BONSAI Garden: parallel knowledge discovery system for amino acid sequences. ISMB 3, 359-366 (1995). [7584459]

Shimozono, S. and Miyano, S.; Complexity of finding alphabet indexing. IEICE Trans. Information and Systems E78-D, 13-18 (1995).

Miyano, S.; Learning theory toward genome informatics. IEICE Trans. Information and Systems E78-D, 560-567 (1995).

Tateishi, E. and Miyano, S.; A greedy strategy for finding motifs from yes-no examples. Proc. Pacific Symposium on Biocomputing '96, pp. 599-613 (1996).

Karasawa, T., Tabuchi, K., Fumoto, M., and Yasukawa, T.; Development of simulation models for protein folding in thermal annealing process - I: a simulation of BPTI folding by pearl necklace model. Comput. Appl. Biosci. 9, 243-251 (1993). [7686806]

Izumisawa, J., Higuti, M., Yoshizawa, T., and Yasukawa, T.; Prediction of protein structure by Hopfield algorithm II: analysis of inter-residue interaction and application to small proteins. Repts. Progr. Polym. Phys. Japan 36, 621-624 (1993).

Fumoto, M. and Yasukawa, T., ; Effects of short range force on the folding processes of proteins. Repts. Progr. Polym. Phys. Japan 37, 719-722 (1994).

Yoshizawa, T., Fumoto, M., and Yasukawa, T., ; Prediction of protein conformations by a spin glass model (II). Repts. Progr. Polym. Phys. Japan 38, 593-596 (1995).

Yokomori, T., Ishida, N., and Kobayashi, S.; Learning local languages and its application to protein alpha-chain identification. Proc. 27th Hawaii International Conference on System Sciences, pp. 113-122 (1994).

Nakaya, A., Yamamoto, K., and Yonezawa., A.; RNA secondary structure prediction using highly parallel computers. Comput. Appl. Biosci. 11, 685-692 (1995). [8808586]

Nakaya, A., Taura, K., Yamamoto, K. and Yonezawa, A.; Visualization of RNA secondary structures using highly parallel computers. Comput. Appl. Biosci. 12, 205-211 (1996). [8872389]