Genome Informatics Workshop 1996

December 2-3, 1996
Yebisu Garden Place, Tokyo, Japan

Published as: Akutsu, T., Asai, K., Hagiya, M., Kuhara, S., Miyano, S., and Nakai, K. (eds.); "Genome Informatics Workshop 1996" Universal Academy Press, Tokyo, 1996.

Preface by Tatsuya Akutsu


Oral Session

[GIW96O01] Louxin Zhang: "On a Mirkin-Muchnik-Smith conjecture for comparing molecular phylogenies" [ps] [pdf]

[GIW96O02] Qian-Ping Gu, Shietung Peng, Hal Sudborough: "Approximation algorithms for genome rearrangements" [ps] [pdf]

[GIW96O03] H. Matsuda, T. Ishihara, A. Hashimoto: "A clustering method for molecular sequences based on pairwise similarity" [ps] [pdf]

[GIW96O04] Fei Shi, Peter Widmayer: "Approximate multiple strings searching by clustering" [ps] [pdf]

[GIW96O05] Tetsuo Shibuya, Hiroshi Imai: "Parametric alignment of multiple biological sequences" [ps] [pdf]

[GIW96O06] Michiyo Yamaguchi, Shinichi Shimozono, Takeshi Shinohara: "Finding minimal multiple generalization over regular patterns with alphabet indexing" [ps] [pdf]

[GIW96O07] Shigehiko Kanaya, Yoshihiro Kudo, Shinya Suzuki, Toshimichi Ikemura: "Systematization of species-specific diversity of genes in codon usage: Comparison of the diversity among bacteria and prediction of the protein production levels in cells" [ps] [pdf]

[GIW96O08] Kenta Nakai: "Refinement of the prediction methods of signal peptides for the genome analyses of Saccharomyces cerevisiae and Bacillus subtilis" [ps] [pdf]

[GIW96O09] M. S. Gelfand, T. V. Astakhova, M. A. Roytberg: "An algorithm for highly specific recognition of protein-coding regions" [ps] [pdf]

[GIW96O10] Kiyoshi Asai, Tetsushi Yada, Katunobu Itou: "Finding genes by hidden Markov models with a protein motif dictionary" [ps] [pdf]

[GIW96O11] Naohiro Furukawa, Satoshi Matsumoto, Ayumi Shinohara, Takayoshi Shoudai, Satoru Miyano: "HAKKE: a multi-strategy prediction system for sequences" [ps] [pdf]

[GIW96O12] Carlos A. Del Carpio, Valentin Gogonea: "Modeling proteins conformation in solution. Part I: a parallel GA engine for protein conformational space mapping" [ps]

[GIW96O13] Nickolai N. Alexandrov, Victor V. Solovyev: "Effect of secondary structure prediction on protein fold recognition and database search" [ps] [pdf]

[GIW96O14] Hiroyuki Ogata, Hidemasa Bono, Wataru Fujibuchi, Susumu Goto, Minoru Kanehisa: "Analysis of binary relations and hierarchies of enzymes in the metabolic pathways" [ps] [pdf]

[GIW96O15] Yasuhiko Kitamura, Hideyuki Nakanishi, Tetsuya Nozaki, Teruhisa Miura, Toru Ishida: "MetaViewer and MetaCommander: WWW tools for genome informatics" [ps]

[GIW96O16] R. Gras, J. Nicolas: "FOREST, a browser for huge DNA sequences" [ps] [pdf]

[GIW96O17] Tomohiro Koike, et al.: "Development of new DDBJ DNA sequence database with data annotation" [ps] [pdf]

Poster Session

[GIW96P01] Hajime Kitakami, Yasuma Mori, Masatoshi Arikawa: "A taxonomy database system for managing multimedia contents" [ps] [pdf]

[GIW96P02] Hiroaki Kato, Yoshimasa Takahashi: "Automated identification of three-dimensional motif in proteins" [ps] [pdf]

[GIW96P03] Takayuki Kamei, Yasuo Yonezawa: "Characterization of enzyme structure by informational complexity" [ps] [pdf]

[GIW96P04] Y. Wada, H. Yasue: "Java version of animal genome database" [ps] [pdf]

[GIW96P05] A. Nakaya, A. Yonezawa, K. Yamamoto: A symbolic representation for RNA secondary structures; towards the construction of RNA secondary structures data base [ps] [pdf]

[GIW96P06] Masamichi Isokawa, Masato Wayama, Toshio Shimizu: "Multiple sequence alignment using a genetic algorithm" [ps] [pdf]

[GIW96P07] Takashi Ishikawa, Shigeki Mitaku, Takao Terano: "Discovering functional sites of amino acid sequences using sorted variable generalization" [ps] [pdf]

[GIW96P08] Takatsugu Hirokawa, Seah Boon-Chieng, Shigeki Mitaku: "Improvement of the transmembrane helix prediction system by three-stage model" [ps] [pdf]

[GIW96P09] Takanori Washio, Masahiko Wada, Masaru Tomita: "Sequence analysis of short tandem repeats in the genomes of H.influenzae and M.genitalium" [ps] [pdf]

[GIW96P10] Yasuhiro Asakawa, Masaru Tomita: "On correlation between G+C contents and introns lengths: Longer introns tend to be more A+T rich" [ps] [pdf]

[GIW96P11] Tom Shimizu, Kouichi Takahashi, Masaru Tomita: "CpG dinucleotide distribution and DNA methylation" [ps] [pdf]

[GIW96P12] Rintaro Saito, Hidekazu Sasaki, Yuko Osada, Masaru Tomita: "Computer analyses of nucleotide patterns around start codons" [ps] [pdf]

[GIW96P13] Yuko Osada, Ryo Matsushima, Masaru Tomita: Computer analyses of overlapping genes in Mycoplasma genitalium [ps] [pdf]

[GIW96P14] Michiko Muraki, Masaru Tomita: "Computer analyses of site-specific variabilities in human Alu sequences" [ps] [pdf]

[GIW96P15] Yoshimi Toda, Masaru Tomita: "Inferring history of genomic duplication using subclassified Alu elements" [ps] [pdf]

[GIW96P16] Y. Fujiwara, M. Asogawa: "Motif extraction: Normalization of scores" [ps] [pdf]

[GIW96P17] Minoru Asogawa: "Beta-sheet prediction using inter-strand residue pairs and refinement with Hopfield neural network" [ps] [pdf]

[GIW96P18] K. Nakata, M. Hayakawa, T. Igarashi, T. Kaminuma: Building a receptor database [ps] [pdf]

[GIW96P19] Naoko Kasahara, Susumu Hiraoka, Keiichi Nagai: "Direct comparison DNA and amino acid sequences based on a dynamic programming method" [ps] [pdf]

[GIW96P20] Hikaru Yamamoto, Takuro Tamura, Katsumi Isono, Takashi Gojobori, Hideaki Sugawara, Ken Nishikawa, Naruya Saitou, Tadashi Imanishi, Kaoru Fukami-Kobayashi, Kazuho Ikeo, Yoshio Tateno: "SAKURA: A new data submission system of DDBJ to meet users' needs in the age of mass production of DNA sequences" [ps] [pdf]

[GIW96P21] Hiroaki Inayoshi, Hitoshi Iba: "Emergent rhythms in an artificial chemical world using 'genetic switches'" [ps] [pdf]

[GIW96P22] Yutaka Ueno, Kiyoshi Asai: "A new software for visualization of large proteins" [ps] [pdf]

[GIW96P23] Tetsushi Yada, Yasushi Totoki, Masato Ishikawa, Kiyoshi Asai: "Automatic discovery of hidden Markov representations for functional sites within DNA sequences" [ps] [pdf]

[GIW96P24] Makoto Hirosawa, Tetsushi Yada: "GeneHacker: "Gene-finding program for the prediction of precise protein coding regions" [ps] [pdf]

[GIW96P25] Yasukazu Nakamura, Nobuyuki Miyajima, Makoto Hirosawa, Takakazu Kaneko, Satoshi Tabata: "CyanoBase: The genome database for Synechocystis sp. strain PCC6803" [ps] [pdf]

[GIW96P26] Mika Hirakawa, Kensaku Imai, Akira Ohyama, Fumihiko Kikuchi: "Management system for sequencing data of human genome - as a part of ALIS -" [ps] [pdf]

[GIW96P27] T. Okazaki, M. Kaizawa, H. Mizushima: "Establishment and management of transcription factor database TFDB" [ps] [pdf]

[GIW96P28] F. Lisacek, N. El Mabrouk: "Very fast identification of tRNA in genomic DNA" [ps] [pdf]

[GIW96P29] Aki Hasegawa, Yasuo Uemura, Satoshi Kobayashi, Takashi Yokomori: "Predicting and learning RNA secondary structures" [ps] [pdf]

[GIW96P30] Valentin Gogonea, Camelia Baleanu-Gogonea, Carlos A. Del Carpio: "Modeling proteins conformation in solution. Part II: a solvent effect model based on the evaluation of solvent-accessible surface area and generalized Born equation" [ps] [pdf]

[GIW96P31] Carlos A. Del Carpio, Valentin Gogonea, Katsuhisa Yamaguchi, Makoto Takei, Kouji Nishimura: "Sense-antisense homology boxes in proteins: Structural motifs enconded in the DNA?" [ps] [pdf]

[GIW96P32] A. Ogiwara, N. Ogasawara, M. Watanabe, T. Takagi: "Construction of the Bacillus subtilis ORF database BSORF DB" [ps] [pdf]

[GIW96P33] Suharnan Sivasundaram, Jun-ichi Takeda, Takeshi Itoh, Keiko Takemoto, Hidemi Watanabe, Hideo Matsuda, Hirotada Mori: "Clustering and evolutional analysis of E. coli proteins" [ps] [pdf]

[GIW96P34] Tomoyasu Takahashi, Katsutoshi Takahashi, Masayuki Nakazawa, Yasuo Watanabe: "High-speed genome scanning analysis based on automated detection and matching spots in autoradiogram images of 2-D gel electrophoresis" [ps] [pdf]

[GIW96P35] F. Ren, H. Tanaka, T. Okayama: "The inference of model-based minimum complexity in reconstructing molecular phylogenetic tree" [ps] [pdf]

[GIW96P36] J. An, T. Nakama, Y. Kubota, A. Sarai: "3DInSight: An integrated relational database and search tool for molecular structures and functional sites" [ps] [pdf]

[GIW96P37] Koji Ohnishi, Hiroshi Yanagawa: "Poly-tRNA structure in the Bacilluis subtilis rrnB operon is a relic of an early peptide-synthesizing ribozyme co-ancestral to the E. coli trpE gene and the exon 2 of the chicken triose-phosphate isomerase gene" [ps] [pdf]

[GIW96P38] S. Minoshima, S. Mitsuyama, N. Shimizu: "Mutation View: A network-transparent database system for mutations in the human disease genes" [ps] [pdf]

[GIW96P39] Nobuyuki Uchikoga, Akira Suyama: "Vestiges of primordial words in base sequences of modern genomes" [ps] [pdf]

[GIW96P40] Daisuke Kihara, Toshio Shimizu, Minoru Kanehisa: "A prediction method for transmembrane segments in proteins utilizing multiple discrimination functions" [ps] [pdf]

[GIW96P41] Kentaro Tomii, Minoru Kanehisa: "A statistical analysis of gene arrangement patterns in bacterial and yeast genomes" [ps] [pdf]

[GIW96P42] Susumu Goto, Nobuhiro Fukushima, Minoru Kanehisa: "Standard Gibbs free energy changes of enzyme reactions in metabolic pathway computation" [ps] [pdf]

[GIW96P43] Wataru Fujibuchi, Susumu Goto, Minoru Kanehisa: "Deductive calculation library for KEGG pathway simulation [ps] [pdf]

[GIW96P44] Hidemasa Bono, Hihoyuki Ogata, Susumu Goto, Minoru Kanehisa: "Genome scale prediction of enzyme genes utilizing the knowledge of metabolic interactions" [ps] [pdf]

[GIW96P45] Kazushige Sato, Toyoko Katsurada, Tomomi Kamiya, Mayuko Egoshi, Minoru Kanehisa: "Java applets for handling genome maps in KEGG" [ps] [pdf]

[GIW96P46] Katsuhiko Murakami, Toshihisa Takagi: "Finding coding region using secondary hexamer measure and two-dimensional linear discriminant analysis" [ps] [pdf]

[GIW96P47] Yoshihiro Ohta, Yasunori Yamamoto, Ikuo Uchiyama, Toshihisa Takagi: "Information finding from biological papers" [ps] [pdf]

[GIW96P48] Yasunori Yamamoto, Yoshihiro Ohta, Ikuo Uchiyama, Toshihisa Takagi: "Constructing a dictionary of biological terms for information extraction" [ps] [pdf]

[GIW96P49] Haretsugu Hishigaki, Kagehiko Kitano, Yusuke Nakamura, Hiroumi Maekawa, Toshihisa Takagi: "A refinement system for large amount of cDNA data" [ps] [pdf]

[GIW96P50] Yoshihisa Yamamura, Yukiko Tsukamoto, Kenji Satou, Emiko Furuichi, Toshihisa Takagi, Satoru Kuhara: "Automatic classification of protein structures with deductive database system" [ps] [pdf]

[GIW96P51] Nobutaka Mitsuhashi, Haretsugu Hishigaki, Toshihisa Takagi: "Application of data mining to genetic linkage analysis" [ps] [pdf]

[GIW96P52] Kazuya Inoue, Osamu Maruyama, Takayoshi Shoudai, Satoru Miyano: "Mining binary diagram rules" [ps] [pdf]

[GIW96P53] Osamu Maruyama, Erika Tateishi, Emiko Furuichi, Satoru Kuhara, Satoru Miyano: "A PAC-learning algorithm for conformation rules and its experiments" [ps] [pdf]

[GIW96P54] Akira Ohyama, Kyotetsu Kanaya, Tatsuya Akutsu, Asao Fujiyama: "An image analysis system for two-dimensional gel electrophoresis" [ps] [pdf]

[GIW96P55] Hidetoshi Kitada, Kazuhiro Tono, Masahito Yamamoto, Tamotsu Mitamura, Azuma Ohuchi, Toshio Ohyanagi, Norio Matsushima: "Multiple alignment of biological sequences containing tandem repeat" [ps] [pdf]

[GIW96P56] Meeta Rani, Chanchal K. Mitra: "Harmonic analysis of protein sequences" [ps] [pdf]

Invited Lectures

[GIW96I01] Gordon M. Crippen: "Failures of inverse folding and threading with gapped alignment" [ps] [pdf]

[GIW96I02] Pavel A. Pevzner: "Transforming men into mice" [ps] [pdf]

[GIW96I03] Hiroaki Kitano: "Toward computer-aided biology: A synthetic approach for understanding life" [ps] [pdf]

[GIW96I04] Susumu Tachi: "Virtual reality and tele-existence" [ps] [pdf]