Genome Informatics Workshop 1994

December 19-20, 1994
Pacific Convention Plaza, Yokohama, Japan

Published as: Miyano, S., Akutsu, T., Imai, H., Gotoh, O., and Takagi, T. (eds.); "Proceedings of Genome Informatics Workshop 1994", Universal Academy Press, Tokyo, 1994.

Preface by Satoru Miyano


Oral Session

[GIW94O01] Tatsuya Akutsu, Kentaro Onizuka, Masato Ishikawa: "New Hashing Techniques for Three-Dimensional Protein Structures" [ps] [pdf]

[GIW94O02] Yo Matsuo, Ken Nishikawa: "Prediction of protein structural similarities using a 3D-1D compatibility method" [ps] [pdf]

[GIW94O03] Hiroshi Mamitsuka, Naoki Abe: "Prediction of Beta-Sheet Structures Using Stochastic Tree Grammars" [ps] [pdf]

[GIW94O04] Satoshi Kobayashi, Takashi Yokomori: "Modeling RNA Secondary Structures Using Tree Grammars" [ps]

[GIW94O05] Hiroki Arimura, Ryoichi Fujino, Takeshi Shinohara, Setsuo Arikawa: "Protein Motif Discovery from Positive Examples by Minimal Multiple Generalization over Regular Patterns" [ps] [pdf]

[GIW94O06] Hugues Ripoche, Engelbert Mephu Nguifo, Jean Sallantin: "Indexing protein sequences with MINOS." [ps] [pdf]

[GIW94O07] Shusaku Tsumoto, Hiroshi Tanaka, Kohei Tsumoto, Izumi Kumagai: "Comparative Analysis of Amino Acid Sequences based on Rough Sets and Domain Knowledge Hierarchy" [ps] [pdf]

[GIW94O08] Makoto Hirosawa, Reiko Tanaka, Hidetoshi Tanaka, Masayuki Akahoshi, Masato Ishikawa: "Simulative representation of biological knowledge using object-oriented database language" [ps] [pdf]

[GIW94O09] Masanori Arita, Masami Hagiya, Tomoki Shiratori: "GEISHA SYSTEM:An Environment for Simulating Protein Interaction" [ps] [pdf]

[GIW94O10] Takahiro Ikeda, Hiroshi Imai: "Fast A* Algorithms for Multiple Sequence Alignment" [ps] [pdf]

[GIW94O11] Jerome Gracy, Jean Sallantin: "Multiple sequence alignment using anchor points through generalized dynamic programming" [ps] [pdf]

[GIW94O12] Masato Ishikawa, Tomoyuki Toya, Yasushi Totoki, Reiko Tanaka: "Multiple RNA-Sequence Alignment Considering Stem Regions" [ps] [pdf]

[GIW94O13] Hideo Matsuda, Hiroshi Yamashita, Yukio Kaneda: "Molecular Phylogenetic Analysis using both DNA and Amino Acid Sequence Data and Its Parallelization" [ps] [pdf]

[GIW94O14] Masahiko Mizuno, Minoru Kanehisa: "Distribution of Base Composition around the Splice Sites in Different Species" [ps] [pdf]

Poster Session

[GIW94P01] Takeshi Itoh, Minoru Yano, Keiko Takemoto, Yutaka Akiyama, Hirotada Mori: "Construction and analysis of Escherichia coli genome database" [ps] [pdf]

[GIW94P02] Hajime Kitakami, Yoshio Tateno, Takashi Gojobori: "YAYOI: Taxonomy Database System over International Computer Networks" [ps] [pdf]

[GIW94P03] Hiroshi Mizushima, Kenshi Hayashi: "Establishment of Transcription Factor Database and Human Mutation Database" [ps] [pdf]

[GIW94P04] Kenji Suzuki, Susumu Goto, Yutaka Akiyama, Minoru Kanehisa: "A Signal Transduction Database" [ps] [pdf]

[GIW94P05] Nobuyuki Miyajima, Shinobu Nakayama, Mitsuyo Kohara, Satoko Hayashi: "The Gene Network: Development of a Database System Showing the Relationships Among the Genes of All Species" [ps] [pdf]

[GIW94P06] Toshio Shimizu, Kenta Nakai: "Construction of a Membrane Protein Database and an Evaluation of Several Prediction Methods of Transmembrane Segments" [ps] [pdf]

[GIW94P07] Makiko Suwa, Takatsugu Hirokawa, Shigeki Mitaku: "The Prediction of Lateral and Rotational Positioning of alpha-Helices in a Membrane Protein" [ps] [pdf]

[GIW94P08] Akira Shimada, Hideki Takehara, Kazunori Toma: "Protein Three Dimensional Structure Prediction on Object Oriented Database" [ps] [pdf]

[GIW94P09] Kenji Satou, Emiko Furuichi, Shin'ichi Hashimoto, Yukiko Tsukamoto, Satoru Kuhara, Toshihisa Takagi, Kazuo Ushijima: "Computing Closures of Indirect Similarity Relationships among Structures in Proteins" [ps] [pdf]

[GIW94P10] Kiyoshi Asai, Kentaro Onizuka, Masayuki Akahoshi, Hidetoshi Tanaka, Katunobu Itou: "Automatic Labeling of Protein Structures by Hidden Markov Models" [ps]

[GIW94P11] Hiroshi Mamitsuka: "A New Method for Predicting Long-range Interactions between Amino Acid Residues Based-on Homological Correlations" [ps] [pdf]

[GIW94P12] Haretsugu Hishigaki, Tamio Yasukawa: "Reverse Evolution of Proteases Studied by a Modified 3D-1D Method" [ps] [pdf]

[GIW94P13] Hiroaki Kato, Yoshimasa Takahashi: "An Approach to Three-Dimensional Motif Finding in Proteins" [ps] [pdf]

[GIW94P14] Motokazu Kamimura, Yoshimasa Takahashi: "Discriminative Analysis of the Conformational Patterns of Protein Amino Acid Residues" [ps] [pdf]

[GIW94P15] Kotoko Nakata: "Protein Secondary Structure Analysis Using Neural Network" [ps] [pdf]

[GIW94P16] Takashi Ishikawa, Shigeki Mitaku, Takao Terano, Takatsugu Hirokawa, Makiko Suwa, Seah Boon Chieng: "Finding Functional Features of Proteins using Machine Learning Techniques" [ps] [pdf]

[GIW94P17] Kenta Nakai, Ayumi Shinohara, Satoru Miyano: "Assignment of Certainty-Factor Parameters with a Given Reasoning Tree for the Prediction of Protein Localization Sites" [ps] [pdf]

[GIW94P18] Hiroshi Nakashima, Ken Nishikawa: "Discrimination of intracellular and extracellular proteins by single residue and residue-pair scores" [ps] [pdf]

[GIW94P19] Yukihiro Eguchi, Yuzo Ueda: "Classification of Possible Proteins from Genome Sequencing" [ps] [pdf]

[GIW94P20] Hideaki Nakakuni, Takeo Okazaki, Satoru Miyano: "Alphabet Indexing by Cluster Analysis: A Method for Knowledge Acquisition from Amino Acid Sequences" [ps] [pdf]

[GIW94P21] Tetsushi Yada, Masato Ishikawa, Hidetoshi Tanaka, Kiyoshi Asai: "DNA Sequence Analysis using Hidden Markov Model and Genetic Algorithm" [ps] [pdf]

[GIW94P22] Mikita Suyama, Takaaki Nishioka, Jun'ichi Oda: "Detecting common amino acid sequence patterns with a gap" [ps] [pdf]

[GIW94P23] Osamu Gotoh: "Multiple Sequence Alignment with a Tree-Based Weighting Syste" [ps] [pdf]

[GIW94P24] Hiroshi Tanaka, Fengrong Ren, Norio Fukuda: "Integration of Minimum Evolution and Maximum Likelihood Method in Constructing Molecular Evolutionary Tree" [ps] [pdf]

[GIW94P25] Shigehiko Kanaya, Toshimichi Ikemura, Yoshihiro Kudo: "Relationship between Gene Function and Codon Usage in Escherichia coli on the basis of Principal Component Analysis" [ps] [pdf]

[GIW94P26] Yasukazu Nakamura, Tatsuo Fukagawa, Kimihiko Sugaya, Toshimichi Ikemura: "Estimation of protein--production levels for ORFs found by E. coli and yeast genome projects, basing on levels of ``optimal codon'' usage, in connection with feasibility of their protein coding ability and with assignment to foreign-type genes." [ps] [pdf]

[GIW94P27] Motoe Sasanuma, Zhong-qing Wang, Kazuhiro Shibata, Syun-ichi Sasanuma, Masashi Ozawa, Eiko Kohriki, Toshihiko Eki, Akinori Sarai, Hideaki Sugawara, Yasufumi Murakami: "A Set of Tools Developed for the Analysis of Open Reading Frames of Yeast (S.cerevisiae) Chromosome VI" [ps] [pdf]

[GIW94P28] Zhong-qing Wang, Yasufumi Murakami, Toshihiko Eki, Akira Oyama, Yukihiro Eguchi, Akinori Sarai, Hideaki Sugawara: "Evaluation of the Sequence Data Assemble Software "Shotgun" " [ps] [pdf]

[GIW94P29] Tetsuo Nishikawa, Susumu Hiraoka, Naoko Kasahara, Keiichi Nagai: "Rapid identity searching program for DNA sequences and its applications to cDNA grouping" [ps] [pdf]

Workstation Session

[GIW94W01] Shinsei Minoshima, Nobuyoshi Shimizu: "Locus-in v.2 and GeneView^{PLUS} : Computer softwares for entry and analysis of the human genome data" [ps] [pdf]

[GIW94W02] Akira Suyama, Akira Ohyama, Masami Hagiya, Yoshiaki Furuhata, Takashi Ito, Asao Fujiyama, Masahira Hattori, Yoshiyuki Sakaki, Toshihisa Takagi: "ContigMaker and SAND: Software Tools for Genome Mapping and Sequencing" [ps] [pdf]

[GIW94W03] Toshiyuki Niiyama, Atsushi Takeuchi, Kouichi Kotani, Ikuo Uchiyama, Atsushi Ogiwara, Kenta Nakai: "Gnome: Recent Developments" [ps] [pdf]

[GIW94W04] Yutaka Akiyama, Takahiro Yakoh, Hirotada Mori, Naotake Ogasawara: "A server-client version of ``Genomatica'' integrated genome information browser" [ps] [pdf]

[GIW94W05] Susumu Goto, Satoru Kuhara, Toshihisa Takagi, Minoru Kanehisa: "Extension of the Integrated Database ``HyperGenome'' for Genome Maps and Sequence Information" [ps] [pdf]

[GIW94W06] Atsushi Ogiwara, Ikuo Uchiyama, Toshihisa Takagi, Minoru Kanehisa: "Further Improvements on SMART: Sequence Motif Analysis and Retrieval Tool" [ps] [pdf]

[GIW94W07] Kagehiko Kitano, Atsushi Ogiwara, Toshihisa Takagi: "Gidre : Genome Integrated Databases Retrieval Environment" [ps] [pdf]

[GIW94W08] Hiroshi Dohi, Hideaki Sugawara: "GenomeCruiser: A Laboratory Notebook for Human Gene Mapping" [ps] [pdf]

[GIW94W09] Akira Ohyama, Masaki Takazawa, Atsuko Kubota, Nobuyuki Miyajima: "A DNA Sequencing Project Monitoring and Sequence Data Quality Control System" [ps] [pdf]

[GIW94W10] Yasuhiko Wada, Kengo Inoue, Hiroshi Yasu: "Animal Genome Database for Network Users" [ps] [pdf]

[GIW94W11] Teruo Yasunaga, Tatsuya Takagi, Takeo Tokimori, Kouichi Kotani, Atsushi Takeuchi, Toshiyuki Niiyama: "Menu System Based on NCSA Mosaic and Programs Forked from the Menu" [ps] [pdf]

[GIW94W12] Hiromi Suzuki, Hiroaki Katoh: "An Attempt to Integrate Various Protein Databases Using an Object-Oriented Database Management System" [ps] [pdf]

[GIW94W13] Akihiro Oda, Jun-ichi Yano, Minoru Kanehisa: "A DNA/protein sequence retrieval system: an Xtpanel application" [ps] [pdf]

[GIW94W14] Susumu Hiraoka, Keiichi Nagai: "Rapid similarity search algorithm of nucleic acid database" [ps] [pdf]

[GIW94W15] Tatsuya Akutsu, Toshio Hyakutake: "Enhancement of the ``PROTEIX'' Database System for Three-Dimensional Protein Structures" [ps] [pdf]

[GIW94W16] Takatsugu Hirokawa, Seah Boon Chieng, Makiko Suwa, Shigeki Mitaku: "A computer system for predicting membrane protein structure" [ps] [pdf]

[GIW94W17] Takayoshi Shoudai, Tomoyuki Uchida, Satoru Miyano, Ayumi Shinohara, Shinichi Shimozono, Takeo Okazaki, Takeshi Shinohara, Satoru Kuhara, Setsuo Arikawa: "BONSAI Garden: Parallel Machine Discovery System for Sequences" [ps] [pdf]

[GIW94W18] Masanori Arita, Masami Hagiya, Tomoki Shiratori: "SIMFLY: The Simulation of a Fly Embryo" [ps] [pdf]

[GIW94W19] Hidetoshi Tanaka, Makoto Hirosawa, Reiko Tanaka, Masayuki Akahoshi, Masato Ishikawa: "A Knowledge Base of Biological Cascades" [ps] [pdf]

[GIW94W20] Susumu Goto, Minoru Kanehisa: "A Knowledge Base for Searching and Browsing Metabolic Pathways" [ps] [pdf]

Invited Lectures

[GIW94I01] Thomas G. Marr: "Application of the genome topographer system to the study of complex human disease" [ps]

[GIW94I02] Amos Bairoch: "Protein sequence databases in the context of genome projects" [ps] [pdf]

[GIW94I03] Stephen H. Bryant: "An Integrated Database of Biological Sequences, Scientific Literature, and 3-Dimensional Structure" [ps] [pdf]