Genome Informatics Workshop IV

Published as: Takagi, T., Imai, H., Miyano, S., Mitaku, S., and Kanehisa, M. (eds.); "Proceedings of Genome Informatics Workshop IV", Universal Academy Press, Tokyo, 1993.

Preface by Minoru Kanehisa

Oral Session - Database

[GIW93O01] Tatsuya Akutsu: "On Pattern Matching Methods for Three Dimensional Protein Structures"

[GIW93O02] Makoto Hirosawa, Reiko Tanaka, Masato Ishikawa: "Motif Knowledge Base Based on Deductive Object-Oriented Database Language"

[GIW93O03] Hideo Matsuda: "Efficient Query Processing on Genomic Database using Data-Parallel Logic Programming Language"

[GIW93O04] Kenji Satou, Emiko Furuichi, Satoru Kuhara, Toshihisa Takagi: "Searches for Topologically and Three Dimensionally Similar Structures in Proteins"

Oral Session - Knowledge Processing

[GIW93O05] Yasubumi Sakakibara, Michael Brown, Rebecca C. Underwood, I. Saira Mian, David Haussler: "Stochastic Context-Free Grammars in Computational Biology: Applications to Modeling RNA"

[GIW93O06] Hiroshi Mamitsuka: "Representing Inter-residue Dependencies in Protein Sequences with Probabilistic Networks"

[GIW93O07] Yukiko Fujiwara, Akihiko Konagaya: "Protein Motif Extraction Using Hidden Markov Model"

[GIW93O08] Masami Hagiya: "A Deductive Method for Construction and Visualization of Contigs in the STS Strategy"

[GIW93O09] Ayumi Shinohara, Shinichi Shimozono, Tomoyuki Uchida, Satoru Miyano, Satoru Kuhara, Setsuo Arikawa: "Running Learning Systems in Parallel for Machine Discovery from Sequences"

Oral Session - Parallel Processing

[GIW93O10] Masato Ishikawa, Tomoyuki Toya, Yasushi Totoki, Akihiko Konagaya: "Parallel Iterative Aligner with Genetic Algorithm"

[GIW93O11] Shiho Araki, Masahiro Goshima, Shin-ichiro Mori, Hiroshi Nakashima, Shinji Tomita, Yutaka Akiyama, Minoru Kanehisa: "Application of Parallelized DP and A* Algorithm to Multiple Sequence Alignment"

[GIW93O12] Naoto Ukiyama, Hiroshi Imai: "Parallel Multiple Alignments and Their Implementation on CM5"

Oral Session - Sequence Analysis

[GIW93O13] Osamu Gotoh: "Extraction of Conserved or Variable Regions from a Multiple Sequence Alignment"

[GIW93O14] Yasuhiko Seto, Yoshinori Ikeuchi, Masaharu Isoyama: "Automatic Extraction of Motif Candidates by Pairwise Sequence Alignment"

[GIW93O15] Gen Shibayama, Hiroshi Imai: "Finding K-best Alignments of Multiple Sequences"

[GIW93O16] Kiyoshi Asai, Hidetoshi Tanaka, Katunobu Itou, Kentaro Onizuka: "Are the Hidden Markov Models Promising in Protein Research?"

Oral Session - Structure Prediction

[GIW93O17] Kentaro Onizuka, Kiyoshi Asai, Masato Ishikawa: "Protein 3D Structure Prediction Based on Multi-Level Description"

[GIW93O18] Nobuhiko Saito, Motonori Ota: "Prediction of Structure of Globular Proteins II. Tertiary Structure"

[GIW93O19] Makiko Suwa, Takatsugu Hirokawa, Shigeki Mitaku: "A Theoretical Method for the Determination of Helix Configuration in Membrane Proteins"

[GIW93O20] Zenmei Ohkubo, Minoru Kanehisa: "A Method for Extracting Spatially Close Peptide Segments in Proteins"

Poster Session

[GIW93P01] Yoichi Iida, Takeshi Masuda: "Quantification Analysis of Translation Initiation Signal Sequences in Vertebrate mRNAs"

[GIW93P02] Koji Tajima: "Multiple Sequence Alignment using Parallel Genetic Algorithms"

[GIW93P03] Tsuyoshi Yoshizawa, Masaki Fumoto, Tamio Yasukawa: "Prediction of Protein Conformations by a Spin Glass Model (I)"

[GIW93P04] Fumiyoshi Sasagawa, Koji Tajima: "Toward Prediction of Multi-states Secondary Structures of Protein by Neural Network"

[GIW93P05] Kotoko Nakata: "Sequence Analysis of Zinc Finger DNA-Binding Protein"

[GIW93P06] Kazuhiro Iida, Hiroshi Mamitsuka: "Protein Sequence Motif Extraction with a Probabilistic Logic Neural Network: Motif Evaluation on a 3-D Structure"

[GIW93P07] Koichi Niijima, Shinichi Shimozono: "Learning Algorithms of Three Layered Neural Networks for Sequence Classification"

[GIW93P08] Hidetoshi Tanaka, Kentaro Onizuka, Kiyoshi Asai: "Classification of Proteins via Successive State Splitting Algorithm of Hidden Markov Network"

[GIW93P09] Shigehiko Kanaya, Yoshihiro Kudo: "Assessment of Species-specific Codon Usage by Principal Component Analysis"

[GIW93P10] Jun Kusuda, Makoto Hirata, Atushi Toyoda, Ichiro Takahashi, Katsuyuki Hashimoto: "A Search for CpG Islands Associated with Genes in Human Genomic Sequences Compiled in the DNA Database"

[GIW93P11] Mikita Suyama, Takaaki Nishioka, Jun'ichi Oda: "Extraciton of the Ligand-related Motifs in Enzymes"

[GIW93P12] Ikuo Uchiyama, Atsushi Ogiwara, Zenmei Ohkubo, Minoru Kanehisa: "Automatic Procedure to Extract Signature Pentapeptides from the Protein Sequence Database"

[GIW93P13] Keiichi Nagai, Tetsuo Nishikawa, Hideki Kambara, Toshihisa Takagi: "A Simple Method for Finding Local Sequence Similarities"

[GIW93P14] Hiroyuki Ogata, Yutaka Akiyama, Minoru Kanehisa: "A Computer Modeling Method for the Three-dimensional Structure of RNA"

[GIW93P15] Wataru Fujibuchi, Minoru Kanehisa: "Construction of a Functional Word Dictionary for Primate Promoter Sequences"

[GIW93P16] Takashi Yokomori, Satoshi Kobayashi: "A Similarity Measure for DNA Sequence Analysis Based on Locality"

[GIW93P17] Yukio Kobayashi, Nobuhiko Saito: "Prediction of Structures of Globular Proteins I. Secondary Structure"

[GIW93P18] Khawaja Sirajuddin, Tomomasa Nagashima, Koichi Ono: "Variation of the Order of Importance in the Base Position for 5'-Splice Site Sequences"

[GIW93P19] Hiroshi Furutani: "Analysis of Abnormal Splicing by Neural Network"

[GIW93P20] Motokazu Kamimura, Yoshimasa Takahashi: "Backbone Conformational Pattern Clustering of Three-Dimensional Peptide Fragments of Proteins"

[GIW93P21] Koji Ohnishi: "Poly-tRNA Theory on the Origin and Evolution of mRNA and Genetic Codes: Evolution from Tandem tRNA-Repeats to Primitive mRNAs Encoding F0-ATPase a Subunit and Glycyl-tRNA Synthetase"

[GIW93P22] Tsukasa Sakai: "Metrics for Protein Sequence Comparison"

[GIW93P23] Takashi Ishikawa, Takao Terano: "Using Analogical Reasoning to Predict a Protein Structure"

[GIW93P24] K.Wada, Y. Wada, S. Tanaka, H. Doi, Y. Nakamura, K. Sugaya, T. Fukagawa, T. Ikemura: "A Sensitive and Efficient Homology Search Method to Find Protein-coding Regions Using "protein-coding region DNA database""

Workstation Session

[GIW93W01] Susumu Goto, Norihiro Sakamoto, Toshihisa Takagi: "Integration of Genome Databases Using a Deductive Object-Oriented Database"

[GIW93W02] Takahiko Suzuki, Susumu Nakashima, Toshihisa Takagi, Satoru Kuhara, Minoru Kanehisa: "Enhancement of the Integrated Database "HyperGenome" for Genome Maps and Sequence Information"

[GIW93W03] Shinsei Minoshima, Nobuyoshi Shimizu: "Locus-in: A New Database System with Graphical Front End to Integrate Mapping Data"

[GIW93W04] Akira Suyama, Masami Hagiya, Takashi Ito, Asao Fujiyama, Akira Ohyama, Toshihisa Takagi: "ContigMaker: Software Tool for Contig Map Construction

[GIW93W05] Toshiyuki Niiyama, Takeo Tokimori, Atsushi Ogiwara, Ikuo Uchiyama, Kenta Nakai: "GNOME: A Sequence Data Management Tool to Access Homology, Motif, and Other Data Analysis Servers"

[GIW93W06] Yutaka Akiyama, Hirotada Mori, Satoru Kuhara, Naoki Ogasawara, Nobuyuki Miyajima, Tetsuya Furukawa, Kenji Sato, Yasufumi Murakami: "Genomatica: An Integrated Data Management and Analysis Tool for Genome Sequencing Projects"

[GIW93W07] Atsushi Ogiwara, Ikuo Uchiyama, Minoru Kanehisa: "Sequence Motif Analysis and Retrieval Tool"

[GIW93W08] Makoto Hirosawa, Yasushi Totoki, Masato Ishikawa: "Constraint Based Alignment Editor with Automatic Alinger and Motif Dictionary Retriever"

[GIW93W09] Masayuki Akahoshi, Kentaro Onizuka, Masato Ishikawa, Kiyoshi Asai: "A Three-Dimensional Graphic System for Protein Structure Analysis"

[GIW93W10] Tatsuya Akutsu: "PROTEIX: An Interactive Database System for Three Dimensional Protein Structures"

[GIW93W11] Takatsugu Hirokawa, Makiko Suwa, Shigeki Mitaku: "A Computer System for Predicting Membrane Protein Structure"

[GIW93W12] Yoshinori Ikeuchi, Masaharu Isoyama, Yasuhiko Seto: "Knowledge Library of Proteins on Anonymous FTP / Genome Network"

[GIW93W13] Hiroshi Mizushima, Yoshiyuki Kuchino: "Development of a Genetic Information System for Institute Engaged in Molecular Biology"

[GIW93W14] Asao Fujiyama: "Human Gene Database for a Personal Computer with Graphical Interface"

Invited Lectures

[GIW93I01] Richard Durbin: "The ACEDB Genome Database: Support for Large Scale Sequencing Projects"

[GIW93I02] Otto Ritter: "Towards an Information Managemenet System for Genomic Objects and Processes"

[GIW93I03] Robert J. Robbins: "The Transformation of GDB"

[GIW93I04] Stephen F. Altschul: "Scoring Systems for Macromolecular Sequence Comparison:

[GIW93I05] Thomas Lengauer: "Algorithmic Research Problems in Molecular Bioinformatics"

[GIW93I06] Hidehiko Tanaka: "Super Parallel Computing Project: Scientific Research on Priority Areas for Ministry of Education"

[GIW93I07] James W. Fickett: "Eukaryotic Gene Identification Algorithms"

[GIW93I08] Phil Green: "Genome Sequence Analysis: Identifying and Classifying Genes"